Diagenode

Bioruptor

2182 publications found.

Targeting the mSWI/SNF Complex in POU2F-POU2AF Transcription Factor-Driven Malignancies
Published: January, 2024

Abstract: The POU2F3-POU2AF2/3 (OCA-T1/2) transcription factor complex is the master regulator of the tuft cell lineage and tuft cell-like small cell lung cancer (SCLC). Here, we found that the POU2F3 molecular subtype of SCLC (SCLC-P) exhibits an exquisite...
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The Effect of Metformin and Carbohydrate-Controlled Diet onDNA Methylation and Gene Expression in the Endometrium of Womenwith Polycystic Ovary Syndrome.
Published: April, 2023

Abstract: Polycystic ovary syndrome (PCOS) is an endocrine disease associated with infertility and metabolic disorders in reproductive-aged women. In this study, we evaluated the expression of eight genes related to endometrial function and their DNA methyl...
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A Systemic and Integrated Analysis of p63-Driven RegulatoryNetworks in Mouse Oral Squamous Cell Carcinoma.
Published: January, 2023

Abstract: Oral squamous cell carcinoma (OSCC) is the most common malignancy of the oral cavity and is linked to tobacco exposure, alcohol consumption, and human papillomavirus infection. Despite therapeutic advances, a lack of molecular understanding of dis...
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Balance between autophagy and cell death is maintained byPolycomb-mediated regulation during stem cell differentiation.
Published: November, 2022

Abstract: Autophagy is a conserved cytoprotective process, aberrations in which lead to numerous degenerative disorders. While the cytoplasmic components of autophagy have been extensively studied, the epigenetic regulation of autophagy genes, especially in...
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Smc5/6 silences episomal transcription by a three-step function.
Published: September, 2022

Abstract: In addition to its role in chromosome maintenance, the six-membered Smc5/6 complex functions as a restriction factor that binds to and transcriptionally silences viral and other episomal DNA. However, the underlying mechanism is unknown. Here, we ...
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Exploration of nuclear body-enhanced sumoylation reveals that PMLrepresses 2-cell features of embryonic stem cells.
Published: September, 2022

Abstract: Membrane-less organelles are condensates formed by phase separation whose functions often remain enigmatic. Upon oxidative stress, PML scaffolds Nuclear Bodies (NBs) to regulate senescence or metabolic adaptation. PML NBs recruit many partner prot...
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Loss of epigenetic regulation disrupts lineage integrity, inducesaberrant alveogenesis and promotes breast cancer.
Published: September, 2022

Abstract: Systematically investigating the scores of genes mutated in cancer and discerning disease drivers from inconsequential bystanders is a prerequisite for Precision Medicine but remains challenging. Here, we developed a somatic CRISPR/Cas9 mutagenesi...
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A complex epigenome-splicing crosstalk governs epithelial-to-mesenchymaltransition in metastasis and brain development.
Published: August, 2022

Abstract: Epithelial-to-mesenchymal transition (EMT) renders epithelial cells migratory properties. While epigenetic and splicing changes have been implicated in EMT, the mechanisms governing their crosstalk remain poorly understood. Here we discovered that...
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The Arabidopsis APOLO and human UPAT sequence-unrelated longnoncoding RNAs can modulate DNA and histone methylation machineries inplants.
Published: August, 2022

Abstract: BACKGROUND: RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcr...
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Prolonged FOS activity disrupts a global myogenic transcriptionalprogram by altering 3D chromatin architecture in primary muscleprogenitor cells.
Published: August, 2022

Abstract: BACKGROUND: The AP-1 transcription factor, FBJ osteosarcoma oncogene (FOS), is induced in adult muscle satellite cells (SCs) within hours following muscle damage and is required for effective stem cell activation and muscle repair. However, why FO...
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Hexokinase 2 is a transcriptional target and a positive modulator ofAHR signalling.
Published: May, 2022

Abstract: The aryl hydrocarbon receptor (AHR) regulates the expression of numerous genes in response to activation by agonists including xenobiotics. Although it is well appreciated that environmental signals and cell intrinsic features may modulate this tr...
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Epigenetic Mechanisms Mediating Cell State Transitions in Chondrocytes
Published: May, 2022

Abstract: Epigenetic modifications play critical roles in regulating cell lineage differentiation, but the epigenetic mechanisms guiding specific differentiation steps within a cell lineage have rarely been investigated. To decipher such mechanisms, we used...
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The CpG Island-Binding Protein SAMD1 Contributes to anUnfavorable Gene Signature in HepG2 Hepatocellular CarcinomaCells.
Published: April, 2022

Abstract: The unmethylated CpG island-binding protein SAMD1 is upregulated in many human cancer types, but its cancer-related role has not yet been investigated. Here, we used the hepatocellular carcinoma cell line HepG2 as a cancer model and investigated t...
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MLL-AF4 and a murinized pSer-variant thereof are turning on thenucleolar stress pathway.
Published: April, 2022

Abstract: BACKGROUND: Recent pathomolecular studies on the MLL-AF4 fusion protein revealed that the murinized version of MLL-AF4, the MLL-Af4 fusion protein, was able to induce leukemia when expressed in murine or human hematopoietic stem/progenitor cells (...
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ZBTB11 dysfunction: spectrum of brain abnormalities, biochemicalsignature and cellular consequences.
Published: February, 2022

Abstract: Bi-allelic pathogenic variants in ZBTB11 have been associated with Intellectual Developmental Disorder, autosomal recessive 69 (MRT69; OMIM 618383). We report five patients from three families with novel, bi-allelic variants in ZBTB11. We expand t...
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Effects of GSK-J4 on JMJD3 Histone Demethylase in MouseProstate Cancer Xenografts.
Published: January, 2022

Abstract: BACKGROUND/AIM: Histone methylation status is required to control gene expression. H3K27me3 is an epigenetic tri-methylation modification to histone H3 controlled by the demethylase JMJD3. JMJD3 is dysregulated in a wide range of cancers and has b...
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Comprehensive characterization of the epigenetic landscape in Multiple Myeloma
Published: January, 2022

Abstract: Background: Human multiple myeloma (MM) cell lines (HMCLs) have been widely used to understand the molecular processes that drive MM biology. Epigenetic modifications are involved in MM development, progression, and drug resistance. A comprehensiv...
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Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos
Published: January, 2022

Abstract: DNA accessibility of cis-regulatory elements (CREs) dictates transcriptional activity and drives cell differentiation during development. While many genes regulating embryonic development have been identified, the underlying CRE dynamics controlli...
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SUV39 SET domains mediate crosstalk of heterochromatic histone marks.
Published: September, 2021

Abstract: The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poor...
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Quantification and epigenetic evaluation of the residual pool of hepatitisB covalently closed circular DNA in long-term nucleoside analogue-treatedpatients.
Published: December, 2020

Abstract: Hepatitis B virus (HBV) covalently closed circular (ccc)DNA is the key genomic form responsible for viral persistence and virological relapse after treatment withdrawal. The assessment of residual intrahepatic cccDNA levels and activity after long...
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The epigenetic regulator RINF (CXXC5) maintains SMAD7 expression in human immature erythroid cells and sustains red blood cellsexpansion.
Published: November, 2020

Abstract: The gene CXXC5, encoding a Retinoid-Inducible Nuclear Factor (RINF), is located within a region at 5q31.2 commonly deleted in myelodysplastic syndrome (MDS) and adult acute myeloid leukemia (AML). RINF may act as an epigenetic regulator and has be...
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A genetic variant controls interferon-β gene expression in human myeloidcells by preventing C/EBP-β binding on a conserved enhancer.
Published: November, 2020

Abstract: Interferon β (IFN-β) is a cytokine that induces a global antiviral proteome, and regulates the adaptive immune response to infections and tumors. Its effects strongly depend on its level and timing of expression. Therefore, the transcrip...
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Combined treatment with CBP and BET inhibitors reverses inadvertentactivation of detrimental super enhancer programs in DIPG cells.
Published: August, 2020

Abstract: Diffuse intrinsic pontine gliomas (DIPG) are the most aggressive brain tumors in children with 5-year survival rates of only 2%. About 85% of all DIPG are characterized by a lysine-to-methionine substitution in histone 3, which leads to global H3K...
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N-Methyladenosine co-transcriptionally directs the demethylation of histoneH3K9me2.
Published: August, 2020

Abstract: A dynamic epigenome is critical for appropriate gene expression in development and health. Central to this is the intricate process of transcription, which integrates cellular signaling with chromatin changes, transcriptional machinery and modific...
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Methylation in pericytes after acute injury promotes chronic kidneydisease.
Published: August, 2020

Abstract: The origin and fate of renal myofibroblasts is not clear after acute kidney injury (AKI). Here, we demonstrate that myofibroblasts were activated from quiescent pericytes (qPericytes) and the cell numbers increased after ischemia/reperfusion injur...
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Exploring the virulence gene interactome with CRISPR/dCas9 in the humanmalaria parasite.
Published: August, 2020

Abstract: Mutually exclusive expression of the var multigene family is key to immune evasion and pathogenesis in Plasmodium falciparum, but few factors have been shown to play a direct role. We adapted a CRISPR-based proteomics approach to identify novel fa...
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Targeted bisulfite sequencing for biomarker discovery.
Published: August, 2020

Abstract: Cytosine methylation is one of the best studied epigenetic modifications. In mammals, DNA methylation patterns vary among cells and is mainly found in the CpG context. DNA methylation is involved in important processes during development and diffe...
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Battle of the sex chromosomes: competition between X- and Y-chromosomeencoded proteins for partner interaction and chromatin occupancy drivesmulti-copy gene expression and evolution in muroid rodents.
Published: July, 2020

Abstract: Transmission distorters (TDs) are genetic elements that favor their own transmission to the detriments of others. Slx/Slxl1 (Sycp3-like-X-linked and Slx-like1) and Sly (Sycp3-like-Y-linked) are TDs which have been co-amplified on the X and Y chrom...
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Proteomics Links Ubiquitin Chain Topology Change to Transcription Factor Activation.
Published: August, 2019

Abstract: A surprising complexity of ubiquitin signaling has emerged with identification of different ubiquitin chain topologies. However, mechanisms of how the diverse ubiquitin codes control biological processes remain poorly understood. Here, we use quan...
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Regulation of Co-transcriptional Pre-mRNA Splicing by mA through the Low-Complexity Protein hnRNPG.
Published: July, 2019

Abstract: N-methyladenosine (mA) modification occurs co-transcriptionally and impacts pre-mRNA processing; however, the mechanism of co-transcriptional mA-dependent alternative splicing regulation is still poorly understood. Heterogeneous nuclear ribonucleo...
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p73 regulates epidermal wound healing and induced keratinocyte programming.
Published: June, 2019

Abstract: p63 is a transcriptional regulator of ectodermal development that is required for basal cell proliferation and stem cell maintenance. p73 is a closely related p53 family member that is expressed in select p63-positive basal cells and can heterodim...
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P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress.
Published: April, 2019

Abstract: DNA damage response (DDR) involves dramatic transcriptional alterations, the mechanisms of which remain ill defined. Here, we show that following genotoxic stress, the RNA-binding motif protein 7 (RBM7) stimulates RNA polymerase II (Pol II) transc...
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A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation.
Published: March, 2019

Abstract: Humoral immunity depends on efficient activation of B cells and their subsequent differentiation into antibody-secreting cells (ASCs). The transcription factor NFκB cRel is critical for B cell proliferation, but incorporating its known regul...
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TF-ChIP Method for Tissue-Specific Gene Targets.
Published: March, 2019

Abstract: Chromatin immunoprecipitation (ChIP) is an assay developed in order to define the dynamic nature of transcription processes. This method has been widely employed to identify methylated and acetylated DNA sequences in a variety of organs both in an...
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Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development
Published: March, 2019

Abstract: Malaria pathogenesis results from the asexual replication of Plasmodium falciparum within human red blood cells, which relies on a precisely timed cascade of gene expression over a 48-hour life cycle. Although substantial post-transcriptional regu...
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Chromatin activity at GWAS loci identifies T cell states driving complex immune diseases
Published: March, 2019

Abstract: Complex immune disease variants are enriched in active chromatin regions of T cells and macrophages. However, whether these variants function in specific cell states or stages of cell activation is unknown. We stimulated T cells and macrophages in...
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A Lamina-Associated Domain Border Governs Nuclear Lamina Interactions, Transcription, and Recombination of the Tcrb Locus.
Published: November, 2018

Abstract: Tcrb locus V(D)J recombination is regulated by positioning at the nuclear periphery. Here, we used DamID to profile Tcrb locus interactions with the nuclear lamina at high resolution. We identified a lamina-associated domain (LAD) border composed ...
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SIRT1-dependent epigenetic regulation of H3 and H4 histone acetylation in human breast cancer
Published: July, 2018

Abstract: Breast cancer is the most frequently diagnosed malignancy in women worldwide. It is well established that the complexity of carcinogenesis involves profound epigenetic deregulations that contribute to the tumorigenesis process. Deregulated H3 and ...
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Interplay of cell–cell contacts and RhoA/MRTF‐A signaling regulates cardiomyocyte identity
Published: May, 2018

Abstract: Cell–cell and cell–matrix interactions guide organ development and homeostasis by controlling lineage specification and maintenance, but the underlying molecular principles are largely unknown. Here, we show that in human developing ca...
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Functional interplay between E2F7 and ribosomal rRNA gene transcription regulates protein synthesis
Published: May, 2018

Abstract: A prerequisite for protein synthesis is the transcription of ribosomal rRNA genes by RNA polymerase I (Pol I), which controls ribosome biogenesis. UBF (upstream binding factor) is one of the main Pol I transcription factors located in the nucleolu...
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Local adaptation and ecological differentiation under selection, migration and drift in Arabidopsis lyrata
Published: May, 2018

Abstract: How the balance between selection, migration and drift influences the evolution of local adaptation has been under intense theoretical scrutiny. Yet, empirical studies that relate estimates of local adaptation to quantification of gene flow and ef...
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The chromatin remodeling factor SPOC1 acts as a cellular restriction factor against human cytomegalovirus by repressing the major immediate-early promoter
Published: May, 2018

Abstract: The cellular protein SPOC1 (survival time-associated PHD finger protein in ovarian cancer 1) acts as a regulator of chromatin structure and DNA damage response. It binds H3K4me2/3 containing chromatin and promotes DNA condensation by recruiting co...
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Nuclear fate of yeast snoRNA is determined by co-transcriptional Rnt1 cleavage
Published: May, 2018

Abstract: Small nucleolar RNA (snoRNA) are conserved and essential non-coding RNA that are transcribed by RNA Polymerase II (Pol II). Two snoRNA classes, formerly distinguished by their structure and ribonucleoprotein composition, act as guide RNA to target...
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SUN2 Modulates HIV-1 Infection and Latency through Association with Lamin A/C To Maintain the Repressive Chromatin
Published: May, 2018

Abstract: The postintegrational latency of HIV-1 is characterized by reversible silencing of long terminal repeat (LTR)-driven transcription of the HIV genome. It is known that the formation of repressive chromatin at the 5′-LTR of HIV-1 proviral DN...
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Viral targeting of TFIIB impairs de novo polymerase II recruitment and affects antiviral immunity
Published: April, 2018

Abstract: Viruses have evolved a plethora of mechanisms to target host antiviral responses. Here, we propose a yet uncharacterized mechanism of immune regulation by the orthomyxovirus Thogoto virus (THOV) ML protein through engaging general transcription fa...
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HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types
Published: April, 2018

Abstract: Processes like cellular senescence are characterized by complex events giving rise to heterogeneous cell populations. However, the early molecular events driving this cascade remain elusive. We hypothesized that senescence entry is triggered by an...
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Generation of a PAX6 knockout glioblastoma cell line with changes in cell cycle distribution and sensitivity to oxidative stress
Published: April, 2018

Abstract: The transcription factor PAX6 is expressed in various cancers. In anaplastic astrocytic glioma, PAX6 expression is inversely related to tumor grade, resulting in low PAX6 expression in Glioblastoma, the highest-grade astrocytic glioma. The aim o...
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MYCN acts as a direct co-regulator of p53 in MYCN amplified neuroblastoma
Published: April, 2018

Abstract: The MYC oncogenes and p53 have opposing yet interrelated roles in normal development and tumorigenesis. How MYCN expression alters the biology and clinical responsiveness of pediatric neuroblastoma remains poorly defined. Neuroblastoma is p53 wild...
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Analysis of Meiotic Double-Strand Break Initiation in Mammals
Published: March, 2018

Abstract: The repair of programmed DNA double-strand breaks (DSBs) physically tethers homologous chromosomes in meiosis to allow for accurate segregation through meiotic cell divisions. This process, known as recombi...
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Lyar-mediated recruitment of Brd2 to the chromatin attenuates Nanog downregulation following induction of differentiation
Published: March, 2018

Abstract: During development, cellular differentiation programs need of tight regulation for proper display of the activity of multiple factors in time and space. Chromatin adaptors of the BET family (Brd2, Brd3, Brd4 and Brdt in vertebrates) are transcript...
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A novel long noncoding RNA LINC00844 regulates prostate cancer cell migration and invasion through androgen receptor signaling
Published: January, 2018

Abstract: The majority of the human genome is transcribed, yielding a rich repository of non-coding transcripts that are involved in a myriad of biological processes including cancer. However, how non-coding transcripts such as long non-coding RNAs (lncRNAs...
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The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes
Published: December, 2017

Abstract: Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. ...
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Repeated methamphetamine and modafinil induce differential cognitive effects and specific histone acetylation and DNA methylation profiles in the mouse medial prefrontal cortex
Published: December, 2017

Abstract: Methamphetamine (METH) and modafinil are psychostimulants with different long-term cognitive profiles: METH is addictive and leads to cognitive decline, whereas modafinil has little abuse liability and is a cognitive enhancer. Increasing evi...
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Super enhancer associated RAI14 is a new potential biomarker in lung adenocarcinoma
Published: December, 2017

Abstract: Tyrosine kinase inhibitors (TKIs) are widely used to treat lung adenocarcinoma patients with EGFR mutations or ALK-fusions. However, patients with wild-type genes or TKIs-resistant mutations lack effective therapeutic targets. Extensive studies re...
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Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours.
Published: October, 2017

Abstract: The dynamic and reversible acetylation of proteins, catalysed by histone acetyltransferases (HATs) and histone deacetylases (HDACs), is a major epigenetic regulatory mechanism of gene transcription and is associated with multiple diseases. Histone...
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MEIS homeodomain proteins facilitate PARP1/ARTD1-mediated eviction of histone H1
Published: July, 2017

Abstract: Pre–B-cell leukemia homeobox (PBX) and myeloid ecotropic viral integration site (MEIS) proteins control cell fate decisions in many physiological and pathophysiological contexts, but how these proteins function mechanistically remains poorly...
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Genomic Characterization of Murine Monocytes Reveals C/EBPβ Transcription Factor Dependence of Ly6C- Cells
Published: May, 2017

Abstract: Monocytes are circulating, short-lived mononuclear phagocytes, which in mice and man comprise two main subpopulations. MurineLy6C+ monocytes display developmental plasticity and are recruited to complement tissue-resident macrophages and dendritic...
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The adaptor protein ARA55 and the nuclear kinase HIPK1 assist c-Myb in recruiting p300 to chromatin
Published: May, 2017

Abstract: LIM-domain proteins, containing multiple cysteine-rich zinc finger-like motifs, have been shown to play diverse roles in several cellular processes. A common theme is that they mediate important protein-protein interactions that are key to their f...
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Novel Molecular Mechanism of Regulation of CD40 Ligand by the Transcription Factor GLI2
Published: April, 2017

Abstract: The interaction between tumor cells and their surrounding microenvironment is essential for the growth and persistence of cancer cells. This interaction is mediated, in part, by cytokines. Although the role of cytokines in normal and malignant cel...
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Genomic responses of mouse synovial fibroblasts during TNF-driven arthritogenesis greatly mimic those of human rheumatoid arthritis
Published: April, 2017

Abstract: OBJECTIVE: Aberrant activation of synovial fibroblasts (SFs) is a key determinant in the pathogenesis of rheumatoid arthritis (RA). We aimed to produce a map of gene expression and epigenetic changes occurring in this cell type during disease pro...
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The Rhomboid Protease GlpG Promotes the Persistence of Extraintestinal Pathogenic Escherichia coli within the Gut
Published: April, 2017

Abstract: Extraintestinal pathogenic Escherichia coli (ExPEC) strains are typically benign within the  mammalian gut, but can disperse to extraintestinal sites to cause disease. As occupation of the  intestinal tract is often a prerequisite for Ex...
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The antiproliferative ELF2 isoform, ELF2B, induces apoptosis in vitro and perturbs early lymphocytic development in vivo
Published: March, 2017

Abstract: Background ELF2 (E74-like factor 2) also known as NERF (new Ets-related factor), a member of the Ets family of transcription factors, regulates genes important in B and T cell development, cell cycle progression, and angiogenesis. Conserved ELF...
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Islet-1 induces the differentiation of mesenchymal stem cells into cardiomyocyte-like cells through the regulation of Gcn5 and DNMT-1
Published: March, 2017

Abstract: Previous studies from this group demonstrated that insulin gene enhancer binding protein ISL-1 (Islet-1) specifically induces the differentiation of mesenchymal stem cells (MSCs) into cardiomyocyte‑like cells through histone acetylation. However, ...
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Differentiation of Mouse Enteric Nervous System Progenitor Cells is Controlled by Endothelin 3 and Requires Regulation of Ednrb by SOX10 and ZEB2
Published: January, 2017

Abstract: Background & Aims Maintenance and differentiation of progenitor cells in the developing enteric nervous system (ENS) are controlled by molecules such as the signaling protein endothelin 3 (EDN3), its receptor (the endothelin receptor type B...
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m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition
Published: December, 2016

Abstract: The maternal-to-zygotic transition (MZT) is one of the most profound and tightly orchestrated processes during the early life of embryos, yet factors that shape the temporal pattern of vertebrate MZT are largely unknown. Here we show that over one...
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Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression
Published: December, 2016

Abstract: ATP-dependent chromatin remodeling complexes are important regulators of gene expression in Eukaryotes. In plants, SWI/SNF-type complexes have been shown critical for transcriptional control of key developmental processes, growth and stress respon...
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Stem cell-like transcriptional reprogramming mediates metastatic
Published: December, 2016

Abstract: Inhibitors of the mechanistic target of rapamycin (mTOR) are currently used to treat advanced metastatic breast cancer. However, whether an aggressive phenotype is sustained through adaptation or resistance to mTOR inhibition remains unknown. Here...
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Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples
Published: December, 2016

Abstract: We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Br...
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Nitric oxide modulates histone acetylation at stress genes by inhibition of histone deacetylases
Published: December, 2016

Abstract: Histone acetylation, which is an important mechanism to regulate gene expression, is controlled by the opposing action of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In animals, several HDACs are subjected to regulation by ...
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Alu repeats as transcriptional regulatory platforms in macrophage responses to M. tuberculosis infection
Published: December, 2016

Abstract: To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo...
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Distinct and Shared Determinants of Cardiomyocyte Contractility in Multi-Lineage Competent Ethnically Diverse Human iPSCs
Published: December, 2016

Abstract: The realization of personalized medicine through human induced pluripotent stem cell (iPSC) technology can be advanced by transcriptomics, epigenomics, and bioinformatics that inform on genetic pathways directing tissue development and function. W...
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TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells
Published: November, 2016

Abstract: BACKGROUND: Ten-eleven translocation (TET) enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their effect on transposable ele...
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β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance
Published: November, 2016

Abstract: Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as lipopolysaccharide (LPS). We apply an integrated epigenomic ap...
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EPOP Functionally Links Elongin and Polycomb in Pluripotent Stem Cells
Published: November, 2016

Abstract: The cellular plasticity of pluripotent stem cells is thought to be sustained by genomic regions that display both active and repressive chromatin properties. These regions exhibit low levels of gene expression, yet the mechanisms controlling these...
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Genome-wide DNA promoter methylation and transcriptome analysis in human adipose tissue unravels novel candidate genes for obesity
Published: November, 2016

Abstract: Objective/methods DNA methylation plays an important role in obesity and related metabolic complications. We examined genome-wide DNA promoter methylation along with mRNA profiles in paired samples of human subcutaneous adipose tissue (SAT) and o...
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The Hematopoietic Transcription Factors RUNX1 and ERG Prevent AML1-ETO Oncogene Overexpression and Onset of the Apoptosis Program in t(8;21) AMLs
Published: November, 2016

Abstract: The t(8;21) acute myeloid leukemia (AML)-associated oncoprotein AML1-ETO disrupts normal hematopoietic differentiation. Here, we have investigated its effects on the transcriptome and epigenome in t(8,21) patient cells. AML1-ETO binding was found ...
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A set of novel automated quantitative microproteomics protocols for small sample amounts and its application to kidney tissue substructures
Published: November, 2016

Abstract: Here we assessed the ability of an automated sample preparation device equipped with disposable microcolumns to prepare mass-limited samples for high-sensitivity quantitative proteomics, using both label-free and isobaric labeling approaches. Firs...
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Transcriptional Activation of Pericentromeric Satellite Repeats and Disruption of Centromeric Clustering upon Proteasome Inhibition
Published: November, 2016

Abstract: Heterochromatinisation of pericentromeres, which in mice consist of arrays of major satellite repeats, are important for centromere formation and maintenance of genome stability. The dysregulation of this process has been linked to genomic stress ...
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Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks
Published: October, 2016

Abstract: As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and pr...
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Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer
Published: October, 2016

Abstract: Clear cell renal cell carcinoma (ccRCC) is characterized by loss of function of the von Hippel-Lindau tumour suppressor (VHL) and unrestrained activation of hypoxia-inducible transcription factors (HIFs). Genetic and epigenetic determinants have a...
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DNA fragmentation and quality control analysis
Published: September, 2016

Abstract: Optimal data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor®, Megaruptor®, and Fragment A...
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Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing
Published: September, 2016

Abstract: Gene silencing is instrumental to interrogate gene function and holds promise for therapeutic applications. Here, we repurpose the endogenous retroviruses' silencing machinery of embryonic stem cells to stably silence three highly expressed g...
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Converging disease genes in ICF syndrome: ZBTB24 controls expression of CDCA7 in mammals
Published: July, 2016

Abstract: For genetically heterogeneous diseases a better understanding of how the underlying gene defects are functionally interconnected will be important for dissecting disease etiology. The Immunodeficiency, Centromeric instability, Facial anomalies (IC...
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Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots
Published: July, 2016

Abstract: Background In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modi...
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UMI-4C for quantitative and targeted chromosomal contact profiling
Published: July, 2016

Abstract: We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (umis) to derive high-complexity quantitative chromosome contact profiles with controlled signal-to-noise ratios. UMI-4C detects chromosom...
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The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation
Published: July, 2016

Abstract: Although the core subunits of Polycomb group (PcG) complexes are well characterized, little is known about the dynamics of these protein complexes during cellular differentiation. We used quantitative interaction proteomics and genome-wide profili...
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Osterix and RUNX2 are Transcriptional Regulators of Sclerostin in Human Bone
Published: May, 2016

Abstract: Sclerostin, encoded by the SOST gene, works as an inhibitor of the Wnt pathway and therefore is an important regulator of bone homeostasis. Due to its potent action as an inhibitor of bone formation, blocking sclerostin activity is the purpose of ...
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Characterization of novel Bovine Leukemia Virus (BLV) antisense transcripts by deep sequencing reveals constitutive expression in tumors and transcriptional interaction with viral microRNAs
Published: May, 2016

Abstract: Background Bovine Leukemia Virus (BLV) is a deltaretrovirus closely related to the Human T cell leukemia virus-1 (HTLV-1). Cattle are the natural host of BLV where it integrates into B-cells, producing a lifelong infection. Most infected animals ...
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Mutations in GAS8, A Gene Encoding A Nexin-Dynein Regulatory Complex Subunit, Cause Primary Ciliary Dyskinesia With Axonemal Disorganization
Published: April, 2016

Abstract: Primary ciliary dyskinesia (PCD) is an autosomal recessive disease characterized by chronic respiratory infections of the upper and lower airways, hypofertility, and, in approximately half of the cases, situs inversus. This complex phenotype resul...
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Histamine 1 receptor-Gβγ-cAMP/PKA-CFTR pathway mediates the histamine-induced resetting of the suprachiasmatic circadian clock
Published: March, 2016

Abstract: Background Recent evidence indicates that histamine, acting on histamine 1 receptor (H1R), resets the circadian clock in the mouse suprachiasmatic nucleus (SCN) by increasing intracellular Ca2+ concentration ([Ca2+]i) through the activation of Ca...
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saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription
Published: February, 2016

Abstract: Small activating RNAs (saRNAs) targeting specific promoter regions are able to stimulate gene expression at the transcriptional level, a phenomenon known as RNA activation (RNAa). It is known that RNAa depends on Ago2 and is associated with epigen...
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Methylated DNA Immunoprecipitation Analysis of Mammalian Endogenous Retroviruses.
Published: February, 2016

Abstract: Endogenous retroviruses are repetitive sequences found abundantly in mammalian genomes which are capable of modulating host gene expression. Nevertheless, most endogenous retrovirus copies are under tight epigenetic control via histone-repressive ...
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ARTD1 regulates osteoclastogenesis and bone homeostasis by dampening NF-κB-dependent transcription of IL-1β
Published: February, 2016

Abstract: While ADP-ribosyltransferase diphtheria toxin-like 1 (ARTD1, formerly PARP1) and its enzymatic activity have been shown to be important for reprogramming and differentiation of cells, such as during adipogenesis, their role and mechanism in regula...
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RecG Directs DNA Synthesis during Double-Strand Break Repair
Published: February, 2016

Abstract: Homologous recombination provides a mechanism of DNA double-strand break repair (DSBR) that requires an intact, homologous template for DNA synthesis. When DNA synthesis associated with DSBR is convergent, the broken DNA strands are replaced and r...
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The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis
Published: February, 2016

Abstract: The association between impaired fetal growth and postnatal development of obesity has been demonstrated before. By comparing adipocytes differentiated from Mesenchymal Stem Cells (MSCs) taken from the umbilical cord and derived from normal and gr...
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Desensitization and incomplete recovery of hepatic target genes after chronic thyroid hormone treatment and withdrawal in male adult mice
Published: February, 2016

Abstract: Here, we examined changes in hepatic gene expression and serum TH/thyrotropin (TSH) levels in adult male mice treated either with a single T3 (20 g/100 g body weight) injection (acute T3) or daily injections for 14 days (chronic T3) followed ...
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Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes
Published: January, 2016

Abstract: Rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) is a method that allows the study of protein complexes, in particular chromatin and transcription factor complexes, in a rapid and robust manner by mass spectrometry (MS). Th...
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Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo
Published: January, 2016

Abstract: Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and silencing of genes mediate the response of plants to environmental signals and developmental cues...
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Analysis of EZH2: micro-RNA network in low and high grade astrocytic tumors
Published: January, 2016

Abstract: Enhancer of Zeste homologue2 (EZH2) is an epigenetic regulator that functions as oncogene in astrocytic tumors, however, EZH2 regulation remains little studied. In this study, we measured EZH2 levels in low (Gr-II,DA) and high grade (Gr-IV,GBM) as...
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Transducin-like enhancer of split-1 is expressed and functional in human macrophages
Published: December, 2015

Abstract: Macrophages display heterogeneous phenotypes, including the classical M1 proinflammatory and the alternative M2 anti-inflammatory polarization states. The transducin-like enhancer of split-1 (TLE1) is a transcriptional corepressor whose functions ...
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Epigenome-wide effects of vitamin D and their impact on the transcriptome of human monocytes involve CTCF
Published: December, 2015

Abstract: The physiological functions of vitamin D are mediated by its metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) activating the transcription factor vitamin D receptor (VDR). The chromatin-organizing protein CTCF bound to 14% of the 1,25(OH)2...
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Standardizing chromatin research: a simple and universal method for ChIP-seq
Published: December, 2015

Abstract: Here we demonstrate that harmonization of ChIP-seq workflows across cell types and conditions is possible when obtaining chromatin from properly isolated nuclei. We established an ultrasound-based nuclei extraction method (Nuclei Extraction b...
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HNF1β drives glutathione (GSH) synthesis underlying intrinsic carboplatin resistance of ovarian clear cell carcinoma (OCCC)
Published: October, 2015

Abstract: Chemoresistance to platinum-based antineoplastic agents is a consistent feature among ovarian carcinomas; however, whereas high-grade serous carcinoma (OSC) acquires resistance during chemotherapy, ovarian clear cell carcinoma (OCCC) is intrinsica...
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NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program
Published: October, 2015

Abstract: Abstract Cell fate specification relies on the action of critical transcription factors that become available at distinct stages of embryonic development. One such factor is NeuroD1, which is essential for eliciting the neuronal development progr...
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Acetylations of Ftz-F1 and histone H4K5 are required for the fine-tuning of ecdysone biosynthesis during Drosophila metamorphosis.
Published: August, 2015

Abstract: The molting during Drosophila development is tightly regulated by the ecdysone hormone. Several steps of the ecdysone biosynthesis have been already identified but the regulation of the entire process has not been clarified yet. We have previously...
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Acetylation of intragenic histones on HPV16 correlates with enhanced HPV16 gene expression.
Published: August, 2015

Abstract: We report that many histone modifications are unevenly distributed over the HPV16 genome in cervical cancer cells as well as in HPV16-immortalized keratinocytes. For example, H3K36me3 and H3K9Ac that are common in highly expressed cellular genes a...
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Folic acid administration inhibits amyloid β-peptide accumulation in APP/PS1 transgenic mice.
Published: August, 2015

Abstract: Alzheimer's disease (AD) is associated with malnutrition, altered one-carbon metabolism and increased hippocampal amyloid-β peptide (Aβ) accumulation. Aberrant DNA methylation may be an epigenetic mechanism that underlies AD pathogenesis...
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Enhancer of zeste homolog-2 (EZH2) methyltransferase regulates transgelin/smooth muscle-22α expression in endothelial cells in response to interleukin-1β and transforming growth factor-β2.
Published: August, 2015

Abstract: Smooth muscle-22α (SM22α), encoded by transgelin (TAGLN), is expressed in mesenchymal lineage cells, including myofibroblasts and smooth muscle cells. It is an F-actin binding protein that regulates the organization of actin cytoskelet...
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The Nuclear DNA Sensor IFI16 Acts as a Restriction Factor for Human Papillomavirus Replication through Epigenetic Modifications of the Viral Promoters.
Published: August, 2015

Abstract: UNLABELLED: The human interferon-inducible IFI16 protein, an innate immune sensor of intracellular DNA, was recently demonstrated to act as a restriction factor for human cytomegalovirus (HCMV) and herpes simplex virus 1 (HSV-1) infection by inhib...
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Sox9 Controls Self-Renewal of Oncogene Targeted Cells and Links Tumor Initiation and Invasion.
Published: July, 2015

Abstract: Sox9 is a transcription factor expressed in most solid tumors. However, the molecular mechanisms underlying Sox9 function during tumorigenesis remain unclear. Here, using a genetic mouse model of basal cell carcinoma (BCC), the most frequent cance...
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Regulation of the expression of claudin 23 by the enhancer of zeste 2 polycomb group protein in colorectal cancer.
Published: July, 2015

Abstract: Altered epigenetic mechanisms, similar to gene mutations, contribute to the pathogenesis and molecular heterogeneity of neoplasms, including colorectal cancer (CRC). Enhancer of zeste 2 (EZH2) is a histone methyltransferase, which is involved in e...
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GCDCA down-regulates gene expression by increasing Sp1 binding to the NOS-3 promoter in an oxidative stress dependent manner.
Published: July, 2015

Abstract: During the course of cholestatic liver diseases, the toxic effect of bile acids accumulation has been related to the decreased expression of endothelial nitric oxide synthase (NOS-3) and cellular oxidative stress increase. In the present study, we...
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Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells
Published: June, 2015

Abstract: Transposable elements comprise roughly 40% of mammalian genomes. They have an active role in genetic variation, adaptation and evolution through the duplication or deletion of genes or their regulatory elements, and transposable elements themselve...
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Lysine-specific demethylase (LSD1/KDM1A) and MYCN cooperatively repress tumor suppressor genes in neuroblastoma.
Published: June, 2015

Abstract: The chromatin-modifying enzyme lysine-specific demethylase 1, KDM1A/LSD1 is involved in maintaining the undifferentiated, malignant phenotype of neuroblastoma cells and its overexpression correlated with aggressive disease, poor differentiation an...
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Concurrent whole-genome haplotyping and copy-number profiling of single cells.
Published: June, 2015

Abstract: Methods for haplotyping and DNA copy-number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-geno...
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Disruption of BRD4 at H3K27Ac-enriched enhancer region correlates with decreased c-Myc expression in Merkel cell carcinoma.
Published: June, 2015

Abstract: Pathologic c-Myc expression is frequently detected in human cancers, including Merkel cell carcinoma (MCC), an aggressive skin cancer with no cure for metastatic disease. Bromodomain protein 4 (BRD4) regulates gene transcription by binding to acet...
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Gene chip analysis of Arabidopsis thaliana genomic DNA methylation and gene expression in response to carbendazim.
Published: June, 2015

Abstract: OBJECTIVES: To examine the effects of carbendazim on Arabidopsis genomic DNA methylation and gene expression. RESULTS: Carbendazim caused widespread changes in gene loci methylation and gene expression. With 0.1 mM (D2) and 0.2 mM (D3) carbendazim...
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Yap7 is a transcriptional repressor of nitric oxide oxidase in yeasts, which arose from neofunctionalization after whole genome duplication.
Published: June, 2015

Abstract: Flavohemoglobins are the main detoxifiers of nitric oxide (NO) in bacteria and fungi and are induced in response to nitrosative stress. In fungi, the flavohemoglobin encoding gene YHB1 is positively regulated by transcription factors which are act...
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Transcription of Nrdp1 by the androgen receptor is regulated by nuclear filamin A in prostate cancer.
Published: June, 2015

Abstract: Prostate cancer (PCa) progression is regulated by the androgen receptor (AR); however, patients undergoing androgen-deprivation therapy (ADT) for disseminated PCa eventually develop castration-resistant PCa (CRPC). Results of previous studies indi...
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Proteomic analysis of the herpes simplex virus 1 virion protein 16 transactivator protein in infected cells.
Published: June, 2015

Abstract: The herpes simplex virus 1 virion protein 16 (VP16) tegument protein forms a transactivation complex with the cellular proteins host cell factor 1 (HCF-1) and octamer-binding transcription factor 1 (Oct-1) upon entry into the host cell. VP16 has a...
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A SNP in the HTT promoter alters NF-κB binding and is a bidirectional genetic modifier of Huntington disease.
Published: June, 2015

Abstract: Cis-regulatory variants that alter gene expression can modify disease expressivity, but none have previously been identified in Huntington disease (HD). Here we provide in vivo evidence in HD patients that cis-regulatory variants in the HTT promot...
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Th2 Cytokines Augment IL-31/IL-31RA Interactions via STAT6-dependent IL-31RA Expression.
Published: May, 2015

Abstract: Interleukin 31 receptor α (IL-31RA) is a novel Type I cytokine receptor that pairs with oncostatin M receptor to mediate IL-31 signaling. Binding of IL-31 to its receptor results in the phosphorylation and activation of STATs, MAPK, and JNK signal...
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The N-terminal Set-β Protein Isoform Induces Neuronal Death.
Published: May, 2015

Abstract: Set-β protein plays different roles in neurons, but the diversity of Set-β neuronal isoforms and their functions have not been characterized. The expression and subcellular localization of Set-β are altered in Alzheimer disease, cleavage of Set-β ...
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Opposing role for Egr3 in nucleus accumbens cell subtypes in cocaine action.
Published: May, 2015

Abstract: An imbalance in molecular signaling cascades and transcriptional regulation in nucleus accumbens (NAc) medium spiny neuron (MSN) subtypes, those enriched in dopamine D1 versus D2 receptors, is implicated in the behavioral responses to psychostimul...
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Glucocorticoid receptor and Klf4 co-regulate anti-inflammatory genes in keratinocytes.
Published: May, 2015

Abstract: The glucocorticoid (GC) receptor (GR) and Kruppel-like factor Klf4 are transcription factors that play major roles in skin homeostasis. However, whether these transcription factors cooperate in binding genomic regulatory regions in epidermal kerat...
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Involvement of RNA Polymerase III in Immune Responses.
Published: May, 2015

Abstract: Inflammation in the tumor microenvironment has many tumor-promoting effects. In particular, tumor-associated macrophages (TAMs) produce many cytokines which can support tumor growth by promoting survival of malignant cells, angiogenesis, and metas...
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Control of brain patterning by Engrailed paracrine transfer: a new function of the Pbx interaction domain.
Published: May, 2015

Abstract: Homeoproteins of the Engrailed family are involved in the patterning of mesencephalic boundaries through a mechanism classically ascribed to their transcriptional functions. In light of recent reports on the paracrine activity of homeoproteins, in...
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The Novel Gene CRNDE Encodes a Nuclear Peptide (CRNDEP) Which Is Overexpressed in Highly Proliferating Tissues.
Published: May, 2015

Abstract: CRNDE, recently described as the lncRNA-coding gene, is overexpressed at RNA level in human malignancies. Its role in gametogenesis, cellular differentiation and pluripotency has been suggested as well. Herein, we aimed to verify our hypothesis th...
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Aerobic glycolysis tunes YAP/TAZ transcriptional activity.
Published: May, 2015

Abstract: Increased glucose metabolism and reprogramming toward aerobic glycolysis are a hallmark of cancer cells, meeting their metabolic needs for sustained cell proliferation. Metabolic reprogramming is usually considered as a downstream consequence of t...
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Snai1 regulates cell lineage allocation and stem cell maintenance in the mouse intestinal epithelium
Published: May, 2015

Abstract: Snail family members regulate epithelial-to-mesenchymal transition (EMT) during invasion of intestinal tumours, but their role in normal intestinal homeostasis is unknown. Studies in breast and skin epithelia indicate that Snail proteins promote a...
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Antisense RNA Controls LRP1 Sense Transcript Expression through Interaction with a Chromatin-Associated Protein, HMGB2.
Published: May, 2015

Abstract: Long non-coding RNAs (lncRNAs), including natural antisense transcripts (NATs), are expressed more extensively than previously anticipated and have widespread roles in regulating gene expression. Nevertheless, the molecular mechanisms of action of...
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Experimental acute lung injury induces multi-organ epigenetic modifications in key angiogenic genes implicated in sepsis-associated endothelial dysfunction.
Published: May, 2015

Abstract: INTRODUCTION: The Tie2/angiopoietin (Tie2/Ang) and vascular endothelial growth factor receptor-ligand systems (VEGFR/VEGF) are recognized to play important roles in the regulation of microvascular endothelial function. Downregulation of these gen...
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Paclitaxel targets FOXM1 to regulate KIF20A in mitotic catastrophe and breast cancer paclitaxel resistance.
Published: May, 2015

Abstract: FOXM1 has been implicated in taxane resistance, but the molecular mechanism involved remains elusive. In here, we show that FOXM1 depletion can sensitize breast cancer cells and mouse embryonic fibroblasts into entering paclitaxel-induced senescen...
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TGF-β1-induced EMT promotes targeted migration of breast cancer cells through the lymphatic system by the activation of CCR7/CCL21-mediated chemotaxis.
Published: May, 2015

Abstract: Tumor cells frequently disseminate through the lymphatic system during metastatic spread of breast cancer and many other types of cancer. Yet it is not clear how tumor cells make their way into the lymphatic system and how they choose between lymp...
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Characterization of genome-wide ordered sequence-tagged Mycobacterium mutant libraries by Cartesian Pooling-Coordinate Sequencing.
Published: May, 2015

Abstract: Reverse genetics research approaches require the availability of methods to rapidly generate specific mutants. Alternatively, where these methods are lacking, the construction of pre-characterized libraries of mutants can be extremely valuable. Ho...
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Roles of hepatic glucokinase in intertissue metabolic communication: Examination of novel liver-specific glucokinase knockout mice.
Published: May, 2015

Abstract: Glucokinase is expressed principally in pancreatic β-cells and hepatocytes, and catalyzes the phosphorylation of glucose to glucose-6-phosphate, a rate-limiting step of glycolysis. To better understand the roles of hepatic glucokinase, we generate...
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Type I interferons regulate eomesodermin expression and the development of unconventional memory CD8(+) T cells.
Published: May, 2015

Abstract: CD8(+) T-cell memory phenotype and function are acquired after antigen-driven activation. Memory-like cells may also arise in absence of antigenic exposure in the thymus or in the periphery. Eomesodermin (Eomes) is a key transcription factor for t...
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Within-host diversity of MRSA antimicrobial resistances.
Published: May, 2015

Abstract: OBJECTIVES: MRSA is a major antimicrobial resistance (AMR) pathogen. The reservoir of infecting isolates is colonization, which is the site of evolutionary selection. The aim was to identify if AMRs in colonizing MRSA populations diversified and p...
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The Basal Transcription Complex Component TAF3 Transduces Changes in Nuclear Phosphoinositides into Transcriptional Output.
Published: May, 2015

Abstract: Phosphoinositides (PI) are important signaling molecules in the nucleus that influence gene expression. However, if and how nuclear PI directly affects the transcriptional machinery is not known. We report that the lipid kinase PIP4K2B regulates n...
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Interaction with WDR5 Promotes Target Gene Recognition and Tumorigenesis by MYC.
Published: May, 2015

Abstract: MYC is an oncoprotein transcription factor that is overexpressed in the majority of malignancies. The oncogenic potential of MYC stems from its ability to bind regulatory sequences in thousands of target genes, which depends on interaction of MYC ...
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Supp. informations: Interaction with WDR5 Promotes Target Gene Recognition and Tumorigenesis by MYC.
Published: May, 2015

Abstract: MYC is an oncoprotein transcription factor that is overexpressed in the majority of malignancies. The oncogenic potential of MYC stems from its ability to bind regulatory sequences in thousands of target genes, which depends on interaction of MYC ...
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A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins
Published: May, 2015

Abstract: The field of population genetics is rapidly moving into population genomics as the quantity of data generated by high-throughput sequencing platforms increases. In this study, we used restriction-site-associated DNA sequencing (RADSeq) to recover ...
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Non-coding RNA Generated following Lariat Debranching Mediates Targeting of AID to DNA.
Published: May, 2015

Abstract: Transcription through immunoglobulin switch (S) regions is essential for class switch recombination (CSR), but no molecular function of the transcripts has been described. Likewise, recruitment of activation-induced cytidine deaminase (AID) to S r...
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Uvrag targeting by Mir125a and Mir351 modulates autophagy associated with Ewsr1 deficiency.
Published: May, 2015

Abstract: The EWSR1 (EWS RNA-binding protein 1/Ewing Sarcoma Break Point Region 1) gene encodes a RNA/DNA binding protein that is ubiquitously expressed and involved in various cellular processes. EWSR1 deficiency leads to impairment of development and acce...
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Evidence Supporting a Role for TopBP1 and Brd4 in the Initiation but Not Continuation of Human Papillomavirus 16 E1/E2-Mediated DNA Replication.
Published: May, 2015

Abstract: UNLABELLED: To replicate the double-stranded human papillomavirus 16 (HPV16) DNA genome, viral proteins E1 and E2 associate with the viral origin of replication, and E2 can also regulate transcription from adjacent promoters. E2 interacts with hos...
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Telomerase regulates MYC-driven oncogenesis independent of its reverse transcriptase activity.
Published: May, 2015

Abstract: Constitutively active MYC and reactivated telomerase often coexist in cancers. While reactivation of telomerase is thought to be essential for replicative immortality, MYC, in conjunction with cofactors, confers several growth advantages to cancer...
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Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases.
Published: May, 2015

Abstract: The treatment of drug-resistant tuberculosis cases is challenging, as drug options are limited, and the existing diagnostics are inadequate. Whole-genome sequencing (WGS) has been used in a clinical setting to investigate six cases of suspected ex...
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Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms.
Published: May, 2015

Abstract: Most disease associations detected by genome-wide association studies (GWAS) lie outside coding genes, but very few have been mapped to causal regulatory variants. Here, we present a method for detecting regulatory quantitative trait loci (QTLs) t...
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Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.
Published: May, 2015

Abstract: To identify chromatin mechanisms of neuronal differentiation, we characterized chromatin accessibility and gene expression in cerebellar granule neurons (CGNs) of the developing mouse. We used DNase-seq to map accessibility of cis-regulatory eleme...
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A lncRNA regulates alternative splicing via establishment of a splicing-specific chromatin signature.
Published: May, 2015

Abstract: Alternative pre-mRNA splicing is a highly cell type-specific process essential to generating protein diversity. However, the mechanisms responsible for the establishment and maintenance of heritable cell-specific alternative-splicing programs are ...
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Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.
Published: May, 2015

Abstract: Technologies that enable targeted manipulation of epigenetic marks could be used to precisely control cell phenotype or interrogate the relationship between the epigenome and transcriptional control. Here we describe a programmable, CRISPR-Cas9-ba...
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C2H2 zinc finger proteins greatly expand the human regulatory lexicon.
Published: May, 2015

Abstract: Cys2-His2 zinc finger (C2H2-ZF) proteins represent the largest class of putative human transcription factors. However, for most C2H2-ZF proteins it is unknown whether they even bind DNA or, if they do, to which sequences. Here, by combining data f...
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Linking the aryl hydrocarbon receptor with altered DNA methylation patterns and developmentally induced aberrant antiviral CD8+ T cell responses.
Published: May, 2015

Abstract: Successfully fighting infection requires a properly tuned immune system. Recent epidemiological studies link exposure to pollutants that bind the aryl hydrocarbon receptor (AHR) during development with poorer immune responses later in life. Yet, h...
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Global regulation of heterochromatin spreading by Leo1.
Published: May, 2015

Abstract: Heterochromatin plays important roles in eukaryotic genome regulation. However, the repressive nature of heterochromatin combined with its propensity to self-propagate necessitates robust mechanisms to contain heterochromatin within defined bounda...
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Development of microsatellite primers in the protected species Viola elatior (Violaceae) using next-generation sequencing.
Published: May, 2015

Abstract: PREMISE OF THE STUDY: Viola elatior (Violaceae) is a Eurasian perennial plant species in which French populations are threatened by anthropogenic pressures. Microsatellite primers were developed to investigate its genetic structure and diversity. ...
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The interaction of mycobacterial protein Rv2966c with host chromatin is mediated through non-CpG methylation and histone H3/H4 binding.
Published: April, 2015

Abstract: To effectively modulate the gene expression within an infected mammalian cell, the pathogen Mycobacterium tuberculosis would need to bring about epigenetic modifications at appropriate genomic loci. Working on this hypothesis, we show in this stud...
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Truncated HBx-dependent silencing of GAS2 promotes hepatocarcinogenesis through deregulation of cell cycle, senescence and p53-mediated apoptosis
Published: April, 2015

Abstract: Hepatocellular carcinoma (HCC) is a worldwide threat to public health, especially in China, where chronic hepatitis B virus (HBV) infection is found in 80-90% of all HCCs. The HBV-encoded X antigen (HBx) is a trans-regulatory protein involved in v...
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Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation.
Published: April, 2015

Abstract: Inflammation is a beneficial host response to infection but can contribute to inflammatory disease if unregulated. The Th17 lineage of T helper (Th) cells can cause severe human inflammatory diseases. These cells exhibit both instability (they can...
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Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling.
Published: April, 2015

Abstract: A bimodal switch model is widely used to describe transcriptional regulation by the thyroid hormone receptor (TR). In this model, the unliganded TR forms stable, chromatin-bound complexes with transcriptional co-repressors to repress transcription...
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Spt6 Is Essential for rRNA Synthesis by RNA Polymerase I
Published: April, 2015

Abstract: Spt6 has many roles in transcription initiation and elongation by RNA polymerase (Pol) II. These effects are mediated through interactions with histones, transcription factors, and the RNA polymerase. Two lines of evidence suggest that Spt6 also p...
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Suppression of Interferon β gene transcription by inhibitors of Bromodomain and Extra-Terminal (BET) family members.
Published: April, 2015

Abstract: Polo-Like Kinase (PLK) inhibitors, such as BI-2536, have been reported to suppress interferon β (IFNβ) gene transcription induced by ligands that activate TLR3 and TLR4. Here, we report that BI-2536 is likely to exert this effect by preventing the...
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RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements.
Published: April, 2015

Abstract: In mouse embryonic cells, ligand-activated retinoic acid receptors (RARs) play a key role in inhibiting pluripotency-maintaining genes and activating some major actors of cell differentiation. To investigate the mechanism underlying this dual regu...
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Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells.
Published: April, 2015

Abstract: Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections, and comprise nearly 8% of the human genome. The most recently acquired human ERV is HERVK(HML-2), which repeatedly infected the primate lineage both before and after the...
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Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.
Published: April, 2015

Abstract: Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end ...
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The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers.
Published: April, 2015

Abstract: While the importance of gene enhancers in transcriptional regulation is well established, the mechanisms and the protein factors that determine enhancers activity have only recently begun to be unravelled. Recent studies have shown that progestero...
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Genome-Wide Analysis of Phosphorylated PhoP Binding to Chromosomal DNA Reveals Several Novel Features of the PhoPR-Mediated Phosphate Limitation Response in Bacillus subtilis.
Published: April, 2015

Abstract: UNLABELLED: The PhoPR two-component signal transduction system controls one of three responses activated by Bacillus subtilis to adapt to phosphate-limiting conditions (PHO response). The response involves the production of enzymes and transporter...
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High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq.
Published: April, 2015

Abstract: Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexi...
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Transcriptional co-repressor function of the hippo pathway transducers YAP and TAZ.
Published: April, 2015

Abstract: YAP (yes-associated protein) and TAZ are oncogenic transcriptional co-activators downstream of the Hippo tumor-suppressor pathway. However, whether YAP and/or TAZ (YAP/TAZ) engage in transcriptional co-repression remains relatively unexplored. Her...
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Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain.
Published: April, 2015

Abstract: Embryogenesis requires the precise activation and repression of many transcriptional regulators. The Polycomb group proteins and the associated H3K27me3 histone mark are essential to maintain the inactive state of many of these genes. Mammalian Ho...
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Divergent androgen regulation of unfolded protein response pathways drives prostate cancer
Published: April, 2015

Abstract: The unfolded protein response (UPR) is a homeostatic mechanism to maintain endoplasmic reticulum (ER) function. The UPR is activated by various physiological conditions as well as in disease states, such as cancer. As androgens regulate secretion ...
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Impact of oxidative stress defense on bacterial survival and morphological change in Campylobacter jejuni under aerobic conditions.
Published: April, 2015

Abstract: Campylobacter jejuni, a microaerophilic foodborne pathogen, inescapably faces high oxygen tension during its transmission to humans. Thus, the ability of C. jejuni to survive under oxygen-rich conditions may significantly impact C. jejuni viabilit...
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The Paf1 complex represses small-RNA-mediated epigenetic gene silencing.
Published: April, 2015

Abstract: RNA interference (RNAi) refers to the ability of exogenously introduced double-stranded RNA to silence expression of homologous sequences. Silencing is initiated when the enzyme Dicer processes the double-stranded RNA into small interfering RNAs (...
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Draft genome sequences of 26 porphyromonas strains isolated from the canine oral microbiome.
Published: April, 2015

Abstract: We present the draft genome sequences for 26 strains of Porphyromonas (P. canoris, P. gulae, P. cangingavalis, P. macacae, and 7 unidentified) and an unidentified member of the Porphyromonadaceae family. All of these strains were isolated from the...
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Characterization of the transcriptome of nascent hair cells and identification of direct targets of the Atoh1 transcription factor.
Published: April, 2015

Abstract: Hair cells are sensory receptors for the auditory and vestibular system in vertebrates. The transcription factor Atoh1 is both necessary and sufficient for the differentiation of hair cells, and is strongly upregulated during hair-cell regeneratio...
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Quantitative analysis of the TNF-α-induced phosphoproteome reveals AEG-1/MTDH/LYRIC as an IKKβ substrate.
Published: April, 2015

Abstract: The inhibitor of the nuclear factor-κB (IκB) kinase (IKK) complex is a key regulator of the canonical NF-κB signalling cascade and is crucial for fundamental cellular functions, including stress and immune responses. The majority of IKK complex fu...
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Zinc regulates a switch between primary and alternative S18 ribosomal proteins in Mycobacterium tuberculosis.
Published: April, 2015

Abstract: The Mycobacterium tuberculosis genome encodes five putative 'alternative' ribosomal proteins whose expression is repressed at high Zn(2+) concentration. Each alternative protein has a primary homologue that is predicted to bind Zn(2+) . We hypothe...
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Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp plantarum is a later heterotypic synonym of Bacillus methylotrophicus.
Published: April, 2015

Abstract: The rhizosphere isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These...
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Long-lasting pro-inflammatory suppression of microglia by LPS-preconditioning is mediated by RelB-dependent epigenetic silencing.
Published: April, 2015

Abstract: Microglia, the innate immune cells of the central nervous system (CNS), react to endotoxins like bacterial lipopolysaccharides (LPS) with a pronounced inflammatory response. To avoid excess damage to the CNS, the microglia inflammatory response ne...
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A Role for the Serine/Arginine-Rich (SR) Protein B52/SRSF6 in Cell Growth and Myc Expression in Drosophila.
Published: April, 2015

Abstract: Serine-/arginine-rich (SR) proteins are RNA-binding proteins that are primarily involved in alternative splicing. Expression of some SR proteins is frequently upregulated in tumors, and previous reports have demonstrated that these proteins can di...
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Effect of poly(ADP-ribose)polymerase and DNA topoisomerase I inhibitors on the p53/p63-dependent survival of carcinoma cells.
Published: April, 2015

Abstract: Depending on their genetic background (p53(wt) versus p53(null)), carcinoma cells are more or less sensitive to drug-induced cell cycle arrest and/or apoptosis. Among the members of the p53 family, p63 is characterized by two N-terminal isoforms, ...
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Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment.
Published: April, 2015

Abstract: The North American carnivorous pitcher plant genus Sarracenia (Sarraceniaceae) is a relatively young clade (
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Targeting the MLL complex in castration-resistant prostate cancer.
Published: April, 2015

Abstract: Resistance to androgen deprivation therapies and increased androgen receptor (AR) activity are major drivers of castration-resistant prostate cancer (CRPC). Although prior work has focused on targeting AR directly, co-activators of AR signaling, w...
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Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
Published: April, 2015

Abstract: Protein quality control is essential for clearing misfolded and aggregated proteins from the cell, and its failure is associated with many neurodegenerative disorders. Here, we identify two genes, ufd-2 and spr-5, that when inactivated, synergisti...
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STAT3 and HIF1alpha Signalling Drives Oncogenic Cellular Phenotypes in Malignant Peripheral Nerve Sheath Tumors (MPNSTs).
Published: April, 2015

Abstract: Therapeutic options are limited for Neurofibromatosis type 1 (NF1) associated malignant peripheral nerve sheath tumours(MPNSTs) and clinical trials using drug agents have so far been unsuccessful. This lack of clinical success is likely attributed...
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Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding.
Published: April, 2015

Abstract: Genome-wide association studies (GWAS) have identified over 40 loci that affect risk of coronary artery disease (CAD) and the causal mechanisms at the majority of loci are unknown. Recent studies have suggested that many causal GWAS variants influ...
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5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer.
Published: April, 2015

Abstract: BACKGROUND: The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferati...
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The epigenetic regulator G9a mediates tolerance to RNA virus infection in Drosophila.
Published: April, 2015

Abstract: Little is known about the tolerance mechanisms that reduce the negative effects of microbial infection on host fitness. Here, we demonstrate that the histone H3 lysine 9 methyltransferase G9a regulates tolerance to virus infection by shaping the r...
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Oxyntomodulin regulates resetting of the liver circadian clock by food
Published: March, 2015

Abstract: Circadian clocks coordinate 24-hr rhythms of behavior and physiology. In mammals, a master clock residing in the suprachiasmatic nucleus (SCN) is reset by the light-dark cycle, while timed food intake is a potent synchronizer of peripheral clocks ...
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GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters
Published: March, 2015

Abstract: Previous studies have shown that GAGA Factor (GAF) is enriched on promoters with paused RNA Polymerase II (Pol II), but its genome-wide function and mechanism of action remain largely uncharacterized. We assayed the levels of transcriptionally-eng...
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CXCR4 expression on pathogenic T cells facilitates their bone marrow infiltration in a mouse model of aplastic anemia.
Published: March, 2015

Abstract: Aplastic anemia (AA) is a disease characterized by T-cell-mediated destruction of bone marrow (BM) hematopoietic stem and progenitor cells. Physiologically, T cells migrate to the BM in response to chemokines, such as SDF-1α, the ligand for CXCR4....
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Induction of hematopoietic and endothelial cell program orchestrated by ETS transcription factor ER71/ETV2
Published: March, 2015

Abstract: The ETS factor ETV2 (aka ER71) is essential for the generation of the blood and vascular system, as ETV2 deficiency leads to a complete block in blood and endothelial cell formation and embryonic lethality in the mouse. However, the ETV2-mediated ...
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SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation.
Published: March, 2015

Abstract: Short interspersed nuclear elements (SINEs), such as Alu, spread by retrotransposition, which requires their transcripts to be copied into DNA and then inserted into new chromosomal sites. This can lead to genetic damage through insertional mutage...
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Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis).
Published: March, 2015

Abstract: BACKGROUND: Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of wh...
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Polyploidy can drive rapid adaptation in yeast.
Published: March, 2015

Abstract: Polyploidy is observed across the tree of life, yet its influence on evolution remains incompletely understood. Polyploidy, usually whole-genome duplication, is proposed to alter the rate of evolutionary adaptation. This could occur through comple...
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Targeting Nrf2 in healthy and malignant ovarian epithelial cells: Protection versus promotion.
Published: March, 2015

Abstract: Risk factors indicate the importance of oxidative stress during ovarian carcinogenesis. To tolerate oxidative stress, cells activate the transcription factor Nrf2 (Nfe2l2), the master regulator of antioxidant and cytoprotective genes. Indeed, for ...
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Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis.
Published: March, 2015

Abstract: BACKGROUND: Bambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers ha...
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Breeding scheme and maternal small RNAs affect the efficiency of transgenerational inheritance of a paramutation in mice.
Published: March, 2015

Abstract: Paramutations result from interactions between two alleles at a single locus, whereby one induces a heritable change in the other. Although common in plants, paramutations are rarely studied in animals. Here, we report a new paramutation mouse mod...
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Epigenetic modulation with HDAC inhibitor CG200745 induces anti-proliferation in non-small cell lung cancer cells.
Published: March, 2015

Abstract: Histone modification plays a pivotal role on gene regulation, as regarded as global epigenetic markers, especially in tumor related genes. Hence, chemical approaches targeting histone-modifying enzymes have emerged onto the main stage of anticance...
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Impact of Thyroid Hormones on Estrogen Receptor α-Dependent Transcriptional Mechanisms in Ventromedial Hypothalamus and Preoptic Area.
Published: March, 2015

Abstract: Elevated levels of thyroid hormones (TH) reduce estradiol (E2)-dependent female sexual behavior. E2 stimulates progesterone receptor (Pgr) and oxytocin receptor (Oxtr) within the ventromedial hypothalamus and preoptic area, critical hypothalamic n...
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Adipose tissue-derived stem cells from obese subjects contribute to inflammation and reduced insulin response in adipocytes through differential regulation of the Th1/Th17 balance and monocyte activation.
Published: March, 2015

Abstract: Obesity, through low-grade inflammation, can drive insulin-resistance and type 2 diabetes. While infiltration of adipose tissue (AT) with mononuclear cells (MNC) is well established in obesity, the functional consequences of these interactions are...
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The nuclear receptor nr4a1 controls CD8 T cell development through transcriptional suppression of runx3.
Published: March, 2015

Abstract: The NR4A nuclear receptor family member Nr4a1 is strongly induced in thymocytes undergoing selection, and has been shown to control the development of Treg cells; however the role of Nr4a1 in CD8(+) T cells remains undefined. Here we report a nove...
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Genome wide expression profiling of p53 regulated miRNAs in neuroblastoma.
Published: March, 2015

Abstract: Restoration of the antitumor activity of p53 could offer a promising approach for the treatment of neuroblastoma. MicroRNAs (miRNAs) are important mediators of p53 activity, but their role in the p53 response has not yet been comprehensively addre...
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Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency.
Published: March, 2015

Abstract: The mechanisms by which transcription factor haploinsufficiency alters the epigenetic and transcriptional landscape in human cells to cause disease are unknown. Here, we utilized human induced pluripotent stem cell (iPSC)-derived endothelial cells...
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H3K4me3 demethylation by the histone demethylase KDM5C/JARID1C promotes DNA replication origin firing.
Published: March, 2015

Abstract: DNA replication is a tightly regulated process that initiates from multiple replication origins and leads to the faithful transmission of the genetic material. For proper DNA replication, the chromatin surrounding origins needs to be remodeled. Ho...
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Identification of FOXM1 as a therapeutic target in B-cell lineage acute lymphoblastic leukaemia.
Published: March, 2015

Abstract: Despite recent advances in the cure rate of acute lymphoblastic leukaemia (ALL), the prognosis for patients with relapsed ALL remains poor. Here we identify FOXM1 as a candidate responsible for an aggressive clinical course. We show that FOXM1 lev...
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PW1/Peg3 expression regulates key properties that determine mesoangioblast stem cell competence.
Published: March, 2015

Abstract: Mesoangioblasts are vessel-associated progenitor cells that show therapeutic promise for the treatment of muscular dystrophy. Mesoangioblasts have the ability to undergo skeletal muscle differentiation and cross the blood vessel wall regardless of...
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AtEAF1 is a potential platform protein for Arabidopsis NuA4 acetyltransferase complex.
Published: March, 2015

Abstract: BACKGROUND: Histone acetyltransferase complex NuA4 and histone variant exchanging complex SWR1 are two chromatin modifying complexes which act cooperatively in yeast and share some intriguing structural similarities. Protein subunits of NuA4 and S...
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Nuclear matrix binding protein SMAR1 regulates T-cell differentiation and allergic airway disease.
Published: March, 2015

Abstract: Asthma is a complex airway allergic disease involving the interplay of various cell types, cytokines, and transcriptional factors. Though many factors contribute to disease etiology, the molecular control of disease phenotype and responsiveness is...
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Genome-wide mapping reveals conservation of promoter DNA methylation following chicken domestication.
Published: March, 2015

Abstract: It is well-known that environment influences DNA methylation, however, the extent of heritable DNA methylation variation following animal domestication remains largely unknown. Using meDIP-chip we mapped the promoter methylomes for 23,316 genes in...
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Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells
Published: March, 2015

Abstract: DNA methylation is thought to be robust to environmental perturbations on a short time scale. Here, we challenge that view by demonstrating that the infection of human dendritic cells (DCs) with a pathogenic bacteria is associated with rapid chang...
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Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.
Published: March, 2015

Abstract: Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns...
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Taspase1-dependent TFIIA cleavage coordinates head morphogenesis by limiting Cdkn2a locus transcription.
Published: March, 2015

Abstract: Head morphogenesis requires complex signal relays to enable precisely coordinated proliferation, migration, and patterning. Here, we demonstrate that, during mouse head formation, taspase1-mediated (TASP1-mediated) cleavage of the general transcri...
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Rad51-mediated replication fork reversal is a global response to genotoxic treatments in human cells.
Published: March, 2015

Abstract: Replication fork reversal protects forks from breakage after poisoning of Topoisomerase 1. We here investigated fork progression and chromosomal breakage in human cells in response to a panel of sublethal genotoxic treatments, using other topoisom...
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Exon-intron circular RNAs regulate transcription in the nucleus.
Published: March, 2015

Abstract: Noncoding RNAs (ncRNAs) have numerous roles in development and disease, and one of the prominent roles is to regulate gene expression. A vast number of circular RNAs (circRNAs) have been identified, and some have been shown to function as microRNA...
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Essential role of the iron-sulfur cluster binding domain of the primase regulatory subunit Pri2 in DNA replication initiation.
Published: March, 2015

Abstract: DNA primase catalyzes de novo synthesis of a short RNA primer that is further extended by replicative DNA polymerases during initiation of DNA replication. The eukaryotic primase is a heterodimeric enzyme comprising a catalytic subunit Pri1 and a ...
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The Integrator complex controls the termination of transcription at diverse classes of gene targets.
Published: March, 2015

Abstract: Complexes containing INTS3 and either NABP1 or NABP2 were initially characterized in DNA damage responses, but their biochemical function remained unknown. Using affinity purifications and HIV Integration targeting-sequencing (HIT-Seq), we find th...
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The DREAM complex promotes gene body H2A.Z for target repression.
Published: March, 2015

Abstract: The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle genes, but its mechanism of action is poorly understood. Here we show that Caenorhabditis elegans DREAM targets have an unusual p...
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Genome-wide redistribution of BRD4 binding sites in transformation resistant cells.
Published: March, 2015

Abstract: Hutchinson-Gilford progeria syndrome (HGPS) patients do not develop cancer despite a significant accumulation of DNA damage in their cells. We have recently reported that HGPS cells are refractory to experimental oncogenic transformation and we id...
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The histone chaperone complex HIR *maintains *nucleosome occupancy and counterbalances impaired histone deposition in CAF-1 mutants.
Published: March, 2015

Abstract: Chromatin organization is essential for coordinated gene expression, genome stability, and inheritance of epigenetic information. Main components of chromatin assembly are specific complexes such as CHROMATIN ASSEMBLY FACTOR 1 (CAF-1) and HISTONE ...
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FUBP1: a new protagonist in splicing regulation of the DMD gene.
Published: February, 2015

Abstract: We investigated the molecular mechanisms for in-frame skipping of DMD exon 39 caused by the nonsense c.5480T>A mutation in a patient with Becker muscular dystrophy. RNase-assisted pull down assay coupled with mass spectrometry revealed that the mu...
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Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy
Published: February, 2015

Abstract: To gain insights into the interrelationships among childhood undernutrition, the gut microbiota, and gut mu- cosal immune/barrier function, we purified bacterial strains targeted by immunoglobulin A (IgA) from the fecal microbiota of two cohorts o...
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Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae.
Published: February, 2015

Abstract: DNA methylation is an important epigenetic modification that regulates development of plants and mammals. To investigate the roles of DNA methylation in fungal development, we profiled genome-wide methylation patterns at single-nucleotide resoluti...
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A Meier-Gorlin Syndrome Mutation Impairs the ORC1-Nucleosome Association.
Published: February, 2015

Abstract: Recent studies have identified several genetic mutations within the BAH domain of human Origin Recognition Complex subunit 1 (hORC1BAH), including the R105Q mutation, implicated in Meier-Gorlin Syndrome (MGS). However, the pathological role of the...
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MCPH1 maintains long-term epigenetic silencing of ANGPT2 in chronic lymphocytic leukemia.
Published: February, 2015

Abstract: The microcephalin gene (MCPH1) [also known as inhibitor of human telomerase reverse transcriptase (hTERT) expression] is a tumor suppressor gene that is functionally involved in the DNA damage response. Angiopoietin 2 (ANGPT2) is a crucial factor ...
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Silica nanoparticles induce oxidative stress, inflammation, and endothelial dysfunction in vitro via activation of the MAPK/Nrf2 pathway and nuclear factor-κB signaling.
Published: February, 2015

Abstract: Abstract: Despite the widespread application of silica nanoparticles (SiNPs) in industrial, commercial, and biomedical fields, their response to human cells has not been fully elucidated. Overall, little is known about the toxicological effec...
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Intermediate DNA methylation is a conserved signature of genome regulation.
Published: February, 2015

Abstract: The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions of intermediate methylation and their quantitative relationship with gene activity, we apply integrative and comparative epigenomics to 25 hum...
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Epigenetic and transcriptional determinants of the human breast.
Published: February, 2015

Abstract: While significant effort has been dedicated to the characterization of epigenetic changes associated with prenatal differentiation, relatively little is known about the epigenetic changes that accompany post-natal differentiation where fully funct...
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MEK guards proteome stability and inhibits tumor-suppressive amyloidogenesis via HSF1.
Published: February, 2015

Abstract: Signaling through RAS/MAP kinase pathway is central to biology. ERK has long been perceived as the only substrate for MEK. Here, we report that HSF1, the master regulator of the proteotoxic stress response, is a new MEK substrate. Beyond mediating...
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p73 engages A2B receptor signalling to prime cancer cells to chemotherapy-induced death.
Published: February, 2015

Abstract: Tumour cells often acquire the ability to escape cell death, a key event leading to the development of cancer. In almost half of all human cancers, the capability to induce cell death is reduced by the mutation and inactivation of p53, a tumour su...
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Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
Published: February, 2015

Abstract: Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequ...
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The Activation of IL-1-Induced Enhancers Depends on TAK1 Kinase Activity and NF-κB p65.
Published: February, 2015

Abstract: The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the genome-wide binding of the TAK1-controlled NF-...
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Circulating nucleic acids damage DNA of healthy cells by integrating into their genomes
Published: February, 2015

Abstract: Whether nucleic acids that circulate in blood have any patho-physiological functions in the host have not been explored.We report here that far from being inert molecules, circulating nucleic acids have significant biological activities of their o...
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Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics.
Published: February, 2015

Abstract: Ten eleven translocation (Tet) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be further excised by thymine-DNA glycosylase (Tdg). Here, we present...
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Genipin as a novel chemical activator of EBV lytic cycle.
Published: February, 2015

Abstract: Epstein-Barr virus (EBV) is a ubiquitous gammaherpesvirus that causes acute infection and establishes life-long latency. EBV causes several human cancers, including Burkitt's lymphoma, nasopharyngeal and gastric carcinoma. Antiviral agents can be ...
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Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling.
Published: February, 2015

Abstract: Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically...
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Increased HDAC3 and decreased miRNA-130a expression in PBMCs through recruitment HDAC3 in patients with spinal cord injuries
Published: February, 2015

Abstract: The study was performed to investigate the molecular mechanism for SCI patients. The interaction between miRNA-130a and HDAC was demonstrated in PBMCs from SCI patients. Increased HDAC3 and decreased miRNA-130a were observed in PBMCs from AS patie...
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Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli.
Published: February, 2015

Abstract: Escherichia coli endoribonuclease E has a major influence on gene expression. It is essential for the maturation of ribosomal and transfer RNA as well as the rapid degradation of messenger RNA. The latter ensures that translation closely follows p...
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Tat predominantly associates with host promoter elements in HIV-1-infected T-cells - regulatory basis of transcriptional repression of c-Rel.
Published: February, 2015

Abstract: UNLABELLED: HIV-1 Tat is a multifunctional regulatory protein that, in addition to its primary function of transactivating viral transcription, also tends to modulate cellular gene expression, for which the molecular mechanism remains to be clarif...
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Polycomb YY1 is a critical interface between epigenetic code and miRNA machinery after exposure to hypoxia in malignancy.
Published: January, 2015

Abstract: Yin Yang 1 (YY1) is a member of polycomb protein family involved in epigenetic modifications and transcriptional controls. We have shown that YY1 acts as positive regulator of tumor growth and angiogenesis by interfering with the VEGFA network. Ye...
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Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan.
Published: January, 2015

Abstract: Several pathways modulating longevity and stress resistance converge on translation by targeting ribosomal proteins or initiation factors, but whether this involves modifications of ribosomal RNA is unclear. Here, we show that reduced levels of th...
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Curcumin inhibits anchorage-independent growth of HT29 human colon cancer cells by targeting epigenetic restoration of the tumor suppressor gene DLEC1.
Published: January, 2015

Abstract: Colorectal cancer remains the most prevalent malignancy in humans. The impact of epigenetic alterations on the development of this complex disease is now being recognized. The dynamic and reversible nature of epigenetic modifications makes them a ...
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Reduced Expression of MYC Increases Longevity and Enhances Healthspan.
Published: January, 2015

Abstract: MYC is a highly pleiotropic transcription factor whose deregulation promotes cancer. In contrast, we find that Myc haploinsufficient (Myc(+/-)) mice exhibit increased lifespan. They show resistance to several age-associated pathologies, including ...
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Ligand-dependent enhancer activation regulated by topoisomerase-I activity.
Published: January, 2015

Abstract: The discovery that enhancers are regulated transcription units, encoding eRNAs, has raised new questions about the mechanisms of their activation. Here, we report an unexpected molecular mechanism that underlies ligand-dependent enhancer activatio...
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A small peptide derived from p53 linker region can resume the apoptotic activity of p53 by sequestering iASPP with p53.
Published: January, 2015

Abstract: One of the most important tumor suppression functions of p53 is its ability to induce apoptosis. iASPP is an inhibitory member of the ASPP protein family. It can specifically inhibit the normal function of p53 as a suppressor. The mechanism of iAS...
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Coexistent ARID1A-PIK3CA mutations promote ovarian clear-cell tumorigenesis through pro-tumorigenic inflammatory cytokine signalling.
Published: January, 2015

Abstract: Ovarian clear-cell carcinoma (OCCC) is an aggressive form of ovarian cancer with high ARID1A mutation rates. Here we present a mutant mouse model of OCCC. We find that ARID1A inactivation is not sufficient for tumour formation, but requires concur...
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Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome.
Published: January, 2015

Abstract: BackgroundBy comparing fibroblasts collected from animals at 5-months or 16-months of age we have previously found that the cultures from older animals produce much more IL-8 in response to lipopolysaccharide (LPS) stimulation. We now expand this ...
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Pharmacologically relevant doses of valproate upregulate CD20 expression in three diffuse large B-cell lymphoma patients in vivo
Published: January, 2015

Abstract: Background Epigenetic code modifications by histone deacetylase inhibitors (HDACi) have been proposed as potential new therapies for lymphoid malignancies. Diffuse large B-cell lymphoma (DLBCL) is the most common type of aggressive lymphoma for ...
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Dppa3 expression is critical for generation of fully reprogrammed iPS cells and maintenance of Dlk1-Dio3 imprinting.
Published: January, 2015

Abstract: Reprogramming of mouse somatic cells into induced pluripotent stem cells (iPSCs) often generates partially reprogrammed iPSCs (pre-iPSCs), low-grade chimera forming iPSCs (lg-iPSCs) and fully reprogrammed, high-grade chimera production competent i...
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Genome-wide DNA methylation analysis in Graves' disease.
Published: January, 2015

Abstract: As an autoimmune disease, Graves' disease (GD) is associated with many genetic and environmental risk factors. Although the exact mechanism remains unclear, epigenetic determinants, such as DNA methylation, are thought to contribute to the pathoge...
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Dynamic Regulation of Schwann Cell Enhancers after Peripheral Nerve Injury.
Published: January, 2015

Abstract: Myelination of the peripheral nervous system is required for axonal function and long term stability. After peripheral nerve injury, Schwann cells transition from axon myelination to a demyelinated state that supports neuronal survival and ultimat...
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An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations.
Published: January, 2015

Abstract: Combined chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) has enabled genome-wide epigenetic profiling of numerous cell lines and tissue types. A major limitation of ChIP-seq, however, is the large number of cells required t...
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USP7 COOPERATES WITH SCML2 TO REGULATE THE ACTIVITY OF PRC1.
Published: January, 2015

Abstract: USP7 is a protein deubiquitinase with an essential role in development. Here, we provide evidence that USP7 regulates the activity of the Polycomb Repressive Complex 1 (PRC1) in coordination with SCML2. There are six versions of PRC1 defined by th...
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Alternative splicing regulates the expression of G9A and SUV39H2 methyltransferases, and dramatically changes SUV39H2 functions.
Published: January, 2015

Abstract: Alternative splicing is the main source of proteome diversity. Here, we have investigated how alternative splicing affects the function of two human histone methyltransferases (HMTase): G9A and SUV39H2. We show that exon 10 in G9A and exon 3 in SU...
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Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature
Published: January, 2015

Abstract: Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, which control key regulators of flowering and elo...
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PU.1 Opposes IL-7-Dependent Proliferation of Developing B Cells with Involvement of the Direct Target Gene Bruton Tyrosine Kinase.
Published: January, 2015

Abstract: Deletion of genes encoding the E26 transformation-specific transcription factors PU.1 and Spi-B in B cells (CD19-CreΔPB mice) leads to impaired B cell development, followed by B cell acute lymphoblastic leukemia at 100% incidence and with a median...
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Transcription-coupled recruitment of human CHD1 and CHD2 influences chromatin accessibility and histone H3 and H3.3 occupancy at active chromatin regions
Published: January, 2015

Abstract: Background CHD1 and CHD2 chromatin remodeling enzymes play important roles in development, cancer and differentiation. At a molecular level, the mechanisms are not fully understood but include transcriptional regulation, nucleosome organization a...
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Recurrent ETNK1 mutations in atypical chronic myeloid leukemia.
Published: January, 2015

Abstract: Despite the recent identification of recurrent SETBP1 mutations in atypical chronic myeloid leukemia (aCML), a complete description of the somatic lesions responsible for the onset of this disorder is still lacking. To find additional somatic abno...
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The Integrase Cofactor LEDGF/p75 Associates with Iws1 and Spt6 for Postintegration Silencing of HIV-1 Gene Expression in Latently Infected Cells.
Published: January, 2015

Abstract: The persistence of a latent reservoir containing transcriptionally silent, but replication-competent, integrated provirus is a serious challenge to HIV eradication. HIV integration is under the control of LEDGF/p75, the cellular cofactor of viral ...
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Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation
Published: January, 2015

Abstract: The CAG repeat expansion in the Huntington's disease gene HTT extends a polyglutamine tract in mutant huntingtin that enhances its ability to facilitate polycomb repressive complex 2 (PRC2). To gain insight into this dominant gain of function, we ...
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Genetic evidence for ecological divergence in kokanee salmon.
Published: January, 2015

Abstract: The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has p...
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Thyroid hormone receptor sumoylation is required for preadipocyte differentiation and proliferation.
Published: January, 2015

Abstract: Thyroid hormone and thyroid hormone receptor (TR) play an essential role in metabolic regulation. However, the role of TR in adipogenesis is not established. We previously reported that TR sumoylation is essential for TR-mediated gene regulation a...
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Phosphorylation of TET proteins is regulated via O-GlcNAcylation by the glycosyltransferase OGT.
Published: January, 2015

Abstract: TET proteins oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC) and 5-carboxylcytosine (caC) and thus provide a possible means for active DNA demethylation in mammals. Although their catalytic mechanism is well c...
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STAT2/IRF9 directs a prolonged ISGF3-like transcriptional response and antiviral activity in the absence of STAT1.
Published: January, 2015

Abstract: Evidence is accumulating for the existence of a STAT2/IRF9-dependent, STAT1-independent IFNα signaling pathway. However, no detailed insight exists in the genome-wide transcriptional regulation and the biological implications of STAT2/IRF9 depende...
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NTR1 is required for transcription elongation checkpoints at alternative exons in Arabidopsis
Published: January, 2015

Abstract: The interconnection between transcription and splicing is a subject of intense study. We report that Arabidopsis homologue of spliceosome disassembly factor NTR1 is required for correct expression and splicing of DOG1, a regulator of seed dormancy...
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Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF.
Published: January, 2015

Abstract: CTCF is a master regulator that plays important roles in genome architecture and gene expression. How CTCF is recruited in a locus-specific manner is not fully understood. Evidence from epigenetic processes, such as X chromosome inactivation (XCI)...
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Genome-wide methylation analysis in Silver-Russell syndrome patients.
Published: January, 2015

Abstract: Silver-Russell syndrome (SRS) is a clinically heterogeneous disorder characterised by severe in utero growth restriction and poor postnatal growth, body asymmetry, irregular craniofacial features and several additional minor malformations. The aet...
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The human urine virome in association with urinary tract infections
Published: January, 2015

Abstract: While once believed to represent a sterile environment, the human urinary tract harbors a unique cellular microbiota. We sought to determine whether the human urinary tract also is home to viral communities whose membership might reflect urinary t...
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STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer.
Published: January, 2015

Abstract: BACKGROUND: Transient induction of the Src oncoprotein in a non-transformed breast cell line can initiate an epigenetic switch to a cancer cell via a positive feedback loop that involves activation of the signal transducer and activator of transcr...
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Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq.
Published: January, 2015

Abstract: BACKGROUND: Chromatin-Immunoprecipitation coupled with deep sequencing (ChIP-seq) is used to map transcription factor occupancy and generate epigenetic profiles genome-wide. The requirement of nano-scale ChIP DNA for generation of sequencing libra...
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Histone H3 Phosphorylation in GBM: a New Rational to Guide the Use of Kinase Inhibitors in anti-GBM Therapy
Published: January, 2015

Abstract: Histones post-translational modifications (PTMs) are crucial components of diverse processes that modulate chromatin. Among the histones PTMs, the histones phosphorylation appears such crucial since it plays a significant role into DNA repair stru...
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Prolonged TNFα primes fibroblast-like synoviocytes in a gene-specific manner by altering chromatin.
Published: January, 2015

Abstract: Objective: During the course of rheumatoid arthritis (RA) fibroblast-like synoviocytes (FLS) are chronically exposed to an inflammatory milieu. In the current study we test the hypothesis that chronic exposure of FLS to TNFα augments inflammatory ...
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Trichoderma reesei meiosis generates segmentally aneuploid progeny with higher xylanase-producing capability.
Published: January, 2015

Abstract: BACKGROUND: Hypocrea jecorina is the sexual form of the industrial workhorse fungus Trichoderma reesei that secretes cellulases and hemicellulases to degrade lignocellulosic biomass into simple sugars, such as glucose and xylose. H. jecorina CBS99...
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CpG signalling, H2A.Z/H3 acetylation and microRNA-mediated deferred self-attenuation orchestrate foetal NOS3 expression.
Published: January, 2015

Abstract: BACKGROUND: An adverse intrauterine environment leads to permanent physiological changes including vascular tone regulation, potentially influencing the risk for adult vascular diseases. We therefore aimed to monitor responsive NOS3 expression in ...
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Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line.
Published: January, 2015

Abstract: BACKGROUND: Spi-B and PU.1 are highly related members of the E26-transformation-specific (ETS) family of transcription factors that have similar, but not identical, roles in B cell development. PU.1 and Spi-B are both expressed in B cells, and hav...
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ERK signaling regulates opposing roles of JUN family transcription factors at ETS/AP-1 sites and in cell migration.
Published: January, 2015

Abstract: JUN transcription factors bind DNA as part of the AP-1 complex, regulate many cellular processes, and play a key role in oncogenesis. The three JUN proteins (c-JUN, JUNB, and JUND) can have both redundant and unique functions depending on the biol...
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Initiation and maintenance of pluripotency gene expression in the absence of cohesin.
Published: January, 2015

Abstract: Cohesin is implicated in establishing and maintaining pluripotency. Whether this is because of essential cohesin functions in the cell cycle or in gene regulation is unknown. Here we tested cohesin's contribution to reprogramming in systems that r...
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Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing
Published: January, 2015

Abstract: DNA methylation is a major epigenetic mark associated with multiple aspects of retrotransposons within the mammalian genome. In order to study DNA methylation of a large number of retrotransposons on an individual-locus basis, we have developed a ...
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Extracellular signal-related kinase 2/specificity protein 1/specificity protein 3/repressor element-1 silencing transcription factor pathway is involved in Aroclor 1254-induced toxicity in SH-SY5Y neuronal cells.
Published: January, 2015

Abstract: Polychlorinated biphenyls (PCBs) cause a wide spectrum of toxic effects in the brain through undefined mechanisms. Exposure to the PCB mixture Aroclor-1254 (A1254) increases the repressor element-1 silencing transcription factor (REST) expression,...
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Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals.
Published: January, 2015

Abstract: BACKGROUND: There are over a half a million copies of L1 retroelements in the human genome which are responsible for as much as 0.5% of new human genetic diseases. Most new L1 inserts arise from young source elements that are polymorphic in the hu...
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BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence.
Published: January, 2015

Abstract: Prostate cancer is driven by a combination of genetic and/or epigenetic alterations. Epigenetic alterations are frequently observed in all human cancers, yet how aberrant epigenetic signatures are established is poorly understood. Here we show tha...
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An integrated functional genomic analysis identifies the antitumorigenic mechanism of action for PPARγ in lung cancer cells
Published: January, 2015

Abstract: Integrating the analysis of the cistrome of a transcription factor by ChIP-Seq with the study of its transcriptional output by microarray or RNA-Seq analysis is a powerful approach to elucidate the genomic functions of a tran- scriptionfactor. Rec...
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Ezh2 represses the basal cell lineage during lung endoderm development.
Published: January, 2015

Abstract: The development of the lung epithelium is regulated in a stepwise fashion to generate numerous differentiated and stem cell lineages in the adult lung. How these different lineages are generated in a spatially and temporally restricted fashion rem...
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Transcriptomic profiles of aging in purified human immune cells.
Published: January, 2015

Abstract: BACKGROUND: Transcriptomic studies hold great potential towards understanding the human aging process. Previous transcriptomic studies have identified many genes with age-associated expression levels; however, small samples sizes and mixed cell ty...
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Transcriptional complexity and roles of Fra-1/AP-1 at the uPA/Plau locus in aggressive breast cancer.
Published: January, 2015

Abstract: Plau codes for the urokinase-type plasminogen activator (uPA), critical in cancer metastasis. While the mechanisms driving its overexpression in tumorigenic processes are unknown, it is regulated by the AP-1 transcriptional complex in diverse situ...
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Molecular and Biochemical Characterization of a Novel Multidomain Xylanase from Arthrobacter sp. GN16 Isolated from the Feces of Grus nigricollis.
Published: January, 2015

Abstract: A novel glycosyl hydrolase family 10 (GH 10) xylanase (XynAGN16), consisting of five domains, was revealed from the genome sequence of Arthrobacter sp. GN16 isolated from the feces of Grus nigricollis. XynAGN16 and its truncated derivatives XynAGN...
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DNA Methylation Analysis of the Macrosatellite Repeat Associated with FSHD Muscular Dystrophy at Single Nucleotide Level.
Published: December, 2014

Abstract: Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common inherited diseases of the skeletal muscle. It is characterized by asymmetric muscle weakness and variable penetrance. FSHD is linked to a reduction in copy number of the D4Z4 ...
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Paclitaxel resistance increases oncolytic adenovirus efficacy via upregulated CAR expression and dysfunctional cell cycle control.
Published: December, 2014

Abstract: Resistance to paclitaxel chemotherapy frequently develops in ovarian cancer. Oncolytic adenoviruses are a novel therapy for human malignancies that are being evaluated in early phase trials. However, there are no reliable predictive biomarkers for...
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A novel Cd8-cis-regulatory element preferentially directs expression in CD44hiCD62L+ CD8+ T cells and in CD8αα+ dendritic cells.
Published: December, 2014

Abstract: CD8 coreceptor expression is dynamically regulated during thymocyte development and is tightly controlled by the activity of at least 5 different cis-regulatory elements. Despite the detailed characterization of the Cd8 loci, the regulation of the...
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Epigenetic modification of the PD-1 (Pdcd1) promoter in effector CD4(+) T cells tolerized by peptide immunotherapy.
Published: December, 2014

Abstract: Clinically effective antigen-based immunotherapy must silence antigen-experienced effector T cells (Teff) driving ongoing immune pathology. Using CD4(+) autoimmune Teff cells, we demonstrate that peptide immunotherapy (PIT) is strictly dependent u...
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Cryosectioning the intestinal crypt-villus axis: an ex vivo method to study the dynamics of epigenetic modifications from stem cells to differentiated cells
Published: December, 2014

Abstract: The intestinal epithelium is a particularly attractive biological adult model to study epigenetic mechanisms driving adult stem cell renewal and cell differentiation. Since epigenetic modifications are dynamic, we have developed an original ex viv...
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Whole-exome sequencing identify a new mutation of MYH7 in a Chinese family with left ventricular noncompaction.
Published: December, 2014

Abstract: BACKGROUND: Left ventricular noncompaction (LVNC) is a genetic cardiomyopathy results from the failure of myocardial development during embryogenesis. Previous reports show that defects in TAZ, SCN5A, TPM1, YWHAE, MYH7, ACTC1 and TNNT2 are associa...
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ChIPping Away at the Drosophila Clock
Published: December, 2014

Abstract: In eukaryotes, the circadian clock controls 24 h rhythms in physiology, metabolism, and behavior via cell autonomous transcriptional feedback loops. These feedback loops keep circadian time and control rhythmic outputs by driving rhythms in transc...
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Methods to Study Molecular Mechanisms of the Neurospora Circadian Clock
Published: December, 2014

Abstract: Eukaryotic circadian clocks are comprised of interlocked autoregulatory feedback loops that control gene expression at the levels of transcription and translation. The filamentous fungus Neurospora crassa is an excellent model for the complex mole...
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Purification and Analysis of PERIOD Protein Complexes of the Mammalian Circadian Clock
Published: December, 2014

Abstract: In mammals, circadian rhythms are generated at least in part by a cell-autonomous transcriptional feedback loop in which the three PERIOD (PER) and two CRYPTOCHROME (CRY) proteins inhibit the activity of the dimeric transcription factor CLOCK-BMAL...
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Next-generation sequencing workflow for assembly of non-model mitogenomes exemplified with North Pacific Albatrosses (Phoebastria spp.).
Published: December, 2014

Abstract: Use of complete mitochondrial genomes (mitogenomes) can greatly increase the resolution achievable in phylogeographic and historical demographic studies. Using next generation sequencing methods, it is now feasible to efficiently sequence mitogeno...
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Cold acclimation induces distinctive changes in the chromatin state and transcript levels of COR genes in Cannabis sativa varieties with contrasting cold acclimation capacities.
Published: December, 2014

Abstract: Little is known about the capacity of Cannabis sativa to cold acclimate and develop freezing tolerance. This study investigates the cold acclimation capacity of nine C. sativa varieties and the underlying genetic and epigenetic responses. The vari...
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NCOA3-mediated upregulation of mucin expression via transcriptional and post-translational changes during the development of pancreatic cancer.
Published: December, 2014

Abstract: Pancreatic cancer (PC) is characterized by aberrant overexpression of mucins that contribute to its pathogenesis. Although the inflammatory cytokines contribute to mucin overexpression, the mucin profile of PC is markedly distinct from that of nor...
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Frequency and phenotypic spectrum of germline mutations in POLE and seven other polymerase genes in 266 patients with colorectal adenomas and carcinomas.
Published: December, 2014

Abstract: In a number of families with colorectal adenomatous polyposis or suspected Lynch syndrome / HNPCC, no germline alteration in the APC, MUTYH, or mismatch repair (MMR) genes are found. Missense mutations in the polymerase genes POLE and POLD1 have r...
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RNA Chromatin Immunoprecipitation (RNA-ChIP) in Caenorhabditis elegans
Published: December, 2014

Abstract: The RNA chromatin immunoprecipitation assay (RNA-ChIP) allows detection and quantification of RNA–protein interactions using in vivo cross-linking with formaldehyde followed by immunoprecipitation of the RNA–protein complexes. Here we describe th...
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Activation of aryl hydrocarbon receptor promotes invasion of clear cell renal cell carcinoma and is associated with poor prognosis and cigarette smoke.
Published: December, 2014

Abstract: Although exposure to environmental pollutants is one of the risk factors for renal cell carcinoma (RCC), its relationship with carcinogenesis and the progression of RCC remains unknown. The present study was designed to elucidate the role of the a...
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Modulation of p53 and met expression by Krüppel-like factor 8 regulates zebrafish cerebellar development.
Published: December, 2014

Abstract: Krüppel-like factor 8 (Klf8) is a zinc-finger transcription factor implicated in cell proliferation, and cancer cell survival and invasion; however, little is known about its role in normal embryonic development. Here, we show that Klf8 is re...
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Product Binding Enforces the Genomic Specificity of a Yeast Polycomb Repressive Complex.
Published: December, 2014

Abstract: We characterize the Polycomb system that assembles repressive subtelomeric domains of H3K27 methylation (H3K27me) in the yeast Cryptococcus neoformans. Purification of this PRC2-like protein complex reveals orthologs of animal PRC2 components as w...
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An AUTS2-Polycomb complex activates gene expression in the CNS.
Published: December, 2014

Abstract: Naturally occurring variations of Polycomb repressive complex 1 (PRC1) comprise a core assembly of Polycomb group proteins and additional factors that include, surprisingly, autism susceptibility candidate 2 (AUTS2). Although AUTS2 is often disrup...
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Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences.
Published: December, 2014

Abstract: Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic eleme...
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A novel analytical brain block tool to enable functional annotation of discriminatory transcript biomarkers among discrete regions of the fronto-limbic circuit in primate brain.
Published: December, 2014

Abstract: Fronto-limbic circuits in the primate brain are responsible for executive function, learning and memory, and emotions, including fear. Consequently, changes in gene expression in cortical and subcortical brain regions housing these circuits are as...
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MiR-127 Modulates Macrophage Polarization and Promotes Lung Inflammation and Injury by Activating the JNK Pathway.
Published: December, 2014

Abstract: A polarized macrophage response is presumed to have a pivotal role in a variety of immunological pathophysiology. However, the molecular mechanism underlying macrophage functional shaping remains largely unknown. In this study, we reveal a pivotal...
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Histone Deacetylase 6 is a FoxO transcription factor-dependent effector in skeletal muscle atrophy.
Published: December, 2014

Abstract: Skeletal muscle atrophy is a severe condition of muscle mass loss. Muscle atrophy is caused by a downregulation of protein synthesis and by an increase of protein breakdown due to the ubiquitin-proteasome system and autophagy activation. Upregulat...
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Promoter occupancy of STAT1 in interferon responses is regulated by processive transcription.
Published: December, 2014

Abstract: Interferons regulate immunity by inducing DNA-binding of the transcription factor STAT1 through Y701 phosphorylation. Transcription by STAT1 needs to be restricted to minimize adverse effects of prolonged immune responses. It remains unclear how S...
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The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase (FPGS).
Published: December, 2014

Abstract: Mutations in the brown midrib4 (bm4) gene affect the accumulation and composition of lignin in maize. Fine mapping analysis of bm4 narrowed the candidate region to an ~105 kb interval on chromosome 9 containing six genes. Only one of these six gen...
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NFAT Targets Signaling Molecules to Gene Promoters in Pancreatic β Cells.
Published: December, 2014

Abstract: Nuclear factor of activated T cells (NFAT) is activated by calcineurin in response to calcium signals derived by metabolic and inflammatory stress to regulate genes in pancreatic islets. Here we show that NFAT targets MAPKs, p300, and histone deac...
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A Distal Locus Element Mediates IFN-γ Priming of Lipopolysaccharide-Stimulated TNF Gene Expression.
Published: December, 2014

Abstract: Interferon γ (IFN-γ) priming sensitizes monocytes and macrophages to lipopolysaccharide (LPS) stimulation, resulting in augmented expression of a set of genes including TNF. Here, we demonstrate that IFN-γ priming of LPS-stimulated TNF transcripti...
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RB Maintains Quiescence and Prevents Premature Senescence through Upregulation of DNMT1 in Mesenchymal Stromal Cells
Published: December, 2014

Abstract: Many cell therapies currently being tested are based on mesenchymal stromal cells (MSCs). However, MSCs start to enter the senescent state upon long-term expansion. The role of retinoblastoma (RB) protein in regulating MSC properties is not well s...
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Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears.
Published: December, 2014

Abstract: Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed...
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Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation.
Published: December, 2014

Abstract: Argonaute (AGO) family proteins are conserved key components of small RNA-induced silencing pathways. In the RNA-directed DNA methylation (RdDM) pathway in Arabidopsis, AGO6 is generally considered to be redundant with AGO4. In this report, our co...
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Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome.
Published: December, 2014

Abstract: Eukaryotic DNA replication initiates from multiple sites on each chromosome called replication origins (origins). In the budding yeast Saccharomyces cerevisiae, origins are defined at discrete sites. Regular spacing and diverse firing characterist...
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CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells.
Published: December, 2014

Abstract: The pluripotency of embryonic stem cells (ESCs) is maintained by a small group of master transcription factors including Oct4, Sox2 and Nanog. These core factors form a regulatory circuit controlling the transcription of a number of pluripotency f...
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STAT1-Dependent Signal Integration between IFNγ and TLR4 in Vascular Cells Reflect Pro-Atherogenic Responses in Human Atherosclerosis
Published: December, 2014

Abstract: Signal integration between IFNγ and TLRs in immune cells has been associated with the host defense against pathogens and injury, with a predominant role of STAT1. We hypothesize that STAT1-dependent transcriptional changes in vascular cells involv...
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Retromer vesicles interact with RNA granules in haploid male germ cells.
Published: December, 2014

Abstract: Spermatozoa are produced during spermatogenesis as a result of mitotic proliferation, meiosis and cellular differentiation. Postmeiotic spermatids are exceptional cells given their haploid genome and remarkable sperm-specific structural transforma...
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Environment drives selection and function of enhancers controlling tissue-specific macrophage identities.
Published: December, 2014

Abstract: Macrophages reside in essentially all tissues of the body and play key roles in innate and adaptive immune responses. Distinct populations of tissue macrophages also acquire context-specific functions that are important for normal tissue homeostas...
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Nuclear envelope remodelling during human spermiogenesis involves somatic B-type lamins and a spermatid-specific B3 lamin isoform.
Published: December, 2014

Abstract: The nuclear lamina (NL) is a filamentous protein meshwork, composed essentially of lamins, situated between the inner nuclear membrane and the chromatin. There is mounting evidence that the NL plays a role in spermatid differentiation during sperm...
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The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development.
Published: December, 2014

Abstract: It was recently reported that the sizes of many mRNAs change when budding yeast cells exit mitosis and enter the meiotic differentiation pathway. These differences were attributed to length variations of their untranslated regions. The function of...
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Genome-wide DNA methylation analysis in precursor B-cells.
Published: December, 2014

Abstract: DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order...
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Foxk proteins repress the initiation of starvation-induced atrophy and autophagy programs.
Published: December, 2014

Abstract: Autophagy is the primary catabolic process triggered in response to starvation. Although autophagic regulation within the cytosolic compartment is well established, it is becoming clear that nuclear events also regulate the induction or repression...
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Transcription bypass of DNA lesions enhances cell survival but attenuates transcription coupled DNA repair.
Published: December, 2014

Abstract: Transcription-coupled DNA repair (TCR) is a subpathway of nucleotide excision repair (NER) dedicated to rapid removal of DNA lesions in the transcribed strand of actively transcribed genes. The precise nature of the TCR signal and how the repair m...
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RAN-Binding Protein 9 is Involved in Alternative Splicing and is Critical for Male Germ Cell Development and Male Fertility.
Published: December, 2014

Abstract: As a member of the large Ran-binding protein family, Ran-binding protein 9 (RANBP9) has been suggested to play a critical role in diverse cellular functions in somatic cell lineages in vitro, and this is further supported by the neonatal lethality...
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Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.
Published: December, 2014

Abstract: DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the rece...
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Degradation of DNA damage-independently stalled RNA polymerase II is independent of the E3 ligase Elc1.
Published: December, 2014

Abstract: Transcription elongation is a highly dynamic and discontinuous process, which includes frequent pausing of RNA polymerase II (RNAPII). RNAPII complexes that stall persistently on a gene during transcription elongation block transcription and thus ...
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Evaluation of methods to detect CALR mutations in myeloproliferative neoplasms
Published: November, 2014

Abstract: The recent discovery of somatically acquired CALR mutations in a substantial proportion of patients with myeloproliferative neoplasms has provided a new marker of clonal disease, advancing both diagnosis and prognosis in these previously difficult...
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Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast.
Published: November, 2014

Abstract: Our current understanding of how natural genetic variation affects gene expression beyond well-annotated coding genes is still limited. The use of deep sequencing technologies for the study of expression quantitative trait loci (eQTLs) has the pot...
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Regulation of anti-sense transcription by Mot1p and NC2 via removal of TATA-binding protein (TBP) from the 3'-end of genes.
Published: November, 2014

Abstract: The activity and dynamic nature of TATA-binding protein (TBP) crucial to RNA polymerase II-mediated transcription is under control of the Mot1p and NC2 complexes. Here we show that both TBP regulatory factors play 'hidden' roles in ensuring transc...
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Long non-coding RNA-mediated transcriptional interference of a permease gene confers drug tolerance in fission yeast.
Published: November, 2014

Abstract: Most long non-coding RNAs (lncRNAs) encoded by eukaryotic genomes remain uncharacterized. Here we focus on a set of intergenic lncRNAs in fission yeast. Deleting one of these lncRNAs exhibited a clear phenotype: drug sensitivity. Detailed analyses...
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Epigenetic memory of the first cell fate decision prevents complete ES cell reprogramming into trophoblast.
Published: November, 2014

Abstract: Embryonic (ES) and trophoblast (TS) stem cells reflect the first, irrevocable cell fate decision in development that is reinforced by distinct epigenetic lineage barriers. Nonetheless, ES cells can seemingly acquire TS-like characteristics upon ma...
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O-GlcNAcylation Prevents Aggregation of the Polycomb Group Repressor Polyhomeotic.
Published: November, 2014

Abstract: The glycosyltransferase Ogt adds O-linked N-Acetylglucosamine (O-GlcNAc) moieties to nuclear and cytosolic proteins. Drosophila embryos lacking Ogt protein arrest development with a remarkably specific Polycomb phenotype, arising from the failure ...
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Cryptogenic stroke and small fiber neuropathy of unknown etiology in patients with alpha-galactosidase A -10T genotype.
Published: November, 2014

Abstract: BackgroundFabry disease (FD) is a multisystemic disorder with typical neurological manifestations such as stroke and small fiber neuropathy (SFN), caused by mutations of the alpha-galactosidase A (GLA) gene. We analyzed 15 patients carrying the GL...
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Synergistic template-free synthesis of dsDNA by Thermococcus nautili primase PolpTN2, DNA polymerase PolB, and pTN2 helicase.
Published: November, 2014

Abstract: A combination of three enzymes from the hyperthermophilic archaeon Thermococcus nautili, DNA primase PolpTN2, DNA polymerase PolB, and pTN2 DNA helicase, was found to synthesize up to 300-400 ng/µl dsDNA from deoxynucleotide triphosphates in less ...
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MiR-98 delays skeletal muscle differentiation by downregulating E2F5.
Published: November, 2014

Abstract: A genome-wide screen had previously shown that knocking down miR-98 and let-7g, two miRNAs of the let-7 family, leads to a dramatic increase of terminal myogenic differentiation. Here we report that a transcriptomic analysis of human myoblasts whe...
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Cell cycle-linked MeCP2 phosphorylation modulates adult neurogenesis involving the Notch signalling pathway.
Published: November, 2014

Abstract: Neuronal activity regulates the phosphorylation states at multiple sites on MeCP2 in postmitotic neurons. The precise control of the phosphorylation status of MeCP2 in neurons is critical for the normal development and function of the mammalian br...
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Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.
Published: November, 2014

Abstract: Developmental history shapes the epigenome and biological function of differentiated cells. Epigenomic patterns have been broadly attributed to the three embryonic germ layers. Here we investigate how developmental origin influences epigenomes. We...
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Single mutations in sasA enable a simpler ΔcikA gene network architecture with equivalent circadian properties.
Published: November, 2014

Abstract: The circadian input kinase of the cyanobacterium Synechococcus elongatus PCC 7942 (CikA) is important both for synchronizing circadian rhythms with external environmental cycles and for transferring temporal information between the oscillator and ...
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RNA helicase DDX21 coordinates transcription and ribosomal RNA processing.
Published: November, 2014

Abstract: DEAD-box RNA helicases are vital for the regulation of various aspects of the RNA life cycle, but the molecular underpinnings of their involvement, particularly in mammalian cells, remain poorly understood. Here we show that the DEAD-box RNA helic...
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Neuropeptide Y promotes adipogenesis in chicken adipose cells in vitro.
Published: November, 2014

Abstract: Neuropeptide Y is an evolutionarily conserved neurotransmitter that stimulates food intake in higher vertebrate species and promotes adipogenesis in mammals. The objective of this study was to determine if NPY also enhances adipogenesis in birds, ...
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Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo.
Published: November, 2014

Abstract: Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock. We have determined the underlying mechanisms by measuring nascent RNA transcr...
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Identification by high-throughput imaging of the histone methyltransferase EHMT2 as an epigenetic regulator of VEGFA alternative splicing.
Published: November, 2014

Abstract: Recent evidence points to a role of chromatin in regulation of alternative pre-mRNA splicing (AS). In order to identify novel chromatin regulators of AS, we screened an RNAi library of chromatin proteins using a cell-based high-throughput in vivo ...
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Global quantitative proteomics reveals novel factors in the ecdysone signaling pathway in Drosophila melanogaster.
Published: November, 2014

Abstract: The ecdysone signaling pathway plays a major role in various developmental transitions in insects. Recent advances in the understanding of ecdysone action have relied to a large extent on the application of molecular genetic tools in Drosophila. H...
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Identification of Cdca7 as a novel Notch transcriptional target involved in hematopoietic stem cell emergence.
Published: November, 2014

Abstract: Hematopoietic stem cell (HSC) specification occurs in the embryonic aorta and requires Notch activation; however, most of the Notch-regulated elements controlling de novo HSC generation are still unknown. Here, we identify putative direct Notch ta...
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Protein arginine methyltransferase 5 is a key regulator of the MYCN oncoprotein in neuroblastoma cells.
Published: November, 2014

Abstract: Approximately half of poor prognosis neuroblastomas (NBs) are characterized by pathognomonic MYCN gene amplification and MYCN over-expression. Here we present data showing that short-interfering RNA mediated depletion of the protein arginine methy...
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MicroRNAs 206 and 21 Cooperate To Promote RAS-Extracellular Signal-Regulated Kinase Signaling by Suppressing the Translation of RASA1 and SPRED1.
Published: November, 2014

Abstract: Despite the low prevalence of activating point mutation of RAS or RAF genes, the RAS-extracellular signal-regulated kinase (ERK) pathway is implicated in breast cancer pathogenesis. Indeed, in triple-negative breast cancer (TNBC), there is recurre...
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Fission yeast Cactin restricts telomere transcription and elongation by controlling Rap1 levels.
Published: November, 2014

Abstract: The telomeric transcriptome comprises multiple long non-coding RNAs generated by transcription of linear chromosome ends. In a screening performed in Schizosaccharomyces pombe, we identified factors modulating the cellular levels of the telomeric ...
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Inhibition of osteoclastogenesis and inflammatory bone resorption by targeting BET proteins and epigenetic regulation.
Published: November, 2014

Abstract: Emerging evidence suggests that RANKL-induced changes in chromatin state are important for osteoclastogenesis, but these epigenetic mechanisms are not well understood and have not been therapeutically targeted. In this study, we find that the smal...
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Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals
Published: November, 2014

Abstract: To understand the evolutionary dynamics between transcription factor (TF) binding and gene expression in mammals, we compared transcriptional output and the binding intensities for three tissue-specific TFs in livers from four closely related mous...
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Structure-guided mutational analysis reveals the functional requirements for product specificity of DOT1 enzymes.
Published: November, 2014

Abstract: DOT1 enzymes are conserved methyltransferases that catalyse the methylation of lysine 79 on histone H3 (H3K79). Most eukaryotes contain one DOT1 enzyme, whereas African trypanosomes have two homologues, DOT1A and DOT1B, with different enzymatic ac...
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Epigenetic Modification of Histone 3 Lysine 27: Mediator Subunit MED25 is Required for the Dissociation of Polycomb Repressive Complex 2 from the Promoter of Cytochrome P450 2C9.
Published: November, 2014

Abstract: The Mediator complex is vital for the transcriptional regulation of eukaryotic genes. Mediator binds to nuclear receptors at target response elements and recruits chromatin modifying enzymes and RNA Pol II. Here, we examine the involvement of Medi...
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Suppression of the FOXM1 transcriptional programme via novel small molecule inhibition.
Published: November, 2014

Abstract: The transcription factor FOXM1 binds to sequence-specific motifs on DNA (C/TAAACA) through its DNA-binding domain (DBD) and activates proliferation- and differentiation-associated genes. Aberrant overexpression of FOXM1 is a key feature in oncogen...
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HIV-1 Integrase Variants Retarget Viral Integration and Are Associated with Disease Progression in a Chronic Infection Cohort.
Published: November, 2014

Abstract: Distinct integration patterns of different retroviruses, including HIV-1, have puzzled virologists for over 20 years. A tetramer of the viral integrase (IN) assembles on the two viral cDNA ends, docks onto the target DNA (tDNA), and catalyzes vira...
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Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system.
Published: November, 2014

Abstract: Saccharomyces cerevisiae has a complex system for switching the mating type of haploid cells, requiring the genome to have three mating-type (MAT)-like loci and a mechanism for silencing two of them. How this system originated is unknown, because ...
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Heavy transcription of yeast genes correlates with differential loss of histone H2B relative to H4 and queued RNA polymerases.
Published: November, 2014

Abstract: Eukaryotic chromatin is composed of nucleosomes, which contain nearly two coils of DNA wrapped around a central histone octamer. The octamer contains an H3-H4 tetramer and two H2A-H2B dimers. Gene activation is associated with chromatin disruption...
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Serine Deprivation Enhances Anti-neoplastic Activity of Biguanides.
Published: November, 2014

Abstract: Metformin, a biguanide widely used in the treatment of type II diabetes, clearly exhibits anti-neoplastic activity in experimental models and has been reported to reduce cancer incidence in diabetics. . There are ongoing clinical trials to evaluat...
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Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation.
Published: November, 2014

Abstract: DNA CpG methylation is a widespread epigenetic mark in high eukaryotes including mammals. DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and c...
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DNA Copy-Number Control through Inhibition of Replication Fork Progression.
Published: November, 2014

Abstract: Proper control of DNA replication is essential to ensure faithful transmission of genetic material and prevent chromosomal aberrations that can drive cancer progression and developmental disorders. DNA replication is regulated primarily at the lev...
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Silica nanoparticles induce autophagy and endothelial dysfunction via the PI3K/Akt/mTOR signaling pathway.
Published: November, 2014

Abstract: Although nanoparticles have a great potential for biomedical applications, there is still a lack of a correlative safety evaluation on the cardiovascular system. This study is aimed to clarify the biological behavior and influence of silica nanopa...
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The repair of oxidized purines in the DNA of human lymphocytes requires an activation involving NF-YA-mediated upregulation of OGG1.
Published: November, 2014

Abstract: 8-Oxoguanine DNA glycosylase (OGG1), which initiates the repair of DNA purine modifications such as 8-oxo-7,8-dihydroguanine (8-oxoG), is often regarded as a house keeping protein ubiquitously active in mammalian cells. We have analysed the repair...
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A phylogenomic analysis of turtles.
Published: November, 2014

Abstract: Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved el...
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A variably occupied CTCF binding site in the Ultrabithorax gene in the Drosophila Bithorax Complex.
Published: November, 2014

Abstract: Although the majority of genomic binding sites for the insulator protein CTCF are constitutively occupied, a subset show variably occupancy. Such variable sites provide an opportunity to assess context-specific CTCF functions in gene regulation. H...
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Detection of single nucleotide polymorphisms in Plasmodium falciparum by PCR primer extension and lateral flow immunoassay.
Published: November, 2014

Abstract: Resistance of Plasmodium falciparum to some antimalarial drugs is linked to single nucleotide polymorphisms (SNPs). Currently there are no methods for identification of resistant parasites that are sufficiently simple, cheap and fast to be perform...
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Deregulation of Rb-E2F1 axis causes chromosomal instability by engaging the transactivation function of Cdc20-APC/C complex.
Published: November, 2014

Abstract: E2F family of transcription factors regulate genes involved in various aspects of cell cycle. Beyond the well-documented role in G1/S transition, mitotic regulation by E2F has also been reported. Proper mitotic progression is monitored by spindle ...
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A Novel Mouse Model for the Hyper-IgM Syndrome: A Spontaneous Activation-Induced Cytidine Deaminase Mutation Leading to Complete Loss of Ig Class Switching and Reduced Somatic Hypermutation.
Published: November, 2014

Abstract: We describe a spontaneously derived mouse line that completely failed to induce Ig class switching in vitro and in vivo. The mice inherited abolished IgG serum titers in a recessive manner caused by a spontaneous G→A transition mutation in codon 1...
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Continuous requirement for the TCR in regulatory T cell function.
Published: November, 2014

Abstract: Foxp3(+) regulatory T cells (Treg cells) maintain immunological tolerance, and their deficiency results in fatal multiorgan autoimmunity. Although heightened signaling via the T cell antigen receptor (TCR) is critical for the differentiation of Tr...
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Blocking of JB6 Cell Transformation by Tanshinone IIA: Epigenetic Reactivation of Nrf2 Antioxidative Stress Pathway.
Published: November, 2014

Abstract: Increasing numbers of natural products have been found to possess anticancer effects. Nuclear factor erythroid-2-related factor-2 (Nrf2) is a master regulator of the antioxidative stress response, and our previous studies found that epigenetic mod...
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Characterization of microsatellite markers for pinedrops, Pterospora andromedea (Ericaceae), from Illumina MiSeq sequencing.
Published: November, 2014

Abstract: UNLABELLED: • PREMISE OF THE STUDY: Pterospora andromedea (Ericaceae) is a mycoheterotrophic plant endemic to North America with a disjunct distribution. Eastern populations are in decline compared to western populations. Microsatellite loci will ...
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RNA Processing Factors Swd2.2 and Sen1 Antagonize RNA Pol III-Dependent Transcription and the Localization of Condensin at Pol III Genes.
Published: November, 2014

Abstract: Condensin-mediated chromosome condensation is essential for genome stability upon cell division. Genetic studies have indicated that the association of condensin with chromatin is intimately linked to gene transcription, but what transcription-ass...
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Genome-wide identification of aberrantly methylated promoters in ovarian tissue of prenatally androgenized rats.
Published: November, 2014

Abstract: OBJECTIVE: To identify aberrantly methylated candidate genes that are involved in the development of polycystic ovary syndrome (PCOS). DESIGN: Animal model. SETTING: University-affiliated laboratory. ANIMAL(S): Sprague-Dawley rats. INTERVENTION(S)...
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Epstein-Barr virus nuclear antigen 3A protein regulates CDKN2B transcription via interaction with MIZ-1.
Published: November, 2014

Abstract: The Epstein-Barr virus (EBV) nuclear antigen 3 family of protein is critical for the EBV-induced primary B-cell growth transformation process. Using a yeast two-hybrid screen we identified 22 novel cellular partners of the EBNA3s. Most importantly...
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Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae.
Published: October, 2014

Abstract: Recent developments in DNA-assembly methods make the synthesis of synthetic chromosomes a reachable goal. However, the redesign of primary chromosomes bears high risks and still requires enormous resources. An alternative approach is the addition ...
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IL-6, IL-8, MMP-2, MMP-9 are overexpressed in Fanconi anemia cells through a NF-κB/TNF-α dependent mechanism.
Published: October, 2014

Abstract: Fanconi anemia (FA) is a rare autosomal recessive genetic disorder associated with a bone-marrow failure, genome instability, hypersensitivity to DNA crosslinking agents and a predisposition to cancer. Mutations have been documented in 16 FA genes...
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Ultrasensitive proteome analysis using paramagnetic bead technology.
Published: October, 2014

Abstract: In order to obtain a systems-level understanding of a complex biological system, detailed proteome information is essential. Despite great progress in proteomics technologies, thorough interrogation of the proteome from quantity-limited biological...
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Androgen receptor-interacting protein HSPBAP1 facilitates growth of prostate cancer cells in androgen-deficient conditions.
Published: October, 2014

Abstract: Hormonal therapies targeting androgen receptor (AR) are effective in prostate cancer (PCa), but often the cancers progress to fatal castrate-resistant disease. Improved understanding of the cellular events during androgen deprivation would help to...
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Enantioselective regulation of lactate racemization by LarR in Lactobacillus plantarum.
Published: October, 2014

Abstract: Lactobacillus plantarum is a lactic acid bacterium that produces a racemic mixture of L- and D-lactate from sugar fermentation. The inter-conversion of lactate isomers is performed by a lactate racemase (Lar) that is transcriptionally controlled b...
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Loss of Nucleolar Histone Chaperone NPM1 Triggers Rearrangement of Heterochromatin and Synergizes with a Deficiency in DNA Methyltransferase DNMT3A to Drive Ribosomal DNA Transcription.
Published: October, 2014

Abstract: Nucleoli are prominent nuclear structures assembled and organized around actively transcribed ribosomal DNA (rDNA). The nucleolus has emerged as a platform for the organization of chromatin enriched for repressive histone modifications associated ...
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BET bromodomain inhibition suppresses transcriptional responses to cytokine-Jak-STAT signaling in a gene-specific manner in human monocytes.
Published: October, 2014

Abstract: Disruption of the interaction of bromo and extraterminal (BET) proteins with acetylated histones using small molecule inhibitors suppresses Myc-driven cancers and TLR-induced inflammation in mouse models. The predominant mechanism of BET inhibitor...
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Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment
Published: October, 2014

Abstract: The generation of naïve T lymphocytes is critical for immune function yet the mechanisms governing their maturation remain incompletely understood. We have identified a mouse mutant, bloto, that harbors a hypomorphic mutation in the zinc finger pr...
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Epigenetic regulation of inflammatory gene expression in macrophages by selenium.
Published: October, 2014

Abstract: Acetylation of histone and non-histone proteins by histone acetyltransferases plays a pivotal role in the expression of proinflammatory genes. Given the importance of dietary selenium in mitigating inflammation, we hypothesized that selenium suppl...
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AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation.
Published: October, 2014

Abstract: The recognition of modified histones by "reader" proteins constitutes a key mechanism regulating gene expression in the chromatin context. Compared with the great variety of readers for histone methylation, few protein modules that recognize histo...
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Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.
Published: October, 2014

Abstract: The gastrointestinal tracts of mammals are colonized by hundreds of microbial species that contribute to health, including colonization resistance against intestinal pathogens. Many antibiotics destroy intestinal microbial communities and increase...
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Next Generation Sequencing Identifies a Novel Rearrangement in the HBB Cluster Permitting to-the-Base Characterization
Published: October, 2014

Abstract: Genetic testing for hemoglobinopathies is required for prenatal diagnosis, understanding complex cases where multiple pathogenic variants may be present or investigating cases of unexplained anemia. Characterization of disease causing variants tha...
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RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells.
Published: October, 2014

Abstract: A fraction of cancer cells maintain telomeres through the telomerase-independent, 'Alternative Lengthening of Telomeres' (ALT) pathway. ALT relies on homologous recombination (HR) between telomeric sequences; yet, what makes ALT telomeres recombin...
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Polycomb Repressive Complex 2 Regulates Lineage Fidelity during Embryonic Stem Cell Differentiation.
Published: October, 2014

Abstract: Polycomb Repressive Complex 2 (PRC2) catalyzes histone H3 lysine 27 tri-methylation (H3K27me3), an epigenetic modification associated with gene repression. H3K27me3 is enriched at the promoters of a large cohort of developmental genes in embryonic...
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The miR-155-PU.1 axis acts on Pax5 to enable efficient terminal B cell differentiation.
Published: October, 2014

Abstract: A single microRNA (miRNA) can regulate the expression of many genes, though the level of repression imparted on any given target is generally low. How then is the selective pressure for a single miRNA/target interaction maintained across long evol...
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Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment - A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses.
Published: October, 2014

Abstract: We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intr...
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In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9.
Published: October, 2014

Abstract: Probing gene function in the mammalian brain can be greatly assisted with methods to manipulate the genome of neurons in vivo. The clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated endonuclease (Cas)9 from Streptococc...
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Transforming Growth Factor β1 (TGF-β1) Enhances Expression of Profibrotic Genes through a Novel Signaling Cascade and MicroRNAs in Renal Mesangial Cells.
Published: October, 2014

Abstract: Increased expression of transforming growth factor-β1 (TGF-β1) in glomerular mesangial cells (MC) augments extracellular matrix accumulation and hypertrophy during the progression of diabetic nephropathy (DN), a debilitating renal complication of ...
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A nanobody modulates the p53 transcriptional program without perturbing its functional architecture.
Published: October, 2014

Abstract: The p53 transcription factor plays an important role in genome integrity. To perform this task, p53 regulates the transcription of genes promoting various cellular outcomes including cell cycle arrest, apoptosis or senescence. The precise regulati...
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Drosophila oncogene Gas41 is RNAi modulator that intersects heterochromatin and siRNA pathway.
Published: October, 2014

Abstract: Glioma amplified sequence41 (Gas41) is a highly conserved putative transcription factor that is frequently abundant in human gliomas. Gas41 shows oncogenic activity by promoting cell growth and viability. Here we show Gas41 is required for proper ...
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KDM5 Interacts with Foxo to Modulate Cellular Levels of Oxidative Stress
Published: October, 2014

Abstract: Increased cellular levels of oxidative stress are implicated in a large number of human diseases. Here we describe the transcription co-factor KDM5 (also known as Lid) as a new critical regulator of cellular redox state. Moreover, this occurs thro...
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Sperm DNA Methylation Analysis in Swine Reveals Conserved and Species-Specific Methylation Patterns and Highlights an Altered Methylation at the GNAS Locus in Infertile Boars.
Published: October, 2014

Abstract: Male infertility is an increasing health issue in today's society, for both human or livestock populations. In livestock, male infertility slows the improvement of animal selection programs and agricultural productivity. There are increasing evide...
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Neural crest specification and migration independently require NSD3-related lysine methyltransferase activity.
Published: October, 2014

Abstract: Neural crest precursors express genes that cause them to become migratory, multipotent cells, distinguishing them from adjacent stationary neural progenitors in the neurepithelium. Histone methylation spatiotemporally regulates neural crest gene e...
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Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells.
Published: October, 2014

Abstract: Naive embryonic stem cells hold great promise for research and therapeutics as they have broad and robust developmental potential. While such cells are readily derived from mouse blastocysts it has not been possible to isolate human equivalents ea...
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ASCL1 is a lineage oncogene providing therapeutic targets for high-grade neuroendocrine lung cancers.
Published: October, 2014

Abstract: Aggressive neuroendocrine lung cancers, including small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), represent an understudied tumor subset that accounts for approximately 40,000 new lung cancer cases per year in the United Stat...
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Cross-talking noncoding RNAs contribute to cell-specific neurodegeneration in SCA7.
Published: October, 2014

Abstract: What causes the tissue-specific pathology of diseases resulting from mutations in housekeeping genes? Specifically, in spinocerebellar ataxia type 7 (SCA7), a neurodegenerative disorder caused by a CAG-repeat expansion in ATXN7 (which encodes an e...
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MeDIP-on-Chip for Methylation Profiling
Published: October, 2014

Abstract: DNA methylation is an important regulatory step in gene expression. Knowledge of the alterations in DNA methylation at a whole genome scale improves our understanding of gene regulation and potential correlations with biological events or disease ...
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Chromatin features of plant telomeric sequences at terminal versus internal positions
Published: October, 2014

Abstract: Epigenetic mechanisms are involved in regulation of crucial cellular processes in eukaryotic organisms. Data on the epigenetic features of plant telomeres and their epigenetic regulation were published mostly for Arabidopsis thaliana, in which the...
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Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis.
Published: October, 2014

Abstract: Diatoms are unicellular photosynthetic algae with promise for green production of fuels and other chemicals. Recent genome-editing techniques have greatly improved the potential of many eukaryotic genetic systems, including diatoms, to enable know...
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Notch signaling regulates myogenic regenerative capacity of murine and human mesoangioblasts.
Published: October, 2014

Abstract: Somatic stem cells hold attractive potential for the treatment of muscular dystrophies (MDs). Mesoangioblasts (MABs) constitute a myogenic subset of muscle pericytes and have been shown to efficiently regenerate dystrophic muscles in mice and dogs...
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HDAC6-ubiquitin interaction controls the duration of HSF1 activation after heat-shock.
Published: October, 2014

Abstract: After heat-shock, HSF1 controls a major cellular transcriptional response involving the activation of early (Hsp70) and late (Hsp25) heat shock gene expression. Here we show that a full response to heat shock (activation of both Hsp70 and Hsp25) d...
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cAMP Responsive Element Binding Protein (CREB) and cAMP Co-regulate Activator Protein 1 (AP1)-Dependent Regeneration-Associated Gene Expression and Neurite Growth.
Published: October, 2014

Abstract: To regenerate damaged axons, neurons must express a cassette of regeneration-associated genes (RAGs) that increases intrinsic growth capacity and confers resistance to extrinsic inhibitory cues. Here we show that dibutyrl-cAMP or forskolin combine...
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ETS1 is a genome-wide effector of RAS/ERK signaling in epithelial cells.
Published: October, 2014

Abstract: The RAS/ERK pathway is commonly activated in carcinomas and promotes oncogenesis by altering transcriptional programs. However, the array of cis-regulatory elements and trans-acting factors that mediate these transcriptional changes is still uncle...
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Cellular uptake behaviour, photothermal therapy performance, and cytotoxicity of gold nanorods with various coatings.
Published: October, 2014

Abstract: With the development of Au nanorods for a number of biomedical applications, understanding their cellular responses has become increasingly important. In this study, we systematically evaluated the cellular uptake behaviour and cytotoxicity of Au ...
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The Polycomb Group Gene EMF2B is essential for maintenance of floral meristem determinacy in rice.
Published: October, 2014

Abstract: The Polycomb Repressive Complex 2 (PRC2) represses transcriptional activity of target genes through trimethylation of Lysine 27 of Histone H3. The functions of the plant PRC2 have been chiefly described in Arabidopsis but specific functions in oth...
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Obesity increases histone H3 lysine 9 and 18 acetylation at Tnfa and Ccl2 genes in mouse liver
Published: October, 2014

Abstract: Obesity contributes to the development of non‑alcoholic fatty liver disease (NAFLD), which is characterized by the upregulated expression of two key inflammatory mediators: tumor necrosis factor (Tnfa) and monocyte chemotactic protein 1 (Mcp1; als...
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Altered promoter nucleosome positioning is an early event in gene silencing.
Published: October, 2014

Abstract: Gene silencing in cancer frequently involves hypermethylation and dense nucleosome occupancy across promoter regions. How a promoter transitions to this silent state is unclear. Using colorectal adenomas, we investigated nucleosome positioning, DN...
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SOX11 promotes tumor angiogenesis through transcriptional regulation of PDGFA in mantle cell lymphoma.
Published: October, 2014

Abstract: SOX11 is overexpressed in several solid tumors and in the vast majority of aggressive mantle cell lymphomas (MCLs). We have recently proven that SOX11 silencing reduces tumor growth in a MCL xenograft model, consistent with the indolent clinical c...
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Integrator Regulates Transcriptional Initiation and Pause Release following Activation.
Published: October, 2014

Abstract: In unicellular organisms, initiation is the rate-limiting step in transcription; in metazoan organisms, the transition from initiation to productive elongation is also important. Here, we show that the RNA polymerase II (RNAPII)-associated multipr...
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Predicting interactome networks perturbations in human cancer: application to gene fusions in acute lymphoblastic leukemia.
Published: October, 2014

Abstract: Genomic variations such as point mutations and gene fusions are directly or indirectly associated with human diseases. They are recognized as diagnostic, prognostic markers and therapeutic targets. However, predicting the functional impact of thes...
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Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model.
Published: October, 2014

Abstract: Agrobacterium rhizogenes (or Rhizobium rhizogenes) is able to transform plant genomes and induce the production of hairy roots. We describe the use of A. rhizogenes in tomato (Solanum spp.) to rapidly assess gene expression and function. Gene expr...
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The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity.
Published: October, 2014

Abstract: Histone variant H3.3 is deposited in chromatin at active sites, telomeres, and pericentric heterochromatin by distinct chaperones, but the mechanisms of regulation and coordination of chaperone-mediated H3.3 loading remain largely unknown. We show...
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Epigenetic mechanisms regulate placental c-myc and hTERT in normal and pathological pregnancies; c-myc as a novel fetal DNA epigenetic marker for pre-eclampsia.
Published: October, 2014

Abstract: Placental development is known for its resemblance with tumor development, such as in the expression of oncogenes (c-myc) and telomerase (hTERT). The expression of c-myc and hTERT is up-regulated during early pregnancy and gestational trophoblasti...
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A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia.
Published: October, 2014

Abstract: Efforts to identify and annotate cancer driver genetic lesions have been focused primarily on the analysis of protein-coding genes; however, most genetic abnormalities found in human cancer are located in intergenic regions. Here we identify a new...
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Head formation: OTX2 regulates Dkk1 and Lhx1 activity in the anterior mesendoderm.
Published: October, 2014

Abstract: The Otx2 gene encodes a paired-type homeobox transcription factor that is essential for the induction and the patterning of the anterior structures in the mouse embryo. Otx2 knockout embryos fail to form a head. Whereas previous studies have shown...
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Genome-wide mapping of yeast histone chaperone anti-silencing function 1 reveals its role in condensin binding with chromatin.
Published: September, 2014

Abstract: Genome-wide participation and importance of the histone chaperone Asf1 (Anti-Silencing Function 1) in diverse DNA transactions like replication, repair, heterochromatic silencing and transcription are well documented. Yet its genome-wide targets h...
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c-Rel Regulates Ezh2 Expression in Activated Lymphocytes and Malignant Lymphoid Cells.
Published: September, 2014

Abstract: The Polycomb group protein Ezh2 is a histone methyltransferase that modifies chromatin structure to alter gene expression during embryonic development, lymphocyte activation and tumorigenesis. The mechanism by which Ezh2 expression is regulated is...
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Co-regulated expression of Na+/phosphate Pho89 transporter and Ena1 Na+-ATPase allows their functional coupling under high pH stress.
Published: September, 2014

Abstract: The yeast Saccharomyces cerevisiae has two main high-affinity inorganic phosphate (Pi) transporters, Pho84 and Pho89, functionally relevant at acidic/neutral pH and alkaline pH, respectively. Upon Pi starvation PHO84 and PHO89 are induced by activ...
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Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells.
Published: September, 2014

Abstract: In the current study, we have used HT-TREBS to individually analyze the DNA methylation pattern of 4799 IAP LTR retrotransposons in embryonic stem, somatic and Neuro2A cells. According to the results, half of the loci within this family show const...
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An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.
Published: September, 2014

Abstract: Throughout evolution primate genomes have been modified by waves of retrotransposon insertions. For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells, ...
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Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform.
Published: September, 2014

Abstract: Despite the recent advance of single-cell gene expression analyses, co-measurement of both genomic and transcriptional signatures at the single-cell level has not been realized. However such analysis is necessary in order to accurately delineate h...
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Significance of glioma-associated oncogene homolog 1 (GLI1) expression in claudin-low breast cancer and crosstalk with the nuclear factor kappa-light-chain-enhancer of activated B cells (NF¿B) pathway.
Published: September, 2014

Abstract: IntroductionThe recently identified claudin-low subtype of breast cancer is enriched for cells with stem-like and mesenchymal-like characteristics. This subtype is most often triple-negative (lacking the estrogen and progesterone receptors (ER, PR...
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Vitamin d receptor-mediated stromal reprogramming suppresses pancreatitis and enhances pancreatic cancer therapy.
Published: September, 2014

Abstract: The poor clinical outcome in pancreatic ductal adenocarcinoma (PDA) is attributed to intrinsic chemoresistance and a growth-permissive tumor microenvironment. Conversion of quiescent to activated pancreatic stellate cells (PSCs) drives the severe ...
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Skeletal Muscle PGC-1α1 Modulates Kynurenine Metabolism and Mediates Resilience to Stress-Induced Depression.
Published: September, 2014

Abstract: Depression is a debilitating condition with a profound impact on quality of life for millions of people worldwide. Physical exercise is used as a treatment strategy for many patients, but the mechanisms that underlie its beneficial effects remain ...
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5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation.
Published: September, 2014

Abstract: In mammals, cytosine methylation (5mC) is widely distributed throughout the genome but is notably depleted from active promoters and enhancers. While the role of DNA methylation in promoter silencing has been well documented, the function of this ...
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Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.
Published: September, 2014

Abstract: GWAS have identified a breast cancer susceptibility locus on 2q35. Here we report the fine mapping of this locus using data from 101,943 subjects from 50 case-control studies. We genotype 276 SNPs using the 'iCOGS' genotyping array and impute geno...
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Asparagine synthetase deficiency detected by whole exome sequencing causes congenital microcephaly, epileptic encephalopathy and psychomotor delay.
Published: September, 2014

Abstract: Deficiency of Asparagine Synthetase (ASNSD, MIM 615574) is a very rare autosomal recessive disorder presenting with some brain abnormalities. Affected individuals have congenital microcephaly and progressive encephalopathy associated with severe i...
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Measuring fast gene dynamics in single cells with timelapse luminescence microscopy
Published: September, 2014

Abstract: Timelapse fluorescence microscopy is an important tool for measuring in vivo gene dynamics in single cells. However, fluorescent proteins are limited by slow chromophore maturation times and the cellular auto-fluorescence or photo-toxicity that ar...
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Genome-wide map of regulatory interactions in the human genome.
Published: September, 2014

Abstract: Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, G...
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SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer.
Published: September, 2014

Abstract: EPHB3 is a critical cellular guidance factor in the intestinal epithelium and an important tumor suppressor in colorectal cancer (CRC) whose expression is frequently lost at the adenoma-carcinoma transition when tumor cells become invasive. The mo...
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Genome-wide CNV analysis in 221 unrelated patients and targeted high-throughput sequencing reveal novel causative candidate genes for colorectal adenomatous polyposis.
Published: September, 2014

Abstract: To uncover novel causative genes in patients with unexplained adenomatous polyposis, a model disease for colorectal cancer, we performed a genome-wide analysis of germline copy number variants (CNV) in a large, well characterized APC and MUTYH mut...
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6-methoxyflavone inhibits NFAT translocation into the nucleus and suppresses T cell activation.
Published: September, 2014

Abstract: NFAT plays a crucial role in the immune system by regulating the transcription of inducible genes during immune responses. In T cells, NFAT proteins govern various cellular events related to T cell development, activation, tolerance induction, and...
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TELP, a sensitive and versatile library construction method for next-generation sequencing.
Published: September, 2014

Abstract: Next-generation sequencing has been widely used for the genome-wide profiling of histone modifications, transcription factor binding and gene expression through chromatin immunoprecipitated DNA sequencing (ChIP-seq) and cDNA sequencing (RNA-seq). ...
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Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers.
Published: September, 2014

Abstract: The transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas9) utlilize distinct molecular mechanisms in targeting site recognition. The two protein...
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Shigella flexneri targets the HP1γ subcode through the phosphothreonine lyase OspF.
Published: September, 2014

Abstract: HP1 proteins are transcriptional regulators that, like histones, are targets for post-translational modifications defining an HP1-mediated subcode. HP1γ has multiple phosphorylation sites, including serine 83 (S83) that marks it to sites of active...
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The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation.
Published: September, 2014

Abstract: BACKGROUND: The DEK gene is highly expressed in a wide range of cancer cells, and a recurrent translocation partner in acute myeloid leukemia. While DEK has been identified as one of the most abundant proteins in human chromatin, its function and ...
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Up to date sample preparation of proteins for mass spectrometric analysis.
Published: September, 2014

Abstract: Abstract For the identification of proteins from biological samples by mass spectrometry there are two scenarios. Proteins are pre-fractionated in some way or are analysed as a complex mixture (shotgun). Shotgun proteomics recently became more pop...
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Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera.
Published: September, 2014

Abstract: Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, ...
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Neural stem cell differentiation is dictated by distinct actions of nuclear receptor corepressors and histone deacetylases.
Published: September, 2014

Abstract: Signaling factors including retinoic acid (RA) and thyroid hormone (T3) promote neuronal, oligodendrocyte, and astrocyte differentiation of cortical neural stem cells (NSCs). However, the functional specificity of transcriptional repressor checkpo...
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NKCC1 mediates traumatic brain injury-induced hippocampal neurogenesis through CREB phosphorylation and HIF-1α expression.
Published: September, 2014

Abstract: Traumatic brain injury (TBI) is one of the most prevalent causes of worldwide mortality and morbidity. We previously had evidenced that TBI induced Na-K-2Cl co-transporter (NKCC1) upregulation in hippocampus. Here, we aim to investigate the role o...
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PDYN, a gene implicated in brain/mental disorders, is targeted by REST in the adult human brain.
Published: September, 2014

Abstract: The dynorphin κ-opioid receptor system is implicated in mental health and brain/mental disorders. However, despite accumulating evidence that PDYN and/or dynorphin peptide expression is altered in the brain of individuals with brain/mental disorde...
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PaperClip: rapid multi-part DNA assembly from existing libraries.
Published: September, 2014

Abstract: Assembly of DNA 'parts' to create larger constructs is an essential enabling technique for bioengineering and synthetic biology. Here we describe a simple method, PaperClip, which allows flexible assembly of multiple DNA parts from currently exist...
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Somatic mutations in DROSHA and DICER1 impair microRNA biogenesis through distinct mechanisms in Wilms tumours.
Published: September, 2014

Abstract: Wilms tumour is the most common childhood kidney cancer. Here we report the whole-exome sequencing of 44 Wilms tumours, identifying missense mutations in the microRNA (miRNA)-processing enzymes DROSHA and DICER1, and novel mutations in MYCN, SMARC...
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The pro-apoptotic activity of Drosophila Rbf1 involves dE2F2-dependent downregulation of diap1 and buffy mRNA.
Published: September, 2014

Abstract: The retinoblastoma gene, rb, ensures at least its tumor suppressor function by inhibiting cell proliferation. Its role in apoptosis is more complex and less described than its role in cell cycle regulation. Rbf1, the Drosophila homolog of Rb, has ...
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Identification of a Face Enhancer Reveals Direct Regulation of LIM homeobox 8 (Lhx8) by Wingless-Int (WNT)/β-catenin Signaling.
Published: September, 2014

Abstract: Development of the mammalian face requires a large number of genes that are expressed with spatio-temporal specificity, and transcriptional regulation mediated by enhancers plays a key role in the precise control of gene expression. Using chromati...
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Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation.
Published: September, 2014

Abstract: Overexpression of the histone methyltransferase MMSET in t(4;14)+ multiple myeloma patients is believed to be the driving factor in the pathogenesis of this subtype of myeloma. MMSET catalyzes dimethylation of lysine 36 on histone H3 (H3K36me2), a...
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Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors.
Published: September, 2014

Abstract: Cell type-specific master transcription factors (TFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that the ubiquito...
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Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells.
Published: September, 2014

Abstract: REV1-deficient chicken DT40 cells are compromised in replicating G quadruplex (G4)-forming DNA. This results in localised, stochastic loss of parental chromatin marks and changes in gene expression. We previously proposed that this epigenetic inst...
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Pregnane X receptor activation and silencing promote steatosis of human hepatic cells by distinct lipogenic mechanisms.
Published: September, 2014

Abstract: In addition to its well-characterized role in the regulation of drug metabolism and transport by xenobiotics, pregnane X receptor (PXR) critically impacts on lipid homeostasis. In mice, both ligand-dependent activation and knockout of PXR were pre...
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A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation.
Published: September, 2014

Abstract: CCCTC-binding factor (CTCF) is a ubiquitously expressed multifunctional transcription factor characterized by chromatin binding patterns often described as largely invariant. In this context, how CTCF chromatin recruitment and functionalities are ...
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Mechanism-based genotoxicity screening of metal oxide nanoparticles using the ToxTracker panel of reporter cell lines.
Published: September, 2014

Abstract: BACKGROUND: The rapid expansion of manufacturing and use of nano-sized materials fuels the demand for fast and reliable assays to identify their potential hazardous properties and underlying mechanisms. The ToxTracker assay is a recently developed...
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Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.
Published: September, 2014

Abstract: The autism susceptibility candidate 2 gene (AUTS2) has been associated with multiple neurological diseases including autism spectrum disorders (ASDs). Previous studies showed that AUTS2 has an important neurodevelopmental function and is a suspect...
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Highly conserved ENY2/Sus1 protein binds to Drosophila CTCF and is required for barrier activity.
Published: September, 2014

Abstract: Chromatin insulators affect interactions between promoters and enhancers/silencers and function as barriers for the spreading of repressive chromatin. Drosophila insulator protein dCTCF marks active promoters and boundaries of many histone H3K27 t...
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A thermo-halo-tolerant and proteinase-resistant endoxylanase from Bacillus sp. HJ14.
Published: September, 2014

Abstract: A glycosyl hydrolase family 10 endoxylanase from Bacillus sp. HJ14 was grouped in a separated cluster with another six Bacillus endoxylanases which have not been characterized. These Bacillus endoxylanases showed less than 52% amino acid sequence ...
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Nanog induces hyperplasia without initiating tumors.
Published: September, 2014

Abstract: Though expression of the homeobox transcription factor Nanog is generally restricted to pluripotent cells and early germ cells, many contradictory reports about Nanog's involvement in tumorigenesis exist. To address this, a modified Tet-On system ...
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Chromatin enrichment for proteomics.
Published: September, 2014

Abstract: During interphase, chromatin hosts fundamental cellular processes, such as gene expression, DNA replication and DNA damage repair. To analyze chromatin on a proteomic scale, we have developed chromatin enrichment for proteomics (ChEP), which is a ...
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Early lineage restriction in temporally distinct populations of Mesp1 progenitors during mammalian heart development.
Published: September, 2014

Abstract: Cardiac development arises from two sources of mesoderm progenitors, the first heart field (FHF) and the second (SHF). Mesp1 has been proposed to mark the most primitive multipotent cardiac progenitors common for both heart fields. Here, using clo...
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Hypomethylated pollen bypasses the interploidy hybridization barrier in Arabidopsis.
Published: September, 2014

Abstract: Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier that is established in the endosperm. Deregulated parent-of-origin specific genes cause the response to interploidy hybridizations, revealing an epigenet...
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Transgenic analysis of the Leishmania MAP kinase MPK10 reveals an auto-inhibitory mechanism crucial for stage-regulated activity and parasite viability.
Published: September, 2014

Abstract: Protozoan pathogens of the genus Leishmania have evolved unique signaling mechanisms that can sense changes in the host environment and trigger adaptive stage differentiation essential for host cell infection. The signaling mechanisms underlying p...
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Dopamine signaling leads to loss of polycomb repression and aberrant gene activation in experimental parkinsonism.
Published: September, 2014

Abstract: Polycomb group (PcG) proteins bind to and repress genes in embryonic stem cells through lineage commitment to the terminal differentiated state. PcG repressed genes are commonly characterized by the presence of the epigenetic histone mark H3K27me3...
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Y chromosomes of 40% Chinese descend from three Neolithic super-grandfathers.
Published: August, 2014

Abstract: Demographic change of human populations is one of the central questions for delving into the past of human beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp of the non-rec...
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oxBS-450K: A method for analysing hydroxymethylation using 450K BeadChips.
Published: August, 2014

Abstract: DNA methylation analysis has become an integral part of biomedical research. For high-throughput applications such as epigenome-wide association studies, the Infinium HumanMethylation450 (450K) BeadChip is currently the platform of choice. However...
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Differences among brain tumor stem cell types and fetal neural stem cells in focal regions of histone modifications and DNA methylation, broad regions of modifications, and bivalent promoters.
Published: August, 2014

Abstract: BACKGROUND: Aberrational epigenetic marks are believed to play a major role in establishing the abnormal features of cancer cells. Rational use and development of drugs aimed at epigenetic processes requires an understanding of the range, extent, ...
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Mediator can regulate mitotic entry and direct periodic transcription in fission yeast.
Published: August, 2014

Abstract: Cdk8 is required for correct timing of mitotic progression in fission yeast. How the activity of Cdk8 is regulated is unclear, since the kinase is not activated by T-loop phosphorylation and its partner CycC, does not oscillate. Cdk8 is however a ...
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Histone methylation has distinct dynamics from histone acetylation in cell cycle re-entry from quiescence.
Published: August, 2014

Abstract: Cell growth is attuned to nutrient availability to sustain homeostatic biosynthetic processes. In unfavorable environments, cells enter a non-proliferative state termed quiescence, but rapidly return to the cell cycle once conditions support energ...
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Immunogenetics. Chromatin state dynamics during blood formation.
Published: August, 2014

Abstract: Chromatin modifications are crucial for development, yet little is known about their dynamics during differentiation. Hematopoiesis provides a well-defined model to study chromatin state dynamics; however, technical limitations impede profiling of...
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Interferon γ-inducible protein (IFI) 16 transcriptionally regulates type i interferons and other interferon-stimulated genes and controls the interferon response to both DNA and RNA viruses.
Published: August, 2014

Abstract: The interferon γ-inducible protein 16 (IFI16) has recently been linked to the detection of nuclear and cytosolic DNA during infection with herpes simplex virus-1 and HIV. IFI16 binds dsDNA via HIN200 domains and activates stimulator of interferon ...
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The ROS-sensitive microRNA-9/9* controls the expression of mitochondrial tRNA-modifying enzymes and is involved in the molecular mechanism of MELAS syndrome.
Published: August, 2014

Abstract: Mitochondrial dysfunction activates mitochondria-to-nucleus signaling pathways whose components are mostly unknown. Identification of these components is important to understand the molecular mechanisms underlying mitochondrial diseases and to dis...
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Hierarchical molecular events driven by oocyte-specific factors lead to rapid and extensive reprogramming.
Published: August, 2014

Abstract: Nuclear transfer to oocytes is an efficient way to transcriptionally reprogram somatic nuclei, but its mechanisms remain unclear. Here, we identify a sequence of molecular events that leads to rapid transcriptional reprogramming of somatic nuclei ...
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A Macrohistone Variant Links Dynamic Chromatin Compaction to BRCA1-Dependent Genome Maintenance.
Published: August, 2014

Abstract: Appropriate DNA double-strand break (DSB) repair factor choice is essential for ensuring accurate repair outcome and genomic integrity. The factors that regulate this process remain poorly understood. Here, we identify two repressive chromatin com...
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Mfn2 downregulation in excitotoxicity causes mitochondrial dysfunction and delayed neuronal death.
Published: August, 2014

Abstract: Mitochondrial fusion and fission is a dynamic process critical for the maintenance of mitochondrial function and cell viability. During excitotoxicity neuronal mitochondria are fragmented, but the mechanism underlying this process is poorly unders...
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Haematopoietic stem cell induction by somite-derived endothelial cells controlled by meox1.
Published: August, 2014

Abstract: Haematopoietic stem cells (HSCs) are self-renewing stem cells capable of replenishing all blood lineages. In all vertebrate embryos that have been studied, definitive HSCs are generated initially within the dorsal aorta (DA) of the embryonic vascu...
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Polycomb Protein EED is Required for Silencing of Pluripotency Genes upon ESC Differentiation.
Published: August, 2014

Abstract: Eed (embryonic ectoderm development) is a core component of the Polycomb Repressive Complex 2 (PRC2) which catalyzes the methylation of histone H3 lysine 27 (H3K27). Trimethylated H3K27 (H3K27me3) can act as a signal for PRC1 recruitment in the pr...
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Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia.
Published: August, 2014

Abstract: T-cell acute lymphoblastic leukaemia (T-ALL) is a haematological malignancy with a dismal overall prognosis, including a relapse rate of up to 25%, mainly because of the lack of non-cytotoxic targeted therapy options. Drugs that target the functio...
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The unfolded protein response and the phosphorylations of activating transcription factor 2 in the trans-activation of il23a produced by β-glucans.
Published: August, 2014

Abstract: Current views on the control of IL-23 production focus on the regulation of il23a, the gene encoding IL-23 p19, by NF-κB in combination with other transcription factors. CHOP, XBP1, AP1, SMAD, C/EBPβ, and CREB have been involved in response to LPS...
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Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae.
Published: August, 2014

Abstract: The epigenome of the human malaria vector Anopheles gambiae was characterized in midgut cells by mapping the distribution and levels of two post-translational histone modifications, H3K27ac and H3K27me3. These histone profiles were then correlated...
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KMTase Set7/9 is a critical regulator of E2F1 activity upon genotoxic stress.
Published: August, 2014

Abstract: During the recent years lysine methyltransferase Set7/9 ((Su(var)-3-9, Enhancer-of-Zeste, Trithorax) domain containing protein 7/9) has emerged as an important regulator of different transcription factors. In this study, we report a novel function...
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Temporospatial Coordination of Meiotic DNA Replication and Recombination via DDK Recruitment to Replisomes.
Published: August, 2014

Abstract: It has been long appreciated that, during meiosis, DNA replication is coordinated with the subsequent formation of the double-strand breaks (DSBs) that initiate recombination, but a mechanistic understanding of this process was elusive. We now sho...
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An improved method for including upper size range plasmids in metamobilomes.
Published: August, 2014

Abstract: Two recently developed isolation methods have shown promise when recovering pure community plasmid DNA (metamobilomes/plasmidomes), which is useful in conducting culture-independent investigations into plasmid ecology. However, both methods employ...
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Genome-wide modulation of gene transcription in ovarian carcinoma cells by a new mithramycin analogue.
Published: August, 2014

Abstract: Ovarian cancer has a poor prognosis due to intrinsic or acquired resistance to some cytotoxic drugs, raising the interest in new DNA-binding agents such as mithramycin analogues as potential chemotherapeutic agents in gynecological cancer. Using a...
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A long noncoding RNA protects the heart from pathological hypertrophy.
Published: August, 2014

Abstract: The role of long noncoding RNA (lncRNA) in adult hearts is unknown; also unclear is how lncRNA modulates nucleosome remodelling. An estimated 70% of mouse genes undergo antisense transcription, including myosin heavy chain 7 (Myh7), which encodes ...
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Dynamics of carbon concentrating mechanism induction and protein re-localisation during the dark to light transition in synchronised Chlamydomonas.
Published: August, 2014

Abstract: In the model green alga Chlamydomonas reinhardtii, a carbon concentrating mechanism (CCM) is induced under low CO2 in the light and comprises: active inorganic carbon transport components, carbonic anhydrases and aggregation of Rubisco in the chlo...
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Identification and Validation of Genetic Variants that Influence Transcription Factor and Cell Signaling Protein Levels.
Published: August, 2014

Abstract: Many genetic variants associated with human disease have been found to be associated with alterations in mRNA expression. Although it is commonly assumed that mRNA expression changes will lead to consequent changes in protein levels, methodologica...
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eQTL Mapping of Transposon Silencing Reveals a Position-Dependent Stable Escape from Epigenetic Silencing and Transposition of AtMu1 in the Arabidopsis Lineage.
Published: August, 2014

Abstract: Transposons are massively abundant in all eukaryotic genomes and are suppressed by epigenetic silencing. Transposon activity contributes to the evolution of species; however, it is unclear how much transposition-induced variation exists at a small...
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Inappropriate p53 activation during development induces features of CHARGE syndrome.
Published: August, 2014

Abstract: CHARGE syndrome is a multiple anomaly disorder in which patients present with a variety of phenotypes, including ocular coloboma, heart defects, choanal atresia, retarded growth and development, genitourinary hypoplasia and ear abnormalities. Desp...
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Whole Exome Sequencing for Familial Bicuspid Aortic Valve Identifies Putative Variants.
Published: August, 2014

Abstract: BACKGROUND: -Bicuspid aortic valve (BAV) is the most common congenital cardiovascular malformation (CVM). Although highly heritable, few causal variants have been identified. The purpose of this study was to identify genetic variants underlying B...
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Genetic variants within the second intron of the KCNQ1 gene affect CTCF binding and confer a risk of Beckwith-Wiedemann syndrome upon maternal transmission.
Published: August, 2014

Abstract: BACKGROUND: Disruption of 11p15 imprinting results in two fetal growth disorders with opposite phenotypes: the Beckwith-Wiedemann (BWS; MIM 130650) and the Silver-Russell (SRS; MIM 180860) syndromes. DNA methylation defects account for 60% of BWS ...
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Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3.
Published: August, 2014

Abstract: Insulinoma associated 1 (Insm1) plays an important role in regulating the development of cells in the central and peripheral nervous systems, olfactory epithelium and endocrine pancreas. To better define the role of Insm1 in pancreatic endocrine c...
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Cell isolation induces fate changes of bone marrow mesenchymal cells leading to loss or alternatively to acquisition of new differentiation potentials.
Published: August, 2014

Abstract: Mesenchymal stromal cell populations include a fraction, termed mesenchymal stem cells, exhibiting multipotency. Other cells within this population possess a lesser differentiation range. This was assumed to be due to a mesenchymal cellular cascad...
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Active CREB1 Promotes a Malignant TGFβ2 Autocrine Loop in Glioblastoma.
Published: August, 2014

Abstract: In advanced cancer, including glioblastoma, the TGFβ pathway acts as an oncogenic factor. Some tumors exhibit aberrantly high TGFβ activity, and the mechanisms underlying this phenomenon are not well understood. We have observed that TGFβ can indu...
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Human cytomegalovirus pUL79 is an elongation factor of RNA polymerase II for viral gene transcription.
Published: August, 2014

Abstract: In this study, we have identified a unique mechanism in which human cytomegalovirus (HCMV) protein pUL79 acts as an elongation factor to direct cellular RNA polymerase II for viral transcription during late times of infection. We and others previo...
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Regulation of broad by the Notch pathway affects timing of follicle cell development.
Published: August, 2014

Abstract: During Drosophila oogenesis, activation of Notch signaling in the follicular epithelium (FE) around stage 6 of oogenesis is essential for entry into the endocycle and a series of other changes such as cell differentiation and migration of subsets ...
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Source tracking of an anthrax outbreak in northeastern China using complete genome analysis and MLVA genotyping.
Published: July, 2014

Abstract: Anthrax is caused by Bacillus anthracis, an etiological agent behind zoonotic diseases worldwide. B. anthracis is also one of the most dangerous bioterrorism agents. An anthrax outbreak took place in Liaoning Province in northeastern China in Augu...
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Inhibition of euchromatic histone methyltransferase 1 and 2 sensitizes chronic myeloid leukemia cells to interferon treatment.
Published: July, 2014

Abstract: BACKGROUND: H3K9 methylation is one of the essential histone post-translational modifications for heterochromatin formation and transcriptional repression. Recently, several studies have demonstrated that H3K9 methylation negatively regulates the ...
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SOX2 is a cancer-specific regulator of tumour initiating potential in cutaneous squamous cell carcinoma.
Published: July, 2014

Abstract: Although the principles that balance stem cell self-renewal and differentiation in normal tissue homeostasis are beginning to emerge, it is still unclear whether cancer cells with tumour initiating potential are similarly governed, or whether they...
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Lipid peroxidation product 4-hydroxy-2-nonenal modulates base excision repair in human cells.
Published: July, 2014

Abstract: Oxidative-stress-driven lipid peroxidation (LPO) is involved in the pathogenesis of several human diseases, including cancer. LPO products react with cellular proteins changing their properties, and with DNA bases to form mutagenic etheno-DNA addu...
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Interlocked loops trigger lineage specification and stable fates in the Drosophila nervous system.
Published: July, 2014

Abstract: Multipotent precursors are plastic cells that generate different, stable fates at the correct number, place and time, to allow tissue and organ formation. While fate determinants are known to trigger specific transcriptional programs, the molecula...
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Loss of TBL1XR1 disrupts glucocorticoid receptor recruitment to chromatin and results in glucocorticoid resistance in a B-lymphoblastic leukemia model.
Published: July, 2014

Abstract: Although great advances have been made in the treatment of pediatric acute lymphoblastic leukemia, up to one of five patients will relapse, and their prognosis thereafter is dismal. We have previously identified recurrent deletions in TBL1XR1, whi...
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Histone deacetylase 4 promotes ubiquitin-dependent proteasomal degradation of Sp3 in SH-SY5Y cells treated with di(2-ethylhexyl)phthalate (DEHP), determining neuronal death.
Published: July, 2014

Abstract: Phthalates, phthalic acid esters, are widely used as plasticizers to produce polymeric materials in industrial production of plastics and daily consumable products. Animal studies have shown that di(2-ethylhexyl)phthalate (DEHP) may cause toxic ef...
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H19 and MEST gene expression and histone modification in blastocysts cultured from vitrified and fresh two-cell mouse embryos
Published: July, 2014

Abstract: Vitrification of embryos is a routine procedure in many IVF laboratories. The effect of vitrification on gene expression and some modifications of H3 histone in H19 and MEST imprinted genes in blastocysts produced in vitro from non-vitrified and v...
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AhR and Arnt differentially regulate NF-κB signaling and chemokine responses in human bronchial epithelial cells.
Published: July, 2014

Abstract: BACKGROUND: The aryl hydrocarbon receptor (AhR) has gradually emerged as a regulator of inflammation in the lung and other tissues. AhR may interact with the p65-subunit of the nuclear factor (NF)-κB transcription factors, but reported outcomes of...
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Concerted activities of distinct H4K20 methyltransferases at DNA double-strand breaks regulate 53BP1 nucleation and NHEJ-directed repair.
Published: July, 2014

Abstract: Although selective binding of 53BP1 to dimethylated histone H4 lysine 20 (H4K20me2) at DNA double-strand breaks (DSBs) is a necessary and pivotal determinant of nonhomologous end joining (NHEJ)-directed repair, the enzymes that generate H4K20me2 a...
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DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide.
Published: July, 2014

Abstract: Genomic DNA is under constant assault by endogenous and exogenous DNA damaging agents. DNA breakage can represent a major threat to genome integrity but can also be necessary for genome function. Here we present approaches to map DNA double-strand...
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Homozygous missense variant in the human CNGA3 channel causes cone-rod dystrophy.
Published: July, 2014

Abstract: We assessed a large consanguineous Pakistani family (PKAB157) segregating early onset low vision problems. Funduscopic and electroretinographic evaluation of affected individuals revealed juvenile cone-rod dystrophy (CRD) with maculopathy. Other c...
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Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa.
Published: July, 2014

Abstract: The filamentous fungus Neurospora crassa responds to light in complex ways. To thoroughly study the transcriptional response of this organism to light, RNA-seq was used to analyze capped and polyadenylated mRNA prepared from mycelium grown for 24 ...
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DAB2IP regulates cancer stem cell phenotypes through modulating stem cell factor receptor and ZEB1.
Published: July, 2014

Abstract: Cancer stem cell (CSC), the primary source of cancer-initiating population, is involved in cancer recurrence and drug-resistant phenotypes. This study demonstrates that the loss of DAB2IP, a novel Ras-GTPase activating protein frequently found in ...
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Activating germline mutations in STAT3 cause early-onset multi-organ autoimmune disease.
Published: July, 2014

Abstract: Monogenic causes of autoimmunity provide key insights into the complex regulation of the immune system. We report a new monogenic cause of autoimmunity resulting from de novo germline activating STAT3 mutations in five individuals with a spectrum ...
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Loss of neuronal 3D chromatin organization causes transcriptional and behavioural deficits related to serotonergic dysfunction.
Published: July, 2014

Abstract: The interior of the neuronal cell nucleus is a highly organized three-dimensional (3D) structure where regions of the genome that are linearly millions of bases apart establish sub-structures with specialized functions. To investigate neuronal chr...
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An AUG Codon Conserved for Protein Function Rather than Translational Initiation: The Story of the Protein sElk1.
Published: July, 2014

Abstract: Elk1 belongs to the ternary complex (TCF) subfamily of the ETS-domain transcription factors. Several studies have implicated an important function for Elk1 in the CNS including synaptic plasticity and cell differentiation. Whilst studying ELK1 gen...
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Eaf5/7/3 form a functionally independent NuA4 submodule linked to RNA polymerase II-coupled nucleosome recycling.
Published: July, 2014

Abstract: The NuA4 histone acetyltransferase complex is required for gene regulation, cell cycle progression, and DNA repair. Dissection of the 13-subunit complex reveals that the Eaf7 subunit bridges Eaf5 with Eaf3, a H3K36me3-binding chromodomain protein,...
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Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer.
Published: July, 2014

Abstract: The mechanism for generating double minutes chromosomes (dmin) and homogeneously staining regions (hsr) in cancer is still poorly understood. Through an integrated approach combining next-generation sequencing, single nucleotide polymorphism array...
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Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Published: July, 2014

Abstract: Fetal alcohol spectrum disorder (FASD) is a frequent cause of mental retardation. However, the molecular mechanisms underlying brain development defects induced by maternal alcohol consumption during pregnancy are unclear. We used normal and Hsf2-...
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Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome.
Published: July, 2014

Abstract: Fetal alcohol spectrum disorder (FASD) is a frequent cause of mental retardation. However, the molecular mechanisms underlying brain development defects induced by maternal alcohol consumption during pregnancy are unclear. We used normal and Hsf2-...
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Gambogic acid inhibits multiple myeloma mediated osteoclastogenesis through suppression of chemokine receptor CXCR4 signaling pathways.
Published: July, 2014

Abstract: Bone disease, characterized by the presence of lytic lesions and osteoporosis is the hallmark of multiple myeloma (MM). Stromal cell-derived factor 1α (SDF-1α) and its receptor, CXC chemokine receptor 4 (CXCR4), has been implicated as a regulator ...
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Screening and identification of small molecule inhibitors of ErbB2-induced invasion
Published: July, 2014

Abstract: ERBB2 amplification and overexpression are strongly associated with invasive cancer with high recurrence and poor prognosis. Enhanced ErbB2 signaling induces cysteine cathepsin B and L expression leading to their higher proteolytic activity (zFRas...
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Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys
Published: July, 2014

Abstract: Background The fungal genus Stachybotrys produces several diverse toxins that affect human health. Its strains comprise two mutually-exclusive toxin chemotypes, one producing satratoxins, which are a subclass of trichothecenes, and the other prod...
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Paradoxical role of DNA methylation in activation of FoxA2 gene expression during endoderm development.
Published: July, 2014

Abstract: The transcription factor FoxA2 is a master regulator of endoderm development and pancreatic beta cell gene expression. To elucidate the mechanisms underlying the activation of the FoxA2 gene during differentiation, we have compared the epigenetic ...
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Microsatellite Primers for the Fungi Rhizopogon kretzerae and R. salebrosus (Rhizopogonaceae) from 454 Shotgun Pyrosequencing
Published: July, 2014

Abstract: PREMISE OF THE STUDY: Rhizopogon kretzerae and R. salebrosus (Rhizopogonaceae) are ectomycorrhizal fungi symbiotic with pines and the mycoheterotrophic plant Pterospora andromedea (Ericaceae). Microsatellite loci will allow population genetic stu...
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Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop.
Published: July, 2014

Abstract: The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidop...
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Non-Circadian Expression Masking Clock-Driven Weak Transcription Rhythms in U2OS Cells.
Published: July, 2014

Abstract: U2OS cells harbor a circadian clock but express only a few rhythmic genes in constant conditions. We identified 3040 binding sites of the circadian regulators BMAL1, CLOCK and CRY1 in the U2OS genome. Most binding sites even in promoters do not co...
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Very small deletions within the NESP55 gene in pseudohypoparathyroidism type 1b.
Published: July, 2014

Abstract: Pseudohypoparathyroidism (PHP) is caused by reduced expression of genes within the GNAS cluster, resulting in parathormone resistance. The cluster contains multiple imprinted transcripts, including the stimulatory G protein α subunit (Gs-α) and NE...
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FUS is sequestered in nuclear aggregates in ALS patient fibroblasts.
Published: July, 2014

Abstract: Mutations in the RNA-binding protein FUS have been shown to cause the neurodegenerative disease amyotrophic lateral sclerosis. We investigate whether mutant FUS protein in ALS patient-derived fibroblasts affects normal FUS functions in the nucleus...
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bPeaks: a bioinformatics tool to detect transcription factor binding sites from ChIPseq data in yeasts and other organisms with small genomes.
Published: July, 2014

Abstract: Peak calling is a critical step in ChIPseq data analysis. Choosing the correct algorithm as well as optimized parameters for a specific biological system is an essential task. In this article, we present an original peak calling method (bPeaks) sp...
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Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing.
Published: July, 2014

Abstract: The objective of this study was to examine five different sources of RNA, namely mammary gland tissue (MGT), milk somatic cells (SC), laser microdissected mammary epithelial cells (LCMEC), milk fat globules (MFG) and antibody-captured milk mammary...
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Four methods of preparing mRNA 5' end libraries using the illumina sequencing platform.
Published: July, 2014

Abstract: BACKGROUND: The 5' untranslated regions of mRNA play an important role in their translation. RESULTS: Here, we describe the development of four methods of profiling mRNA 5' ends using the Illumina sequencing platform; the first method utilizes S...
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Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis.
Published: July, 2014

Abstract: Circadian clocks allow organisms to anticipate daily changes in the environment to enhance overall fitness. Transcription factors (TFs) play a prominent role in the molecular mechanism but are incompletely described possibly due to functional redu...
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Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility.
Published: July, 2014

Abstract: A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4(+) T cells that produce type 2 cytokines (TH2 cells). By mapping genome-wide histone modification profiles for subsets of T cells isolated f...
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The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis.
Published: July, 2014

Abstract: Histone variants play crucial roles in gene expression, genome integrity, and chromosome segregation. We report that the four H2A variants in Arabidopsis define different genomic features, contributing to overall genomic organization. The histone ...
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Helicobacter pylori-induced STAT3 activation and signalling network in gastric cancer
Published: July, 2014

Abstract: Background: Helicobacter pylori (H. pylori) is the most important gastric carcinogen. However, the mechanisms of H. pylori induced gastric carcinogenesis through STAT3 activation are largely unknown. We evaluated the effects of H. pylori infection...
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Tissue specific insulator function at H19/Igf2 revealed by deletions at the imprinting control region.
Published: July, 2014

Abstract: Parent-of-origin specific expression at imprinted genes is regulated by allele-specific DNA methylation at imprinting control regions (ICRs). This mechanism of gene regulation, where one element controls allelic expression of multiple genes, is no...
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Synergistic apoptosis in head and neck squamous cell carcinoma cells by co-inhibition of insulin-like growth factor-1 receptor signaling and compensatory signaling pathways.
Published: July, 2014

Abstract: Background: In head and neck squamous cell carcinoma (HNSCC), resistance to single agent targeted therapy may be overcome by co-targeting of compensatory signaling pathways. Methods: A targeted drug screen with 120 combinations was used on 9 HNSCC...
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The interaction of MYC with the trithorax protein ASH2L promotes gene transcription by regulating H3K27 modification.
Published: July, 2014

Abstract: The appropriate expression of the roughly 30,000 human genes requires multiple layers of control. The oncoprotein MYC, a transcriptional regulator, contributes to many of the identified control mechanisms, including the regulation of chromatin, RN...
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Identification of a large protein network involved in epigenetic transmission in replicating DNA of embryonic stem cells.
Published: July, 2014

Abstract: Pluripotency of embryonic stem cells (ESCs) is maintained by transcriptional activities and chromatin modifying complexes highly organized within the chromatin. Although much effort has been focused on identifying genome-binding sites, little is k...
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The telomerase inhibitor Gno1p/PINX1 activates the helicase Prp43p during ribosome biogenesis.
Published: July, 2014

Abstract: We provide evidence that a central player in ribosome synthesis, the ribonucleic acid helicase Prp43p, can be activated by yeast Gno1p and its human ortholog, the telomerase inhibitor PINX1. Gno1p and PINX1 expressed in yeast interact with Prp43p ...
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TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells.
Published: July, 2014

Abstract: TET1 is a 5-methylcytosine dioxygenase and its DNA demethylating activity has been implicated in pluripotency and reprogramming. However, the precise role of TET1 in DNA methylation regulation outside of developmental reprogramming is still unclea...
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The Leishmania donovani chaperone cyclophilin 40 is essential for intracellular infection independent of its stage-specific phosphorylation status.
Published: July, 2014

Abstract: During its life cycle, the protozoan pathogen Leishmania donovani is exposed to contrasting environments inside insect vector and vertebrate host, to which the parasite must adapt for extra- and intracellular survival. Combining null mutant analys...
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From transient transcriptome responses to disturbed neurodevelopment: role of histone acetylation and methylation as epigenetic switch between reversible and irreversible drug effects.
Published: July, 2014

Abstract: The superordinate principles governing the transcriptome response of differentiating cells exposed to drugs are still unclear. Often, it is assumed that toxicogenomics data reflect the immediate mode of action (MoA) of drugs. Alternatively, transc...
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Feasibility of a lateral flow test for neurocysticercosis using novel up-converting nanomaterials and a lightweight strip analyzer.
Published: July, 2014

Abstract: Neurocysticercosis is a frequent parasitic infection of the human brain, occurring in most of the world, and requires imaging of the brain to diagnose. To determine the burden of disease and to simplify diagnosis, a field-friendly rapid lateral fl...
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Interactions with RNA direct the Polycomb group protein SCML2 to chromatin where it represses target genes
Published: July, 2014

Abstract: Polycomb repressive complex-1 (PRC1) is essential for the epigenetic regulation of gene expression. SCML2 is a mammalian homolog of Drosophila SCM, a Polycomb-group protein that associates with PRC1. In this study, we show that SCML2A, an SCML2 is...
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Functional Conservation of the Pre-Sensor One Beta-Finger Hairpin (PS1-hp) Structures in Mini-Chromosome Maintenance Proteins of Saccharomyces cerevisiae and Archaea.
Published: July, 2014

Abstract: Mini-chromosome maintenance (MCM) proteins form complexes that are required for DNA replication and are highly conserved throughout evolution. The replicative helicase of eukaryotic organisms is composed of the six paralogs MCM2-7, which form a he...
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Genome-wide analysis of DNA 5-hmC in peripheral blood of uremia by hMeDIP-chip.
Published: July, 2014

Abstract: Abstract Background: Treatment of uremia is now dominated by dialysis; in some cases, patients are treated with dialysis for decades, but overall outcomes are disappointing. A number of studies have confirmed the relevance of several experimental ...
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Influence of ND10 Components on Epigenetic Determinants of Early KSHV Latency Establishment.
Published: July, 2014

Abstract: We have previously demonstrated that acquisition of intricate patterns of activating (H3K4me3, H3K9/K14ac) and repressive (H3K27me3) histone modifications is a hallmark of KSHV latency establishment. The precise molecular mechanisms that shape the...
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GENOME-WIDE SCREEN OF PROMOTER METHYLATION IDENTIFIES NOVEL MARKERS IN DIET-INDUCED OBESE MICE.
Published: July, 2014

Abstract: OBJECTIVE: To investigate the genome-wide promoter methylation and gene expression for the identification of methylation markers in obesity. METHODS: Using a high-fat, diet-induced obese mouse model, we performed comprehensive DNA methylation prof...
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DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis.
Published: July, 2014

Abstract: RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) are related transcriptional silencing mechanisms that target transposable elements (TEs) and repeats to maintain genome stability in plants. RdDM is mediated by sm...
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Divergent roles of histone deacetylase 6 (HDAC6) and histone deacetylase 11 (HDAC11) on the transcriptional regulation of IL10 in antigen presenting cells.
Published: July, 2014

Abstract: The anti-inflammatory cytokine IL-10 is a key modulator of immune responses. A better understanding of the regulation of this cytokine offers the possibility of tipping the balance of the immune response toward either tolerance, or enhanced immune...
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3β,5α,6β-Cholestanetriol and 25-hydroxycholesterol accumulate in ATP-binding cassette transporter G1 (ABCG1)-deficiency.
Published: July, 2014

Abstract: OBJECTIVE: Oxysterols are oxidized derivatives of sterols that have cytotoxic effects and are potent regulators of diverse cellular functions. Efficient oxysterol removal by the sub-family G member 1 of the ATP-binding cassette transporters (ABCG1...
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Chromatin Profiling Reveals Regulatory Network Shifts and a Protective Role for HNF4A during Colitis.
Published: June, 2014

Abstract: Transcriptional regulatory mechanisms likely contribute to the etiology of Inflammatory Bowel Disease (IBD), as genetic variants associated with the disease are disproportionately found at regulatory elements. However, the transcription factors re...
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Pygo2 regulates β-catenin-induced activation of hair follicle stem/progenitor cells and skin hyperplasia.
Published: June, 2014

Abstract: Understanding the epigenetic mechanisms that control the activation of adult stem cells holds the promise of tissue and organ regeneration. Hair follicle stem cells have emerged as a prime model to study stem cell activation. Wnt/β-catenin signali...
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Characterization of bacteriophage communities and CRISPR profiles from dental plaque.
Published: June, 2014

Abstract: BACKGROUND: Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether...
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Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7.
Published: June, 2014

Abstract: BACKGROUND: Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which ca...
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Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide
Published: June, 2014

Abstract: Introduction: Arsenic i s a widely distributed environmental toxicant that can cause multi-tissue pathologies. Proteomic assays allow for the identification of biological processes modulated by arsenic in diverse tissue types. Method: The altered ...
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Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency.
Published: June, 2014

Abstract: Embryonic stem cells (ESCs) are unique in that they have the capacity to differentiate into all of the cell types in the body. We know a lot about the complex transcriptional control circuits that maintain the naive pluripotent state under self-re...
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MicroRNAs Establish Robustness and Adaptability of a Critical Gene Network to Regulate Progenitor Fate Decisions during Cortical Neurogenesis
Published: June, 2014

Abstract: Over the course of cortical neurogenesis, the transi- tion of progenitors from proliferation to differentia- tion requires a precise regulation of involved gene networks under varying environmental conditions. In order to identify such regulatory ...
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Listeria monocytogenes induces IFNβ expression through an IFI16-, cGAS- and STING-dependent pathway.
Published: June, 2014

Abstract: Listeria monocytogenes is a gram-positive facultative intracellular bacterium, which replicates in the cytoplasm of myeloid cells. Interferon β (IFNβ) has been reported to play an important role in the mechanisms underlying Listeria disease. Altho...
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CD1d-mediated presentation of endogenous lipid antigens by adipocytes requires microsomal triglyceride transfer protein (MTP).
Published: June, 2014

Abstract: Obesity-induced adipose tissue (AT) dysfunction results in a chronic low-grade inflammation that predisposes to the development of insulin resistance and type 2 diabetes. During the development of obesity, the AT-resident immune cell profile alter...
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Chronic inflammation induces telomere dysfunction and accelerates ageing in mice.
Published: June, 2014

Abstract: Chronic inflammation is associated with normal and pathological ageing. Here we show that chronic, progressive low-grade inflammation induced by knockout of the nfkb1 subunit of the transcription factor NF-κB induces premature ageing in mice. We a...
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RPLP1, a Crucial Ribosomal Protein for Embryonic Development of the Nervous System.
Published: June, 2014

Abstract: Ribosomal proteins are pivotal to development and tissue homeostasis. RP Large P1 (Rplp1) overexpression is associated with tumorigenesis. However, the physiological function of Rplp1 in mammalian development remains unknown. In this study, we dis...
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A phosphotyrosine switch determines the antitumor activity of ERβ
Published: June, 2014

Abstract: Estrogen receptors ERα and ERβ share considerable sequence homology yet exert opposite effects on breast cancer cell proliferation. While the proliferative role of ERα in breast tumors is well characterized, it is not clear whether the antitumor a...
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Immunoproteasomes Shape the Transcriptome and Regulate the Function of Dendritic Cells.
Published: June, 2014

Abstract: By regulating protein degradation, constitutive proteasomes (CPs) control practically all cellular functions. In addition to CPs, vertebrates express immunoproteasomes (IPs). The major nonredundant role ascribed to IPs is their enhanced ability to...
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Genomic mapping of cAMP receptor protein (CRPMt) in Mycobacterium tuberculosis: relation to transcriptional start sites and the role of CRPMt as a transcription factor.
Published: June, 2014

Abstract: Chromatin immunoprecipitation identified 191 binding sites of Mycobacterium tuberculosis cAMP receptor protein (CRP(Mt)) at endogenous expression levels using a specific α-CRP(Mt) antibody. Under these native conditions an equal distribution betwe...
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A role for migration-linked genes and genomic islands in divergence of a songbird.
Published: June, 2014

Abstract: Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently there has been a debate around the role of 'genomic islands of divergence' (i.e. blocks of ...
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Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation.
Published: June, 2014

Abstract: Chromatin compaction mediates progenitor to post-mitotic cell transitions and modulates gene expression programs, yet the mechanisms are poorly defined. Snf2h and Snf2l are ATP-dependent chromatin remodelling proteins that assemble, reposition and...
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Epigenetic Regulation by Chromatin Activation Mark H3K4me3 in Primate Progenitor Cells within Adult Neurogenic Niche.
Published: June, 2014

Abstract: Histone 3 lysine 4 trimethylation (H3K4me3) is known to be associated with transcriptionally active or poised genes and required for postnatal neurogenesis within the subventricular zone (SVZ) in the rodent model. Previous comparisons have shown s...
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Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress
Published: June, 2014

Abstract: Background: DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses. Results: In this study, we examined single-base resolution methylomes of Populus under cont...
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ZNF143 is regulated through alternative 3'UTR isoforms.
Published: June, 2014

Abstract: ZNF143 is a ubiquitously expressed transcription factor conserved in all vertebrates, regulating genes involved in primary metabolism and cell growth. It is therefore crucial to tightly maintain the adequate level of this factor in the cell. Altho...
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Cell cycle transition from S-phase to G1 in Caulobacter is mediated by ancestral virulence regulators.
Published: June, 2014

Abstract: Zinc-finger domain transcriptional regulators regulate a myriad of functions in eukaryotes. Interestingly, ancestral versions (MucR) from Alpha-proteobacteria control bacterial virulence/symbiosis. Whether virulence regulators can also control cel...
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Breast cancer cell invasion mediated by Gα12 signaling involves expression of interleukins-6 and -8, and matrix metalloproteinase-2.
Published: June, 2014

Abstract: BACKGROUND: Recent studies on the involvement of the G12 family of heterotrimeric G proteins (Gα12 and Gα13, the products of the GNA12 and GNA13 genes, respectively) in oncogenic pathways have uncovered a link between G12 signaling and cancer prog...
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Loss of Ubp3 increases silencing, decreases unequal recombination in rDNA, and shortens the replicative life span in Saccharomyces cerevisiae.
Published: June, 2014

Abstract: Ubp3 is a conserved ubiquitin protease that acts as an antisilencing factor in MAT and telomeric regions. Here we show that ubp3∆ mutants also display increased silencing in ribosomal DNA (rDNA). Consistent with this, RNA polymerase II occupancy i...
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Two CCAAT box-binding transcription factors redundantly regulate early steps of the legume-rhizobia endosymbiosis.
Published: June, 2014

Abstract: During endosymbiotic interactions between legume plants and nitrogen-fixing rhizobia, successful root infection by bacteria and nodule organogenesis requires the perception and transduction of bacterial lipo-chitooligosaccharidic signal called Nod...
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Protein Phosphatase 2A (PP2A) Regulates Low Density Lipoprotein Uptake through Regulating Sterol Response Element-binding Protein-2 (SREBP-2) DNA Binding.
Published: June, 2014

Abstract: LDL-cholesterol (LDL-C) uptake by Ldlr is regulated at the transcriptional level by the cleavage-dependent activation of membrane-associated sterol response element-binding protein (SREBP-2). Activated SREBP-2 translocates to the nucleus, where it...
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Targeting Polycomb to Pericentric Heterochromatin in Embryonic Stem Cells Reveals a Role for H2AK119u1 in PRC2 Recruitment.
Published: June, 2014

Abstract: The mechanisms by which the major Polycomb group (PcG) complexes PRC1 and PRC2 are recruited to target sites in vertebrate cells are not well understood. Building on recent studies that determined a reciprocal relationship between DNA methylation ...
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Transient accumulation of 5-carboxylcytosine indicates involvement of active demethylation in lineage specification of neural stem cells.
Published: June, 2014

Abstract: 5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene activity during differentiation. Tet dioxygenases oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Both 5fC an...
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Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer.
Published: June, 2014

Abstract: Men who develop metastatic castration-resistant prostate cancer (CRPC) invariably succumb to the disease. Progression to CRPC after androgen ablation therapy is predominantly driven by deregulated androgen receptor (AR) signalling. Despite the suc...
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Epigenetic regulations of immediate early genes expression involved in memory formation by the amyloid precursor protein of Alzheimer disease.
Published: June, 2014

Abstract: We previously demonstrated that APP epigenetically regulates Egr1 expression both in cultured neurons and in vivo. Since Egr1 is an immediate early gene involved in memory formation, we wondered whether other early genes involved in memory were re...
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A Histone Deacetylase Complex Mediates Biofilm Dispersal and Drug Resistance in Candida albicans.
Published: June, 2014

Abstract: UNLABELLED: Biofilms are resilient, surface-associated communities of cells with specialized properties (e.g., resistance to drugs and mechanical forces) that are distinct from those of suspension (planktonic) cultures. Biofilm formation by the op...
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RNAi-Mediated Gene silencing in Zebrafish Triggered by Convergent Transcription.
Published: June, 2014

Abstract: RNAi based strategies to induce gene silencing are commonly employed in numerous model organisms but have not been extensively used in zebrafish. We found that introduction of transgenes containing convergent transcription units in zebrafish embry...
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REGNET: mining context-specific human transcription networks using composite genomic information.
Published: June, 2014

Abstract: BACKGROUND: Genome-wide expression profiles reflect the transcriptional networks specific to the given cell context. However, most statistical models try to estimate the average connectivity of the networks from a collection of gene expression dat...
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Corolla Is a Novel Protein that Contributes to the Architecture of the Synaptonemal Complex of Drosophila.
Published: June, 2014

Abstract: In most organisms the synaptonemal complex (SC) connects paired homologs along their entire length during much of meiotic prophase. To better understand the structure of the SC, we aim to identify its components and to determine how each of these ...
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SOX2 controls tumour initiation and cancer stem-cell functions in squamous-cell carcinoma.
Published: June, 2014

Abstract: Cancer stem cells (CSCs) have been reported in various cancers, including in skin squamous-cell carcinoma (SCC). The molecular mechanisms regulating tumour initiation and stemness are still poorly characterized. Here we find that Sox2, a transcrip...
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COUP-TFI modifies CXCL12 and CXCR4 expression by activating EGF signaling and stimulates breast cancer cell migration.
Published: June, 2014

Abstract: BACKGROUND: The orphan receptors COUP-TF (chicken ovalbumin upstream promoter transcription factor) I and II are members of the nuclear receptor superfamily that play distinct and critical roles in vertebrate organogenesis. The involvement of COUP...
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PARG is dispensable for recovery from transient replicative stress but required to prevent detrimental accumulation of poly(ADP-ribose) upon prolonged replicative stress.
Published: June, 2014

Abstract: Poly(ADP-ribosyl)ation is involved in numerous bio-logical processes including DNA repair, transcription and cell death. Cellular levels of poly(ADP-ribose) (PAR) are regulated by PAR polymerases (PARPs) and the degrading enzyme PAR glycohydrolase...
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NFAT1 and NFAT3 Cooperate with HDAC4 during Regulation of Alternative Splicing of PMCA Isoforms in PC12 Cells.
Published: June, 2014

Abstract: BACKGROUND: The bulk of human genes undergo alternative splicing (AS) upon response to physiological stimuli. AS is a great source of protein diversity and biological processes and is associated with the development of many diseases. Pheochromocyt...
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Conservation of streptococcal CRISPRs on human skin and saliva.
Published: June, 2014

Abstract: BACKGROUND: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are utilized by bacteria to resist encounters with their viruses. Human body surfaces have numerous bacteria that harbor CRISPRs, and their content can provide clues a...
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Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation.
Published: June, 2014

Abstract: Chromatin modifying activities inherent to polycomb repressive complexes PRC1 and PRC2 play an essential role in gene regulation, cellular differentiation, and development. However, the mechanisms by which these complexes recognize their target si...
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Reorganization of enhancer patterns in transition from naive to primed pluripotency.
Published: June, 2014

Abstract: Naive and primed pluripotency is characterized by distinct signaling requirements, transcriptomes, and developmental properties, but both cellular states share key transcriptional regulators: Oct4, Sox2, and Nanog. Here, we demonstrate that transi...
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Retinoblastoma protein (RB) interacts with E2F3 to control terminal differentiation of Sertoli cells.
Published: June, 2014

Abstract: The retinoblastoma protein (RB) is essential for normal cell cycle control. RB function depends, at least in part, on interactions with the E2F family of DNA-binding transcription factors (E2Fs). To study the role of RB in the adult testis, a Sert...
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Hippo pathway activity influences liver cell fate.
Published: June, 2014

Abstract: The Hippo-signaling pathway is an important regulator of cellular proliferation and organ size. However, little is known about the role of this cascade in the control of cell fate. Employing a combination of lineage tracing, clonal analysis, and o...
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The HP1 Homolog Rhino Anchors a Nuclear Complex that Suppresses piRNA Precursor Splicing.
Published: June, 2014

Abstract: piRNAs guide an adaptive genome defense system that silences transposons during germline development. The Drosophila HP1 homolog Rhino is required for germline piRNA production. We show that Rhino binds specifically to the heterochromatic clusters...
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CETP inhibitors downregulate hepatic LDL receptor and PCSK9 expression in vitro and in vivo through a SREBP2 dependent mechanism.
Published: June, 2014

Abstract: BACKGROUND: CETP inhibitors block the transfer of cholesteryl ester from HDL-C to VLDL-C and LDL-C, thereby raising HDL-C and lowering LDL-C. In this study, we explored the effect of CETP inhibitors on hepatic LDL receptor (LDLR) and PCSK9 express...
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Deep sequencing reveals new aspects of progesterone receptor signaling in breast cancer cells.
Published: June, 2014

Abstract: Despite the pleiotropic effects of the progesterone receptor in breast cancer, the molecular mechanisms in play remain largely unknown. To gain a global view of the PR-orchestrated networks, we used next-generation sequencing to determine the prog...
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Frizzled 7 Expression Is Positively Regulated by SIRT1 and β-Catenin in Breast Cancer Cells.
Published: June, 2014

Abstract: The Wnt signaling pathway is often chronically activated in diverse human tumors, and the Frizzled (FZD) family of receptors for Wnt ligands, are central to propagating oncogenic signals in a β-catenin-dependent and independent manner. SIRT1 is a ...
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Insulin regulates carboxypeptidase E by modulating translation initiation scaffolding protein eIF4G1 in pancreatic β cells.
Published: June, 2014

Abstract: Insulin resistance, hyperinsulinemia, and hyperproinsulinemia occur early in the pathogenesis of type 2 diabetes (T2D). Elevated levels of proinsulin and proinsulin intermediates are markers of β-cell dysfunction and are strongly associated with d...
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Functional Analysis of the TRIB1 Associated Locus Linked to Plasma Triglycerides and Coronary Artery Disease.
Published: June, 2014

Abstract: BACKGROUND: The TRIB1 locus has been linked to hepatic triglyceride metabolism in mice and to plasma triglycerides and coronary artery disease in humans. The lipid-associated single nucleotide polymorphisms (SNPs), identified by genome-wide associ...
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Chronic alcohol consumption leads to neurochemical changes in the nucleus accumbens that are not fully reversed by withdrawal.
Published: June, 2014

Abstract: Neuropeptide Y (NPY)- and acetylcholine-containing interneurons of the nucleus accumbens (NAc) seem to play a major role in the rewarding effects of alcohol. This study investigated the relationship between chronic alcohol consumption and subseque...
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Differential regulation of Gli proteins by Sufu in the lung affects PDGF signaling and myofibroblast development.
Published: June, 2014

Abstract: Mammalian Hedgehog (Hh) signaling relies on three Gli transcription factors to mediate Hh responses. This process is controlled in part by a major negative regulator, Sufu, through its effects on Gli protein level, distribution and activity. In th...
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A specific polymorphism in Mycobacterium tuberculosis H37Rv causes differential ESAT-6 expression and identifies WhiB6 as a novel ESX-1 component.
Published: June, 2014

Abstract: The ESX-1 secreted virulence factor ESAT-6 is one of the major and most well-studied virulence factors of Mycobacterium tuberculosis given that its inactivation severely attenuates virulent mycobacteria. In this work we show that clinical isolates...
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Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress.
Published: June, 2014

Abstract: In response to genotoxic stress the TP53 tumour suppressor activates target gene expression to induce cell cycle arrest or apoptosis depending on the extent of DNA damage. These canonical activities can be repressed by TP63 in normal stratifying e...
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The noncoding RNA IPW regulates the imprinted DLK1-DIO3 locus in an induced pluripotent stem cell model of Prader-Willi syndrome.
Published: June, 2014

Abstract: Parental imprinting is a form of epigenetic regulation that results in parent-of-origin differential gene expression. To study Prader-Willi syndrome (PWS), a developmental imprinting disorder, we generated case-derived induced pluripotent stem cel...
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MOZ-Mediated Repression of p16(INK) (4) (a) Is Critical for the Self-Renewal of Neural and Hematopoietic Stem Cells.
Published: June, 2014

Abstract: Although inhibition of p16(INK4a) expression is critical to preserve the proliferative capacity of stem cells, the molecular mechanisms responsible for silencing p16(INK4a) expression remain poorly characterized. Here, we show that the histone ace...
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BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2.
Published: June, 2014

Abstract: Genome instability is central to ageing, cancer and other diseases. It is not only proteins involved in DNA replication or the DNA damage response (DDR) that are important for maintaining genome integrity: from yeast to higher eukaryotes, mutation...
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Genome editing in the human malaria parasite Plasmodium falciparum using the CRISPR-Cas9 system.
Published: June, 2014

Abstract: Genome manipulation in the malaria parasite Plasmodium falciparum remains largely intractable and improved genomic tools are needed to further understand pathogenesis and drug resistance. We demonstrated the CRISPR-Cas9 system for use in P. falcip...
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CPF-Associated Phosphatase Activity Opposes Condensin-Mediated Chromosome Condensation.
Published: June, 2014

Abstract: Functional links connecting gene transcription and condensin-mediated chromosome condensation have been established in species ranging from prokaryotes to vertebrates. However, the exact nature of these links remains misunderstood. Here we show in...
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New lung cancer panel for high-throughput targeted resequencing.
Published: June, 2014

Abstract: We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total len...
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Increased levels of the long intergenic non-protein coding RNA POU3F3 promote DNA methylation in esophageal squamous cell carcinoma cells.
Published: June, 2014

Abstract: BACKGROUND & AIMS: Thousands of long intergenic non-protein coding RNAs (lincRNAs) have been identified in mammals via genome-wide sequencing studies. Many are functional, but are expressed aberrantly by cancer cells. We investigated whether level...
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Phylogenomics of the plant family Araceae.
Published: June, 2014

Abstract: The biogeography, chromosome number evolution, pollination biology and evolutionary history of the plant family Araceae have recently become much clearer (Cabrera et al., 2008; Chartier et al., 2013; Cusimano et al., 2011, 2012; Nauheimer et al., ...
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Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.
Published: June, 2014

Abstract: The development of the human malaria parasite Plasmodium falciparum is controlled by coordinated changes in gene expression throughout its complex life cycle, but the corresponding regulatory mechanisms are incompletely understood. To study the re...
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Engineered zinc-finger transcription factors activate OCT4 (POU5F1), SOX2, KLF4, c-MYC (MYC) and miR302/367.
Published: June, 2014

Abstract: Artificial transcription factors are powerful tools for regulating gene expression. Here we report results with engineered zinc-finger transcription factors (ZF-TFs) targeting four protein-coding genes, OCT4, SOX2, KLF4 and c-MYC, and one noncodin...
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Hydroxymethylation and DNA methylation profiles in the prefrontal cortex of the non-human primate rhesus macaque and the impact of maternal deprivation on hydroxymethylation.
Published: May, 2014

Abstract: 5-Hydroxymethylcytosine (5hmC) is abundant in the brain, suggesting an important role in epigenetic control of neuronal functions. In this paper, we show that 5hmC and 5-methylcytosine (5mC) levels are coordinately distributed in gene promoters of...
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Membrane-Bound Methyltransferase Complex VapA-VipC-VapB Guides Epigenetic Control of Fungal Development.
Published: May, 2014

Abstract: Epigenetic and transcriptional control of gene expression must be coordinated in response to external signals to promote alternative multicellular developmental programs. The membrane-associated trimeric complex VapA-VipC-VapB controls a signal tr...
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Fat specific protein 27 inhibits lipolysis by facilitating the inhibitory effect of Egr1 on transcription of adipose triglyceride lipase.
Published: May, 2014

Abstract: Lipolysis in fat tissue represents a major source of circulating fatty acids. Previously, we have found that lipolysis in adipocytes is controlled by early growth response transcription factor Egr1 that directly inhibits transcription of adipose t...
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A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
Published: May, 2014

Abstract: Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of their target site recognition. Most p...
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Quiescence-Induced LncRNAs Trigger H4K20 Trimethylation and Transcriptional Silencing.
Published: May, 2014

Abstract: A complex network of regulatory pathways links transcription to cell growth and proliferation. Here we show that cellular quiescence alters chromatin structure by promoting trimethylation of histone H4 at lysine 20 (H4K20me3). In contrast to peric...
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Regulating Set-β's Subcellular Localization Toggles Its Function between Inhibiting and Promoting Axon Growth and Regeneration.
Published: May, 2014

Abstract: The failure of the CNS neurons to regenerate axons after injury or stroke is a major clinical problem. Transcriptional regulators like Set-β are well positioned to regulate intrinsic axon regeneration capacity, which declines developmentally in ma...
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Altered oral viral ecology in association with periodontal disease.
Published: May, 2014

Abstract: UNLABELLED: The human oral cavity is home to a large and diverse community of viruses that have yet to be characterized in patients with periodontal disease. We recruited and sampled saliva and oral biofilm from a cohort of humans either periodont...
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Nuclear ARRB1 induces pseudohypoxia and cellular metabolism reprogramming in prostate cancer
Published: May, 2014

Abstract: Tumour cells sustain their high proliferation rate through metabolic reprogramming, whereby cellular metabolism shifts from oxidative phosphorylation to aerobic glycolysis, even under normal oxygen levels. Hypoxia-inducible factor 1A (HIF1A) is a ...
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Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) analysis uncovers broad changes in chromatin structure resulting from hexavalent chromium exposure.
Published: May, 2014

Abstract: The ability of chromatin to switch back and forth from open euchromatin to closed heterochromatin is vital for transcriptional regulation and genomic stability, but its dynamic structure is subject to disruption by exposure to environmental agents...
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Expanding the chemical diversity of natural esters by engineering a polyketide-derived pathway into Escherichia coli.
Published: May, 2014

Abstract: Microbial fatty acid (FA)-derived molecules have emerged as promising alternatives to petroleum-based chemicals for reducing dependence on fossil hydrocarbons. However, native FA biosynthetic pathways often yield limited structural diversity, and ...
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Discovery of transgene insertion sites by high throughput sequencing of mate pair libraries.
Published: May, 2014

Abstract: BACKGROUND: Transgenesis by random integration of a transgene into the genome of a zygote has become a reliable and powerful method for the creation of new mouse strains that express exogenous genes, including human disease genes, tissue specific ...
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Homeostatic maintenance of allele-specific p16 methylation in cancer cells accompanied by dynamic focal methylation and hydroxymethylation.
Published: May, 2014

Abstract: AIM: p16 Methylation frequently occurs in carcinogenesis. While it has been hypothesized that the p16 methylation states are dynamically maintained in cancer cells, direct evidence supporting this hypothesis has not been available until now. METHO...
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Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation.
Published: May, 2014

Abstract: The DNA damage response (DDR) is a vast signaling network that is robustly activated by DNA double-strand breaks, the critical lesion induced by ionizing radiation (IR). Although much of this response operates at the protein level, a critical comp...
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Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency.
Published: May, 2014

Abstract: Hepatocellular carcinoma (HCC) is almost invariably associated with an underlying inflammatory state, whose direct contribution to the acquisition of critical genomic changes is unclear. Here we map acquired genomic alterations in human and mouse ...
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Androgen-dependent Sertoli cell tight junction remodeling is mediated by multiple tight junction components.
Published: May, 2014

Abstract: Sertoli cell tight junctions (SCTJs) of the seminiferous epithelium create a specialized microenvironment in the testis to aid differentiation of spermatocytes and spermatids from spermatogonial stem cells. SCTJs must be chronically broken and re-...
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IL-22 negatively regulates Helicobacter pylori-induced CCL20 expression in gastric epithelial cells.
Published: May, 2014

Abstract: Helicobacter pylori is a Gram-negative bacterium that infects the human gastric mucosa and causes various gastric diseases. H. pylori infection induces the production of inflammatory chemokine CCL20 in gastric mucosa and leads to gastric inflammat...
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Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing
Published: May, 2014

Abstract: The role that mtDNA heteroplasmy plays in healthy aging, familial longevity and the heritability patterns of low levels heteroplasmy in the elderly are largely unknown. We analyzed the low levels of mtDNA heteroplasmy in blood in a cohort of cente...
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IL-15 regulates Bcl-2 family members Bim and Mcl-1 through JAK/STAT and PI3K/AKT pathways in T cells.
Published: May, 2014

Abstract: Maintenance of T cells is determined by their survival capacity, which is regulated by Bcl-2 proteins. Cytokines signalling through the common gamma chains such as IL-2, IL-7 and IL-15 are important for T-cell survival but how these cytokines dete...
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Genomic analysis of the emergence of 20th century epidemic dysentery.
Published: May, 2014

Abstract: BACKGROUND: Shigella dysenteriae type 1 (Sd1) causes recurrent epidemics of dysentery associated with high mortality in many regions of the world. Sd1 infects humans at very low infectious doses (10 CFU), and treatment is complicated by the rapid ...
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The Transcriptional Regulators TAZ and YAP Direct Transforming Growth Factor β-induced Tumorigenic Phenotypes in Breast Cancer Cells.
Published: May, 2014

Abstract: Uncontrolled transforming growth factor-β (TGFβ) signaling promotes aggressive metastatic properties in late-stage breast cancers. However, how TGFβ-mediated cues are directed to induce tumorigenic events is poorly understood, particularly given t...
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Insights into how Spt5 functions in transcription elongation and repressing transcription coupled DNA repair.
Published: May, 2014

Abstract: Spt5, a transcription elongation factor, and Rpb4, a subunit of RNA polymerase II (RNAP II) that forms a subcomplex with Rpb7, play important roles in transcription elongation and repression of transcription coupled DNA repair (TCR) in eukaryotic ...
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Identification of regulators of the three-dimensional polycomb organization by a microscopy-based genome-wide RNAi screen.
Published: May, 2014

Abstract: Polycomb group (PcG) proteins dynamically define cellular identities through epigenetic repression of key developmental genes. PcG target gene repression can be stabilized through the interaction in the nucleus at PcG foci. Here, we report the res...
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Dendritic cell development requires histone deacetylase activity.
Published: May, 2014

Abstract: DCs develop from multipotent progenitors (MPPs), which commit into DC-restricted common dendritic cell progenitors (CDPs). CDPs further differentiate into classical DCs (cDCs) and plasmacytoid DCs (pDCs). Here, we studied the impact of histone ace...
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The extent of error-prone replication-restart by homologous recombination is controlled by Exo1 and checkpoint proteins
Published: May, 2014

Abstract: Genetic instability, a hallmark of cancer, can occur when the replication machinery encounters a barrier. The intra-S phase checkpoint maintains stalled replication forks in a replication-competent configuration by phosphorylating replisome compon...
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Biogeography and phylogenomics of New World Bambusoideae (Poaceae), revisited.
Published: May, 2014

Abstract: • Premise of the study: New World Bambusoideae have only recently been studied in a phylogenomic context. Plastome sequences were determined and analyzed from Arundinaria appalachiana, A. tecta, and Olyra latifolia, to refine our knowledge of thei...
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Myostatin Regulates Energy Homeostasis in the Heart and Prevents Heart Failure.
Published: May, 2014

Abstract: RATIONALE: Myostatin is a major negative regulator of skeletal muscle mass and initiates multiple metabolic changes including enhanced insulin sensitivity. However, the function of Myostatin in the heart is barely understood although it is upregul...
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Fetal programming of adult Leydig cell function by androgenic effects on stem/progenitor cells.
Published: May, 2014

Abstract: Fetal growth plays a role in programming of adult cardiometabolic disorders, which in men, are associated with lowered testosterone levels. Fetal growth and fetal androgen exposure can also predetermine testosterone levels in men, although how is ...
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Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.
Published: May, 2014

Abstract: Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome wide. ...
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EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.
Published: May, 2014

Abstract: BACKGROUND: Next Generation Sequencing technologies have facilitated differential gene expression analysis through RNA-seq and Tag-seq methods. RNA-seq has biases associated with transcript lengths, lacks uniform coverage of regions in mRNA and re...
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Thyroid hormone induction of human cholesterol 7 alpha-hydroxylase (Cyp7a1) in vitro.
Published: May, 2014

Abstract: Thyroid hormone (TH) modulates serum cholesterol by acting on TH receptor β1 (TRβ1) in liver to regulate metabolic gene sets. In rodents, one important TH regulated step involves induction of Cyp7a1, an enzyme in the cytochrome P450 family, which ...
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Highly efficient differentiation of embryonic stem cells into adipocytes by ascorbic acid.
Published: May, 2014

Abstract: Adipocyte differentiation and function have become the major research targets due to the increasing interest in obesity and related metabolic conditions. Although, late stages of adipogenesis have been extensively studied, the early phases remain ...
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MIR146A inhibits JMJD3 expression and osteogenic differentiation in human mesenchymal stem cells.
Published: May, 2014

Abstract: Chromatin remodeling is important for cell differentiation. Histone methyltransferase EZH2 and histone demethylase JMJD3 (KDM6B) modulate levels of histone H3 lysine 27 trimethylation (H3K27me3). Interplay between the two modulators influence line...
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Reassessment of QTLs for Late Blight Resistance in the Tomato Accession L3708 Using a Restriction Site Associated DNA (RAD) Linkage Map and Highly Aggressive Isolates of Phytophthora infestans
Published: May, 2014

Abstract: omato late blight caused by the oomycete pathogen Phytophthora infestans (Mont.) de Bary is a major threat to tomato production in cool and wet environments. Intensified outbreaks of late blight have been observed globally from the 1980s, and are ...
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The plant metacaspase AtMC1 in pathogen-triggered programmed cell death and aging: functional linkage with autophagy.
Published: May, 2014

Abstract: Autophagy is a major nutrient recycling mechanism in plants. However, its functional connection with programmed cell death (PCD) is a topic of active debate and remains not well understood. Our previous studies established the plant metacaspase At...
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Trrap-dependent histone acetylation specifically regulates cell-cycle gene transcription to control neural progenitor fate decisions.
Published: May, 2014

Abstract: Fate decisions in neural progenitor cells are orchestrated via multiple pathways, and the role of histone acetylation in these decisions has been ascribed to a general function promoting gene activation. Here, we show that the histone acetyltransf...
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DNA hypermethylation in prostate cancer is a consequence of aberrant epithelial differentiation and hyperproliferation.
Published: May, 2014

Abstract: Prostate cancer (CaP) is mostly composed of luminal-like differentiated cells, but contains a small subpopulation of basal cells (including stem-like cells), which can proliferate and differentiate into luminal-like cells. In cancers, CpG island h...
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The Ah Receptor Recruits IKKα to Its Target Binding Motifs to Phosphorylate Serine-10 in Histone H3 Required for Transcriptional Activation.
Published: May, 2014

Abstract: Aryl hydrocarbon receptor (AHR) activation by xenobiotic ligands such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is key to their toxicity. Following activation and nuclear translocation, AHR heterodimerizes with the AHR nuclear translocator (AR...
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Early-life stress reduces DNA methylation of the pomc gene in male mice.
Published: May, 2014

Abstract: Early-life stress (ELS) increases the vulnerability thresholds for stress-related diseases such as major depression and anxiety by inducing alterations in the structure and function of neural circuits and endocrine pathways. We previously demonstr...
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The myc 3' wnt-responsive element suppresses colonic tumorigenesis.
Published: May, 2014

Abstract: Mutations in components of the Wnt/β-catenin signaling pathway are commonly found in colorectal cancers, and these mutations cause aberrant expression of genes controlled by Wnt-responsive DNA elements (WREs). While the c-Myc proto-oncogene (Myc) ...
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Function-based identification of mammalian enhancers using site-specific integration.
Published: May, 2014

Abstract: The accurate and comprehensive identification of functional regulatory sequences in mammalian genomes remains a major challenge. Here we describe site-specific integration fluorescence-activated cell sorting followed by sequencing (SIF-seq), an un...
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Unraveling vitamin B12-responsive gene regulation in algae.
Published: May, 2014

Abstract: Photosynthetic microalgae play a vital role in primary productivity and biogeochemical cycling in both marine and freshwater systems across the globe. However, the growth of these cosmopolitan organisms depends on the bioavailability of nutrients ...
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CD4(+) T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2.
Published: May, 2014

Abstract: Molecular mechanisms that maintain lineage integrity of helper T cells are largely unknown. Here we show histone deacetylases 1 and 2 (HDAC1 and HDAC2) as crucial regulators of this process. Loss of HDAC1 and HDAC2 during late T cell development l...
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Signaling by IL-6 promotes alternative activation of macrophages to limit endotoxemia and obesity-associated resistance to insulin.
Published: May, 2014

Abstract: Obesity and resistance to insulin are closely associated with the development of low-grade inflammation. Interleukin 6 (IL-6) is linked to obesity-associated inflammation; however, its role in this context remains controversial. Here we found that...
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Double-Wall Carbon Nanotubes for Wide-Band, Ultrafast Pulse Generation.
Published: May, 2014

Abstract: We demonstrate wide-band ultrafast optical pulse generation at 1, 1.5, and 2 μm using a single-polymer composite saturable absorber based on double-wall carbon nanotubes (DWNTs). The freestanding optical quality polymer composite is prepared from ...
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Monitoring in vivo reversible cysteine oxidation in proteins using ICAT and mass spectrometry.
Published: May, 2014

Abstract: Reversible thiol oxidation of cysteine residues occurs in many intracellular catalytic and signaling processes. Here we describe an optimized protocol, which can be completed in ∼5 d, to unambiguously identify specific cysteine residues that are t...
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Epigenetic changes modulate schistosome egg formation and are a novel target for reducing transmission of schistosomiasis.
Published: May, 2014

Abstract: Treatment and control of schistosomiasis relies on the only available drug, praziquantel, and the search for alternative chemotherapeutic agents is therefore urgent. Egg production is required for the transmission and immunopathology of schistosom...
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R-loops associated with triplet repeat expansions promote gene silencing in Friedreich ataxia and fragile X syndrome.
Published: May, 2014

Abstract: Friedreich ataxia (FRDA) and Fragile X syndrome (FXS) are among 40 diseases associated with expansion of repeated sequences (TREDs). Although their molecular pathology is not well understood, formation of repressive chromatin and unusual DNA struc...
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Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia.
Published: April, 2014

Abstract: BACKGROUND: Aberrant DNA methylation is frequently found in human malignancies including acute myeloid leukemia (AML). While most studies focus on later disease stages, the onset of aberrant DNA methylation events and their dynamics during leukemi...
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Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis.
Published: April, 2014

Abstract: The SMARCA4 (also known as BRG1 in humans) chromatin remodeling factor is critical for establishing lineage-specific chromatin states during early mammalian development. However, the role of SMARCA4 in tissue-specific gene regulation during embryo...
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Primary vitamin D receptor target genes as biomarkers for the vitamin D3 status in the hematopoietic system.
Published: April, 2014

Abstract: Vitamin D3 belongs to the few nutritional compounds that has, via the binding of its metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) to the transcription factor vitamin D receptor (VDR), a direct effect on gene regulation. The relation of thous...
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Breast tumor specific mutation in GATA3 affects physiological mechanisms regulating transcription factor turnover.
Published: April, 2014

Abstract: BACKGROUND: The transcription factor GATA3 is a favorable prognostic indicator in estrogen receptor-alpha (ERalpha)-positive breast tumors in which it participates with ERalpha and FOXA1 in a complex transcriptional regulatory program driving tumo...
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Dynamic ER Interactomes Control the Estrogen-Responsive Trefoil Factor (TFF) Locus Cell-Specific Activities.
Published: April, 2014

Abstract: Estradiol signaling is ideally suited for analyzing molecular and functional linkages between the different layers of information directing transcriptional regulations: DNA sequence, chromatin modifications and the spatial organization of the geno...
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The ETS family member GABPα modulates androgen receptor signalling and mediates an aggressive phenotype in prostate cancer.
Published: April, 2014

Abstract: In prostate cancer (PC), the androgen receptor (AR) is a key transcription factor at all disease stages, including the advanced stage of castrate-resistant prostate cancer (CRPC). In the present study, we show that GABPα, an ETS factor that is up-...
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Targeting vertebrate intron-encoded box C/D 2'-O-methylation guide RNAs into the Cajal body.
Published: April, 2014

Abstract: Post-transcriptional pseudouridylation and 2'-O-methylation of splicesomal small nuclear ribonucleic acids (snRNAs) is mediated by box H/ACA and box C/D small Cajal body (CB)-specific ribonucleoproteins (scaRNPs), respectively. The WD-repeat prote...
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Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells.
Published: April, 2014

Abstract: Bacterial type II CRISPR-Cas9 systems have been widely adapted for RNA-guided genome editing and transcription regulation in eukaryotic cells, yet their in vivo target specificity is poorly understood. Here we mapped genome-wide binding sites of a...
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Specificity Protein 1 (Sp1) Maintains Basal Epithelial Expression of the miR-200 Family: IMPLICATIONS FOR EPITHELIAL-MESENCHYMAL TRANSITION.
Published: April, 2014

Abstract: Epithelial-mesenchymal transition (EMT) is required for the specification of tissues during embryonic development and is recapitulated during the metastatic progression of tumors. The miR-200 family plays a critical role in enforcing the epithelia...
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Gene-Specific Methylation Control of H3K9 and H3K36 on Neurotrophic BDNF versus Astroglial GFAP Genes by KDM4A/C Regulates Neural Stem Cell Differentiation.
Published: April, 2014

Abstract: Neural stem cell (NSC) state and fate depend on spatially and temporally synchronized transcriptional and epigenetic regulation of the expression of extrinsic signaling factors and intrinsic cell-specific genes, but the functional roles for chroma...
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Genome-Wide and Gene-Specific Epigenomic Platforms for Hepatocellular Carcinoma Biomarker Development Trials
Published: April, 2014

Abstract: The majority of the epigenomic reports in hepatocellular carcinoma have focused on identifying novel differentially methylated drivers or passengers of the oncogenic process. Few reports have considered the technologies in place for clinical trans...
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The CpG Island Encompassing the Promoter and First Exon of Human DNMT3L Gene Is a PcG/TrX Response Element (PRE).
Published: April, 2014

Abstract: DNMT3L, a member of DNA methyltransferases family, is present only in mammals. As it provides specificity to the action of de novo methyltransferases, DNMT3A and DNMT3B and interacts with histone H3, DNMT3L has been invoked as the molecule that ca...
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CHD7 interacts with BMP R-SMADs to epigenetically regulate cardiogenesis in mice.
Published: April, 2014

Abstract: Haploinsufficiency for CHD7, an ATP-dependent nucleosome remodeling factor, is the leading cause of CHARGE syndrome. While congenital heart defects (CHDs) are major clinical features of CHARGE syndrome, affecting >75% of patients, it remains uncle...
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Suv39h1 mediates AP-2α-dependent inhibition of C/EBPα expression during adipogenesis.
Published: April, 2014

Abstract: Previous studies show that CCAAT/enhancer-binding protein α (C/EBPα) plays a very important role during adipocyte terminal differentiation and that AP-2α (Activator Protein 2α) acts as a repressor to delay the expression of C/EBPα. However, the me...
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Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1.
Published: April, 2014

Abstract: Genetic deficiencies in transcription factors can lead to the loss of certain types of cells and tissue. The steroidogenic tissue-specific nuclear receptor Ad4BP/SF-1 (NR5A1) is one such gene, because mice in which this gene is disrupted fail to d...
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Acupuncture Promotes Angiogenesis after Myocardial Ischemia through H3K9 Acetylation Regulation at VEGF Gene.
Published: April, 2014

Abstract: BACKGROUND: Acupuncture exerts cardioprotective effects on several types of cardiac injuries, especially myocardial ischemia (MI), but the mechanisms have not yet been well elucidated. Angiogenesis mediated by VEGF gene expression and its modifica...
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Histone Deacetylase 1 and p300 Can Directly Associate with Chromatin and Compete for Binding in a Mutually Exclusive Manner.
Published: April, 2014

Abstract: Lysine acetyltransferases (KATs) and histone deacetylases (HDACs) are important epigenetic modifiers and dynamically cycled on active gene promoters to regulate transcription. Although HDACs are recruited to gene promoters and DNA hypersensitive s...
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Rif1 controls DNA replication timing in yeast through the PP1 phosphatase Glc7.
Published: April, 2014

Abstract: The Rif1 protein, originally identified as a telomere-binding factor in yeast, has recently been implicated in DNA replication control from yeast to metazoans. Here, we show that budding yeast Rif1 protein inhibits activation of prereplication com...
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Epigenetic upregulation of corticotrophin-releasing hormone mediates postnatal maternal separation-induced memory deficiency.
Published: April, 2014

Abstract: Accumulating evidences demonstrated that early postnatal maternal separation induced remarkable social and memory defects in the adult rodents. Early-life stress induced long-lasting functional adaptation of neuroendocrine hypothalamic-pituitary-a...
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ZBED6 Modulates the Transcription of Myogenic Genes in Mouse Myoblast Cells.
Published: April, 2014

Abstract: ZBED6 is a recently discovered transcription factor, unique to placental mammals, that has evolved from a domesticated DNA transposon. It acts as a repressor at the IGF2 locus. Here we show that ZBED6 acts as a transcriptional modulator in mouse m...
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Characterization of an archaeal two-component system that regulates methanogenesis in Methanosaeta harundinacea.
Published: April, 2014

Abstract: Two-component signal transduction systems (TCSs) are a major mechanism used by bacteria in response to environmental changes. Although many sequenced archaeal genomes encode TCSs, they remain poorly understood. Previously, we reported that a metha...
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The transcription factor E4bp4/Nfil3 controls commitment to the NK lineage and directly regulates Eomes and Id2 expression.
Published: April, 2014

Abstract: The transcription factor E4bp4 (Nfil3) is essential for natural killer (NK) cell production. Here, we show that E4bp4 is required at the NK lineage commitment point when NK progenitors develop from common lymphoid progenitors (CLPs) and that E4bp4...
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Multisite phosphorylation of the Sum1 transcriptional repressor by S-phase kinases controls exit from meiotic prophase in yeast.
Published: April, 2014

Abstract: Activation of the meiotic transcription factor Ndt80 is a key regulatory transition in the life-cycle of Saccharomyces cerevisiae because it triggers exit from pachytene and entry into meiosis. The NDT80 promoter is held inactive by a complex cont...
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Whole Exome Sequencing Identifies Recessive PKHD1 Mutations in a Chinese Twin Family with Caroli Disease.
Published: April, 2014

Abstract: BACKGROUND: Mutations in PKHD1 cause autosomal recessive Caroli disease, which is a rare congenital disorder involving cystic dilatation of the intrahepatic bile ducts. However, the mutational spectrum of PKHD1 and the phenotype-genotype correlati...
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Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period.
Published: April, 2014

Abstract: The complex relationship between ontogeny and phylogeny has been the subject of attention and controversy since von Baer's formulations in the 19th century. The classic concept that embryogenesis progresses from clade general features to species s...
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YY1 Acts as a Transcriptional Activator of Hoxa5 Gene Expression in Mouse Organogenesis.
Published: April, 2014

Abstract: The Hox gene family encodes homeodomain-containing transcriptional regulators that confer positional information to axial and paraxial tissues in the developing embryo. The dynamic Hox gene expression pattern requires mechanisms that differentiall...
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Protein quantitative trait Loci identify novel candidates modulating cellular response to chemotherapy.
Published: April, 2014

Abstract: Annotating and interpreting the results of genome-wide association studies (GWAS) remains challenging. Assigning function to genetic variants as expression quantitative trait loci is an expanding and useful approach, but focuses exclusively on mRN...
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USP7 attenuates hepatic gluconeogenesis through modulation of FoxO1 gene promoter occupancy.
Published: April, 2014

Abstract: Hepatic forkhead protein FoxO1 is a key component of systemic glucose homeostasis via its ability to regulate the transcription of rate-limiting enzymes in gluconeogenesis. Important in the regulation of FoxO1 transcriptional activity are the modi...
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Intronic DNA elements regulate Nrf-2 chemical responsiveness of the human microsomal epoxide hydrolase gene (EPHX1) through a far upstream alternative promoter.
Published: April, 2014

Abstract: In humans, microsomal epoxide hydrolase (mEH) contributes important biological functions that underlie both detoxification and bioactivation fates arising from exposures to foreign chemicals. Previously, we discovered that human mEH gene transcrip...
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ApoER2 processing by presenilin-1 modulates reelin expression.
Published: April, 2014

Abstract: The reelin signaling protein and its downstream components have been associated with synaptic plasticity and neurotransmission. The reelin signaling pathway begins with the binding of reelin to the transmembrane lipoprotein receptor apolipoprotein...
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LORD-Q: a long-run real-time PCR-based DNA-damage quantification method for nuclear and mitochondrial genome analysis.
Published: April, 2014

Abstract: DNA damage is tightly associated with various biological and pathological processes, such as aging and tumorigenesis. Although detection of DNA damage is attracting increasing attention, only a limited number of methods are available to quantify D...
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Length-dependent processing of telomeres in the absence of telomerase.
Published: April, 2014

Abstract: In the absence of telomerase, telomeres progressively shorten with every round of DNA replication, leading to replicative senescence. In telomerase-deficient Saccharomyces cerevisiae, the shortest telomere triggers the onset of senescence by activ...
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CpG domains downstream of TSSs promote high levels of gene expression.
Published: April, 2014

Abstract: CpG dinucleotides are known to play a crucial role in regulatory domains, affecting gene expression in their natural context. Here, we demonstrate that intragenic CpG frequency and distribution impacts transgene and genomic gene expression levels ...
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The antineoplastic effect of carnosine is accompanied by induction of PDK4 and can be mimicked by L-histidine.
Published: April, 2014

Abstract: Carnosine (β-alanyl-L-histidine) is a naturally occurring dipeptide that shows antineoplastic effects in cell culture as well as in animal experiments. Since its mode of action and the targets at the molecular level have not yet been elucidated, w...
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Suppression of intragenic transcription requires the MOT1 and NC2 regulators of TATA-binding protein.
Published: April, 2014

Abstract: Chromatin structure in transcribed regions poses a barrier for intragenic transcription. In a comprehensive study of the yeast chromatin remodelers and the Mot1p-NC2 regulators of TATA-binding protein (TBP), we detected synthetic genetic interacti...
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Folic acid stimulation of neural stem cell proliferation is associated with altered methylation profile of PI3K/Akt/CREB.
Published: April, 2014

Abstract: Proliferation of neural stem cells (NSCs) is required for development and repair in the nervous system. NSC amplification in vitro is a necessary step towards using NSC transplantation therapy to treat neurodegenerative diseases. Folic acid (FA) h...
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Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2.
Published: April, 2014

Abstract: Seven linker histone H1 variants are present in human somatic cells with distinct prevalence across cell types. Despite being key structural components of chromatin, it is not known whether the different variants have specific roles in the regulat...
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Transcriptional Derepression of the ERVWE1 Locus following Influenza A Virus Infection.
Published: April, 2014

Abstract: UNLABELLED: Syncytin-1, a fusogenic protein encoded by a human endogenous retrovirus of the W family (HERV-W) element (ERVWE1), is expressed in the syncytiotrophoblast layer of the placenta. This locus is transcriptionally repressed in adult tissu...
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HMGA1 recruits CTIP2-repressed P-TEFb to the HIV-1 and cellular target promoters.
Published: April, 2014

Abstract: Active positive transcription elongation factor b (P-TEFb) is essential for cellular and human immunodeficiency virus type 1 (HIV-1) transcription elongation. CTIP2 represses P-TEFb activity in a complex containing 7SK RNA and HEXIM1. Recently, th...
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Anp32e, a higher eukaryotic histone chaperone directs preferential recognition for H2A.Z.
Published: April, 2014

Abstract: H2A.Z is a highly conserved histone variant in all species. The chromatin deposition of H2A.Z is specifically catalyzed by the yeast chromatin remodeling complex SWR1 and its mammalian counterpart SRCAP. However, the mechanism by which H2A.Z is pr...
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High-throughput sequencing exclusively identified a novel Torque teno virus genotype in serum of a patient with fatal fever.
Published: April, 2014

Abstract: Torque teno virus (TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased sequencing to screen for viruses i...
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MBD4 cooperates with DNMT1 to mediate methyl-DNA repression and protects mammalian cells from oxidative stress.
Published: April, 2014

Abstract: Oxidative stress induces genome-wide remodeling of the chromatin structure. In this study, we identify Methyl-CpG Binding Protein 4 (MBD4), a multifunctional enzyme involved in DNA demethylation, base excision repair, and gene expression regulatio...
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Rad51-Rad52 mediated maintenance of centromeric chromatin in Candida albicans.
Published: April, 2014

Abstract: Specification of the centromere location in most eukaryotes is not solely dependent on the DNA sequence. However, the non-genetic determinants of centromere identity are not clearly defined. While multiple mechanisms, individually or in concert, m...
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TAp73 is essential for germ cell adhesion and maturation in testis.
Published: March, 2014

Abstract: A core evolutionary function of the p53 family is to protect the genomic integrity of gametes. However, the role of p73 in the male germ line is unknown. Here, we reveal that TAp73 unexpectedly functions as an adhesion and maturation factor of the...
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High-resolution chromatin immunoprecipitation (ChIP) sequencing reveals novel binding targets and prognostic role for SOX11 in mantle cell lymphoma.
Published: March, 2014

Abstract: Sex determining region Y-box 11 (SOX11) expression is specific for mantle cell lymphoma (MCL) as compared with other non-Hodgkin's lymphomas. However, the function and direct-binding targets of SOX11 in MCL are largely unknown. We used high-resolu...
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Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline.
Published: March, 2014

Abstract: Mapping genome-wide data to human subtelomeres has been problematic due to the incomplete assembly and challenges of low-copy repetitive DNA elements. Here, we provide updated human subtelomere sequence assemblies that were extended by filling tel...
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Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids.
Published: March, 2014

Abstract: Pulmonary carcinoids are rare neuroendocrine tumours of the lung. The molecular alterations underlying the pathogenesis of these tumours have not been systematically studied so far. Here we perform gene copy number analysis (n=54), genome/exome (n...
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Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.
Published: March, 2014

Abstract: Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon...
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Modelling mutational landscapes of human cancers in vitro.
Published: March, 2014

Abstract: Experimental models that recapitulate mutational landscapes of human cancers are needed to decipher the rapidly expanding data on human somatic mutations. We demonstrate that mutation patterns in immortalised cell lines derived from primary murine...
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High-throughput quantitative proteomic analysis of dengue virus type 2 infected A549 cells.
Published: March, 2014

Abstract: Disease caused by dengue virus is a global health concern with up to 390 million individuals infected annually worldwide. There are no vaccines or antiviral compounds available to either prevent or treat dengue disease which may be fatal. To incre...
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Hic-5 influences genomic and non-genomic actions of the androgen receptor in prostate myofibroblasts.
Published: March, 2014

Abstract: There is extensive knowledge of androgen receptor (AR) signaling in cancer cells, but less regarding androgen action in stromal cells of the tumor microenvironment. We report here the genome-wide effects of a stromal cell specific molecular adapte...
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GABA and glutamate pathways are spatially and developmentally affected in the brain of Mecp2-deficient mice.
Published: March, 2014

Abstract: Proper brain functioning requires a fine-tuning between excitatory and inhibitory neurotransmission, a balance maintained through the regulation and release of glutamate and GABA. Rett syndrome (RTT) is a rare genetic disorder caused by mutations ...
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Calcineurin/NFAT signaling represses genes Vamp1 and Vamp2 via PMCA-dependent mechanism during dopamine secretion by Pheochromocytoma cells.
Published: March, 2014

Abstract: BACKGROUND: Plasma membrane Ca(2+)-ATPases (PMCA) extrude Ca(2+) ions out of the cell and contribute to generation of calcium oscillations. Calcium signaling is crucial for transcriptional regulation of dopamine secretion by neuroendocrine PC12 ce...
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Identification of protein partners in mycobacteria using a single-step affinity purification method.
Published: March, 2014

Abstract: Tuberculosis is a leading cause of death in developing countries. Efforts are being made to both prevent its spread and improve curability rates. Understanding the biology of the bacteria causing the disease, Mycobacterium tuberculosis (M. tubercu...
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Hmga2 is required for canonical WNT signaling during lung development.
Published: March, 2014

Abstract: BACKGROUND: The high-mobility-group (HMG) proteins are the most abundant non-histone chromatin-associated proteins. HMG proteins are present at high levels in various undifferentiated tissues during embryonic development and their levels are stron...
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Large-scale analysis of tandem repeat variability in the human genome.
Published: March, 2014

Abstract: Tandem repeats are short DNA sequences that are repeated head-to-tail with a propensity to be variable. They constitute a significant proportion of the human genome, also occurring within coding and regulatory regions. Variation in these repeats c...
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Integrative ChIP-seq/microarray analysis identifies a CTNNB1 target signature enriched in intestinal stem cells and colon cancer.
Published: March, 2014

Abstract: BACKGROUND: Deregulation of canonical Wnt/CTNNB1 (beta-catenin) pathway is one of the earliest events in the pathogenesis of colon cancer. Mutations in APC or CTNNB1 are highly frequent in colon cancer and cause aberrant stabilization of CTNNB1, w...
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PI3K-p110-alpha-subtype signalling mediates survival, proliferation and neurogenesis of cortical progenitor cells via activation of mTORC2.
Published: March, 2014

Abstract: Development of the cerebral cortex is controlled by growth factors among which transforming growth factor beta (TGFβ) and insulin-like growth factor 1 (IGF1) have a central role. The TGFβ- and IGF1-pathways cross-talk and share signalling molecule...
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Fine mapping of genome activation in bovine embryos by RNA sequencing.
Published: March, 2014

Abstract: During maternal-to-embryonic transition control of embryonic development gradually switches from maternal RNAs and proteins stored in the oocyte to gene products generated after embryonic genome activation (EGA). Detailed insight into the onset of...
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Synthesis of multifunctional lipid–polymer conjugates: application to the elaboration of bright far-red fluorescent lipid probes
Published: March, 2014

Abstract: A new class of lipid-ended polymer conjugates presenting reactive sites regularly distributed along the polymer chain were synthesized using RAFT polymerization. The chosen modular approach enables preparation of different lipid families by tuning...
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Hook is an adapter that coordinates kinesin-3 and dynein cargo attachment on early endosomes.
Published: March, 2014

Abstract: Bidirectional membrane trafficking along microtubules is mediated by kinesin-1, kinesin-3, and dynein. Several organelle-bound adapters for kinesin-1 and dynein have been reported that orchestrate their opposing activity. However, the coordination...
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The circadian clock regulates rhythmic activation of the NRF2/glutathione-mediated antioxidant defense pathway to modulate pulmonary fibrosis.
Published: March, 2014

Abstract: The disruption of the NRF2 (nuclear factor erythroid-derived 2-like 2)/glutathione-mediated antioxidant defense pathway is a critical step in the pathogenesis of several chronic pulmonary diseases and cancer. While the mechanism of NRF2 activation...
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MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain.
Published: March, 2014

Abstract: MBD5 and MBD6 are two members of the methyl-CpG-binding domain (MBD) family of proteins that are poorly characterized. Studies performed thus far have failed to show binding of the MBD5 and MBD6 MBD to methylated DNA. Here, we show that both MBD5 ...
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Counteracting Activities of OCT4 and KLF4 during Reprogramming to Pluripotency.
Published: March, 2014

Abstract: Differentiated cells can be reprogrammed into induced pluripotent stem cells (iPSCs) after overexpressing four transcription factors, of which Oct4 is essential. To elucidate the role of Oct4 during reprogramming, we investigated the immediate tra...
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Sequence capture using PCR-generated probes: a cost-effective method of targeted high-throughput sequencing for nonmodel organisms.
Published: March, 2014

Abstract: Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To multiplex large numbers of indexed samples while sequen...
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Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression.
Published: March, 2014

Abstract: To systematically investigate the impact of immune stimulation upon regulatory variant activity, we exposed primary monocytes from 432 healthy Europeans to interferon-γ (IFN-γ) or differing durations of lipopolysaccharide and mapped expression qua...
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Citrullination regulates pluripotency and histone H1 binding to chromatin.
Published: March, 2014

Abstract: Citrullination is the post-translational conversion of an arginine residue within a protein to the non-coded amino acid citrulline. This modification leads to the loss of a positive charge and reduction in hydrogen-bonding ability. It is carried o...
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RNAi screen in Drosophila larvae identifies histone deacetylase 3 as a positive regulator of the hsp70 heat shock gene expression during heat shock.
Published: March, 2014

Abstract: The transcription regulation of the Drosophila hsp70 gene is a complex process that involves the regulation of multiple steps, including the establishment of paused Pol II and release of Pol II into elongation upon heat shock activation. While the...
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β-agonists selectively modulate proinflammatory gene expression in skeletal muscle cells via non-canonical nuclear crosstalk mechanisms.
Published: March, 2014

Abstract: The proinflammatory cytokine Tumour Necrosis Factor (TNF)-α is implicated in a variety of skeletal muscle pathologies. Here, we have investigated how in vitro cotreatment of skeletal muscle C2C12 cells with β-agonists modulates the TNF-α-induced i...
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The transcription factor CREB has no non-redundant functions in hepatic glucose metabolism in mice.
Published: March, 2014

Abstract: AIMS/HYPOTHESIS: Excessive hepatic glucose production is a hallmark of insulin resistance in type 2 diabetes. The cAMP responsive transcription factor cAMP responsive element binding protein (CREB), thought to be a key activator of the hepatic glu...
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Polycomb binding precedes early-life stress responsive DNA methylation at the Avp enhancer.
Published: March, 2014

Abstract: Early-life stress (ELS) in mice causes sustained hypomethylation at the downstream Avp enhancer, subsequent overexpression of hypothalamic Avp and increased stress responsivity. The sequence of events leading to Avp enhancer methylation is present...
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A lipid-mediated conformational switch modulates the thermosensing activity of DesK.
Published: March, 2014

Abstract: The thermosensor DesK is a multipass transmembrane histidine-kinase that allows the bacterium Bacillus subtilis to adjust the levels of unsaturated fatty acids required to optimize membrane lipid fluidity. The cytoplasmic catalytic domain of DesK ...
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mMAPS: a flow-proteometric technique to analyze protein-protein interactions in individual signaling complexes.
Published: March, 2014

Abstract: Signal transduction is a dynamic process that regulates cellular functions through multiple types of biomolecular interactions, such as the interactions between proteins and between proteins and nucleic acids. However, the techniques currently ava...
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Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis.
Published: March, 2014

Abstract: Genetic variation at the chromosome 9p21 risk locus promotes cardiovascular disease; however, it is unclear how or which proteins encoded at this locus contribute to disease. We have previously demonstrated that loss of one candidate gene at this ...
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Contesting the dogma of an age-related heat shock response impairment: implications for cardiac-specific age-related disorders.
Published: March, 2014

Abstract: Ageing is associated with the reduced performance of physiological processes and has been proposed as a major risk factor for disease. An age-related decline in stress response pathways has been widely documented in lower organisms. In particular,...
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Peroxisome proliferator-activated receptor γ and C/EBPα synergistically activate key metabolic adipocyte genes by assisted loading.
Published: March, 2014

Abstract: Peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key activators of adipogenesis. They mutually induce the expression of each other and have been reported to cooperate in...
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Promoter occupancy of the basal class I transcription factor A differs strongly between active and silent VSG expression sites in Trypanosoma brucei.
Published: March, 2014

Abstract: Monoallelic expression within a gene family is found in pathogens exhibiting antigenic variation and in mammalian olfactory neurons. Trypanosoma brucei, a lethal parasite living in the human bloodstream, expresses variant surface glycoprotein (VSG...
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Identification of HilD-regulated genes in Salmonella enterica serovar Typhimurium.
Published: March, 2014

Abstract: Salmonella enterica serovar Typhimurium (S. Typhimurium) pathogenicity island 1 (SPI-1) encodes a type III secretion system required for invasion of host gut epithelial cells. Expression of SPI-1 virulence genes is controlled by a complex hierarch...
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SH2B1β interacts with STAT3 and enhances fibroblast growth factor 1-induced gene expression during neuronal differentiation.
Published: March, 2014

Abstract: Neurite outgrowth is an essential process during neuronal differentiation as well as neuroregeneration. Thus, understanding the molecular and cellular control of neurite outgrowth will benefit patients with neurological diseases. We have previousl...
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Telomere repeat binding proteins are functional components of Arabidopsis telomeres and interact with telomerase.
Published: March, 2014

Abstract: Although telomere-binding proteins constitute an essential part of telomeres, in vivo data indicating the existence of a structure similar to mammalian shelterin complex in plants are limited. Partial characterization of a number of candidate prot...
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Decreased genetic dosage of hepatic yin yang 1 causes diabetic-like symptoms.
Published: March, 2014

Abstract: Insulin sensitivity in liver is characterized by the ability of insulin to efficiently inhibit glucose production and fatty acid oxidation as well as promote de novo lipid biosynthesis. Specific dysregulation of glucose and lipid metabolism in liv...
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Transcription factor Runx3 regulates interleukin-15-dependent natural killer cell activation.
Published: March, 2014

Abstract: Natural killer cells belong to the family of innate lymphoid cells comprising the frontline defense against infected and transformed cells. Development and activation of natural killer cells is highly dependent on interleukin-15 signaling. However...
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Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and Drosophila santomea.
Published: March, 2014

Abstract: Interspecific hybridization provides the unique opportunity for species to tap into genetic variation present in a closely related species and potentially take advantage of beneficial alleles. It has become increasingly clear that when hybridizati...
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The transcriptional regulator Aire coopts the repressive ATF7ip-MBD1 complex for the induction of immunotolerance.
Published: March, 2014

Abstract: The maintenance of immunological tolerance requires the deletion of self-reactive T cells in the thymus. The expression of genes encoding tissue-specific antigens (TSAs) by thymic epithelial cells is critical for this process and depends on activi...
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Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells.
Published: March, 2014

Abstract: Mass spectrometry (MS)-based proteomics typically employs multistep sample-preparation workflows that are subject to sample contamination and loss. We report an in-StageTip method for performing sample processing, from cell lysis through elution o...
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Stage-specific control of early B cell development by the transcription factor Ikaros.
Published: March, 2014

Abstract: The transcription factor Ikaros is an essential regulator of lymphopoiesis. Here we studied its B cell-specific function by conditional inactivation of the gene encoding Ikaros (Ikzf1) in pro-B cells. B cell development was arrested at an aberrant...
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FoxA1 directs the lineage and immunosuppressive properties of a novel regulatory T cell population in EAE and MS.
Published: March, 2014

Abstract: The defective generation or function of regulatory T (Treg) cells in autoimmune disease contributes to chronic inflammation and tissue injury. We report the identification of FoxA1 as a transcription factor in T cells that, after ectopic expressio...
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Centromeric histone H2B monoubiquitination promotes noncoding transcription and chromatin integrity.
Published: March, 2014

Abstract: Functional centromeres are essential for proper cell division. Centromeres are established largely by epigenetic processes resulting in incorporation of the histone H3 variant CENP-A. Here, we demonstrate the direct involvement of H2B monoubiquiti...
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The chromatin regulator Brg1 suppresses formation of intraductal papillary mucinous neoplasm and pancreatic ductal adenocarcinoma.
Published: March, 2014

Abstract: Pancreatic ductal adenocarcinoma (PDA) develops through distinct precursor lesions, including pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasia (IPMN). However, genetic features resulting in IPMN-associated ...
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Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components.
Published: March, 2014

Abstract: To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture ...
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Sequencing and assembly of the 22-gb loblolly pine genome.
Published: March, 2014

Abstract: Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the lobloll...
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BMP4 promotes EMT and mesodermal commitment in human embryonic stem cells via SLUG and MSX2.
Published: March, 2014

Abstract: Bone morphogenetic proteins (BMPs) initiate differentiation in human embryonic stem cells (hESCs) but the exact mechanisms have not been fully elucidated. We demonstrate here that SLUG and MSX2, transcription factors involved in epithelial-mesench...
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Live cell imaging unveils multiple domain requirements for in vivo dimerization of the glucocorticoid receptor.
Published: March, 2014

Abstract: Glucocorticoids are essential for life, but are also implicated in disease pathogenesis and may produce unwanted effects when given in high doses. Glucocorticoid receptor (GR) transcriptional activity and clinical outcome have been linked to its o...
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PGC7 suppresses TET3 for protecting DNA methylation.
Published: March, 2014

Abstract: Ten-eleven translocation (TET) family enzymes convert 5-methylcytosine to 5-hydroxylmethylcytosine. However, the molecular mechanism that regulates this biological process is not clear. Here, we show the evidence that PGC7 (also known as Dppa3 or ...
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Characterization of two different Asf1 histone chaperones with distinct cellular localizations and functions in Trypanosoma brucei.
Published: March, 2014

Abstract: The anti-silencing function protein 1 (Asf1) is a chaperone that forms a complex with histones H3 and H4 facilitating dimer deposition and removal from chromatin. Most eukaryotes possess two different Asf1 chaperones but their specific functions a...
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The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors.
Published: March, 2014

Abstract: Genome-wide association studies have identified numerous loci linked to breast cancer susceptibility, but the mechanism by which variations at these loci influence susceptibility is usually unknown. Some variants are only associated with particula...
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A recently evolved class of alternative 3'-terminal exons involved in cell cycle regulation by topoisomerase inhibitors.
Published: February, 2014

Abstract: Alternative 3'-terminal exons, which use intronic polyadenylation sites, are generally less conserved and expressed at lower levels than the last exon of genes. Here we discover a class of human genes, in which the last exon appeared recently duri...
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Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity.
Published: February, 2014

Abstract: Cells differentiate when transcription factors bind accessible cis-regulatory elements to establish specific gene expression programs. In differentiating embryonic stem cells, chromatin at lineage-restricted genes becomes sequentially accessible, ...
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Epigenomic alterations define lethal CIMP-positive ependymomas of infancy.
Published: February, 2014

Abstract: Ependymomas are common childhood brain tumours that occur throughout the nervous system, but are most common in the paediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not furth...
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Maintenance of Heterochromatin Boundary and Nucleosome Composition at Promoters by the Asf1 Histone Chaperone and SWR1-C Chromatin Remodeler in Saccharomyces cerevisiae.
Published: February, 2014

Abstract: Chromatin remodeling complexes cooperate to regulate gene promoters and to define chromatin neighborhoods. Here, we identified genetic and functional connections between two silencing-related chromatin factors in the maintenance of native heteroch...
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Epigenetic upregulation of endogenous VEGF-A reduces myocardial infarct size in mice.
Published: February, 2014

Abstract: "Epigenetherapy" alters epigenetic status of the targeted chromatin and modifies expression of the endogenous therapeutic gene. In this study we used lentiviral in vivo delivery of small hairpin RNA (shRNA) into hearts in a murine infarction model...
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Sequencing-based large-scale genomics approaches with small numbers of isolated maize meiocytes.
Published: February, 2014

Abstract: High-throughput sequencing has become the large-scale approach of choice to study global gene expression and the distribution of specific chromatin marks and features. However, the limited availability of large amounts of purified cells made it ve...
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Reversible Top1 cleavage complexes are stabilized strand-specifically at the ribosomal replication fork barrier and contribute to ribosomal DNA stability.
Published: February, 2014

Abstract: Various topological constraints at the ribosomal DNA (rDNA) locus impose an extra challenge for transcription and DNA replication, generating constant torsional DNA stress. The topoisomerase Top1 is known to release such torsion by single-strand n...
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The FOS transcription factor family differentially controls trophoblast migration and invasion.
Published: February, 2014

Abstract: Extravillous trophoblast invasion is a fundamental component of human placentation. Invading trophoblast cells promote blood flow to the conceptus by actively remodeling the uterine vasculature. The extent of trophoblast invasion is tightly regula...
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Myc and max genome-wide binding sites analysis links the Myc regulatory network with the polycomb and the core pluripotency networks in mouse embryonic stem cells.
Published: February, 2014

Abstract: Myc is a master transcription factor that has been demonstrated to be required for embryonic stem cell (ESC) pluripotency, self-renewal, and inhibition of differentiation. Although recent works have identified several Myc-targets in ESCs, the list...
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Geriatric muscle stem cells switch reversible quiescence into senescence.
Published: February, 2014

Abstract: Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline with ageing. Here we report that geriatric satellite cells are incap...
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Runx1t1 (Runt-related transcription factor 1; translocated to, 1) epigenetically regulates the proliferation and nitric oxide production of microglia.
Published: February, 2014

Abstract: BACKGROUND: Microglia, the resident immune cells of the brain, undergo rapid proliferation and produce several proinflammatory molecules and nitric oxide (NO) when activated in neuropathological conditions. Runx1t1 (Runt-related transcription fact...
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Glial wingless/Wnt regulates glutamate receptor clustering and synaptic physiology at the Drosophila neuromuscular junction.
Published: February, 2014

Abstract: Glial cells are emerging as important regulators of synapse formation, maturation, and plasticity through the release of secreted signaling molecules. Here we use chromatin immunoprecipitation along with Drosophila genomic tiling arrays to define ...
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The long non-coding RNA Paupar regulates the expression of both local and distal genes.
Published: February, 2014

Abstract: Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites ...
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Genome-wide binding patterns of thyroid hormone receptor beta.
Published: February, 2014

Abstract: Thyroid hormone (TH) receptors (TRs) play central roles in metabolism and are major targets for pharmaceutical intervention. Presently, however, there is limited information about genome wide localizations of TR binding sites. Thus, complexities o...
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Long-term parental methamphetamine exposure of mice influences behavior and hippocampal DNA methylation of the offspring.
Published: February, 2014

Abstract: The high rate of methamphetamine (METH) abuse among young adults and women of childbearing age makes it imperative to determine the long-term effects of METH exposure on the offspring. We hypothesized that parental METH exposure modulates offsprin...
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CDK phosphorylation of SLD-2 is required for replication initiation and germline development in C. elegans.
Published: February, 2014

Abstract: Cyclin-dependent kinase (CDK) plays a vital role in proliferation control across eukaryotes. Despite this, how CDK mediates cell cycle and developmental transitions in metazoa is poorly understood. In this paper, we identify orthologues of Sld2, a...
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Reduced Euchromatin histone methyltransferase 1 causes developmental delay, hypotonia, and cranial abnormalities associated with increased bone gene expression in Kleefstra syndrome mice.
Published: February, 2014

Abstract: Haploinsufficiency of Euchromatin histone methyltransferase 1 (EHMT1), a chromatin modifying enzyme, is the cause of Kleefstra syndrome (KS). KS is an intellectual disability (ID) syndrome, with general developmental delay, hypotonia, and craniofa...
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Sp1 and Sp3 transcription factors regulate the basal expression of human microsomal epoxide hydrolase (EPHX1) through interaction with the E1b far upstream promoter.
Published: February, 2014

Abstract: Microsomal epoxide hydrolase (mEH, EPHX1) is a critical biotransformation enzyme, catalyzing the metabolism of many xenobiotics. Human mEH is transcribed using alternative promoters. The upstream E1 promoter is active in liver while the far upstre...
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C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells.
Published: February, 2014

Abstract: CCAAT/enhancer binding protein-α (C/EBPα) induces transdifferentiation of B cells into macrophages at high efficiencies and enhances reprogramming into induced pluripotent stem (iPS) cells when co-expressed with the transcription factors Oct4 (Pou...
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Nonstochastic reprogramming from a privileged somatic cell state.
Published: February, 2014

Abstract: Reprogramming somatic cells to induced pluripotency by Yamanaka factors is usually slow and inefficient and is thought to be a stochastic process. We identified a privileged somatic cell state, from which acquisition of pluripotency could occur in...
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A deterministic analysis of genome integrity during neoplastic growth in Drosophila.
Published: February, 2014

Abstract: The development of cancer has been associated with the gradual acquisition of genetic alterations leading to a progressive increase in malignancy. In various cancer types this process is enabled and accelerated by genome instability. While genome ...
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Sumoylation of the THO complex regulates the biogenesis of a subset of mRNPs.
Published: February, 2014

Abstract: Assembly of messenger ribonucleoparticles (mRNPs) is a pivotal step in gene expression, but only a few molecular mechanisms contributing to its regulation have been described. Here, through a comprehensive proteomic survey of mRNP assembly, we dem...
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c-Myc-dependent transcriptional regulation of cell cycle and nucleosomal histones during oligodendrocyte differentiation.
Published: February, 2014

Abstract: Oligodendrocyte progenitor cells (OPCs) have the ability to divide or to growth arrest and differentiate into myelinating oligodendrocytes in the developing brain. Due to their high number and the persistence of their proliferative capacity in the...
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Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome.
Published: February, 2014

Abstract: Metagenomic approaches are widespread in microbiological research, but so far, the knowledge on extrachromosomal DNA diversity and composition has largely remained dependant on cultivating host organisms. Even with the emergence of metagenomics, c...
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A Drosophila in vivo screen identifies store-operated calcium entry as a key regulator of adiposity.
Published: February, 2014

Abstract: To unravel the evolutionarily conserved genetic network underlying energy homeostasis, we performed a systematic in vivo gene knockdown screen in Drosophila. We used a transgenic RNAi library enriched for fly orthologs of human genes to functional...
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Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain.
Published: February, 2014

Abstract: DNA methylation has critical roles in the nervous system and has been traditionally considered to be restricted to CpG dinucleotides in metazoan genomes. Here we show that the single base-resolution DNA methylome from adult mouse dentate neurons c...
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Hypoxia perturbs aryl hydrocarbon receptor signaling and CYP1A1 expression induced by PCB 126 in human skin and liver-derived cell lines.
Published: February, 2014

Abstract: The aryl hydrocarbon receptor (AhR) is an important mediator of toxic responses after exposure to xenobiotics including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and dioxin-like polychlorinated biphenyls (PCBs). Activation of AhR responsive genes...
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Adult glucocorticoid exposure leads to transcriptional and DNA methylation changes in nuclear steroid receptors in the hippocampus and kidney of mouse male offspring.
Published: February, 2014

Abstract: Synthetic glucocorticoids (sGCs) are commonly prescribed for the management of inflammatory and endocrine disorders. However, nothing is known regarding the effects of sGC on adult germline methylome and whether these effects can be transmitted to...
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The BAF60 Subunit of the SWI/SNF Chromatin-Remodeling Complex Directly Controls the Formation of a Gene Loop at FLOWERING LOCUS C in Arabidopsis.
Published: February, 2014

Abstract: SWI/SNF complexes mediate ATP-dependent chromatin remodeling to regulate gene expression. Many components of these complexes are evolutionarily conserved, and several subunits of Arabidopsis thaliana SWI/SNF complexes are involved in the control o...
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DSSylation, a novel protein modification targets proteins induced by oxidative stress, and facilitates their degradation in cells.
Published: February, 2014

Abstract: Timely removal of oxidatively damaged proteins is critical for cells exposed to oxidative stresses; however, cellular mechanism for clearing oxidized proteins is not clear. Our study reveals a novel type of protein modification that may play a rol...
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A cohesin-independent role for NIPBL at promoters provides insights in CdLS.
Published: February, 2014

Abstract: The cohesin complex is crucial for chromosome segregation during mitosis and has recently also been implicated in transcriptional regulation and chromatin architecture. The NIPBL protein is required for the loading of cohesin onto chromatin, but h...
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The role of plasma membrane estrogen receptors in mediating the estrogen induction of progesterone receptors in hypothalamic ventromedial neurons.
Published: February, 2014

Abstract: Progesterone is well known for its role in the modulation of sexual behavior. In the ventromedial nucleus (VMN), a part of the mediobasal hypothalamus which regulates sexual behavior in female rodents, estrogens induce the expression of progestero...
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Human RECQ5 helicase promotes repair of DNA double-strand breaks by synthesis-dependent strand annealing.
Published: February, 2014

Abstract: Most mitotic homologous recombination (HR) events proceed via a synthesis-dependent strand annealing mechanism to avoid crossing over, which may give rise to chromosomal rearrangements and loss of heterozygosity. The molecular mechanisms controlli...
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The chromatin remodeller CHD8 is required for E2F-dependent transcription activation of S-phase genes.
Published: February, 2014

Abstract: The precise regulation of S-phase-specific genes is critical for cell proliferation. How the repressive chromatin configuration mediated by the retinoblastoma protein and repressor E2F factors changes at the G1/S transition to allow transcription ...
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A highly conserved region within H2B is important for FACT to act on nucleosomes.
Published: February, 2014

Abstract: Histone N-terminal tails play crucial roles in chromatin-related processes. The tails of histones H3 and H4 are highly conserved and well characterized, but much less is known about the functions of the tails of histones H2A and H2B and their sequ...
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The Mef2 transcription network is disrupted in myotonic dystrophy heart tissue, dramatically altering miRNA and mRNA expression.
Published: January, 2014

Abstract: Cardiac dysfunction is the second leading cause of death in myotonic dystrophy type 1 (DM1), primarily because of arrhythmias and cardiac conduction defects. A screen of more than 500 microRNAs (miRNAs) in a DM1 mouse model identified 54 miRNAs th...
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Assembly of the genome of the disease vector Aedes aegypti onto a genetic linkage map allows mapping of genes affecting disease transmission.
Published: January, 2014

Abstract: The mosquito Aedes aegypti transmits some of the most important human arboviruses, including dengue, yellow fever and chikungunya viruses. It has a large genome containing many repetitive sequences, which has resulted in the genome being poorly as...
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ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state.
Published: January, 2014

Abstract: Glioblastoma (GBM) harbors subpopulations of therapy-resistant tumor-initiating cells (TICs) that are self-renewing and multipotent. To understand the regulation of the TIC state, we performed an image-based screen for genes regulating GBM TIC mai...
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Inhibition of HDAC1 and DNMT1 modulate RGS10 expression and decrease ovarian cancer chemoresistance.
Published: January, 2014

Abstract: RGS10 is an important regulator of cell survival and chemoresistance in ovarian cancer. We recently showed that RGS10 transcript expression is suppressed during acquired chemoresistance in ovarian cancer. The suppression of RGS10 is due to DNA hyp...
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The role of DNA methylation in regulation of the murine Lhx3 gene.
Published: January, 2014

Abstract: LHX3 is a LIM-homeodomain transcription factor with critical roles in pituitary and nervous system development. Mutations in the LHX3 gene are associated with pediatric diseases featuring severe hormone deficiencies, hearing loss, developmental de...
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A role for peroxisome proliferator-activated receptor γ coactivator 1 (PGC-1) in the regulation of cardiac mitochondrial phospholipid biosynthesis.
Published: January, 2014

Abstract: The energy demands of the adult mammalian heart are met largely by ATP generated via oxidation of fatty acids in a high capacity mitochondrial system. Peroxisome proliferator-activated receptor γ coactivator 1 (PGC-1)-α and -β serve as inducible t...
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Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin.
Published: January, 2014

Abstract: JARID2 is an accessory component of Polycomb repressive complex-2 (PRC2) required for the differentiation of embryonic stem cells (ESCs). A role for JARID2 in the recruitment of PRC2 to target genes silenced during differentiation has been put for...
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An Easy, Convenient Cell and Tissue Extraction Protocol for Nuclear Magnetic Resonance Metabolomics.
Published: January, 2014

Abstract: INTRODUCTION: As a complement to the classic metabolomics biofluid studies, the visualisation of the metabolites contained in cells or tissues could be a very powerful tool to understand how the local metabolism and biochemical pathways could be a...
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Suppression of UV-B stress responses by flg22 is regulated at the chromatin level via histone modification.
Published: January, 2014

Abstract: Genes of the flavonol pathway are activated by UV-B, but suppressed by concomitant flg22 application in Arabidopsis. Analysis at the metabolite level suggested that this regulation allows the plant to focus its secondary metabolism on the plant de...
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Lysine-specific demethylase 1 regulates differentiation onset and migration of trophoblast stem cells.
Published: January, 2014

Abstract: Propagation and differentiation of stem cell populations are tightly regulated to provide sufficient cell numbers for tissue formation while maintaining the stem cell pool. Embryonic parts of the mammalian placenta are generated from differentiati...
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Lysine deacetylase inhibition prevents diabetes by chromatin-independent immunoregulation and β-cell protection.
Published: January, 2014

Abstract: Type 1 diabetes is due to destruction of pancreatic β-cells. Lysine deacetylase inhibitors (KDACi) protect β-cells from inflammatory destruction in vitro and are promising immunomodulators. Here we demonstrate that the clinically well-tolerated KD...
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Structural basis for the inhibition of the chromatin repressor BAHD1 by the bacterial nucleomodulin LntA.
Published: January, 2014

Abstract: UNLABELLED: The nucleus has emerged as a key target for nucleomodulins, a family of effectors produced by bacterial pathogens to control host transcription or other nuclear processes. The virulence factor LntA from Listeria monocytogenes stimulate...
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Hsp70 cochaperones HspBP1 and BAG-1M differentially regulate steroid hormone receptor function.
Published: January, 2014

Abstract: Hsp70 binding protein 1 (HspBP1) and Bcl2-associated athanogene 1 (BAG-1), the functional orthologous nucleotide exchange factors of the heat shock protein 70 kilodalton (Hsc70/Hsp70) chaperones, catalyze the release of ADP from Hsp70 while induci...
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Peroxisome proliferator-activated receptor γ regulates genes involved in insulin/insulin-like growth factor signaling and lipid metabolism during adipogenesis through functionally distinct enhancer classes.
Published: January, 2014

Abstract: The nuclear receptor peroxisome proliferator-activated receptor (PPAR) is a transcription factor whose expression is induced during adipogenesis and that is required for the acquisition and control of mature adipocyte functions. Indeed, PPAR induc...
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SPBP is a sulforaphane induced transcriptional coactivator of NRF2 regulating expression of the autophagy receptor p62/SQSTM1.
Published: January, 2014

Abstract: Organisms exposed to oxidative stress respond by orchestrating a stress response to prevent further damage. Intracellular levels of antioxidant agents increase, and damaged components are removed by autophagy induction. The KEAP1-NRF2 signaling pa...
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Depletion of sirtuin 1 (SIRT1) leads to epigenetic modifications of telomerase (TERT) gene in hepatocellular carcinoma cells.
Published: January, 2014

Abstract: Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD)-dependent deacetylase that is implicated in plethora of biological processes, including metabolism, aging, stress response, and tumorigenesis. Telomerase (TERT) is essential for telome...
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mRNA levels of related Abcb genes change opposite to each other upon histone deacetylase inhibition in drug-resistant rat hepatoma cells.
Published: January, 2014

Abstract: The multidrug-resistant phenotype of tumor cells is acquired via an increased capability of drug efflux by ABC transporters and causes serious problems in cancer treatment. With the aim to uncover whether changes induced by epigenetic mechanisms i...
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DUSP1 is a novel target for enhancing pancreatic cancer cell sensitivity to gemcitabine.
Published: January, 2014

Abstract: Pancreatic ductal adenocarcinoma (PDAC) is a deadly cancer with a poor prognosis that is characterized by excessive mitogenic pathway activation and marked chemoresistance to a broad spectrum of chemotherapeutic drugs. Dual specificity protein pho...
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The thyroid hormone receptor β induces DNA damage and premature senescence.
Published: January, 2014

Abstract: There is increasing evidence that the thyroid hormone (TH) receptors (THRs) can play a role in aging, cancer and degenerative diseases. In this paper, we demonstrate that binding of TH T3 (triiodothyronine) to THRB induces senescence and deoxyribo...
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A role for FACT in repopulation of nucleosomes at inducible genes.
Published: January, 2014

Abstract: Xenobiotic drugs induce Pleiotropic Drug Resistance (PDR) genes via the orthologous Pdr1/Pdr3 transcription activators. We previously identified the Mediator transcription co-activator complex as a key target of Pdr1 orthologs and demonstrated tha...
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Mutations in POGLUT1, encoding protein O-glucosyltransferase 1, cause autosomal-dominant Dowling-Degos disease.
Published: January, 2014

Abstract: Dowling-Degos disease (DDD) is an autosomal-dominant genodermatosis characterized by progressive and disfiguring reticulate hyperpigmentation. We previously identified loss-of-function mutations in KRT5 but were only able to detect pathogenic muta...
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CLOCK:BMAL1 is a pioneer-like transcription factor.
Published: January, 2014

Abstract: The mammalian circadian clock relies on the master genes CLOCK and BMAL1 to drive rhythmic gene expression and regulate biological functions under circadian control. Here we show that rhythmic CLOCK:BMAL1 DNA binding promotes rhythmic chromatin op...
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Integrated transcriptome analysis of mouse spermatogenesis.
Published: January, 2014

Abstract: BACKGROUND: Differentiation of primordial germ cells into mature spermatozoa proceeds through multiple stages, one of the most important of which is meiosis. Meiotic recombination is in turn a key part of meiosis. To achieve the highly specialized...
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The genome-wide landscape of DNA methylation and hydroxymethylation in response to sleep deprivation impacts on synaptic plasticity genes.
Published: January, 2014

Abstract: Sleep is critical for normal brain function and mental health. However, the molecular mechanisms mediating the impact of sleep loss on both cognition and the sleep electroencephalogram remain mostly unknown. Acute sleep loss impacts brain gene exp...
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Genome-wide profiling of transcription factor binding and epigenetic marks in adipocytes by ChIP-seq.
Published: January, 2014

Abstract: The recent advances in high-throughput sequencing combined with various other technologies have allowed detailed and genome-wide insight into the transcriptional networks that control adipogenesis. Chromatin immunoprecipitation (ChIP) combined wit...
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Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor.
Published: January, 2014

Abstract: BACKGROUND: Identifying the target genes of transcription factors is important for unraveling regulatory networks in all types of organisms. Our interest was precisely to uncover the spectrum of loci regulated by a widespread plant transcription f...
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Analyzing the functions and structure of the human lipodystrophy protein seipin.
Published: January, 2014

Abstract: Disruption of the gene BSCL2, which encodes the protein seipin, causes severe generalized lipodystrophy in humans with a near complete absence of adipose tissue. Moreover, cell culture studies have demonstrated that seipin plays a critical cell-au...
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Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants.
Published: January, 2014

Abstract: BACKGROUND: The source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW,
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Differential methylation of the TRPA1 promoter in pain sensitivity.
Published: January, 2014

Abstract: Chronic pain is a global public health problem, but the underlying molecular mechanisms are not fully understood. Here we examine genome-wide DNA methylation, first in 50 identical twins discordant for heat pain sensitivity and then in 50 further ...
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Negative regulation of the peptidylarginine deiminase type IV promoter by NF-κB in human myeloid cells.
Published: January, 2014

Abstract: High titers of anti-citrullinated protein/peptide antibodies (ACPAs) have been detected in sera of rheumatoid arthritis (RA) patients, implicating citrullinating enzymes in the pathogenesis of RA. Peptidylarginine deiminase type IV (PAD4) is a mem...
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Differential expression of histone H3 genes and selective association of the variant H3.7 with a specific sequence class in Stylonychia macronuclear development.
Published: January, 2014

Abstract: BACKGROUND: Regulation of chromatin structure involves deposition of selective histone variants into nucleosome arrays. Numerous histone H3 variants become differentially expressed by individual nanochromosomes in the course of macronuclear differ...
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Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice.
Published: January, 2014

Abstract: BACKGROUND: Methylation on the fifth position of cytosine (5-mC) is an essential epigenetic mark that is linked to both normal neurodevelopment and neurological diseases. The recent identification of another modified form of cytosine, 5-hydroxymet...
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Viral aetiology influenza like illnesses in Santa Cruz, Bolivia (2010-2012).
Published: January, 2014

Abstract: BACKGROUND: Acute respiratory infections represent a serious public health issue worldwide but virological aetiologies of Influenza Like Illnesses (ILIs) remain largely unknown in developing countries. This study represents the first attempt to ch...
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Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum.
Published: January, 2014

Abstract: BACKGROUND: Advances in high-throughput sequencing have led to the discovery of widespread transcription of natural antisense transcripts (NATs) in a large number of organisms, where these transcripts have been shown to play important roles in the...
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Histone Deacetylase inhibition with Valproic Acid down-regulates Osteocalcin gene expression in Human Dental Pulp Stem Cells and Osteoblasts: Evidence for HDAC2 involvement.
Published: January, 2014

Abstract: Adult mesenchymal stem cells, such as dental pulp stem cells, are of great interest for cell-based tissue engineering strategies because they can differentiate into a variety of tissue-specific cells, above all, into osteoblasts. In recent years, ...
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Histone Deacetylase Classes I and II Regulate Kaposi's Sarcoma-Associated Herpesvirus Reactivation.
Published: January, 2014

Abstract: In primary effusion lymphoma (PEL) cells infected with latent Kaposi's sarcoma-associated herpesvirus (KSHV), the promoter of the viral lytic switch gene, Rta, is organized into bivalent chromatin, similar to cellular developmental switch genes. H...
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Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis.
Published: January, 2014

Abstract: The contribution of cis-regulatory mutations to human disease remains poorly understood. Whole-genome sequencing can identify all noncoding variants, yet the discrimination of causal regulatory mutations represents a formidable challenge. We used ...
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Meis2 is a Pax6 co-factor in neurogenesis and dopaminergic periglomerular fate specification in the adult olfactory bulb.
Published: January, 2014

Abstract: Meis homeodomain transcription factors control cell proliferation, cell fate specification and differentiation in development and disease. Previous studies have largely focused on Meis contribution to the development of non-neuronal tissues. By co...
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Regulation of the neuronal transcription factor NPAS4 by REST and microRNAs.
Published: January, 2014

Abstract: NPAS4 is a brain restricted, activity-induced transcription factor which regulates the expression of inhibitory synapse genes to control homeostatic excitatory/inhibitory balance in neurons. NPAS4 is required for normal social interaction and cont...
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Human cytomegalovirus major immediate early 1 protein targets host chromosomes by docking to the acidic pocket on the nucleosome surface.
Published: January, 2014

Abstract: The 72-kDa immediate early 1 (IE1) protein encoded by human cytomegalovirus (hCMV) is a nuclearly localized promiscuous regulator of viral and cellular transcription. IE1 has long been known to associate with host mitotic chromatin, yet the mechan...
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Large conserved domains of low DNA methylation maintained by Dnmt3a.
Published: January, 2014

Abstract: Gains and losses in DNA methylation are prominent features of mammalian cell types. To gain insight into the mechanisms that promote shifts in DNA methylation and contribute to changes in cell fate, including malignant transformation, we performed...
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Inactivating CUX1 mutations promote tumorigenesis.
Published: January, 2014

Abstract: A major challenge in cancer genetics is to determine which low-frequency somatic mutations are drivers of tumorigenesis. Here we interrogate the genomes of 7,651 diverse human cancers and find inactivating mutations in the homeodomain transcriptio...
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Genome-wide methylation and gene expression changes in newborn rats following maternal protein restriction and reversal by folic acid.
Published: December, 2013

Abstract: A large body of evidence from human and animal studies demonstrates that the maternal diet during pregnancy can programme physiological and metabolic functions in the developing fetus, effectively determining susceptibility to later disease. The m...
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Molecular mechanisms of regulation and action of microRNA-199a in testicular germ cell tumor and glioblastomas.
Published: December, 2013

Abstract: MicroRNA-199a (miRNA-199a) has been shown to have comprehensive functions and behave differently in different systems and diseases. It is encoded by two loci in the human genome, miR-199a-1 in chromosome 19 and miR-199a-2 in chromosome 1. Both loc...
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Anti-androgen resistance in prostate cancer cells chronically induced by interleukin-1β
Published: December, 2013

Abstract: Chronic inflammation has been linked to cancer initiation and progression in a variety of tissues, yet the impact of acute and chronic inflammatory signaling on androgen receptor function has not been widely studied. In this report, we examine the...
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Novel CTCF binding at a site in exon1A of BCL6 is associated with active histone marks and a transcriptionally active locus.
Published: December, 2013

Abstract: BCL6 is a zinc-finger transcriptional repressor, which is highly expressed in germinal centre B-cells and is essential for germinal centre formation and T-dependent antibody responses. Constitutive BCL6 expression is sufficient to produce lymphoma...
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Rapid and pervasive changes in genome-wide enhancer usage during mammalian development.
Published: December, 2013

Abstract: Enhancers are distal regulatory elements that can activate tissue-specific gene expression and are abundant throughout mammalian genomes. Although substantial progress has been made toward genome-wide annotation of mammalian enhancers, their tempo...
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Prmt7 is dispensable in tissue culture models for adipogenic differentiation
Published: December, 2013

Abstract: Protein arginine methylation is a common posttranslational modification that has been implicated in numerous biological processes including gene expression. The mammalian genome encodes nine protein arginine methyltransferases (Prmts) that catalyz...
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H19 lncRNA controls gene expression of the Imprinted Gene Network by recruiting MBD1.
Published: December, 2013

Abstract: The H19 gene controls the expression of several genes within the Imprinted Gene Network (IGN), involved in growth control of the embryo. However, the underlying mechanisms of this control remain elusive. Here, we identified the methyl-CpG-binding ...
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Nfatc1 orchestrates aging in hair follicle stem cells.
Published: December, 2013

Abstract: Hair production is fueled by stem cells (SCs), which transition between cyclical bouts of rest and activity. Here, we explore why hair growth wanes with age. We show that aged hair follicle SCs (HFSCs) in mice exhibit enhanced resting and abbrevia...
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Langerhans cells are generated by two distinct PU.1-dependent transcriptional networks.
Published: December, 2013

Abstract: Langerhans cells (LCs) are the unique dendritic cells found in the epidermis. While a great deal of attention has focused on defining the developmental origins of LCs, reports addressing the transcriptional network ruling their differentiation rem...
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UTX coordinates steroid hormone-mediated autophagy and cell death.
Published: December, 2013

Abstract: Correct spatial and temporal induction of numerous cell type-specific genes during development requires regulated removal of the repressive histone H3 lysine 27 trimethylation (H3K27me3) modification. Here we show that the H3K27me3 demethylase dUT...
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Local depletion of DNA methylation identifies a repressive p53 regulatory region in the NEK2 promoter.
Published: December, 2013

Abstract: Genome-scale mapping suggests that the function of DNA methylation varies with genomic context beyond transcriptional repression. However, the use of DNA-demethylating agents (e.g. 5-aza-2'-deoxycytidine (5aza-dC)) to study epigenetic regulation o...
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miR-16 and miR-26a target checkpoint kinases Wee1 and Chk1 in response to p53 activation by genotoxic stress.
Published: December, 2013

Abstract: The tumour suppressor p53 is a crucial regulator of cell cycle arrest and apoptosis by acting as a transcription factor to regulate a variety of genes. At least in part, this control is exerted by p53 via regulating expression of numerous microRNA...
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p53 status determines the role of autophagy in pancreatic tumour development.
Published: December, 2013

Abstract: Macroautophagy (hereafter referred to as autophagy) is a process in which organelles termed autophagosomes deliver cytoplasmic constituents to lysosomes for degradation. Autophagy has a major role in cellular homeostasis and has been implicated in...
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β-Globin cis-elements determine differential nuclear targeting through epigenetic modifications.
Published: December, 2013

Abstract: Increasing evidence points to nuclear compartmentalization as a contributing mechanism for gene regulation, yet mechanisms for compartmentalization remain unclear. In this paper, we use autonomous targeting of bacterial artificial chromosome (BAC)...
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The maize glossy13 gene, cloned via BSR-Seq and Seq-walking encodes a putative ABC transporter required for the normal accumulation of epicuticular waxes.
Published: December, 2013

Abstract: Aerial plant surfaces are covered by epicuticular waxes that among other purposes serve to control water loss. Maize glossy mutants originally identified by their "glossy" phenotypes exhibit alterations in the accumulation of epicuticular waxes. B...
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Oncogenic K-Ras and loss of Smad4 mediate invasion by activating an EGFR/NF-κB Axis that induces expression of MMP9 and uPA in human pancreas progenitor cells.
Published: December, 2013

Abstract: Activating K-Ras mutations and inactivating mutations of Smad4 are two common genetic alterations that occur in the development and progression of pancreatic ductal adenocarcinomas (PDAC). To further study the individual and combinatorial roles of...
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Reprogramming of lysosomal gene expression by interleukin-4 and Stat6
Published: December, 2013

Abstract: Background Lysosomes play important roles in multiple aspects of physiology, but the problem of how the transcription of lysosomal genes is coordinated remains incompletely understood. The goal of this study was to illuminate the physiological c...
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The role of Ctk1 kinase in termination of small non-coding RNAs.
Published: December, 2013

Abstract: Transcription termination in Saccharomyces cerevisiae can be performed by at least two distinct pathways and is influenced by the phosphorylation status of the carboxy-terminal domain (CTD) of RNA polymerase II (Pol II). Late termination of mRNAs ...
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Transcriptional activation of Mina by Sp1/3 factors.
Published: December, 2013

Abstract: Mina is an epigenetic gene regulatory protein known to function in multiple physiological and pathological contexts, including pulmonary inflammation, cell proliferation, cancer and immunity. We showed previously that the level of Mina gene expres...
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ZRF1 controls the retinoic acid pathway and regulates leukemogenic potential in acute myeloid leukemia.
Published: December, 2013

Abstract: Acute myeloid leukemia (AML) is frequently linked to epigenetic abnormalities and deregulation of gene transcription, which lead to aberrant cell proliferation and accumulation of undifferentiated precursors. ZRF1, a recently characterized epigene...
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Distinctive patterns of epigenetic marks are associated with promoter regions of mouse LINE-1 and LTR retrotransposons.
Published: December, 2013

Abstract: BACKGROUND: The long terminal repeat (LTR) retrotransposons and the non-LTR retrotransposons (LINE-1 or L1) make up more than one-third of the mouse genome. Because of their abundance, the retrotransposons are the major players in genomic structur...
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Elevated levels of FOXA1 facilitate androgen receptor chromatin binding resulting in a CRPC-like phenotype.
Published: December, 2013

Abstract: Castration-resistant prostate cancer (CRPC) continues to pose a significant clinical challenge with new generation second-line hormonal therapies affording limited improvement in disease outcome. As the androgen receptor (AR) remains a critical dr...
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Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions.
Published: December, 2013

Abstract: Distal regulatory elements, including enhancers, play a critical role in regulating gene activity. Transcription factor binding to these elements correlates with Low Methylated Regions (LMRs) in a process that is poorly understood. Here we ask whe...
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The PAF complex and Prf1/Rtf1 delineate distinct Cdk9-dependent pathways regulating transcription elongation in fission yeast.
Published: December, 2013

Abstract: Cyclin-dependent kinase 9 (Cdk9) promotes elongation by RNA polymerase II (RNAPII), mRNA processing, and co-transcriptional histone modification. Cdk9 phosphorylates multiple targets, including the conserved RNAPII elongation factor Spt5 and RNAPI...
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Rapid Transposon Liquid Enrichment Sequencing (TnLE-seq) for Gene Fitness Evaluation in Underdeveloped Bacterial Systems.
Published: December, 2013

Abstract: Whole-genome fitness analysis in microbes that uses saturating transposon mutagenesis combined with massively parallel sequencing (Tn-seq) is providing a measure of the contribution of each gene to a given growth condition. With this technique, ge...
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Alternative End-Joining and Classical Nonhomologous End-Joining Pathways Repair Different Types of Double-Strand Breaks during Class-Switch Recombination.
Published: December, 2013

Abstract: Classical nonhomologous end-joining (C-NHEJ) and alternative end-joining (A-EJ) are the main DNA double-strand break (DSB) repair pathways when a sister chromatid is not available. However, it is not clear how one pathway is chosen over the other ...
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Two Histone Deacetylases, FfHda1 and FfHda2, Are Important for Fusarium fujikuroi Secondary Metabolism and Virulence.
Published: December, 2013

Abstract: Histone modifications are crucial for the regulation of secondary metabolism in various filamentous fungi. Here we studied the involvement of histone deacetylases (HDACs) in secondary metabolism in the phytopathogenic fungus Fusarium fujikuroi, a ...
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Genome-wide chromatin analysis in mature mouse and human spermatozoa.
Published: December, 2013

Abstract: At the end of mammalian spermatogenesis, chromatin in differentiating germ cells is extensively remodeled, with the majority of nucleosomes being removed and ultimately exchanged by highly basic proteins named protamines. Residual nucleosomes are,...
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The microRNA miR-433 promotes renal fibrosis by amplifying the TGF-β/Smad3-Azin1 pathway.
Published: December, 2013

Abstract: The TGF-β/Smad3 pathway plays a major role in tissue fibrosis, but the precise mechanisms are not fully understood. Here we identified microRNA miR-433 as an important component of TGF-β/Smad3-driven renal fibrosis. The miR-433 was upregulated fol...
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Mediator links transcription and DNA repair by facilitating Rad2/XPG recruitment.
Published: December, 2013

Abstract: Mediator is a large multiprotein complex conserved in all eukaryotes. The crucial function of Mediator in transcription is now largely established. However, we found that this complex also plays an important role by connecting transcription with D...
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Oral administration of transforming growth factor-β1 (TGF-β1) protects the immature gut from injury via Smad protein-dependent suppression of epithelial nuclear factor κB (NF-κB) signaling and proinflammatory cytokine production.
Published: November, 2013

Abstract: Inflammatory immune responses play an important role in mucosal homeostasis and gut diseases. Nuclear factor κB (NF-κB), central to the proinflammatory cascade, is activated in necrotizing enterocolitis (NEC), a devastating condition of intestinal...
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BORIS/CTCFL is an RNA-binding protein that associates with polysomes.
Published: November, 2013

Abstract: BACKGROUND: BORIS (CTCFL), a paralogue of the multifunctional and ubiquitously expressed transcription factor CTCF, is best known for its role in transcriptional regulation. In the nucleus, BORIS is particularly enriched in the nucleolus, a crucia...
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A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice.
Published: November, 2013

Abstract: Diet-induced obesity is a lifestyle-associated medical condition that increases the risk of developing cardiovascular disease, type 2 diabetes and certain types of cancer. Here we report the design of a closed-loop genetic circuit that constantly ...
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Toxoplasma gondii inhibits IFN-γ- and IFN-β-induced host cell STAT1 transcriptional activity by increasing the association of STAT1 with DNA.
Published: November, 2013

Abstract: The IFN-γ response, mediated by the STAT1 transcription factor, is crucial for host defense against the intracellular pathogen Toxoplasma gondii, but prior infection with Toxoplasma can inhibit this response. Recently it was reported that th...
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A quantitative telomeric chromatin isolation protocol identifies different telomeric states.
Published: November, 2013

Abstract: Telomere composition changes during tumourigenesis, aging and in telomere syndromes in a poorly defined manner. Here we develop a quantitative telomeric chromatin isolation protocol (QTIP) for human cells, in which chromatin is cross-linked, immun...
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Reactive Oxygen Species Induce Epigenetic Instability through the Formation of 8-Hydroxydeoxyguanosine in Human Hepatocarcinogenesis.
Published: November, 2013

Abstract: Chronic hepatitis C (CHC) triggers oxidative stress and contributes to the emergence of hepatocellular carcinoma (HCC). We previously reported that tumor suppressor gene (TSG) methylation is a critical factor during the early stages of hepatocarci...
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The nuclear receptor Rev-erbα controls circadian thermogenic plasticity.
Published: November, 2013

Abstract: Circadian oscillation of body temperature is a basic, evolutionarily conserved feature of mammalian biology. In addition, homeostatic pathways allow organisms to protect their core temperatures in response to cold exposure. However, the mechanism ...
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Transcriptome surveillance by selective termination of noncoding RNA synthesis.
Published: November, 2013

Abstract: Pervasive transcription of eukaryotic genomes stems to a large extent from bidirectional promoters that synthesize mRNA and divergent noncoding RNA (ncRNA). Here, we show that ncRNA transcription in the yeast S. cerevisiae is globally restricted b...
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Suggestive linkage of familial mesial temporal lobe epilepsy to chromosome 3q26.
Published: November, 2013

Abstract: PURPOSE: To describe the clinical findings in a family with a benign form of mesial temporal lobe epilepsy and to identify the causative genetic factors. METHODS: All participants were personally interviewed and underwent neurologic examination. T...
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PRH/HHex inhibits the migration of breast and prostate epithelial cells through direct transcriptional regulation of Endoglin.
Published: November, 2013

Abstract: PRH/HHex (proline-rich homeodomain protein) is a transcription factor that controls cell proliferation and cell differentiation in a variety of tissues. Aberrant subcellular localisation of PRH is associated with breast cancer and thyroid cancer. ...
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Pluripotency factors and Polycomb Group proteins repress aryl hydrocarbon receptor expression in murine embryonic stem cells.
Published: November, 2013

Abstract: The aryl hydrocarbon receptor (AHR) is a transcription factor and environmental sensor that regulates expression of genes involved in drug-metabolism and cell cycle regulation. Chromatin immunoprecipitation analyses, Ahr ablation in mice and studi...
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Adenovirus precursor pVII protein stability is regulated by its propeptide sequence.
Published: November, 2013

Abstract: Adenovirus encodes for the pVII protein, which interacts and modulates virus DNA structure in the infected cells. The pVII protein is synthesized as the precursor protein and undergoes proteolytic processing by viral proteinase Avp, leading to rel...
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Structural variation-associated expression changes are paralleled by chromatin architecture modifications.
Published: November, 2013

Abstract: UNLABELLED: Copy number variants (CNVs) influence the expression of genes that map not only within the rearrangement, but also to its flanks. To assess the possible mechanism(s) underlying this "neighboring effect", we compared intrachromosomal in...
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Drosophila UTX Coordinates with p53 to Regulate ku80 Expression in Response to DNA Damage.
Published: November, 2013

Abstract: UTX is known as a general factor that activates gene transcription during development. Here, we demonstrate an additional essential role of UTX in the DNA damage response, in which it upregulates the expression of ku80 in Drosophila, both in cultu...
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Frequent alteration of the protein synthesis of enzymes for glucose metabolism in hepatocellular carcinomas.
Published: November, 2013

Abstract: BACKGROUND: Cancer cells show enhanced glycolysis and inhibition of oxidative phosphorylation, even in the presence of sufficient oxygen (aerobic glycolysis). Glycolysis is much less efficient for energy production than oxidative phosphorylation, ...
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Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques.
Published: November, 2013

Abstract: The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cos...
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High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.
Published: November, 2013

Abstract: The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. A...
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MAP Kinase Signaling Mediates Phosphorylation of Polycomb Ortholog Cbx7.
Published: November, 2013

Abstract: Cbx7 is one of five mammalian orthologs of the Drosophila Polycomb (Pc). Cbx7 recognizes methylated lysine residues on the histone H3 tail and contributes to gene silencing in the context of the Polycomb Repressive Complex 1 (PRC1). However, our k...
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Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network.
Published: November, 2013

Abstract: Metabolic diseases and comorbidities represent an ever-growing epidemic where multiple cell types impact tissue homeostasis. Here, the link between the metabolic and gene regulatory networks was studied through experimental and computational analy...
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Insulin-dependent transcriptional control in L6 rat myotubes is associated with modulation of histone acetylation and accumulation of the histone variant H2A.Z in the proximity of the transcriptional start site
Published: November, 2013

Abstract: Besides its direct metabolic effects, insulin induces transcriptional alterations in its target tissues. However, whether such changes are accompanied by epigenetic changes on the chromatin template encompassing insulin responsive genes is unclear...
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Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.
Published: November, 2013

Abstract: It is currently not possible to resolve the genome-wide relationship of transcription factors (TFs) and nucleosomes at the level of individual chromatin templates despite rapidly increasing data on TF and nucleosome occupancy in the human genome. ...
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Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis.
Published: November, 2013

Abstract: The development and severity of inflammatory bowel diseases and other chronic inflammatory conditions can be influenced by host genetic and environmental factors, including signals derived from commensal bacteria. However, the mechanisms that inte...
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Precision-cut liver slices of Atlantic cod (Gadus morhua): An in vitro system for studying the effects of environmental contaminants.
Published: November, 2013

Abstract: The Atlantic cod (Gadus morhua) is an economically important species commonly consumed by humans. The widespread distribution of cod in the North Atlantic Ocean makes it vulnerable to effluents from human activities, such as coastal industries and...
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Promiscuous RNA binding by Polycomb repressive complex 2.
Published: November, 2013

Abstract: Polycomb repressive complex 2 (PRC2) is a histone methyltransferase required for epigenetic silencing during development and cancer. Long noncoding RNAs (lncRNAs) recruit PRC2 to chromatin, but the general role of RNA in maintaining repressed chro...
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MEF2 Is a Converging Hub for Histone Deacetylase 4 and Phosphatidylinositol 3-Kinase/Akt-Induced Transformation.
Published: November, 2013

Abstract: The MEF2-class IIa histone deacetylase (HDAC) axis operates in several differentiation pathways and in numerous adaptive responses. We show here that nuclear active HDAC4 and HDAC7 display transforming capability. HDAC4 oncogenic potential depends...
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Regulation of hypothalamic corticotropin-releasing hormone transcription by elevated glucocorticoids.
Published: November, 2013

Abstract: Negative glucocorticoid feedback is essential for preventing the deleterious effects of excessive hypothalamic pituitary adrenal axis axis activation, with an important target being CRH transcription in the hypothalamic paraventricular nucleus. Th...
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Genomic and proteomic analyses of prdm5 reveal interactions with insulator binding proteins in embryonic stem cells.
Published: November, 2013

Abstract: PRDM proteins belong to the SET domain protein family, which is involved in the regulation of gene expression. Although few PRDM members possess histone methyltransferase activity, the molecular mechanisms by which the other members exert transcri...
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A chromatin immunoprecipitation (ChIP) protocol for use in whole human adipose tissue.
Published: November, 2013

Abstract: Chromatin immunoprecipitation (ChIP) has become a central method when studying in vivo protein-DNA interactions, with the major challenge being the hope to capture "authentic" interactions. While ChIP protocols have been optimized for use with spe...
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Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation.
Published: November, 2013

Abstract: Although intergenic long noncoding RNAs (lincRNAs) have been linked to gene regulation in various tissues, little is known about lincRNA transcriptomes in the T cell lineages. Here we identified 1,524 lincRNA clusters in 42 T cell samples, from ea...
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Lipopolysaccharide Increases the Incidence of Collagen-Induced Arthritis in Mice Through Induction of Protease HTRA-1 Expression.
Published: November, 2013

Abstract: OBJECTIVE: The protease HTRA-1 is closely associated with rheumatoid arthritis (RA). The molecular mechanisms that control HTRA-1 expression are currently unknown. This study was undertaken to determine the regulatory role of Toll-like receptors (...
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PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells.
Published: November, 2013

Abstract: EZH2 is the catalytic subunit of PRC2, a central epigenetic repressor essential for development processes in vivo and for the differentiation of embryonic stem cells (ESCs) in vitro. The biochemical function of PRC2 in depositing repressive H3K27m...
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Mitochondrial-related proteomic changes during obesity and fasting in mice are greater in the liver than skeletal muscles.
Published: November, 2013

Abstract: Although mitochondrial dysfunction is implicated in the pathogenesis of obesity, the molecular mechanisms underlying obesity-related metabolic abnormalities are not well established. We performed mitochondrial quantitative proteomic and whole tran...
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The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex.
Published: November, 2013

Abstract: Prostate cancers remain indolent in the majority of individuals but behave aggressively in a minority. The molecular basis for this clinical heterogeneity remains incompletely understood. Here we characterize a long noncoding RNA termed SChLAP1 (s...
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Dynamics of 1α,25-dihydroxyvitamin D3-dependent chromatin accessibility of early vitamin D receptor target genes.
Published: November, 2013

Abstract: The signaling cascade of the transcription factor vitamin D receptor (VDR) is triggered by its specific ligand 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3). In this study we demonstrate that in THP-1 human monocytic leukemia cells 87.4% of the 1034 mo...
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Mouse BAZ1A (ACF1) is dispensable for double-strand break repair but is essential for averting improper gene expression during spermatogenesis.
Published: November, 2013

Abstract: ATP-dependent chromatin remodelers control DNA access for transcription, recombination, and other processes. Acf1 (also known as BAZ1A in mammals) is a defining subunit of the conserved ISWI-family chromatin remodelers ACF and CHRAC, first purifie...
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The THO complex component Thp2 counteracts telomeric R-loops and telomere shortening.
Published: October, 2013

Abstract: Telomere maintenance by the conventional DNA replication machinery and telomerase is assisted by specialized DNA helicases, nucleases and telomere binding proteins. Here, we identify the THO components at telomeres and define critical roles of thi...
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Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.
Published: October, 2013

Abstract: Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing ...
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Fine-Mapping an Association of FSHR with Preterm Birth in a Finnish Population.
Published: October, 2013

Abstract: Preterm birth is a complex disorder defined by gestations of less than 37 weeks. While preterm birth is estimated to have a significant genetic component, relative few genes have been associated with preterm birth. Polymorphism in one such gene, f...
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Diet Alters Both the Structure and Taxonomy of the Ovine Gut Microbial Ecosystem.
Published: October, 2013

Abstract: We surveyed the ruminal metagenomes of 16 sheep under two different diets using Illumina pair-end DNA sequencing of raw microbial DNA extracted from rumen samples. The resulting sequence data were bioinformatically mapped to known prokaryotic 16S ...
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Mu-seq: Sequence-Based Mapping and Identification of Transposon Induced Mutations.
Published: October, 2013

Abstract: Mutations tagged by transposon insertions can be readily mapped and identified in organisms with sequenced genomes. Collections of such mutants allow a systematic analysis of gene function, and can be sequence-indexed to build invaluable resources...
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Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants.
Published: October, 2013

Abstract: A locus on human chromosome 11q23 tagged by marker rs3802842 was associated with colorectal cancer (CRC) in a genome-wide association study; this finding has been replicated in case-control studies worldwide. In order to identify biologic factors ...
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A missense mutation accelerating the gating of the lysosomal Cl-/H+-exchanger ClC-7/Ostm1 causes osteopetrosis with gingival hamartomas in cattle.
Published: October, 2013

Abstract: Chloride/proton exchange by the lysosomal anion transporter ClC-7/Ostm1 is of pivotal importance for the physiology of lysosomes and bone resorption. Mice lacking either ClC-7 or Ostm1 develop a lysosomal storage disease and mutations in either pr...
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A molecular evolution approach to study the roles of tropomyosin in fission yeast.
Published: October, 2013

Abstract: Tropomyosin, a coiled-coil protein that binds along the length of the actin filament, is a universal regulator of the actin cytoskeleton. We have taken a bioinformatics/proteomic approach to studying structure-function relationships in this protei...
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The double PHD finger domain of MOZ/MYST3 induces α-helical structure of the histone H3 tail to facilitate acetylation and methylation sampling and modification.
Published: October, 2013

Abstract: Histone tail modifications control many nuclear processes by dictating the dynamic exchange of regulatory proteins on chromatin. Here we report novel insights into histone H3 tail structure in complex with the double PHD finger (DPF) of the lysine...
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A functionally conserved Polycomb response element from mouse HoxD complex responds to heterochromatin factors.
Published: October, 2013

Abstract: Anterior-posterior body axis in all bilaterians is determined by the Hox gene clusters that are activated in a spatio-temporal order. This expression pattern of Hox genes is established and maintained by regulatory mechanisms that involve higher o...
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Early adipogenesis is regulated through USP7-mediated deubiquitination of the histone acetyltransferase TIP60.
Published: October, 2013

Abstract: Transcriptional coregulators, including the acetyltransferase Tip60, have a key role in complex cellular processes such as differentiation. Whereas post-translational modifications have emerged as an important mechanism to regulate transcriptional...
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Genome-wide and cell-specific epigenetic analysis challenges the role of polycomb in Drosophila spermatogenesis.
Published: October, 2013

Abstract: The Drosophila spermatogenesis cell differentiation pathway involves the activation of a large set of genes in primary spermatocytes. Most of these genes are activated by testis-specific TATA-binding protein associated factors (tTAFs). In the curr...
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IL-4 blocks TH1-polarizing/inflammatory cytokine gene expression during monocyte-derived dendritic cell differentiation through histone hypoacetylation.
Published: October, 2013

Abstract: BACKGROUND: Whereas recent research has characterized the mechanism by which dendritic cells (DCs) induce TH1/TH17 responses, the functional specialization enabling DCs to polarize TH2 responses remains undefined. Because IL-4 is essential during ...
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Gene dysregulation by histone variant H2A.Z in bladder cancer
Published: October, 2013

Abstract: Background The incorporation of histone variants into nucleosomes is one of the main strategies that the cell uses to regulate the structure and function of chromatin. Histone H2A.Z is an evolutionarily conserved histone H2A variant that is pref...
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The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana.
Published: October, 2013

Abstract: How alternative splicing (AS) is regulated in plants has not yet been elucidated. Previously, we have shown that the nuclear cap-binding protein complex (AtCBC) is involved in AS in Arabidopsis thaliana. Here we show that both subunits of AtCBC (A...
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Gene regulatory scenarios of primary 1,25-dihydroxyvitamin d3 target genes in a human myeloid leukemia cell line.
Published: October, 2013

Abstract: Genome- and transcriptome-wide data has significantly increased the amount of available information about primary 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) target genes in cancer cell models, such as human THP-1 myelomonocytic leukemia cells. In this...
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Evidence of population bottleneck in Astragalus michauxii (Fabaceae), a narrow endemic of the southeastern United States
Published: October, 2013

Abstract: Genetic factors such as decreased genetic diversity and increased homozygosity can have detrimental effects on rare species, and may ultimately limit potential adaptation and exacerbate population declines. The Gulf and Atlantic Coastal Plain phys...
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Blimp1 (Prdm1) prevents re-specification of photoreceptors into retinal bipolar cells by restricting competence.
Published: October, 2013

Abstract: During retinal development, photoreceptors and bipolar cells express the transcription factor Otx2. Blimp1 is transiently expressed in Otx2+ cells. Blimp1 deletion results in excess bipolar cell formation at the expense of photoreceptors. In princ...
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CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation.
Published: October, 2013

Abstract: CTCF (CCCTC-binding factor) is a highly conserved multifunctional DNA-binding protein with thousands of binding sites genome-wide. Our previous work suggested that differences in CTCF's binding site sequence may affect the regulation of CTCF recru...
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Global analysis of eukaryotic mRNA degradation reveals Xrn1-dependent buffering of transcript levels.
Published: October, 2013

Abstract: The rates of mRNA synthesis and degradation determine cellular mRNA levels and can be monitored by comparative dynamic transcriptome analysis (cDTA) that uses nonperturbing metabolic RNA labeling. Here we present cDTA data for 46 yeast strains lac...
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NLRP7 affects trophoblast lineage differentiation, binds to overexpressed YY1 and alters CpG methylation.
Published: October, 2013

Abstract: Maternal-effect mutations in NLRP7 cause rare biparentally inherited hydatidiform moles (BiHMs), abnormal pregnancies containing hypertrophic vesicular trophoblast but no embryo. BiHM trophoblasts display abnormal DNA methylation patterns affectin...
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Sox2 Expression Is Regulated by a Negative Feedback Loop in Embryonic Stem Cells That Involves AKT Signaling and FoxO1.
Published: October, 2013

Abstract: The self-renewal and pluripotency of embryonic stem cells (ESC) is regulated by a highly integrated network of essential transcription factors, which includes Sox2. Previous studies have shown that elevating Sox2 on its own in mouse ESC induces di...
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Combined modulation of polycomb and trithorax genes rejuvenates β cell replication.
Published: October, 2013

Abstract: Inadequate functional β cell mass underlies both type 1 and type 2 diabetes. β Cell growth and regeneration also decrease with age through mechanisms that are not fully understood. Age-dependent loss of enhancer of zeste homolog 2 (EZH2) prevents ...
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Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast.
Published: October, 2013

Abstract: Spt6 is a highly conserved histone chaperone that interacts directly with both RNA polymerase II and histones to regulate gene expression. To gain a comprehensive understanding of the roles of Spt6, we performed genome-wide analyses of transcripti...
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Membrane-to-nucleus signaling links insulin-like growth factor-1- and stem cell factor-activated pathways.
Published: October, 2013

Abstract: STEM CELL FACTOR (MOUSE: Kitl, human: KITLG) and insulin-like growth factor-1 (IGF1), acting via KIT and IGF1 receptor (IGF1R), respectively, are critical for the development and integrity of several tissues. Autocrine/paracrine KITLG-KIT and IGF1...
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A Conserved Protein Motif Is Required for Full Modulatory Activity of Negative Elongation Factor Subunits NELF-A and NELF-B in Modifying Glucocorticoid Receptor-Regulated Gene Induction Properties.
Published: October, 2013

Abstract: NELF-B is a BRCA1-interacting protein and subunit (with NELF-A, -C/D, and -E) of the human negative elongation factor (NELF) complex, which participates in RNA polymerase II pausing shortly after transcription initiation, especially for synchroniz...
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Angiomodulin is required for cardiogenesis of embryonic stem cells and is maintained by a feedback loop network of p63 and Activin-A.
Published: October, 2013

Abstract: The transcription factor p63, member of the p53 gene family, encodes for two main isoforms, TAp63 and ΔNp63 with distinct functions on epithelial homeostasis and cancer. Recently, we discovered that TAp63 is essential for in vitro cardiogenesis an...
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Class I Lysine Deacetylases Facilitate Glucocorticoid-induced Transcription.
Published: October, 2013

Abstract: Nuclear receptors use lysine acetyltransferases and lysine deacetylases (KDACs) in regulating transcription through histone acetylation. Lysine acetyltransferases interact with steroid receptors upon binding of an agonist and are recruited to targ...
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PRMT5-mediated histone H4 arginine-3 symmetrical dimethylation marks chromatin at G + C-rich regions of the mouse genome.
Published: October, 2013

Abstract: Symmetrical dimethylation on arginine-3 of histone H4 (H4R3me2s) has been reported to occur at several repressed genes, but its specific regulation and genomic distribution remained unclear. Here, we show that the type-II protein arginine methyltr...
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Genomic organization of human transcription initiation complexes.
Published: October, 2013

Abstract: The human genome is pervasively transcribed, yet only a small fraction is coding. Here we address whether this non-coding transcription arises at promoters, and detail the interactions of initiation factors TATA box binding protein (TBP), transcri...
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A three-component signaling system finetunes expression kinetics of HPPK responsible for folate synthesis by positive feedback loop during stress response of Xanthomonas campestris.
Published: October, 2013

Abstract: During adaptation to environments, bacteria employ two-component signal transduction systems, which contain histidine kinases and response regulators, to sense and respond to exogenous and cellular stimuli in an accurate spatiotemporal manner. Alt...
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ErbB2 upregulates the Na+,HCO3--cotransporter NBCn1/SLC4A7 in human breast cancer cells via Akt, ERK, Src, and Kruppel-like factor 4.
Published: October, 2013

Abstract: Misregulation of acid-base transport plays central roles in cancer development. We previously demonstrated the strong up-regulation of the Na(+),HCO3(-) cotransporter NBCn1 (SLC4A7) in MCF-7 breast cancer cells by a truncated, constitutively activ...
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Whole-exome sequencing supports genetic heterogeneity in childhood apraxia of speech.
Published: October, 2013

Abstract: The genetic basis of complex neurological disorders involving language are poorly understood, partly due to the multiple additive genetic risk factors that are thought to be responsible. Furthermore, these conditions are often syndromic in that th...
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DNMT1 Is Regulated by ATP-Citrate Lyase and Maintains Methylation Patterns during Adipocyte Differentiation.
Published: October, 2013

Abstract: During adipocyte differentiation, significant epigenomic changes occur in association with the implementation of the adipogenic program. We have previously shown that histone acetylation increases during differentiation in a manner dependent on ac...
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The APSES transcription factor Efg1 is a global regulator that controls morphogenesis and biofilm formation in Candida parapsilosis.
Published: October, 2013

Abstract: Efg1 (a member of the APSES family) is an important regulator of hyphal growth and of the white-to-opaque transition in Candida albicans and very closely related species. We show that in Candida parapsilosis Efg1 is a major regulator of a differen...
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Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation.
Published: October, 2013

Abstract: Despite numerous studies on specific sumoylated transcriptional regulators, the global role of SUMO on chromatin in relation to transcription regulation remains largely unknown. Here, we determined the genome-wide localization of SUMO1 and SUMO2/3...
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Cell-Autonomous Regulation of Brown Fat Identity Gene UCP1 by Unliganded Vitamin D Receptor.
Published: October, 2013

Abstract: White adipose tissue stores energy in the form of lipids, and brown adipose tissue expends energy via uncoupled fatty acid oxidation, which leads to the generation of heat. Obesity reflects an imbalance between energy storage and energy expenditur...
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Dissection of the elements of osmotic stress response transcription factor Hot1 involved in the interaction with MAPK Hog1 and in the activation of transcription.
Published: October, 2013

Abstract: The response to hyperosmotic stress is mediated by the HOG pathway. The MAP kinase Hog1 activates several transcription factors, regulates chromatin-modifying enzymes and, through its interaction with RNA polymerase II, it directs this enzyme to o...
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Pregnenolone activates CLIP-170 to promote microtubule growth and cell migration.
Published: October, 2013

Abstract: Pregnenolone (P5) is a neurosteroid that improves memory and neurological recovery. It is also required for zebrafish embryonic development. However, its mode of action is unclear. Here we show that P5 promotes cell migration and microtubule polym...
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MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma.
Published: October, 2013

Abstract: MEF2B encodes a transcriptional activator and is mutated in ∼11% of diffuse large B cell lymphomas (DLBCLs) and ∼12% of follicular lymphomas (FLs). Here we found that MEF2B directly activated the transcription of the proto-oncogene BCL6 in normal ...
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Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine.
Published: October, 2013

Abstract: To uncover the function of and interplay between the mammalian cytosine modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), new techniques and advances in current technology are needed. To this end, we have developed oxidative...
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Early histone modifications in the ventromedial hypothalamus and preoptic area following oestradiol administration.
Published: October, 2013

Abstract: Expression of the primary female sex behaviour, lordosis, in laboratory animals depends on oestrogen-induced expression of progesterone receptor (PgR) within a defined cell group in the ventrolateral portion of the ventromedial nucleus of the hypo...
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Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues.
Published: October, 2013

Abstract: Mammalian development requires cytosine methylation, a heritable epigenetic mark of cellular memory believed to maintain a cell's unique gene expression pattern. However, it remains unclear how dynamic DNA methylation relates to cell type-specific...
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Sequestration by IFIT1 impairs translation of 2'O-unmethylated capped RNA.
Published: October, 2013

Abstract: Viruses that generate capped RNA lacking 2'O methylation on the first ribose are severely affected by the antiviral activity of Type I interferons. We used proteome-wide affinity purification coupled to mass spectrometry to identify human and mous...
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tRNA methyltransferase homolog gene TRMT10A mutation in young onset diabetes and primary microcephaly in humans.
Published: October, 2013

Abstract: We describe a new syndrome of young onset diabetes, short stature and microcephaly with intellectual disability in a large consanguineous family with three affected children. Linkage analysis and whole exome sequencing were used to identify the ca...
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Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes.
Published: October, 2013

Abstract: The nuclear lamina is implicated in the organization of the eukaryotic nucleus. Association of nuclear lamins with the genome occurs through large chromatin domains including mostly, but not exclusively, repressed genes. How lamin interactions wit...
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Cap Completion and C-Terminal Repeat Domain Kinase Recruitment Underlie the Initiation-Elongation Transition of RNA Polymerase II.
Published: October, 2013

Abstract: After transcription initiation, RNA polymerase (Pol) II escapes from the promoter and recruits elongation factors. The molecular basis for the initiation-elongation factor exchange during this transition remains poorly understood. Here, we used ch...
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Genome-wide profiling reveals stimulus-specific functions of p53 during differentiation and DNA damage of human embryonic stem cells.
Published: September, 2013

Abstract: How tumor suppressor p53 selectively responds to specific signals, especially in normal cells, is poorly understood. We performed genome-wide profiling of p53 chromatin interactions and target gene expression in human embryonic stem cells (hESCs) ...
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Tissue-specific differences in the regulation of KIBRA gene expression involve transcription factor TCF7L2 and a complex alternative promoter system.
Published: September, 2013

Abstract: KIBRA has been described as a key regulator of the Hippo signaling pathway, regulating organ size control, cell contact inhibition, cell growth, as well as tumorigenesis and cystogenesis. Since there is scarce information on KIBRA gene expression ...
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Gene regulation and priming by topoisomerase IIα in embryonic stem cells.
Published: September, 2013

Abstract: Topoisomerases resolve torsional stress, while their function in gene regulation, especially during cellular differentiation, remains unknown. Here we find that the expression of topo II isoforms, topoisomerase IIα and topoisomerase IIβ, is the ch...
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Human SNP Links Differential Outcomes in Inflammatory and Infectious Disease to a FOXO3-Regulated Pathway.
Published: September, 2013

Abstract: The clinical course and eventual outcome, or prognosis, of complex diseases varies enormously between affected individuals. This variability critically determines the impact a disease has on a patient's life but is very poorly understood. Here, we...
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Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells.
Published: September, 2013

Abstract: Polycomb repressive complex 2 (PRC2) regulates gene expression during lineage specification through trimethylation of lysine 27 on histone H3 (H3K27me3). In Drosophila, polycomb binding sites are dynamic chromatin regions enriched with the histone...
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Addiction of t(8;21) and inv(16) acute myeloid leukemia to native RUNX1.
Published: September, 2013

Abstract: The t(8;21) and inv(16) chromosomal aberrations generate the oncoproteins AML1-ETO (A-E) and CBFβ-SMMHC (C-S). The role of these oncoproteins in acute myeloid leukemia (AML) etiology has been well studied. Conversely, the function of native RUNX1 ...
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Insulin-activated Elk-1 recruits the TIP60/NuA4 complex to increase prolactin gene transcription.
Published: September, 2013

Abstract: Insulin increases prolactin gene expression in GH4 cells through phosphorylation of Elk-1 (Jacob and Stanley, 2001). We preformed a reverse two-hybrid screen using Elk-1-B42 as bait to identify proteins from GH4 cells that might serve as co-activa...
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Dnmt3L antagonizes DNA methylation at bivalent promoters and favors DNA methylation at gene bodies in ESCs.
Published: September, 2013

Abstract: The de novo DNA methyltransferase 3-like (Dnmt3L) is a catalytically inactive DNA methyltransferase that cooperates with Dnmt3a and Dnmt3b to methylate DNA. Dnmt3L is highly expressed in mouse embryonic stem cells (ESCs), but its function in these...
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Identification of an Enhancer That Increases miR-200b~200a~429 Gene Expression in Breast Cancer Cells.
Published: September, 2013

Abstract: The miR-200b~200a~429 gene cluster is a key regulator of EMT and cancer metastasis, however the transcription-based mechanisms controlling its expression during this process are not well understood. We have analyzed the miR-200b~200a~429 locus for...
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The Reelin receptors ApoER2 and VLDLR are direct target genes of HIC1 (Hypermethylated In Cancer 1).
Published: September, 2013

Abstract: The tumor suppressor gene HIC1 (Hypermethylated In Cancer 1) is located in 17p13.3 a region frequently hypermethylated or deleted in tumors and in a contiguous-gene syndrome, the Miller-Dieker syndrome which includes classical lissencephaly (smoot...
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Genome-Wide Analysis of DNA Methylation in Soybean.
Published: September, 2013

Abstract: Cytosine methylation is an important mechanism for dynamical regulation of gene expression. We identified 2162 differentially methylated regions in different soybean organs and further analyzed the interplays among DNA methylation, smRNA abundance...
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The BTB-Containing Protein Kctd15 Is SUMOylated In Vivo.
Published: September, 2013

Abstract: Potassium Channel Tetramerization Domain containing 15 (Kctd15) has a role in regulating the neural crest (NC) domain in the embryo. Kctd15 inhibits NC induction by antagonizing Wnt signaling and by interaction with the transcription factor AP-2α ...
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Verification of Intraovum Transmission of a Microsporidium of Vertebrates: Pseudoloma neurophilia Infecting the Zebrafish, Danio rerio.
Published: September, 2013

Abstract: Direct transmission from parents to offspring, referred to as vertical transmission, occurs within essentially all major groups of pathogens. Several microsporidia (Phylum Microsporidia) that infect arthropods employ this mode of transmission, and...
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An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer
Published: September, 2013

Abstract: Background Pancreatic cancer is a highly lethal cancer with limited diagnostic and therapeutic modalities. Methods To begin to explore the genomic landscape of pancreatic cancer, we used massively parallel sequencing to catalog and compare tran...
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Human telomeres that carry an integrated copy of human herpesvirus 6 are often short and unstable, facilitating release of the viral genome from the chromosome.
Published: September, 2013

Abstract: Linear chromosomes are stabilized by telomeres, but the presence of short dysfunctional telomeres triggers cellular senescence in human somatic tissues, thus contributing to ageing. Approximately 1% of the population inherits a chromosomally integ...
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Geminin Is Required for the Maintenance of Pluripotency
Published: September, 2013

Abstract: Pluripotency requires the expression of the three core transcriptions factors Oct4, Sox2 and Nanog, as well as further, complementary proteins. The geminin protein is part of this network, and was shown to play a role in the regulation of DNA repl...
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Recent Diversification of a Marine Genus (Tursiops spp.) Tracks Habitat Preference and Environmental Change.
Published: September, 2013

Abstract: Understanding the evolution of diversity and the resulting systematics in marine systems is confounded by the lack of clear boundaries in oceanic habitats, especially for highly mobile species like marine mammals. Dolphin populations and sibling s...
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Epigenetic Induction of EGR-1 Expression by the Amyloid Precursor Protein during Exposure to Novelty.
Published: September, 2013

Abstract: Following transcriptome comparison of primary cultures isolated from brain of mice expressing or not the amyloid precursor protein APP, we found transcription of the EGR-1 gene to be regulated by APP. In primary cultures of cortical neurons, APP s...
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MiR-210 Is Induced by Oct-2, Regulates B Cells, and Inhibits Autoantibody Production.
Published: September, 2013

Abstract: MicroRNAs (MiRs) are small, noncoding RNAs that regulate gene expression posttranscriptionally. In this study, we show that MiR-210 is induced by Oct-2, a key transcriptional mediator of B cell activation. Germline deletion of MiR-210 results in t...
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Multivalent Engagement of TFIID to Nucleosomes.
Published: September, 2013

Abstract: The process of eukaryotic transcription initiation involves the assembly of basal transcription factor complexes on the gene promoter. The recruitment of TFIID is an early and important step in this process. Gene promoters contain distinct DNA seq...
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Target Capture and Massively Parallel Sequencing of Ultraconserved Elements (UCEs) for Comparative Studies at Shallow Evolutionary Time Scales
Published: September, 2013

Abstract: Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily d...
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Direct activation of a mouse Hoxd11 axial expression enhancer by Gdf11/Smad signalling.
Published: September, 2013

Abstract: A Hoxd11/lacZ reporter, expressed with a Hoxd11-like axial expression pattern in transgenic mouse embryos, is stimulated in tailbud fragments when cultured in presence of Gdf11, a TGF-β growth/differentiation factor. The same construct is also sti...
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Proteomics identifies ubiquitin-proteasome targets and new roles for chromatin-remodeling in the Arabidopsis response to phosphate starvation.
Published: September, 2013

Abstract: In order to identify new regulators of the phosphate (Pi) starvation signaling pathway in plants, we analyzed variation in the abundance of nuclear-enriched proteins isolated from Arabidopsis roots that depends on Pi supply. We used 2-D fluorescen...
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Exome sequencing identifies recurring FLT3 N676K mutations in core-binding factor leukemia.
Published: September, 2013

Abstract: The t(8;21) and inv(16)/t(16;16) rearrangements affecting the core-binding factors RUNX1 and CBFB, respectively, are found in 15% to 20% of adult de novo acute myeloid leukemia (AML) cases and are associated with a favorable prognosis. Since the e...
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Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences.
Published: September, 2013

Abstract: Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the co...
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Evidence from mouse and man for a role of neuregulin 3 in nicotine dependence.
Published: September, 2013

Abstract: Addiction to nicotine and the ability to quit smoking are influenced by genetic factors. We used functional genomic approaches (chromatin immunoprecipitation (ChIP) and whole-genome sequencing) to identify cAMP response element-binding protein (CR...
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The p130 Isoform of Angiomotin Is Required for Yap-Mediated Hepatic Epithelial Cell Proliferation and Tumorigenesis
Published: September, 2013

Abstract: The Hippo-Yap signaling pathway regulates a number of developmental and adult cellular processes, including cell fate determination, tissue growth, and tumorigenesis. Members of the scaffold protein angiomotin (Amot) family interact with several H...
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Global alterations of DNA methylation in cholangiocarcinoma targets the Wnt signaling pathway
Published: September, 2013

Abstract: The molecular mechanisms underlying the genesis of cholangiocarcinomas (CCs) are poorly understood. Epigenetic changes such as aberrant hypermethylation and subsequent atypical gene expression are characteristic features of most human cancers. In ...
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Antisense transcripts enhanced by camptothecin at divergent CpG-island promoters associated with bursts of topoisomerase I-DNA cleavage complex and R-loop formation.
Published: September, 2013

Abstract: DNA Topoisomerase I (Top1) is required to relax DNA supercoils generated by RNA polymerases (RNAPs). Top1 is inhibited with high specificity by camptothecin (CPT), an effective anticancer agent, and by oxidative base damage and ribonucleotides in ...
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Phosphorylation of RNA polymerase II is independent of P-TEFb in the C. elegans germline.
Published: September, 2013

Abstract: RNA polymerase II (Pol II) elongation in metazoans is thought to require phosphorylation of serine 2 (Ser2-P) of the Pol II C-terminal domain (CTD) by the P-TEFb complex, CDK-9/cyclin T. Another Ser2 kinase complex, CDK-12/cyclin K, which requires...
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A new strategy for gene targeting and functional proteomics using the DT40 cell line.
Published: September, 2013

Abstract: DT40 cells derived from chicken B lymphocytes exhibit exceptionally high homologous recombination rates. Therefore, they can be used as a convenient tool and model for gene targeting experiments. However, lack of efficient cloning strategies, prot...
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Integrated virus-host methylome analysis in head and neck squamous cell carcinoma
Published: September, 2013

Abstract: One in six cancers worldwide is caused by infection and human papillomavirus (HPV) is one of the main culprits. To better understand the dynamics of HPV integration and its effect on both the viral and host methylomes, we conducted whole-genome DN...
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Chromatin-specific regulation of mammalian rDNA transcription by clustered TTF-I binding sites.
Published: September, 2013

Abstract: Enhancers and promoters often contain multiple binding sites for the same transcription factor, suggesting that homotypic clustering of binding sites may serve a role in transcription regulation. Here we show that clustering of binding sites for t...
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Ago1 Interacts with RNA Polymerase II and Binds to the Promoters of Actively Transcribed Genes in Human Cancer Cells.
Published: September, 2013

Abstract: Argonaute proteins are often credited for their cytoplasmic activities in which they function as central mediators of the RNAi platform and microRNA (miRNA)-mediated processes. They also facilitate heterochromatin formation and establishment of re...
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Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans.
Published: September, 2013

Abstract: Aneuploidy is known to be deleterious and underlies several common human diseases, including cancer and genetic disorders such as trisomy 21 in Down's syndrome. In contrast, aneuploidy can also be advantageous and in fungi confers antifungal drug ...
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miR-1/133a clusters cooperatively specify the cardiomyogenic lineage by adjustment of myocardin levels during embryonic heart development.
Published: September, 2013

Abstract: miRNAs are small RNAs directing many developmental processes by posttranscriptional regulation of protein-coding genes. We uncovered a new role for miR-1-1/133a-2 and miR-1-2/133a-1 clusters in the specification of embryonic cardiomyocytes allowin...
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A metagenomic snapshot of taxonomic and functional diversity in an alpine glacier cryoconite ecosystem
Published: September, 2013

Abstract: Cryoconite is a microbe–mineral aggregate which darkens the ice surface of glaciers. Microbial process and marker gene PCR-dependent measurements reveal active and diverse cryoconite microbial communities on polar glaciers. Here, we provide the fi...
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Epigenetic silencing of Bim transcription by Spi-1/PU.1 promotes apoptosis resistance in leukaemia.
Published: September, 2013

Abstract: Deregulation of transcriptional networks contributes to haematopoietic malignancies. The transcription factor Spi-1/PU.1 is a master regulator of haematopoiesis and its alteration leads to leukaemia. Spi-1 overexpression inhibits differentiation a...
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Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome.
Published: September, 2013

Abstract: Here, we present an adaptation of restriction-site-associated DNA sequencing (RAD-seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Réunion grey white-eye (Zosterops ...
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Let-7b and miR-495 Stimulate Differentiation and Prevent Metaplasia of Pancreatic Acinar Cells by Repressing HNF6.
Published: September, 2013

Abstract: BACKGROUND & AIMS: Diseases of the exocrine pancreas are often associated with perturbed differentiation of acinar cells. MicroRNAs (miRNAs) regulate pancreas development, yet little is known about their contribution to acinar cell differentiation...
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The ASAP2 gene is a primary target of 1,25-dihydroxyvitamin D3 in human monocytes and macrophages.
Published: August, 2013

Abstract: A genome-wide data set on vitamin D receptor (VDR) binding sites in human THP-1 cells (monocytes) led us to the genomic region around the ASAP2 (Arf-GAP with SH3 domain, ankyrin repeat and PH domain 2) gene, whose product is involved in the regula...
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Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells.
Published: August, 2013

Abstract: DNA methylation and chromatin remodeling are frequently implicated in the silencing of genes involved in carcinogenesis. Long Range Epigenetic Silencing (LRES) is a mechanism of gene inactivation that affects multiple contiguous CpG islands and ha...
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Endogenous Nuclear RNAi Mediates Behavioral Adaptation to Odor.
Published: August, 2013

Abstract: Most eukaryotic cells express small regulatory RNAs. The purpose of one class, the somatic endogenous siRNAs (endo-siRNAs), remains unclear. Here, we show that the endo-siRNA pathway promotes odor adaptation in C. elegans AWC olfactory neurons. In...
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Transcriptional environment and chromatin architecture interplay dictates globin expression patterns of heterospecific hybrids derived from undifferentiated human embryonic stem cells or from their erythroid progeny.
Published: August, 2013

Abstract: To explore the response of β globin locus with established chromatin domains upon their exposure to new transcriptional environments, we transferred the chromatin-packaged β globin locus of undifferentiated human embryonic stem cells (hESCs) or hE...
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PRC2 Controls Drosophila Oocyte Cell Fate by Repressing Cell Cycle Genes.
Published: August, 2013

Abstract: The oocyte is a unique cell type that undergoes extensive chromosome changes on its way to fertilization, but the chromatin determinants of its fate are unknown. Here, we show that Polycomb group (PcG) proteins of the Polycomb repressive complex 2...
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A signature motif mediating selective interactions of BCL11A with the NR2E/F subfamily of orphan nuclear receptors.
Published: August, 2013

Abstract: Despite their physiological importance, selective interactions between nuclear receptors (NRs) and their cofactors are poorly understood. Here, we describe a novel signature motif (F/YSXXLXXL/Y) in the developmental regulator BCL11A that facilitat...
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Enhanced Chromatin Dynamics by FACT Promotes Transcriptional Restart after UV-Induced DNA Damage.
Published: August, 2013

Abstract: Chromatin remodeling is tightly linked to all DNA-transacting activities. To study chromatin remodeling during DNA repair, we established quantitative fluorescence imaging methods to measure the exchange of histones in chromatin in living cells. W...
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Optical control of mammalian endogenous transcription and epigenetic states.
Published: August, 2013

Abstract: The dynamic nature of gene expression enables cellular programming, homeostasis and environmental adaptation in living systems. Dissection of causal gene functions in cellular and organismal processes therefore necessitates approaches that enable ...
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A GAA repeat expansion reporter model of Friedreich's ataxia recapitulates the genomic context and allows rapid screening of therapeutic compounds.
Published: August, 2013

Abstract: Friedreich's ataxia (FRDA) is caused by large GAA expansions in intron 1 of the frataxin gene (FXN), which lead to reduced FXN expression through a mechanism not fully understood. Understanding such mechanism is essential for the identification of...
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Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses
Published: August, 2013

Abstract: Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA...
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Sexually Dimorphic Genome-Wide Binding of Retinoid X Receptor alpha (RXRα) Determines Male-Female Differences in the Expression of Hepatic Lipid Processing Genes in Mice.
Published: August, 2013

Abstract: Many hepatic functions including lipid metabolism, drug metabolism, and inflammatory responses are regulated in a sex-specific manner due to distinct patterns of hepatic gene expression between males and females. Regulation for the majority of the...
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PARP-1 Controls Immunosuppressive Function of Regulatory T Cells by Destabilizing Foxp3.
Published: August, 2013

Abstract: Poly (ADP-ribose) polymerase-1 (PARP-1) is a nuclear enzyme and transcription factor that is involved in inflammatory response, but its role in T cell response remains largely unknown. We show here that PARP-1 regulates the suppressive function of...
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Mutant IDH1 promotes leukemogenesis in vivo and can be specifically targeted in human AML.
Published: August, 2013

Abstract: Mutations in the metabolic enzymes isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) are frequently found in glioma, acute myeloid leukemia (AML), melanoma, thyroid cancer and chondrosarcoma patients. Mutant IDH produces 2-hydroxyglutarate (2HG), whi...
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Systematic Identification of Proteins Binding to Chromatin-Embedded Ubiquitylated H2B Reveals Recruitment of SWI/SNF to Regulate Transcription.
Published: August, 2013

Abstract: Chromatin posttranslational modifications (PTMs), including monoubiquitylation of histone H2B on lysine 120 (H2Bub1), play a major role in regulating genome functions. To elucidate the molecular mechanisms of H2Bub1 activity, a chromatin template ...
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CDK8-Mediated STAT1-S727 Phosphorylation Restrains NK Cell Cytotoxicity and Tumor Surveillance.
Published: August, 2013

Abstract: The transcription factor STAT1 is important in natural killer (NK) cells, which provide immediate defense against tumor and virally infected cells. We show that mutation of a single phosphorylation site (Stat1-S727A) enhances NK cell cytotoxicity ...
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WT1 regulates the expression of inhibitory chemokines during heart development.
Published: August, 2013

Abstract: The embryonic epicardium is an important source of cardiovascular precursor cells and paracrine factors that are required for adequate heart formation. Signaling pathways regulated by WT1 that promote heart development have started to be described...
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Mod5 protein binds to tRNA gene complexes and affects local transcriptional silencing.
Published: August, 2013

Abstract: The tRNA gene-mediated (tgm) silencing of RNA polymerase II promoters is dependent on subnuclear clustering of the tRNA genes, but genetic analysis shows that the silencing requires additional mechanisms. We have identified proteins that bind tRNA...
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Artd1/Parp1 regulates reprogramming by transcriptional regulation of Fgf4 via Sox2 ADP-ribosylation.
Published: August, 2013

Abstract: The recently established reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) by Takahashi and Yamanaka, represents a valuable tool for future therapeutic applications. To date, the mechanisms underlying this process are stil...
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A Kinase-Independent Function of CDK6 Links the Cell Cycle to Tumor Angiogenesis.
Published: August, 2013

Abstract: In contrast to its close homolog CDK4, the cell cycle kinase CDK6 is expressed at high levels in lymphoid malignancies. In a model for p185(BCR-ABL+) B-acute lymphoid leukemia, we show that CDK6 is part of a transcription complex that induces the ...
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Chromatin-Bound IκBα Regulates a Subset of Polycomb Target Genes in Differentiation and Cancer.
Published: August, 2013

Abstract: IκB proteins are the primary inhibitors of NF-κB. Here, we demonstrate that sumoylated and phosphorylated IκBα accumulates in the nucleus of keratinocytes and interacts with histones H2A and H4 at the regulatory region of HOX and IRX genes. Chroma...
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A three-state model for the regulation of telomerase by TERRA and hnRNPA1.
Published: August, 2013

Abstract: Telomeres, the physical ends of eukaryotic chromosomes, are transcribed into telomeric repeat-containing RNA (TERRA), a large non-coding RNA, which forms an integral part of telomeric heterochromatin. In vitro, naked TERRA molecules are efficient ...
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Ezh1 and Ezh2 differentially regulate PSD-95 gene transcription in developing hippocampal neurons.
Published: August, 2013

Abstract: Polycomb Repressive Complex 2 (PRC2) mediates transcriptional silencing by catalyzing histone H3 lysine 27 trimethylation (H3K27me3), but its role in the maturation of postmitotic mammalian neurons remains largely unknown. We report that the PRC2 ...
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Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells.
Published: August, 2013

Abstract: DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germ line, and may be mediated by Tet (ten eleven t...
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Histone variant Htz1 promotes histone H3 acetylation to enhance nucleotide excision repair in Htz1 nucleosomes.
Published: August, 2013

Abstract: Nucleotide excision repair (NER) is critical for maintaining genome integrity. How chromatin dynamics are regulated to facilitate this process in chromatin is still under exploration. We show here that a histone H2A variant, Htz1 (H2A.Z), in nucle...
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Nanolipodendrosome-loaded glatiramer acetate and myogenic differentiation 1 as augmentation therapeutic strategy approaches in muscular dystrophy.
Published: August, 2013

Abstract: BACKGROND: Muscular dystrophies consist of a number of juvenile and adult forms of complex disorders which generally cause weakness or efficiency defects affecting skeletal muscles or, in some kinds, other types of tissues in all parts of the body...
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Model selection reveals control of cold signalling by evening-phased components of the plant circadian clock.
Published: August, 2013

Abstract: Circadian clocks confer advantages by restricting biological processes to certain times of day through the control of specific phased outputs. Control of temperature signalling is an important function of the plant oscillator, but the architecture...
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Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila.
Published: August, 2013

Abstract: Aims: Mitofusin (Mfn) 2 redundantly promotes mitochondrial outer membrane tethering and organelle fusion with Mfn1, and uniquely functions as the mitochondrial receptor for Parkin during PINK1-Parkin mediated mitophagy. Selective deletion of Mfn2 ...
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A role for SIRT2-dependent histone H3K18 deacetylation in bacterial infection.
Published: August, 2013

Abstract: Pathogens dramatically affect host cell transcription programs for their own profit during infection, but in most cases, the underlying mechanisms remain elusive. We found that during infection with the bacterium Listeria monocytogenes, the host d...
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O-glycosylation as a novel control mechanism of peptidoglycan hydrolase activity.
Published: August, 2013

Abstract: Acm2, the major autolysin of Lactobacillus plantarum, is a tripartite protein. Its catalytic domain is surrounded by an O-glycosylated N-terminal region rich in Ala, Ser, and Thr (AST domain), which is of low complexity and unknown function, and a...
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Genome-wide profiling identifies a subset of methamphetamine (METH)-induced genes associated with METH-induced increased H4K5Ac binding in the rat striatum.
Published: August, 2013

Abstract: BACKGROUND: METH is an illicit drug of abuse that influences gene expression in the rat striatum. Histone modifications regulate gene transcription. METHODS: We therefore used microarray analysis and genome-scale approaches to examine potential re...
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Binding of TFIIIC to SINE Elements Controls the Relocation of Activity-Dependent Neuronal Genes to Transcription Factories.
Published: August, 2013

Abstract: In neurons, the timely and accurate expression of genes in response to synaptic activity relies on the interplay between epigenetic modifications of histones, recruitment of regulatory proteins to chromatin and changes to nuclear structure. To ide...
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H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation.
Published: August, 2013

Abstract: The histone H2A variant H2A.Z is essential for embryonic development and for proper control of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions of amino acid sequence of H2A.Z likely determine its functional...
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Ras-Induced Changes in H3K27me3 Occur after Those in Transcriptional Activity.
Published: August, 2013

Abstract: Oncogenic signaling pathways regulate gene expression in part through epigenetic modification of chromatin including DNA methylation and histone modification. Trimethylation of histone H3 at lysine-27 (H3K27), which correlates with transcriptional...
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Androgen Receptor Drives Transcription of Rat PACAP in Gonadotrope Cells.
Published: August, 2013

Abstract: Gonadotropin expression is precisely regulated within the hypothalamic-pituitary-gonadal axis through the complex interaction of neuropeptides, gonadal steroids. and both gonadal- and pituitary-derived peptides. In the anterior pituitary gland, th...
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High-throughput sequencing reveals principles of adeno-associated virus serotype 2 integration.
Published: August, 2013

Abstract: Viral integrations are important in human biology, yet genome-wide integration profiles have not been determined for many viruses. Adeno-associated virus (AAV) infects most of the human population and is a prevalent gene therapy vector. AAV integr...
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Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells.
Published: August, 2013

Abstract: The effects of diverse stresses on promoter selectivity and transcription regulation by the tumor suppressor p53 are poorly understood. We have taken a comprehensive approach to characterizing the human p53 network that includes p53 levels, bindin...
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Program Specificity for Ptf1a in Pancreas versus Neural Tube Development Correlates with Distinct Collaborating Cofactors and Chromatin Accessibility.
Published: August, 2013

Abstract: The lineage-specific basic helix-loop-helix transcription factor Ptf1a is a critical driver for development of both the pancreas and nervous system. How one transcription factor controls diverse programs of gene expression is a fundamental questio...
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Minotaur is critical for primary piRNA biogenesis.
Published: August, 2013

Abstract: Piwi proteins and their associated small RNAs are essential for fertility in animals. In part, this is due to their roles in guarding germ cell genomes against the activity of mobile genetic elements. piRNA populations direct Piwi proteins to sile...
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Early growth response 2 (Egr2) plays opposing roles in committing C3H10T1/2 stem cells to adipocytes and smooth muscle-like cells.
Published: August, 2013

Abstract: Early growth response 2 (Egr2) is a zinc-finger transcription factor that acts as an important modulator of a variety of physiological processes, such as cell differentiation, proliferation and apoptosis. Here we showed that Egr2 was downregulated...
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Chromatin tandem affinity purification sequencing.
Published: August, 2013

Abstract: Chromatin immunoprecipitation coupled with ultra-high-throughput sequencing (ChIP-seq) is a widely used method for mapping the interactions of proteins with DNA. However, the requirements for ChIP-grade antibodies impede wider application of this ...
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Chromatin-modifying agents reactivate embryonic renal stem/progenitor genes in human adult kidney epithelial cells but abrogate dedifferentiation and stemness.
Published: August, 2013

Abstract: Abstract Recent studies have suggested that epigenetic modulation with chromatin-modifying agents can induce stemness and dedifferentiation and increase developmental plasticity. For instance, valproic acid (VPA), a histone deacetylase (HDAC) inhi...
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Rev-erb-α modulates skeletal muscle oxidative capacity by regulating mitochondrial biogenesis and autophagy.
Published: August, 2013

Abstract: The nuclear receptor Rev-erb-α modulates hepatic lipid and glucose metabolism, adipogenesis and the inflammatory response in macrophages. We show here that Rev-erb-α is highly expressed in oxidative skeletal muscle and that its deficiency in muscl...
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BACH2 mediates negative selection and p53-dependent tumor suppression at the pre-B cell receptor checkpoint.
Published: August, 2013

Abstract: The B cell-specific transcription factor BACH2 is required for affinity maturation of B cells. Here we show that Bach2-mediated activation of p53 is required for stringent elimination of pre-B cells that failed to productively rearrange immunoglob...
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Noncoding RNAs prevent spreading of a repressive histone mark.
Published: August, 2013

Abstract: Transcription of eukaryotic genomes is more widespread than was previously anticipated and results in the production of many non-protein-coding RNAs (ncRNAs) whose functional relevance is poorly understood. Here we demonstrate that ncRNAs can coun...
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Prdm1a directly activates foxd3 and tfap2a during zebrafish neural crest specification.
Published: August, 2013

Abstract: The neural crest comprises multipotent precursor cells that are induced at the neural plate border by a series of complex signaling and genetic interactions. Several transcription factors, termed neural crest specifiers, are necessary for early ne...
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Genome wide association analysis of a founder population identified TAF3 as a gene for MCHC in humans.
Published: July, 2013

Abstract: The red blood cell related traits are highly heritable but their genetics are poorly defined. Only 5-10% of the total observed variance is explained by the genetic loci found to date, suggesting that additional loci should be searched using approa...
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Silencing MED1 sensitizes breast cancer cells to pure anti-estrogen fulvestrant in vitro and in vivo.
Published: July, 2013

Abstract: Pure anti-estrogen fulvestrant has been shown to be a promising ER antagonist for locally advanced and metastatic breast cancer. Unfortunately, a significant proportion of patients developed resistance to this type of endocrine therapy but the mol...
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Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells.
Published: July, 2013

Abstract: Pluripotency is maintained by both known and unknown transcriptional regulatory networks. In the present study, we have identified Zfp819, a KRAB-zinc finger protein, as a novel pluripotency-related factor and characterized its role in pluripotent...
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Synchronous recruitment of epigenetic modifiers to endotoxin synergistically activated Tnf-α gene in acute kidney injury.
Published: July, 2013

Abstract: BACKGROUND: As a consequence of acute kidney injury (AKI), proximal tubular cells hyperrespond to endotoxin (lipopolysaccharide, LPS) by exaggerated renal Tnf-α Production. This LPS hyperresponsiveness is transcriptionally mediated. The epigenetic...
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STAT3 signaling induces the differentiation of human ICOS(+) CD4 T cells helping B lymphocytes.
Published: July, 2013

Abstract: The generation of high-affinity antibodies and the development of B cell memory are dependent on the help provided by CD4 T cells. Mouse studies indicate that STAT3 signaling in CD4 T cells promotes the acquisition of the B cell help function. How...
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DNA unmethylome profiling by covalent capture of CpG sites.
Published: July, 2013

Abstract: Dynamic patterns of cytosine-5 methylation and successive hydroxylation are part of epigenetic regulation in eukaryotes, including humans, which contributes to normal phenotypic variation and disease risk. Here we present an approach for the mappi...
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Chromatin insulator bodies are nuclear structures that form in response to osmotic stress and cell death.
Published: July, 2013

Abstract: Chromatin insulators assist in the formation of higher-order chromatin structures by mediating long-range contacts between distant genomic sites. It has been suggested that insulators accomplish this task by forming dense nuclear foci termed insul...
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DNA methylation of dermal MSCs in psoriasis: Identification of epigenetically dysregulated genes.
Published: July, 2013

Abstract: BACKGROUND: Mesenchymal stem cells (MSCs) are likely involved in pathological processes of immune-related diseases, including psoriasis, because of their immunoregulatory and pro-angiogenic effects. DNA methylation plays an essential role in regul...
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An epigenetic trap stabilizes singular olfactory receptor expression.
Published: July, 2013

Abstract: The molecular mechanisms regulating olfactory receptor (OR) expression in the mammalian nose are not yet understood. Here, we identify the transient expression of histone demethylase LSD1 and the OR-dependent expression of adenylyl cyclase 3 (Adcy...
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Transcriptional profiling by RNA-Seq of peri-attachment porcine embryos generated by a variety of assisted reproductive technologies.
Published: July, 2013

Abstract: Substantial mortality of in vitro manipulated porcine embryos is observed during peri-attachment development. Herein we describe our efforts to characterize the transcriptomes of embryonic disc (ED) and trophectoderm (TE) cells from porcine embryo...
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PfSec13 is an unusual chromatin-associated nucleoporin of Plasmodium falciparum that is essential for parasite proliferation in human erythrocytes.
Published: July, 2013

Abstract: In Plasmodium falciparum, the deadliest form of human malaria, the nuclear periphery has drawn much attention due to its role as a sub-nuclear compartment involved in virulence gene expression. Recent data have implicated components of the nuclear...
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STAT4 and T-bet are required for the plasticity of IFN-γ expression across Th2 ontogeny and influence changes in Ifng promoter DNA methylation.
Published: July, 2013

Abstract: CD4(+) T cells developing toward a Th2 fate express IL-4, IL-5, and IL-13 while inhibiting production of cytokines associated with other Th types, such as the Th1 cytokine IFN- γ. IL-4-producing Th2 effector cells give rise to a long-lived memory ...
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Otx2 and onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors.
Published: July, 2013

Abstract: Cone photoreceptors carry out phototransduction in daylight conditions and provide the critical first step in color vision. Despite their importance, little is known about the developmental mechanisms involved in their generation, particularly how...
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Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states.
Published: July, 2013

Abstract: Eukaryotes can have thousands of 45S ribosomal RNA (rRNA) genes, many of which are silenced during development. Using fluorescence-activated sorting techniques, we show that active rRNA genes in Arabidopsis thaliana are present within sorted nucle...
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Cell-penetrating peptide secures an efficient endosomal escape of an intact cargo upon a brief photo-induction.
Published: July, 2013

Abstract: Since their discovery, cell-penetrating peptides (CPPs) have provided a novel, efficient, and non-invasive mode of transport for various (bioactive) cargos into cells. Despite the ever-growing number of successful implications of the CPP-mediated ...
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Hmgb1 can facilitate activation of the matrilin-1 gene promoter by Sox9 and L-Sox5/Sox6 in early steps of chondrogenesis.
Published: July, 2013

Abstract: The architectural high mobility group box 1 (Hmgb1) protein acts as both a nuclear and an extracellular regulator of various biological processes, including skeletogenesis. Here we report its contribution to the evolutionarily conserved, distincti...
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De Novo Mutations in the Genome Organizer CTCF Cause Intellectual Disability.
Published: July, 2013

Abstract: An increasing number of genes involved in chromatin structure and epigenetic regulation has been implicated in a variety of developmental disorders, often including intellectual disability. By trio exome sequencing and subsequent mutational screen...
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De Novo DNA Methylation in the Male Germ Line Occurs by Default but Is Excluded at Sites of H3K4 Methylation.
Published: July, 2013

Abstract: To understand what dictates the emerging patterns of de novo DNA methylation in the male germline, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells by using methylated CpG island recovery assay (MI...
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PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum
Published: July, 2013

Abstract: The variant antigen Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), which is expressed on the surface of P. falciparum-infected red blood cells, is a critical virulence factor for malaria1. Each parasite has 60 antigenically distinc...
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A robust dry reagent lateral flow assay for diagnosis of active schistosomiasis by detection of Schistosoma circulating anodic antigen.
Published: July, 2013

Abstract: An earlier reported laboratory assay, performed in The Netherlands, to diagnose Schistosoma infections by detection of the parasite antigen CAA in serum was converted to a more user-friendly format with dry reagents. The improved assay requires le...
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Molecular circuit involving KLK4 integrates androgen and mTOR signaling in prostate cancer.
Published: July, 2013

Abstract: The androgen receptor (AR) and the phosphoinositide 3-kinase (PI3K)/protein kinase B/mammalian target of rapamycin (mTOR) signaling are two of the major proliferative pathways in a number of tissues and are the main therapeutic targets in various ...
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Beyond the binding site: in vivo identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development.
Published: July, 2013

Abstract: CNBP is a nucleic acid chaperone implicated in vertebrate craniofacial development, as well as in myotonic dystrophy type 2 (DM2) and sporadic inclusion body myositis (sIBM) human muscle diseases. CNBP is highly conserved among vertebrates and has...
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Digital genotyping of sorghum -- a diverse plant species with a large repeat-rich genome.
Published: July, 2013

Abstract: BACKGROUND: Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genotyping; however, for species...
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PP1α, PP1β and Wip-1 regulate H4S47 phosphorylation and deposition of histone H3 variant H3.3.
Published: July, 2013

Abstract: Phosphorylation of histone H4 serine 47 (H4S47ph) is catalyzed by Pak2, a member of the p21-activated serine/threonine protein kinase (Pak) family and regulates the deposition of histone variant H3.3. However, the phosphatase(s) involved in the re...
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Modifications of Chromatin Dynamics Control the Smad2 Pathway Activation in Aneurysmal Smooth Muscle Cells.
Published: July, 2013

Abstract: Rationale: The activation of the Smad2 signaling pathway is thought to play an important role in human aneurysmal diseases as described by an important body of research. We previously showed that constitutive Smad2 activation is associated with Sm...
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Detection of histone modification by chromatin immunoprecipitation combined zinc finger luciferase-based bioluminescence resonance energy transfer assay.
Published: July, 2013

Abstract: Epigenetic modification such as DNA methylation and histone modification have important roles in gene regulation. Epigenetic modification can be altered by environmental influences and are related to diseases. Therefore, epigenetic modifications m...
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Submergence Confers Immunity Mediated by the WRKY22 Transcription Factor in Arabidopsis.
Published: July, 2013

Abstract: Transcriptional control plays an important role in regulating submergence responses in plants. Although numerous genes are highly induced during hypoxia, their individual roles in hypoxic responses are still poorly understood. Here, we found that ...
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Epigenetic induction of the Ink4a/Arf locus prevents Schwann cell overproliferation during nerve regeneration and after tumorigenic challenge.
Published: July, 2013

Abstract: The number of Schwann cells is fitted to axonal length in peripheral nerves. This relationship is lost when tumorigenic stimuli induce uncontrolled Schwann cell proliferation, generating tumours such us neurofibromas and schwannomas. Schwann cells...
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Changes in RNA polymerase II progression influence somatic hypermutation of Ig-related genes by AID.
Published: July, 2013

Abstract: Somatic hypermutation (SHM) of Ig genes is initiated by the activation-induced cytidine deaminase (AID), and requires target gene transcription. We previously proposed that AID may associate with the RNA polymerase II (Pol). Here, to determine asp...
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Uniform, optimal signal processing of mapped deep-sequencing data.
Published: July, 2013

Abstract: Despite their apparent diversity, many problems in the analysis of high-throughput sequencing data are merely special cases of two general problems, signal detection and signal estimation. Here we adapt formally optimal solutions from signal proce...
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Genome-wide measurement of protein-DNA binding dynamics using competition ChIP.
Published: July, 2013

Abstract: Competition chromatin immunoprecipitation (competition ChIP) enables experimenters to measure protein-DNA dynamics at a single locus or across the entire genome, depending on the detection method. Competition ChIP relies on a cell containing two c...
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Therapeutic targeting of NOTCH signaling ameliorates immune-mediated bone marrow failure of aplastic anemia.
Published: July, 2013

Abstract: Severe aplastic anemia (AA) is a bone marrow (BM) failure (BMF) disease frequently caused by aberrant immune destruction of blood progenitors. Although a Th1-mediated pathology is well described for AA, molecular mechanisms driving disease progres...
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Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency.
Published: July, 2013

Abstract: Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) involves a marked reorganization of chromatin. To identify post-translational histone modifications that change in global abundance during this process, we have applied a q...
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The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals.
Published: July, 2013

Abstract: Glucocorticoid receptor (GR) binds to genomic response elements and regulates gene transcription with cell and gene specificity. Within a response element, the precise sequence to which the receptor binds has been implicated in directing its struc...
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Alu Elements in ANRIL Non-Coding RNA at Chromosome 9p21 Modulate Atherogenic Cell Functions through Trans-Regulation of Gene Networks.
Published: July, 2013

Abstract: The chromosome 9p21 (Chr9p21) locus of coronary artery disease has been identified in the first surge of genome-wide association and is the strongest genetic factor of atherosclerosis known today. Chr9p21 encodes the long non-coding RNA (ncRNA) an...
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Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus.
Published: July, 2013

Abstract: Coronary heart disease (CHD) is the leading cause of mortality in both developed and developing countries worldwide. Genome-wide association studies (GWAS) have now identified 46 independent susceptibility loci for CHD, however, the biological and...
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Stepwise activation of the ATR signaling pathway upon increasing replication stress impacts fragile site integrity.
Published: July, 2013

Abstract: Breaks at common fragile sites (CFS) are a recognized source of genome instability in pre-neoplastic lesions, but how such checkpoint-proficient cells escape surveillance and continue cycling is unknown. Here we show, in lymphocytes and fibroblast...
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Stalled RNAP-II molecules bound to non-coding rDNA spacers are required for normal nucleolus architecture.
Published: July, 2013

Abstract: The correct distribution of nuclear domains is critical for the maintenance of normal cellular processes such as transcription and replication, which are regulated depending on their location and surroundings. The most well-characterized nuclear d...
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A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen.
Published: July, 2013

Abstract: Survival at host temperature is a critical trait for pathogenic microbes of humans. Thermally dimorphic fungal pathogens, including Histoplasma capsulatum, are soil fungi that undergo dramatic changes in cell shape and virulence gene expression in...
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Zeb1 Regulates E-cadherin and Epcam (Epithelial Cell Adhesion Molecule) Expression to Control Cell Behavior in Early Zebrafish Development.
Published: June, 2013

Abstract: The ZEB1 transcription factor is best known as an inducer of epithelial-mesenchymal transitions (EMT) in cancer metastasis, acting through transcriptional repression of CDH1 (encoding E-cadherin) and the EMT-suppressing microRNA-200s (miR-200s). H...
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The genomic landscape of the somatic linker histone subtypes h1.1 to h1.5 in human cells.
Published: June, 2013

Abstract: Human cells contain five canonical, replication-dependent somatic histone H1 subtypes (H1.1, H1.2, H1.3, H1.4, and H1.5). Although they are key chromatin components, the genomic distribution of the H1 subtypes is still unknown, and their role in c...
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Status epilepticus triggers early and late alterations in brain-derived neurotrophic factor and NMDA glutamate receptor Grin2b DNA methylation levels in the hippocampus.
Published: June, 2013

Abstract: Status epilepticus (SE) triggers abnormal expression of genes in the hippocampus, such as glutamate receptor subunit epsilon-2 (Grin2b/Nr2b) and brain-derived neurotrophic factor (Bdnf), that is thought to occur in temporal lobe epilepsy (TLE). We...
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Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo.
Published: June, 2013

Abstract: Developmental regulatory genes have both activating (H3K4me3) and repressive (H3K27me3) histone modifications in embryonic stem cells (ESCs). This bivalent configuration is thought to maintain lineage commitment programs in a poised state. However...
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PLK1 signaling in breast cancer cells cooperates with estrogen receptor-dependent gene transcription.
Published: June, 2013

Abstract: Polo-like kinase 1 (PLK1) is a key regulator of cell division and is overexpressed in many types of human cancers. Compared to its well-characterized role in mitosis, little is known about PLK1 functions in interphase. Here, we report that PLK1 me...
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Cbl-b mediates TGFβ sensitivity by downregulating inhibitory SMAD7 in primary T cells.
Published: June, 2013

Abstract: T cell-intrinsic transforming growth factor β (TGFβ) receptor signaling plays an essential role in controlling immune responses. The RING-type E3 ligase Cbl-b has been shown to mediate the sensitivity of T cells to TGFβ; however, the mechanism und...
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LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data.
Published: June, 2013

Abstract: One big limitation of computational tools for analyzing ChIP-seq data is that most of them ignore non-unique tags (NUTs) that match the human genome even though NUTs comprise up to 60% of all raw tags in ChIP-seq data. Effectively utilizing these ...
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The Role of SIRT6 Protein in Aging and Reprogramming of Human Induced Pluripotent Stem Cells.
Published: June, 2013

Abstract: Aging is known to be the single most important risk factor for multiple diseases. Sirtuin 6, or SIRT6, has recently been identified as a critical regulator of transcription, genome stability, telomere integrity, DNA repair, and metabolic homeostas...
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Epigenetic regulation of microRNA expression in renal cell carcinoma.
Published: June, 2013

Abstract: The underlying mechanisms of microRNA deregulation in cancer cells include epigenetic modifications, which play a crucial role in carcinogenesis. We demonstrate that numerous microRNAs are induced in renal cell carcinoma cell lines after treatment...
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Jpx RNA activates Xist by evicting CTCF.
Published: June, 2013

Abstract: In mammals, dosage compensation between XX and XY individuals occurs through X chromosome inactivation (XCI). The noncoding Xist RNA is expressed and initiates XCI only when more than one X chromosome is present. Current models invoke a dependency...
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Improved genetic testing for monogenic diabetes using targeted next-generation sequencing.
Published: June, 2013

Abstract: AIMS/HYPOTHESIS: Current genetic tests for diagnosing monogenic diabetes rely on selection of the appropriate gene for analysis according to the patient's phenotype. Next-generation sequencing enables the simultaneous analysis of multiple genes in...
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Myc binds the pluripotency factor Utf1 through the basic-helix-loop-helix leucine zipper domain.
Published: June, 2013

Abstract: In order to elucidate the function of Myc in the maintenance of pluripotency and self-renewal in mouse embryonic stem cells (mESCs), we screened for novel ESC-specific interactors of Myc by mass spectrometry. Undifferentiated embryonic cell transc...
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Senescence-associated lncRNAs: senescence-associated long noncoding RNAs.
Published: June, 2013

Abstract: Noncoding RNAs include small transcripts, such as microRNAs and piwi-interacting RNAs, and a wide range of long noncoding RNAs (lncRNAs). Although many lncRNAs have been identified, only a small number of lncRNAs have been characterized functional...
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Distinct Roles for CBP and p300 on the RA-Mediated Expression of the Meiosis Commitment Gene Stra8 in Mouse Embryonic Stem Cells.
Published: June, 2013

Abstract: In mammalian germ cells, meiotic commitment requires the expression of Stimulated by retinoic acid gene 8 (Stra8), which is transcriptionally activated by retinoic acid (RA). However, little is known about the epigenetic mechanism by which RA indu...
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The histone deacetylase inhibitor SAHA acts in synergism with fenretinide and doxorubicin to control growth of rhabdoid tumor cells.
Published: June, 2013

Abstract: BACKGROUND: Rhabdoid tumors are highly aggressive malignancies affecting infants and very young children. In many instances these tumors are resistant to conventional type chemotherapy necessitating alternative approaches. METHODS: Proliferation a...
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Choroid-plexus-derived Otx2 homeoprotein constrains adult cortical plasticity.
Published: June, 2013

Abstract: Brain plasticity is often restricted to critical periods in early life. Here, we show that a key regulator of this process in the visual cortex, Otx2 homeoprotein, is synthesized and secreted globally from the choroid plexus. Consequently, Otx2 is...
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Centromere binding and a conserved role in chromosome stability for SUMO-dependent ubiquitin ligases.
Published: June, 2013

Abstract: The Saccharomyces cerevisiae Slx5/8 complex is the founding member of a recently defined class of SUMO-targeted ubiquitin ligases (STUbLs). Slx5/8 has been implicated in genome stability and transcription, but the precise contribution is unclear. ...
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Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis
Published: June, 2013

Abstract: The gaseous plant hormone ethylene regulates a multitude of growth and developmental processes. How the numerous growth control pathways are coordinated by the ethylene transcriptional response remains elusive. We characterized the dynamic ethyle...
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Discovery of potential new gene variants and inflammatory cytokine associations with fibromyalgia syndrome by whole exome sequencing.
Published: June, 2013

Abstract: Fibromyalgia syndrome (FMS) is a chronic musculoskeletal pain disorder affecting 2% to 5% of the general population. Both genetic and environmental factors may be involved. To ascertain in an unbiased manner which genes play a role in the disorder...
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Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells.
Published: June, 2013

Abstract: BACKGROUND: In mouse embryonic stem cells (mESCs), transcriptional silencing of numerous class I and II endogenous retroviruses (ERVs), including IAP, ETn and MMERVK10C, is dependent upon the H3K9 methyltransferase (KMTase) SETDB1/ESET and its bin...
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Autolysosomal β-catenin degradation regulates Wnt-autophagy-p62 crosstalk
Published: June, 2013

Abstract: The Wnt/β-catenin signalling and autophagy pathways each play important roles during development, adult tissue homeostasis and tumorigenesis. Here we identify the Wnt/β-catenin signalling pathway as a negative regulator of both basal and stress-in...
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HPV-related methylation signature predicts survival in oropharyngeal squamous cell carcinomas.
Published: June, 2013

Abstract: High-risk types of human papilloma virus (HPV) are increasingly associated with oropharyngeal squamous cell carcinoma (OPSCC). Strikingly, patients with HPV-positive OPSCC are highly curable with ionizing radiation and have better survival compare...
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Nuclear receptor/microRNA circuitry links muscle fiber type to energy metabolism.
Published: June, 2013

Abstract: The mechanisms involved in the coordinate regulation of the metabolic and structural programs controlling muscle fitness and endurance are unknown. Recently, the nuclear receptor PPARβ/δ was shown to activate muscle endurance programs in transgeni...
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Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data.
Published: June, 2013

Abstract: In this study, we used restriction site-associated DNA (RAD) sequencing to discover SNP markers suitable for population genetic and parentage analysis with the aim of using them for monitoring the reintroduction of the Eurasian beaver (Castor fibr...
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The Glucocorticoid Receptor and KLF15 Regulate Gene Expression Dynamics and Integrate Signals through Feed-Forward Circuitry.
Published: June, 2013

Abstract: The glucocorticoid receptor (GR) regulates adaptive transcriptional programs that alter metabolism in response to stress. Network properties that allow GR to tune gene expression to match specific physiologic demands are poorly understood. We anal...
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Functional dissection of the PROPEP2 and PROPEP3 promoters reveals the importance of WRKY factors in mediating microbe-associated molecular pattern-induced expression.
Published: June, 2013

Abstract: · In Arabidopsis thaliana, small peptides (AtPeps) encoded by PROPEP genes act as damage-associated molecular patterns (DAMPs) that are perceived by two leucine-rich repeat receptor kinases, PEPR1 and PEPR2, to amplify defense responses. In partic...
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A new strategy for selective targeting of progesterone receptor with passive antagonists.
Published: June, 2013

Abstract: Currently available progesterone (P4) receptor (PR) antagonists, such as mifepristone (RU486), lack specificity and display partial agonist properties, leading to potential drawbacks in their clinical use. Recent x-ray crystallographic studies hav...
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Partial functional redundancy between Hoxa5 and Hoxb5 paralog genes during lung morphogenesis.
Published: June, 2013

Abstract: Hox genes encode transcription factors governing complex developmental processes in several organs. A subset of Hox genes are expressed in the developing lung. Except for Hoxa5, the lack of overt lung phenotype in single mutants suggests that Hox ...
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HOXA13 regulates Aldh1a2 expression in the autopod to facilitate interdigital programmed cell death.
Published: June, 2013

Abstract: Background: Retinoic acid (RA), plays an essential role in the growth and patterning of vertebrate limb. While the developmental processes regulated by RA are well understood, little is known about the transcriptional mechanisms required to precis...
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Dynamic changes in 5-hydroxymethylation signatures underpin early and late events in drug exposed liver.
Published: June, 2013

Abstract: Aberrant DNA methylation is a common feature of neoplastic lesions, and early detection of such changes may provide powerful mechanistic insights and biomarkers for carcinogenesis. Here, we investigate dynamic changes in the mouse liver DNA methyl...
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A novel role for Sem1 and TREX-2 in transcription involves their impact on recruitment and H2B deubiquitylation activity of SAGA.
Published: June, 2013

Abstract: Transcription and mRNA export are linked processes. However, the molecular mechanisms of this coordination are not clear. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator; TREX-2...
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Measurement of phosphoinositides in the zebrafish Danio rerio.
Published: June, 2013

Abstract: Phosphoinositides represent a minor fraction of the total glycerolipids in cells. Despite the fact that phosphoinositides are present in small quantities, they have crucial roles during cell signaling and in regulating numerous intracellular proce...
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Protective role of functionalized single walled carbon nanotubes enhance ex vivo expansion of hematopoietic stem and progenitor cells in human umbilical cord blood.
Published: June, 2013

Abstract: In this study, carboxylic acid functionalized single walled carbon nanotubes (f-SWCNT-COOH) was shown to support the viability and ex vivo expansion of freeze-thawed, non-enriched hematopoietic stem and progenitor cells (HSPC) in human umbilical c...
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Histone acetyl transferase 1 is essential for mammalian development, genome stability, and the processing of newly synthesized histones H3 and H4.
Published: June, 2013

Abstract: Histone acetyltransferase 1 is an evolutionarily conserved type B histone acetyltransferase that is thought to be responsible for the diacetylation of newly synthesized histone H4 on lysines 5 and 12 during chromatin assembly. To understand the fu...
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Characterization of the DNA methylome and its interindividual variation in human peripheral blood monocytes.
Published: June, 2013

Abstract: AIM: Peripheral blood monocytes (PBMs) play multiple and critical roles in the immune response, and abnormalities in PBMs have been linked to a variety of human disorders. However, the DNA methylation landscape in PBMs is largely unknown. In this ...
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Enhanced infra-red emission from sub-millimeter microelectromechanical systems micro hotplates via inkjet deposited carbon nanoparticles and fullerenes
Published: June, 2013

Abstract: In this paper, we demonstrate a micro-inkjet printing technique as a reproducible post-process for the deposition of carbon nanoparticles and fullerene adlayers onto fully CMOS compatible micro-electro-mechanical silicon-on-insulator infrared (IR)...
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Vitamin D induces interleukin-1β expression: paracrine macrophage epithelial signaling controls M. tuberculosis infection.
Published: June, 2013

Abstract: Although vitamin D deficiency is a common feature among patients presenting with active tuberculosis, the full scope of vitamin D action during Mycobacterium tuberculosis (Mtb) infection is poorly understood. As macrophages are the primary site of...
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Bcl11a controls Flt3 expression in early hematopoietic progenitors and is required for pDC development in vivo.
Published: May, 2013

Abstract: Bcl11a is a transcription factor known to regulate lymphoid and erythroid development. Recent bioinformatic analysis of global gene expression patterns has suggested a role for Bcl11a in the development of dendritic cell (DC) lineages. We tested t...
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KDM4B is a Master Regulator of the Estrogen Receptor Signalling Cascade.
Published: May, 2013

Abstract: The importance of the estrogen receptor (ER) in breast cancer (BCa) development makes it a prominent target for therapy. Current treatments, however, have limited effectiveness, and hence the definition of new therapeutic targets is vital. The ER ...
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CREB phosphorylation regulates striatal transcriptional responses in the self-administration model of methamphetamine addiction in the rat.
Published: May, 2013

Abstract: Neuroplastic changes in the dorsal striatum participate in the transition from casual to habitual drug use and might play a critical role in the development of methamphetamine (METH) addiction. We examined the influence of METH self-administration...
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N-linked glycosylation supports cross-talk between receptor tyrosine kinases and androgen receptor.
Published: May, 2013

Abstract: Prostate cancer is the second most common cause of cancer-associated deaths in men and signalling via a transcription factor called androgen receptor (AR) is an important driver of the disease. Androgen treatment is known to affect the expression ...
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Recombination-Induced Tag Exchange (RITE) Cassette Series to Monitor Protein Dynamics in Saccharomyces cerevisiae.
Published: May, 2013

Abstract: Proteins are not static entities. They are highly mobile, and their steady-state levels are achieved by a balance between ongoing synthesis and degradation. The dynamic properties of a protein can have important consequences for its function. For ...
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Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis.
Published: May, 2013

Abstract: Maintaining proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. We demonstrate that most yeast mRNAs are degraded by the cytoplasmic 5'-to-3' pathway (the "...
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Global regulation of promoter melting in naive lymphocytes.
Published: May, 2013

Abstract: Lymphocyte activation is initiated by a global increase in messenger RNA synthesis. However, the mechanisms driving transcriptome amplification during the immune response are unknown. By monitoring single-stranded DNA genome wide, we show that the...
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Bcl6a function is required during optic cup formation to prevent p53-dependent apoptosis and colobomata.
Published: May, 2013

Abstract: Mutations in BCOR (Bcl6 corepressor) are found in patients with oculo-facio-cardio-dental (OFCD) syndrome, a congenital disorder affecting visual system development, and loss-of-function studies in zebrafish and Xenopus demonstrate a role for Bcor...
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Ptc6 Is required for proper rapamycin-induced down-regulation of the genes coding for ribosomal and rRNA processing proteins in S. cerevisiae.
Published: May, 2013

Abstract: Ptc6 is one of the seven components (Ptc1-Ptc7) of the protein phosphatase 2C family in the yeast Saccharomyces cerevisiae. In contrast to other type 2C phosphatases, the cellular role of this isoform is poorly understood. We present here a compre...
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The co-repressor SMRT delays DNA damage-induced caspase activation by repressing pro-apoptotic genes and modulating the dynamics of checkpoint kinase 2 activation.
Published: May, 2013

Abstract: Checkpoint kinase 2 (Chk2) is a major regulator of DNA damage response and can induce alternative cellular responses: cell cycle arrest and DNA repair or programmed cell death. Here, we report the identification of a new role of Chk2 in transcript...
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Role of estrogen receptor α and β in the induction of progesterone receptors in hypothalamic ventromedial neurons.
Published: May, 2013

Abstract: The estrogen induction of progesterone receptors (PRs) in the ventrolateral division of the hypothalamic ventromedial nucleus (VMNvl) is critical for the regulation of female sexual behavior. VMNvl neurons express PRs and both types of estrogen re...
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Overexpression of facioscapulohumeral muscular dystrophy region gene 1 causes primary defects in myogenic stem cells.
Published: May, 2013

Abstract: Overexpression of facioscapulohumeral muscular dystrophy region gene 1 (FRG1) in mice, frogs and worms leads to muscular and vascular abnormalities. Nevertheless, the mechanism that follows FRG1 overexpression and finally leads to muscular defects...
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Polycomb subunits Ezh1 and Ezh2 regulate the Merkel cell differentiation program in skin stem cells
Published: May, 2013

Abstract: While the Polycomb complex is known to regulate cell identity in ES cells, its role in controlling tissue-specific stem cells is not well understood. Here we show that removal of Ezh1 and Ezh2, key Polycomb subunits, from mouse skin results in a m...
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SUMOylation of the Farnesoid X Receptor (FXR) Regulates the Expression of FXR Target Genes.
Published: May, 2013

Abstract: The farnesoid X receptor (FXR) belongs to a family of ligand-activated transcription factors that regulate many aspects of metabolism including bile acid homeostasis. Here we show that FXR is covalently modified by the small ubiquitin-like modifie...
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Androgen-responsive Serum Response Factor target genes regulate prostate cancer cell migration.
Published: May, 2013

Abstract: Progression of prostate cancer (CaP) relies on androgen receptor (AR) signaling, but AR-dependent events that underlie the lethal phenotype remain unknown. Recently, an indirect mechanism of androgen action in which effects of AR on CaP cells are ...
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Homeostasis in intestinal epithelium is orchestrated by the circadian clock and microbiota cues transduced by TLRs.
Published: May, 2013

Abstract: Alterations of symbiosis between microbiota and intestinal epithelial cells (IEC) are associated with intestinal and systemic pathologies. Interactions between bacterial products (MAMPs) and Toll-like receptors (TLRs) are known to be mandatory for...
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LIN9, a subunit of the DREAM complex, regulates mitotic gene expression and proliferation of embryonic stem cells.
Published: May, 2013

Abstract: The DREAM complex plays an important role in regulation of gene expression during the cell cycle. We have previously shown that the DREAM subunit LIN9 is required for early embryonic development and for the maintenance of the inner cell mass in vi...
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Sirt1 ablation promotes stress-induced loss of epigenetic and genomic hematopoietic stem and progenitor cell maintenance.
Published: May, 2013

Abstract: The (histone) deacetylase Sirt1 is a mediator of genomic and epigenetic maintenance, both of which are critical aspects of stem cell homeostasis and tightly linked to their functional decline in aging and disease. We show that Sirt1 ablation in ad...
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Transcriptional regulation of insulin-degrading enzyme modulates mitochondrial amyloid β (Aβ) peptide catabolism and functionality.
Published: May, 2013

Abstract: Studies of post-mortem brains from Alzheimer disease patients suggest that oxidative damage induced by mitochondrial amyloid β (mitAβ) accumulation is associated with mitochondrial dysfunction. However, the regulation of mitAβ metabolism is unknow...
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Estrogen-dependent dynamic profile of eNOS-DNA associations in prostate cancer.
Published: May, 2013

Abstract: In previous work we have documented the nuclear translocation of endothelial NOS (eNOS) and its participation in combinatorial complexes with Estrogen Receptor Beta (ERβ) and Hypoxia Inducible Factors (HIFs) that determine localized chromatin remo...
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Region of difference 4 in alpine Mycobacterium caprae isolates indicates three variants.
Published: May, 2013

Abstract: The lack of complete genome sequence information for Mycobacterium caprae complicates a robust differentiation of M. caprae and Mycobacterium bovis. In this study, the presence or absence of M. caprae-specific single nucleotide polymorphisms in le...
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Sulforaphane enhances Nrf2 expression in prostate cancer TRAMP C1 cells through epigenetic regulation.
Published: May, 2013

Abstract: Growing evidence suggests epigenetic alteration is involved during the development and progression of prostate cancer. Previously, we found Nrf2, a key regulator of cellular antioxidant defense systems, was silenced through epigenetic mechanism du...
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Epigenetic regulation of cholinergic receptor M1 (CHRM1) by histone H3K9me3 impairs Ca(2+) signaling in Huntington's disease.
Published: May, 2013

Abstract: Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by an expanded trinucleotide CAG repeat in the gene coding for huntingtin. Deregulation of chromatin remodeling is linked to the pathogenesis of HD but the mechani...
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Developmentally programmed 3' CpG island methylation confers tissue- and cell-type-specific transcriptional activation.
Published: May, 2013

Abstract: During development, a small but significant number of CpG islands (CGIs) become methylated. The timing of developmentally programmed CGI methylation and associated mechanisms of transcriptional regulation during cellular differentiation, however, ...
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Use of red autofluorescence for monitoring prodiginine biosynthesis.
Published: May, 2013

Abstract: Prodigiosin-like pigments or prodiginines (PdGs) are promising drugs owing to their reported antitumor, antibiotic, and immunosuppressive activities. These natural compounds are produced by several bacteria, including Streptomyces coelicolor and S...
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Epigenetic changes in renal genes dysregulated in mouse and rat models of type 1 diabetes.
Published: May, 2013

Abstract: Epigenetic processes are increasingly being recognized as factors in the pathophysiology of diabetes complications, but few chromatin studies have been done in diabetic nephropathy (DN). We hypothesized that changes in mRNA expression of DN-relate...
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G9a is transactivated by C/EBPβ to facilitate mitotic clonal expansion during 3T3-L1 preadipocyte differentiation.
Published: May, 2013

Abstract: In 3T3-L1 preadipocyte differentiation, the CCAAT/enhancer-binding protein-β (C/EBPβ) is an important early transcription factor that activates cell cycle genes during mitotic clonal expansion (MCE), sequentially activating peroxisome proliferator...
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The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits.
Published: May, 2013

Abstract: Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth and malignant disease such as cancer, also appeared several times independently in lower vertebrates. The genetic mechanisms underlyin...
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A Common histone modification code on C4 genes in maize and its conservation in Sorghum and Setaria italica.
Published: May, 2013

Abstract: C4 photosynthesis evolved more than 60 times independently in different plant lineages. Each time, multiple genes were recruited into C4 metabolism. The corresponding promoters acquired new regulatory features such as high expression, light induct...
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Satb1 regulates the self-renewal of hematopoietic stem cells by promoting quiescence and repressing differentiation commitment.
Published: May, 2013

Abstract: How hematopoietic stem cells (HSCs) coordinate the regulation of opposing cellular mechanisms such as self-renewal and differentiation commitment remains unclear. Here we identified the transcription factor and chromatin remodeler Satb1 as a criti...
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Progesterone receptors induce FOXO1-dependent senescence in ovarian cancer cells.
Published: May, 2013

Abstract: Loss of nuclear progesterone receptors (PR) and low circulating progesterone levels are associated with increased ovarian cancer (OC) risk. However, PR are abundantly expressed in a significant percentage of serous and endometrioid ovarian tumors;...
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G-quadruplex structures are stable and detectable in human genomic DNA.
Published: April, 2013

Abstract: The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome for transcriptional regulation, DNA replication and genome stability, but the nature and distribution of G-quadruplexes...
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Heterochromatin protein 1 promotes self-renewal and triggers regenerative proliferation in adult stem cells
Published: April, 2013

Abstract: Adult stem cells (ASCs) capable of self-renewal and differentiation confer the potential of tissues to regenerate damaged parts. Epigenetic regulation is essential for driving cell fate decisions by rapidly and reversibly modulating gene expressio...
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Coordinate changes in histone modifications, mRNA levels, and metabolite profiles in clonal INS-1 832/13 β-cells accompany functional adaptations to lipotoxicity.
Published: April, 2013

Abstract: Lipotoxicity is a presumed pathogenetic process whereby elevated circulating and stored lipids in type 2 diabetes cause pancreatic β-cell failure. To resolve the underlying molecular mechanisms, we exposed clonal INS-1 832/13 β-cells to palmitate ...
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Balancing of histone H3K4 methylation states by the Kdm5c/SMCX histone demethylase modulates promoter and enhancer function.
Published: April, 2013

Abstract: The functional organization of eukaryotic genomes correlates with specific patterns of histone methylations. Regulatory regions in genomes such as enhancers and promoters differ in their extent of methylation of histone H3 at lysine-4 (H3K4), but ...
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A proteomic characterization of factors enriched at nascent DNA molecules.
Published: April, 2013

Abstract: DNA replication is facilitated by multiple factors that concentrate in the vicinity of replication forks. Here, we developed an approach that combines the isolation of proteins on nascent DNA chains with mass spectrometry (iPOND-MS), allowing a co...
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Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics.
Published: April, 2013

Abstract: TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by ...
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Placing the HIRA histone chaperone complex in the chromatin landscape.
Published: April, 2013

Abstract: The HIRA chaperone complex, comprised of HIRA, UBN1, and CABIN1, collaborates with histone-binding protein ASF1a to incorporate histone variant H3.3 into chromatin in a DNA replication-independent manner. To better understand HIRA's function and m...
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A vitamin D receptor/SMAD genomic circuit gates hepatic fibrotic response.
Published: April, 2013

Abstract: Liver fibrosis is a reversible wound-healing response involving TGFβ1/SMAD activation of hepatic stellate cells (HSCs). It results from excessive deposition of extracellular matrix components and can lead to impairment of liver function. Here, we ...
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Mechanism of Polycomb recruitment to CpG islands revealed by inherited disease-associated mutation.
Published: April, 2013

Abstract: How the transcription repressing complex Polycomb interacts with transcriptional regulators at housekeeping genes in somatic cells is not well understood. By exploiting a CpG island (CGI) point mutation causing a Mendelian disease, we show that DN...
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The response of human macrophages to β-glucans depends on the inflammatory milieu.
Published: April, 2013

Abstract: BACKGROUND: β-glucans are fungal cell wall components that bind to the C-type lectin-like receptor dectin-1. Polymorphisms of dectin-1 gene are associated with susceptibility to invasive fungal infection and medically refractory ulcerative colitis...
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Hypersensitive site 6 of the Th2 locus control region is essential for Th2 cytokine expression.
Published: April, 2013

Abstract: The T helper type 2 (Th2) cytokine genes Il4, Il5, and Il13 are contained within a 140-kb region of mouse chromosome 11 and their expression is controlled by a locus control region (LCR) embedded within this locus. The LCR is composed of a number ...
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The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos.
Published: April, 2013

Abstract: Genome-wide profiling of DNA methylation and histone modifications answered many questions as to how the genes are regulated on a global scale and what their epigenetic makeup is. Yet, little is known about the function of these marks during early...
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Estradiol represses the G(D3) synthase gene ST8SIA1 expression in human breast cancer cells by preventing NFκB binding to ST8SIA1 promoter.
Published: April, 2013

Abstract: Recent data have underlined a possible role of G(D3) synthase (GD3S) and complex gangliosides in Estrogen Receptor (ER) negative breast cancer progression. Here, we describe the main transcript of the GD3S coding gene ST8SIA1 expressed in breast t...
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Association between living environment and human oral viral ecology.
Published: April, 2013

Abstract: The human oral cavity has an indigenous microbiota known to include a robust community of viruses. Very little is known about how oral viruses are spread throughout the environment or to which viruses individuals are exposed. We sought to determin...
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Multiple mechanisms of action of pyridoxine in primary hyperoxaluria type 1.
Published: April, 2013

Abstract: Primary hyperoxaluria type 1 (PH1) is a rare hereditary calcium oxalate kidney stone disease caused by a deficiency of the liver-specific pyridoxal-phosphate-dependent peroxisomal enzyme alanine:glyoxylate aminotransferase (AGT). About one third o...
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Retinoic acid represses invasion and stem cell phenotype by induction of the metastasis suppressors RARRES1 and LXN.
Published: April, 2013

Abstract: The mouse haematopoietic stem cell (SC) regulator Latexin (LXN) is the only known homologue of the retinoic acid receptor responder 1 (RARRES1) gene. Both genes lie adjacent on chromosome 3 and differ mostly by the presence of a transmembrane doma...
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The histone demethylase Jmjd3 sequentially associates with the transcription factors Tbx3 and Eomes to drive endoderm differentiation
Published: April, 2013

Abstract: Stem cell differentiation depends on transcriptional activation driven by lineage-specific regulators as well as changes in chromatin organization. However, the coordination of these events is poorly understood. Here, we show that T-box proteins t...
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Exit from pluripotency is gated by intracellular redistribution of the bHLH transcription factor Tfe3.
Published: April, 2013

Abstract: Factors that sustain self-renewal of mouse embryonic stem cells (ESCs) are well described. In contrast, the machinery regulating exit from pluripotency is ill defined. In a large-scale small interfering RNA (siRNA) screen, we found that knockdown ...
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Methylation-dependent and -independent genomic targeting principles of the MBD protein family.
Published: April, 2013

Abstract: To gain insight into the cellular readout of DNA methylation, we established a strategy for systematically profiling the genome-wide distribution of chromatin-interacting factors. This enabled us to create genomic maps for the methyl-CpG-binding d...
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A Culture-Independent Sequence-Based Metage nomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4
Published: April, 2013

Abstract: Importance Identification of the bacterium responsible for an outbreak can aid in disease management. However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain...
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Distinct roles for Sir2 and RNAi in centromeric heterochromatin nucleation, spreading and maintenance
Published: April, 2013

Abstract: Epigenetically regulated heterochromatin domains govern essential cellular activities. A key feature of heterochromatin domains is the presence of hypoacetylated nucleosomes, which are methylated on lysine 9 of histone H3 (H3K9me). Here, we invest...
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Acyl-CoA synthetase 1 is induced by Gram-negative bacteria and lipopolysaccharide and is required for phospholipid turnover in stimulated macrophages.
Published: April, 2013

Abstract: The enzyme acyl-CoA synthetase 1 (ACSL1) is induced by peroxisome proliferator-activated receptor α (PPARα) and PPARγ in insulin target tissues, such as skeletal muscle and adipose tissue, and plays an important role in β-oxidation in these tissue...
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Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers.
Published: April, 2013

Abstract: Analysis of 4,405 variants in 89,050 European subjects from 41 case-control studies identified three independent association signals for estrogen-receptor-positive tumors at 11q13. The strongest signal maps to a transcriptional enhancer element in...
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Utx is required for proper induction of ectoderm and mesoderm during differentiation of embryonic stem cells.
Published: April, 2013

Abstract: Embryonic development requires chromatin remodeling for dynamic regulation of gene expression patterns to ensure silencing of pluripotent transcription factors and activation of developmental regulators. Demethylation of H3K27me3 by the histone de...
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Akt kinase targets the association of CBP with histone H3 to regulate the acetylation of lysine K18.
Published: April, 2013

Abstract: CREB binding protein (CBP) is an acetyltransferase that plays an important role in many biological processes. Here, we show that Akt phosphorylates CBP at threonine 1871 and suppresses its acetyltransferase activity by impeding the binding of CBP ...
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Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells.
Published: April, 2013

Abstract: Increased physiological levels of oxysterols are major risk factors for developing atherosclerosis and cardiovascular disease. Lipid-loaded macrophages, termed foam cells, are important during the early development of atherosclerotic plaques. To p...
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A systemic transcriptome analysis reveals the regulation of neural stem cell maintenance by an E2F1-miRNA feedback loop.
Published: April, 2013

Abstract: Stem cell fate decisions are controlled by a molecular network in which transcription factors and miRNAs are of key importance. To systemically investigate their impact on neural stem cell (NSC) maintenance and neuronal commitment, we performed a ...
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Control of human adenovirus type 5 gene expression by cellular Daxx/ATRX chromatin-associated complexes.
Published: April, 2013

Abstract: Death domain-associated protein (Daxx) cooperates with X-linked α-thalassaemia retardation syndrome protein (ATRX), a putative member of the sucrose non-fermentable 2 family of ATP-dependent chromatin-remodelling proteins, acting as the core ATPas...
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Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11.
Published: April, 2013

Abstract: ZNF143 is a zinc-finger protein involved in the transcriptional regulation of both coding and non-coding genes from polymerase II and III promoters. Our study deciphers the genome-wide regulatory role of ZNF143 in relation with the two previously ...
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Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method.
Published: April, 2013

Abstract: The genome-wide distribution patterns of the '6th base' 5-hydroxymethylcytosine (5hmC) in many tissues and cells have recently been revealed by hydroxymethylated DNA immunoprecipitation (hMeDIP) followed by high throughput sequencing or tiling arr...
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Multiple functions of Kip-related protein5 connect endoreduplication and cell elongation.
Published: April, 2013

Abstract: Despite considerable progress in our knowledge regarding the cell cycle inhibitor of the Kip-related protein (KRP) family in plants, less is known about the coordination of endoreduplication and cell differentiation. In animals, the role of cyclin...
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A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells.
Published: April, 2013

Abstract: PTEN is a tumor-suppressor gene that has been shown to be under the regulatory control of a PTEN pseudogene expressed noncoding RNA, PTENpg1. Here, we characterize a previously unidentified PTENpg1-encoded antisense RNA (asRNA), which regulates PT...
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Duration of fecal shedding of Shiga toxin-producing Escherichia coli O104:H4 in patients infected during the 2011 outbreak in Germany: a multicenter study.
Published: April, 2013

Abstract: BACKGROUND: In May-July 2011, Germany experienced a large food-borne outbreak of Shiga toxin 2-producing Escherichia coli (STEC O104:H4) with 3842 cases, including 855 cases with hemolytic uremic syndrome (HUS) and 53 deaths. METHODS: A multicente...
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De novo sequencing of hazelnut bacterial artificial chromosomes (BACs) using multiplex Illumina sequencing and targeted marker development for eastern filbert blight resistance
Published: April, 2013

Abstract: Bacterial artificial chromosome (BAC) libraries are widely used in map-based cloning of plant genes. Eastern filbert blight (EFB), caused by the pyrenomycete Anisogramma anomala (Peck) E. Müller, is a devastating disease of European hazelnut (Cory...
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Epigenetic and molecular signature of human umbilical cord blood-derived neural stem cell (HUCB-NSC) neuronal differentiation.
Published: April, 2013

Abstract: In the context of cell therapy, the epigenetic status of core stemness transcription factor (STF) genes regulating the cell proliferation/differentiation program is of primary interest. Our results confirmed that in vitro differentiation of the um...
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Epigenetic upregulation of lncRNAs at 13q14.3 in leukemia is linked to the In Cis downregulation of a gene cluster that targets NF-kB.
Published: April, 2013

Abstract: Non-coding RNAs are much more common than previously thought. However, for the vast majority of non-coding RNAs, the cellular function remains enigmatic. The two long non-coding RNA (lncRNA) genes DLEU1 and DLEU2 map to a critical region at chromo...
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Intrinsic epigenetic regulation of the D4Z4 macrosatellite repeat in a transgenic mouse model for FSHD.
Published: April, 2013

Abstract: Facioscapulohumeral dystrophy (FSHD) is a progressive muscular dystrophy caused by decreased epigenetic repression of the D4Z4 macrosatellite repeats and ectopic expression of DUX4, a retrogene encoding a germline transcription factor encoded in e...
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Multiple IRF- and NFkB-sites cooperate in mediating cell type- and maturation-specific activation of the human CD83 promoter in dendritic cells.
Published: April, 2013

Abstract: CD83 is one of the best-known surface marker for fully mature dendritic cells (DCs) and its cell type- and maturation-specific regulation makes the CD83 promoter an interesting tool for the genetic modulation of DCs. To determine the mechanisms re...
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Single-cell dynamics of genome-nuclear lamina interactions.
Published: March, 2013

Abstract: The nuclear lamina (NL) interacts with hundreds of large genomic regions termed lamina associated domains (LADs). The dynamics of these interactions and the relation to epigenetic modifications are poorly understood. We visualized the fate of LADs...
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The role of proteasome beta subunits in gastrin-mediated transcription of plasminogen activator inhibitor-2 and regenerating protein1.
Published: March, 2013

Abstract: The hormone gastrin physiologically regulates gastric acid secretion and also contributes to maintaining gastric epithelial architecture by regulating expression of genes such as plasminogen activator inhibitor 2 (PAI-2) and regenerating protein 1...
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Topoisomerase IIα promotes activation of RNA polymerase I transcription by facilitating pre-initiation complex formation.
Published: March, 2013

Abstract: Type II DNA topoisomerases catalyse DNA double-strand cleavage, passage and re-ligation to effect topological changes. There is considerable interest in elucidating topoisomerase II roles, particularly as these proteins are targets for anti-cancer...
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Epigenetic reactivation of Nrf2 in murine prostate cancer TRAMP C1 cells by natural phytochemicals Z-ligustilide and Radix angelica sinensis via promoter CpG demethylation.
Published: March, 2013

Abstract: Cancer development has been linked to epigenetic modifications of cancer oncogenes and tumor suppressor genes; in advanced metastatic cancers, severe epigenetic modifications are present. We previously demonstrated that the progression of prostate...
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The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors.
Published: March, 2013

Abstract: We recently reported that Drosophila Insensitive (Insv) promotes sensory organ development and has activity as a nuclear corepressor for the Notch transcription factor Suppressor of Hairless [Su(H)]. Insv lacks domains of known biochemical functio...
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Fission yeast CSL proteins function as transcription factors.
Published: March, 2013

Abstract: BACKGROUND: Transcription factors of the CSL (CBF1/RBP-Jk/Suppressor of Hairless/LAG-1) family are key regulators of metazoan development and function as the effector components of the Notch receptor signalling pathway implicated in various cell f...
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PRC1 coordinates timing of sexual differentiation of female primordial germ cells.
Published: March, 2013

Abstract: In mammals, sex differentiation of primordial germ cells (PGCs) is determined by extrinsic cues from the environment. In mouse female PGCs, expression of stimulated by retinoic acid gene 8 (Stra8) and meiosis are induced in response to retinoic ac...
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Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution.
Published: March, 2013

Abstract: Despite extensive genetic analysis, the evolutionary relationship between polar bears (Ursus maritimus) and brown bears (U. arctos) remains unclear. The two most recent comprehensive reports indicate a recent divergence with little subsequent admi...
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CPEB1 coordinates alternative 3'-UTR formation with translational regulation.
Published: March, 2013

Abstract: More than half of mammalian genes generate multiple messenger RNA isoforms that differ in their 3' untranslated regions (3' UTRs) and therefore in regulatory sequences, often associated with cell proliferation and cancer; however, the mechanisms c...
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Shift from extracellular signal-regulated kinase to AKT/cAMP response element-binding protein pathway increases survival-motor-neuron expression in spinal-muscular-atrophy-like mice and patient cells.
Published: March, 2013

Abstract: Spinal muscular atrophy (SMA), a recessive neurodegenerative disease, is characterized by the selective loss of spinal motor neurons. No available therapy exists for SMA, which represents one of the leading genetic causes of death in childhood. SM...
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Epigenetic hierarchy within the MAGEA1 cancer-germline gene: promoter DNA methylation dictates local histone modifications.
Published: March, 2013

Abstract: Gene MAGEA1 belongs to a group of human germline-specific genes that rely on DNA methylation for repression in somatic tissues. Many of these genes, termed cancer-germline (CG) genes, become demethylated and activated in a wide variety of tumors, ...
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Acetylation limits 53BP1 association with damaged chromatin to promote homologous recombination.
Published: March, 2013

Abstract: The pathogenic sequelae of BRCA1 mutation in human and mouse cells are mitigated by concomitant deletion of 53BP1, which binds histone H4 dimethylated at Lys20 (H4K20me2) to promote nonhomologous end joining, suggesting that a balance between BRCA...
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H2A.Z and H2B.Z double-variant nucleosomes define intergenic regions and dynamically occupy var gene promoters in the malaria parasite Plasmodium falciparum.
Published: March, 2013

Abstract: Histone variants are important components of eukaryotic chromatin and can alter chromatin structure to confer specialized functions. H2B variant histones are rare in nature but have evolved independently in the phyla Apicomplexa and Trypanasomatid...
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Myod and H19-Igf2 locus interactions are required for diaphragm formation in the mouse.
Published: March, 2013

Abstract: The myogenic regulatory factor Myod and insulin-like growth factor 2 (Igf2) have been shown to interact in vitro during myogenic differentiation. In order to understand how they interact in vivo, we produced double-mutant mice lacking both the Myo...
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Chromatin immunoprecipitation of adult murine cardiomyocytes.
Published: March, 2013

Abstract: This unit describes a streamlined two-step protocol for the isolation of adult murine cardiomyocytes with subsequent Chromatin ImmunoPrecipitation (ChIP). Isolation and culturing of cardiomyocytes is a delicate process and the protocol presented h...
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Genome-wide control of RNA polymerase II activity by cohesin.
Published: March, 2013

Abstract: Cohesin is a well-known mediator of sister chromatid cohesion, but it also influences gene expression and development. These non-canonical roles of cohesin are not well understood, but are vital: gene expression and development are altered by mode...
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Activating RNAs associate with Mediator to enhance chromatin architecture and transcription.
Published: February, 2013

Abstract: Recent advances in genomic research have revealed the existence of a large number of transcripts devoid of protein-coding potential in multiple organisms. Although the functional role for long non-coding RNAs (lncRNAs) has been best defined in epi...
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H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation.
Published: February, 2013

Abstract: Histone modifications regulate chromatin-dependent processes, yet the mechanisms by which they contribute to specific outcomes remain unclear. H3K4me3 is a prominent histone mark that is associated with active genes and promotes transcription thro...
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H2-independent growth of the hydrogenotrophic methanogen Methanococcus maripaludis.
Published: February, 2013

Abstract: UNLABELLED: Hydrogenotrophic methanogenic Archaea require reduced ferredoxin as an anaplerotic source of electrons for methanogenesis. H(2) oxidation by the hydrogenase Eha provides these electrons, consistent with an H(2) requirement for growth. ...
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Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor.
Published: February, 2013

Abstract: Estrogen receptor-α (ER) is the driving transcription factor in most breast cancers, and its associated proteins can influence drug response, but direct methods for identifying interacting proteins have been limited. We purified endogenous ER usin...
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SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state.
Published: February, 2013

Abstract: SOX2 is a master regulator of both pluripotent embryonic stem cells (ESCs) and multipotent neural progenitor cells (NPCs); however, we currently lack a detailed understanding of how SOX2 controls these distinct stem cell populations. Here we show ...
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Mitochondrial phylogenomics of modern and ancient equids.
Published: February, 2013

Abstract: The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated...
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Polycomb domain formation depends on short and long distance regulatory cues.
Published: February, 2013

Abstract: BACKGROUND: Polycomb group (PcG) proteins dynamically define cellular identities through the epigenetic repression of key developmental genes. In Drosophila, cis-regulatory regions termed PcG response elements (PREs) act as nucleation sites for Pc...
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Inhibition of neural crest formation by Kctd15 involves regulation of transcription factor AP-2.
Published: February, 2013

Abstract: The neural crest develops in vertebrate embryos within a discrete domain at the neural plate boundary and eventually gives rise to a migrating population of cells that differentiate into a multitude of derivatives. We have shown that the broad-com...
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ARCH domain of XPD, an anchoring platform for CAK that conditions TFIIH DNA repair and transcription activities.
Published: February, 2013

Abstract: The xeroderma pigmentosum group D (XPD) helicase is a subunit of transcription/DNA repair factor, transcription factor II H (TFIIH) that catalyzes the unwinding of a damaged DNA duplex during nucleotide excision repair. Apart from two canonical he...
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Multiple roles for Piwi in silencing Drosophila transposons.
Published: February, 2013

Abstract: Silencing of transposons in the Drosophila ovary relies on three Piwi family proteins--Piwi, Aubergine (Aub), and Ago3--acting in concert with their small RNA guides, the Piwi-interacting RNAs (piRNAs). Aub and Ago3 are found in the germ cell cyto...
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Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer.
Published: February, 2013

Abstract: Histone modifications are key regulators of chromatin function. However, little is known to what extent histone modifications can directly impact on chromatin. Here, we address how a modification within the globular domain of histones regulates ch...
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Krüppel-like factor 2 is required for normal mouse cardiac development.
Published: February, 2013

Abstract: Krüppel-like factor 2 (KLF2) is expressed in endothelial cells in the developing heart, particularly in areas of high shear stress, such as the atrioventricular (AV) canal. KLF2 ablation leads to myocardial thinning, high output cardiac failure an...
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Identification of thyroid hormone response elements in vivo using mice expressing a tagged thyroid hormone receptor alpha 1.
Published: February, 2013

Abstract: Thyroid hormone receptor alpha 1 (TRα1) is well recognized for its importance in brain development. However, due to the difficulties in predicting thyroid hormone response elements (TREs) in silico and the lack of suitable antibodies against TRα1 ...
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SUMOylation of the inducible (c-Fos:c-Jun)/AP-1 transcription complex occurs on target promoters to limit transcriptional activation.
Published: February, 2013

Abstract: The inducible proto-oncogenic (c-Fos:c-Jun)/AP-1 transcription complex binds 12-O-tetradecanoylphorbol 13-acetate (TPA)-responsive elements (TRE) in its target genes. It is tightly controlled at multiple levels to avoid the deleterious effects of ...
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DNA methylation analysis in the intestinal epithelium-effect of cell separation on gene expression and methylation profile.
Published: February, 2013

Abstract: BACKGROUND: Epigenetic signatures are highly cell type specific. Separation of distinct cell populations is therefore desirable for all epigenetic studies. However, to date little information is available on whether separation protocols might infl...
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Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.
Published: February, 2013

Abstract: Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We...
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DNA methylation mediated control of gene expression is critical for development of crown gall tumors.
Published: February, 2013

Abstract: Crown gall tumors develop after integration of the T-DNA of virulent Agrobacterium tumefaciens strains into the plant genome. Expression of the T-DNA-encoded oncogenes triggers proliferation and differentiation of transformed plant cells. Crown ga...
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Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli.
Published: February, 2013

Abstract: Bacterial populations have a remarkable capacity to cope with extreme environmental fluctuations in their natural environments. In certain cases, adaptation to one stressful environment provides a fitness advantage when cells are exposed to a seco...
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Direct molecular regulation of the myogenic determination gene Myf5 by Pax3, with modulation by Six1/4 factors, is exemplified by the -111kb-Myf5 enhancer.
Published: February, 2013

Abstract: The Myf5 gene plays an important role in myogenic determination during mouse embryo development. Multiple genomic regions of the Mrf4-Myf5 locus have been characterized as enhancer sequences responsible for the complex spatiotemporal expression of...
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Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling.
Published: February, 2013

Abstract: Cellular signal transduction generally involves cascades of post-translational protein modifications that rapidly catalyze changes in protein-DNA interactions and gene expression. High-throughput measurements are improving our ability to study eac...
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Histone lysine trimethylation or acetylation can be modulated by phytoestrogen, estrogen or anti-HDAC in breast cancer cell lines.
Published: February, 2013

Abstract: AIM: The isoflavones genistein, daidzein and equol (daidzein metabolite) have been reported to interact with epigenetic modifications, specifically hypermethylation of tumor suppressor genes. The objective of this study was to analyze and understa...
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Bifurcation of Arabidopsis NLR immune signaling via Ca²⁺-dependent protein kinases.
Published: January, 2013

Abstract: Nucleotide-binding domain leucine-rich repeat (NLR) protein complexes sense infections and trigger robust immune responses in plants and humans. Activation of plant NLR resistance (R) proteins by pathogen effectors launches convergent immune respo...
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The Function of the Conserved Regulatory Element within the Second Intron of the Mammalian Csf1r Locus
Published: January, 2013

Abstract: The gene encoding the receptor for macrophage colony-stimulating factor (CSF-1R) is expressed exclusively in cells of the myeloid lineages as well as trophoblasts. A conserved element in the second intron, Fms-Intronic Regulatory Element (FIRE), i...
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LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation.
Published: January, 2013

Abstract: Eukaryotic cells have a layer of heterochromatin at the nuclear periphery. To investigate mechanisms regulating chromatin distribution, we analyzed heterochromatin organization in different tissues and species, including mice with mutations in the...
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Interplay between KLF4 and ZEB2/SIP1 in the regulation of E-cadherin expression
Published: January, 2013

Abstract: E-cadherin expression is repressed by ZEB2/SIP1 while it is induced by KLF4. Independent data from the literature indicate that these two transcription factors could bind close to each other in the proximal region of the E-cadherin gene promoter. ...
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Global Changes in the Mammary Epigenome Are Induced by Hormonal Cues and Coordinated by Ezh2.
Published: January, 2013

Abstract: The mammary epithelium is a dynamic, highly hormone-responsive tissue. To explore chromatin modifications underlying its lineage specification and hormone responsiveness, we determined genome-wide histone methylation profiles of mammary epithelial...
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Specificity and Function of Archaeal DNA Replication Initiator Proteins.
Published: January, 2013

Abstract: Chromosomes with multiple DNA replication origins are a hallmark of Eukaryotes and some Archaea. All eukaryal nuclear replication origins are defined by the origin recognition complex (ORC) that recruits the replicative helicase MCM(2-7) via Cdc6 ...
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Identification of Transcription factors and Co-activators Affected by Dibutyl Phthalate Interactions in Fetal Rat Testes.
Published: January, 2013

Abstract: Previous analysis of in utero dibutylphthalate (DBP)-exposed fetal rat testes indicated that DBP's anti-androgenic effects were mediated in part by indirect inhibition of SF1 suggesting that PPARα might be involved through coactivtor (CBP) sequest...
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Notch pathway activation targets AML-initiating cell homeostasis and differentiation.
Published: January, 2013

Abstract: Notch signaling pathway activation is known to contribute to the pathogenesis of a spectrum of human malignancies, including T cell leukemia. However, recent studies have implicated the Notch pathway as a tumor suppressor in myeloproliferative neo...
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Cell Cycle-Dependent Recruitment of Polycomb Proteins to the ASNS Promoter Counteracts C/ebp-Mediated Transcriptional Activation in Bombyx mori
Published: January, 2013

Abstract: Epigenetic modifiers and transcription factors contribute to developmentally programmed gene expression. Here, we establish a functional link between epigenetic regulation by Polycomb group (PcG) proteins and transcriptional regulation by C/ebp th...
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Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA.
Published: January, 2013

Abstract: How a more plastic chromatin state is maintained and reversed during development is unknown. Heterochromatin-mediated silencing of repetitive elements occurs in differentiated cells. Here, we used repetitive elements, including retrotransposons, a...
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Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes.
Published: January, 2013

Abstract: While most transcription factors exit the chromatin during mitosis and the genome becomes silent, a subset of factors remains and "bookmarks" genes for rapid reactivation as cells progress through the cell cycle. However, it is unknown whether suc...
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Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics.
Published: January, 2013

Abstract: Next-generation sequencing (NGS) is emerging as an efficient and cost-effective tool in population genomic analyses of nonmodel organisms, allowing simultaneous resequencing of many regions of multi-genomic DNA from multiplexed samples. Here, we d...
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MeCP2 modulates gene expression pathways in astrocytes.
Published: January, 2013

Abstract: ABSTRACT: BACKGROUND: Mutations in MECP2 encoding methyl-CpG-binding protein 2 (MeCP2) cause the X-linked neurodevelopmental disorder Rett syndrome. Rett syndrome patients exhibit neurological symptoms that include irregular breathing, impaired mo...
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Valproic acid inhibits the proliferation of cancer cells by re-expressing cyclin D2.
Published: January, 2013

Abstract: In this study, primary murine prostate cancer (PCa) cells were derived using the well-established TRAMP model (transgenic adenocarcinoma mouse prostate). These PCa cells were treated with the histone deacetylase inhibitor (HDACi), valproic acid (V...
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An in vivo hypoxia metagene identifies the novel hypoxia inducible factor target gene SLCO1B3
Published: January, 2013

Abstract: A hypoxia-associated gene signature (metagene) was previously derived via in vivo data-mining. In this study, we aimed to investigate whether this approach could identify novel hypoxia regulated genes. From an initial list of nine genes, three wer...
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SIRT1 Positively Regulates Breast Cancer Associated Human Aromatase (CYP19A1) Expression.
Published: January, 2013

Abstract: Breast cancer remains one of the leading causes of death in women diagnosed with cancer. In breast cancer, aberrant expression of the CYP19A1 gene, which encodes the aromatase enzyme, contributes to increased intratumoral levels of estradiol. Rega...
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Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment.
Published: January, 2013

Abstract: Long noncoding RNAs (lncRNAs) are often expressed in a development-specific manner, yet little is known about their roles in lineage commitment. Here, we identified Braveheart (Bvht), a heart-associated lncRNA in mouse. Using multiple embryonic st...
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In Vivo Epigenomic Profiling of Germ Cells Reveals Germ Cell Molecular Signatures.
Published: January, 2013

Abstract: The limited number of in vivo germ cells poses an impediment to genome-wide studies. Here, we applied a small-scale chromatin immunoprecipitation sequencing (ChIP-seq) method on purified mouse fetal germ cells to generate genome-wide maps of four ...
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RUNX1 Is a Key Target in t(4;11) Leukemias that Contributes to Gene Activation through an AF4-MLL Complex Interaction.
Published: January, 2013

Abstract: The Mixed Lineage Leukemia (MLL) protein is an important epigenetic regulator required for the maintenance of gene activation during development. MLL chromosomal translocations produce novel fusion proteins that cause aggressive leukemias in human...
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Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator.
Published: January, 2013

Abstract: Because regulation of its activity is instrumental either to support cell proliferation and growth or to promote cell death, the universal myo-inositol phosphate synthase (MIPS), responsible for myo-inositol biosynthesis, is a critical enzyme of p...
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The SIRT1 Modulators AROS and DBC1 Regulate HSF1 Activity and the Heat Shock Response
Published: January, 2013

Abstract: The heat shock response, the cellular response to protein damaging stress, is critical in maintaining proteostasis. The heat shock response is regulated by the transcription factor HSF1, which is activated upon heat shock and other stresses to ind...
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Olig2 Targets Chromatin Remodelers to Enhancers to Initiate Oligodendrocyte Differentiation
Published: January, 2013

Abstract: Establishment of oligodendrocyte identity is crucial for subsequent events of myelination in the CNS. Here, we demonstrate that activation of ATP-dependent SWI/SNF chromatin-remodeling enzyme Smarca4/Brg1 at the differentiation onset is necessary ...
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Mechanism of competence activation by the ComRS signaling system in streptococci.
Published: January, 2013

Abstract: In many streptococci, competence for natural DNA transformation is regulated by the Rgg-type regulator ComR and the pheromone ComS, which is sensed intracellularly. We compared the ComRS systems of four model streptococcal species using in vitro a...
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Rapid inactivation and proteasome-mediated degradation of OGG1 contribute to the synergistic effect of hyperthermia on genotoxic treatments
Published: January, 2013

Abstract: Inhibition of DNA repair has been proposed as a mechanism underlying heat-induced sensitization of tumour cells to some anticancer treatments. Base excision repair (BER) constitutes the main pathway for the repair of DNA lesions induced by oxidizi...
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Myb-domain protein Teb1 controls histone levels and centromere assembly in fission yeast.
Published: January, 2013

Abstract: The TTAGGG motif is common to two seemingly unrelated dimensions of chromatin function-the vertebrate telomere repeat and the promoter regions of many Schizosaccharomyces pombe genes, including all of those encoding canonical histones. The essenti...
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Caspase-dependent cleavage of the mono-ADP-ribosyltransferase ARTD10 interferes with its pro-apoptotic function.
Published: January, 2013

Abstract: ADP-ribosylation is a posttranslational modification regulating various physiological processes, including DNA damage repair, gene transcription, and signal transduction. Intracellular ADP-ribosyltransferases (ARTDs or PARPs) modify their substrat...
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Pre-mRNA Splicing Is a Determinant of Nucleosome Organization
Published: January, 2013

Abstract: Chromatin organization affects alternative splicing and previous studies have shown that exons have increased nucleosome occupancy compared with their flanking introns. To determine whether alternative splicing affects chromatin organization we de...
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Dynamic Chromatin Remodeling Mediated by Polycomb Proteins Orchestrates Pancreatic Differentiation of Human Embryonic Stem Cells.
Published: January, 2013

Abstract: Embryonic development is characterized by dynamic changes in gene expression, yet the role of chromatin remodeling in these cellular transitions remains elusive. To address this question, we profiled the transcriptome and select chromatin modifica...
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Histone methyltransferase MLL3 contributes to genome-scale circadian transcription.
Published: January, 2013

Abstract: Daily cyclical expression of thousands of genes in tissues such as the liver is orchestrated by the molecular circadian clock, the disruption of which is implicated in metabolic disorders and cancer. Although we understand much about the circadian...
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Direct Transcriptional Regulation of Human Hepatic Cytochrome P450 3A4 (CYP3A4) by Peroxisome Proliferator-Activated Receptor Alpha (PPARα).
Published: January, 2013

Abstract: The nuclear receptor peroxisome proliferator-activated receptor (PPAR)α is primarily known as a regulator of fatty acid metabolism, energy balance, and inflammation, but there is evidence suggesting a wider role in regulating biotransformation of ...
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Comprehensive histone phosphorylation analysis and identification of pf14-3-3 protein as a histone h3 phosphorylation reader in malaria parasites.
Published: January, 2013

Abstract: The important role of histone posttranslational modifications, particularly methylation and acetylation, in Plasmodium falciparum gene regulation has been established. However, the role of histone phosphorylation remains understudied. Here, we inv...
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Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis.
Published: January, 2013

Abstract: Endogenous microRNAs (miRNAs) modulate gene expression at the post-transcription level. In plants, a vast majority of MIR genes are thought to be transcribed by RNA Polymerase II (Pol II). However, promoter organization is currently unknown for mo...
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The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes.
Published: January, 2013

Abstract: Researchers have long been enthralled with the idea that gene duplication can generate novel functions, crediting this process with great evolutionary importance. Empirical data shows that whole-genome duplications (WGDs) are more likely to be ret...
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Reducing HDAC6 ameliorates cognitive deficits in a mouse model for Alzheimer's disease.
Published: January, 2013

Abstract: Histone deacetylases (HDACs) are currently being discussed as promising therapeutic targets to treat neurodegenerative diseases. However, the role of specific HDACs in cognition and neurodegeneration remains poorly understood. Here, we investigate...
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The WalRK (YycFG) and σ(I) RsgI regulators cooperate to control CwlO and LytE expression in exponentially growing and stressed Bacillus subtilis cells.
Published: January, 2013

Abstract: The WalRK (YycFG) two-component system co-ordinates cell wall metabolism with growth by regulating expression of autolysins and proteins that modulate autolysin activity. Here we extend its role in cell wall metabolism by showing that WalR binds t...
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Bridging Decapentaplegic and Wingless signaling in Drosophila wings through repression of naked cuticle by Brinker.
Published: January, 2013

Abstract: Wnts and bone morphogenetic proteins (BMPs) are signaling elements that are crucial for a variety of events in animal development. In Drosophila, Wingless (Wg, a Wnt ligand) and Decapentaplegic (Dpp, a BMP homolog) are thought to function through ...
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Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing
Published: January, 2013

Abstract: We have developed a method that enriches for methylated cytosines by capturing the fraction of bisulfite-treated DNA with unconverted cytosines. The method, called streptavidin bisulfite ligand methylation enrichment (SuBLiME), involves the specif...
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53BP1 Alters the Landscape of DNA Rearrangements and Suppresses AID-Induced B Cell Lymphoma.
Published: January, 2013

Abstract: Deficiencies in factors that regulate the DNA damage response enhance the incidence of malignancy by destabilizing the genome. However, the precise influence of the DNA damage response on regulation of cancer-associated rearrangements is not well ...
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ATR-like kinase Mec1 facilitates both chromatin accessibility at DNA replication forks and replication fork progression during replication stress.
Published: January, 2013

Abstract: Faithful DNA replication is essential for normal cell division and differentiation. In eukaryotic cells, DNA replication takes place on chromatin. This poses the critical question as to how DNA replication can progress through chromatin, which is ...
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Identification of Novel Imidazo[1,2-a]pyridine Inhibitors Targeting M. tuberculosis QcrB.
Published: December, 2012

Abstract: Mycobacterium tuberculosis is a major human pathogen and the causative agent for the pulmonary disease, tuberculosis (TB). Current treatment programs to combat TB are under threat due to the emergence of multi-drug and extensively-drug resistant T...
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Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression.
Published: December, 2012

Abstract: Poised RNA polymerase II (Pol II) is predominantly found at developmental control genes and is thought to allow their rapid and synchronous induction in response to extracellular signals. How the recruitment of poised RNA Pol II is regulated durin...
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Evolution of cichlid vision via trans-regulatory divergence.
Published: December, 2012

Abstract: ABSTRACT: BACKGROUND: Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within t...
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The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation.
Published: December, 2012

Abstract: Enhancers play a central role in precisely regulating the expression of developmentally regulated genes. However, the machineries required for enhancer-promoter communication have remained largely unknown. We have found that Ell3, a member of the ...
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Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes.
Published: December, 2012

Abstract: ABSTRACT: BACKGROUND: It has recently emerged that common epithelial cancers such as breast cancers have fusion genes like those in leukaemias. In a representative breast cancer cell line, ZR-75-30, we searched for fusion genes, by analysing genom...
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Next-Generation Sequencing Reveals Deep Intronic Cryptic ABCC8 and HADH Splicing Founder Mutations Causing Hyperinsulinism by Pseudoexon Activation.
Published: December, 2012

Abstract: Next-generation sequencing (NGS) enables analysis of the human genome on a scale previously unachievable by Sanger sequencing. Exome sequencing of the coding regions and conserved splice sites has been very successful in the identification of dise...
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AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In Vivo.
Published: December, 2012

Abstract: AMPK is a metabolic sensor that helps maintain cellular energy homeostasis. Despite evidence linking AMPK with tumor suppressor functions, the role of AMPK in tumorigenesis and tumor metabolism is unknown. Here we show that AMPK negatively regulat...
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Epigenetic Regulation of Nestin Expression During Neurogenic Differentiation of Adipose Tissue Stem Cells.
Published: December, 2012

Abstract: Adipose-tissue-derived stem cells (ASCs) have received considerable attention due to their easy access, expansion potential, and differentiation capacity. ASCs are believed to have the potential to differentiate into neurons. However, the mechanis...
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A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells.
Published: December, 2012

Abstract: Factor-induced reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) is inefficient, complicating mechanistic studies. Here, we examined defined intermediate cell populations poised to becoming iPSCs by genome-wide analyses. W...
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The Potential for Isocitrate Dehydrogenase Mutations to Produce 2-Hydroxyglutarate Depends on Allele Specificity and Subcellular Compartmentalization.
Published: December, 2012

Abstract: Monoallelic point mutations in cytosolic isocitrate dehydrogenase 1 (IDH1) and its mitochondrial homolog IDH2 can lead to elevated levels of 2-hydroxyglutarate (2HG) in multiple cancers. Here we report that cellular 2HG production from cytosolic I...
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HDAC1-mSin3a-NCOR1, Dnmt3b-HDAC1-Egr1 and Dnmt1-PCNA-UHRF1-G9a regulate the NY-ESO1 gene expression
Published: December, 2012

Abstract: The NY-ESO1 gene is a cancer/testis antigen considered to be suitable target for the immunotherapy of human malignancies. Despite the identification of the epigenetical silencing of the NY-ESO1 gene in a large variety of tumors, the molecular mech...
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A polycomb group protein is retained at specific sites on chromatin in mitosis.
Published: December, 2012

Abstract: Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states, but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionati...
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Hypoxia-inducible Factor 1α regulates a Socs3-Stat3-adiponectin signal transduction pathway in adipocytes.
Published: December, 2012

Abstract: Obesity has been identified as a major risk factor for type 2 diabetes, characterized by insulin resistance in insulin target tissues. Hypoxia-inducible factor 1α (HIF1α) regulates pathways in energy metabolism that become dysregulated in obesity....
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The EP300, KDM5A, KDM6A and KDM6B Chromatin Regulators Cooperate with KLF4 in the Transcriptional Activation of POU5F1.
Published: December, 2012

Abstract: POU5F1 is essential for maintaining pluripotency in embryonic stem cells (ESCs). It has been reported that the constitutive activation of POU5F1 is sustained by the core transcriptional regulatory circuitry in ESCs; however, the means by which POU...
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Nano-MeDIP-seq: Methylome analysis using low DNA concentrations (Prot 58)
Published: December, 2012

Abstract: To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome - wide analysis should be embraced. This in turn requires a technique that balances accuracy, genome coverage, resolution and cost, yet is low in DNA i...
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A Genome-Wide RNAi Screen Reveals MAP Kinase Phosphatases as Key ERK Pathway Regulators during Embryonic Stem Cell Differentiation.
Published: December, 2012

Abstract: Embryonic stem cells and induced pluripotent stem cells represent potentially important therapeutic agents in regenerative medicine. Complex interlinked transcriptional and signaling networks control the fate of these cells towards maintenance of ...
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TET2 promotes histone O-GlcNAcylation during gene transcription.
Published: December, 2012

Abstract: Ten eleven translocation (TET) enzymes, including TET1, TET2 and TET3, convert 5-methylcytosine to 5-hydroxymethylcytosine and regulate gene transcription. However, the molecular mechanism by which TET family enzymes regulate gene transcription re...
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High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.
Published: December, 2012

Abstract: To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches: strand-specific RNA-seq, to survey the global transcriptome, and ChIP-seq, to monitor the genom...
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STAT3 Protein Up-regulates Gα-interacting Vesicle-associated Protein (GIV)/Girdin Expression, and GIV Enhances STAT3 Activation in a Positive Feedback Loop during Wound Healing and Tumor Invasion/Metastasis.
Published: December, 2012

Abstract: Gα-interacting vesicle-associated protein (GIV) is a guanine nucleotide exchange factor that modulates key signaling pathways during a diverse set of biological processes, e.g. wound healing, macrophage chemotaxis, tumor angiogenesis, vascular rep...
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A Histone Deacetylase Adjusts Transcription Kinetics at Coding Sequences during Candida albicans Morphogenesis.
Published: December, 2012

Abstract: Despite their classical role as transcriptional repressors, several histone deacetylases, including the baker's yeast Set3/Hos2 complex (Set3C), facilitate gene expression. In the dimorphic human pathogen Candida albicans, the homologue of the Set...
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Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing-based approach.
Published: December, 2012

Abstract: Integration of the viral DNA into host chromosomes was found in most of the hepatitis B virus (HBV)-related hepatocellular carcinomas (HCCs). Here we devised a massive anchored parallel sequencing (MAPS) method using next-generation sequencing to ...
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Conserved boundary elements from the Hox complex of mosquito, Anopheles gambiae.
Published: December, 2012

Abstract: The conservation of hox genes as well as their genomic organization across the phyla suggests that this system of anterior-posterior axis formation arose early during evolution and has come under strong selection pressure. Studies in the split Hox...
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Scmh1 has E3 ubiquitin ligase activity for Geminin and histone H2A and regulates Geminin stability directly or indirectly via transcriptional repression of Hoxa9 and Hoxb4.
Published: December, 2012

Abstract: Polycomb-group (PcG) complex 1 acts as an E3 ubiquitin ligase both for histone H2A to silence transcription and for Geminin to regulate its stability. Scmh1 is a sub-stoichiometric component of PcG complex 1 that provides the complex with an inter...
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Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species.
Published: December, 2012

Abstract: Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-re...
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Control of somatic tissue differentiation by the long non-coding RNA TINCR.
Published: December, 2012

Abstract: Several of the thousands of human long non-coding RNAs (lncRNAs) have been functionally characterized; however, potential roles for lncRNAs in somatic tissue differentiation remain poorly understood. Here we show that a 3.7-kilobase lncRNA, termin...
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ATF4 orchestrates a program of BH3-only protein expression in severe hypoxia.
Published: December, 2012

Abstract: Intratumoral hypoxia is associated with poor prognosis, regardless of the mode of therapy. Cancer cells survive this condition through activating several adaptive signaling pathways, including the integrated stress response (ISR) and autophagy. Ac...
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Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.
Published: December, 2012

Abstract: Interleukin 15 (IL-15) and IL-2 have distinct immunological functions even though both signal through the receptor subunit IL-2Rβ and the common γ-chain (γ(c)). Here we found that in the structure of the IL-15-IL-15Rα-IL-2Rβ-γ(c) quaternary comple...
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Genome Sequence of OXA-48 Carbapenemase-Producing Klebsiella pneumoniae KpO3210.
Published: December, 2012

Abstract: Klebsiella pneumoniae KpO3210 is a OXA-48 carbapenemase-producing isolate obtained from a blood culture in the context of an outbreak in Hospital Universitario La Paz (Madrid, Spain) in 2010. It belongs to the major clone detected during the outbr...
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Bone morphogenetic protein-7 regulates Snail signaling in carbon tetrachloride-induced fibrosis in the rat liver.
Published: December, 2012

Abstract: The aim of this study was to explore the molecular mechanism of the bone morphogenetic protein-7 (BMP-7) downregulation of Snail-mediated E-cadherin repression and mesenchymal-epithelial transition (MET) induction, since little is presently known ...
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Ezh2 maintains a key phase of muscle satellite cell expansion but does not regulate terminal differentiation.
Published: November, 2012

Abstract: Tissue generation and repair requires a stepwise process of cell fate restriction to ensure adult stem cells differentiate in a timely and appropriate manner. A crucial role has been implicated for Polycomb-group (PcG) proteins and the H3K27me3 re...
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Cdk11-CyclinL Controls the Assembly of the RNA Polymerase II Mediator Complex.
Published: November, 2012

Abstract: The large Mediator (L-Mediator) is a general coactivator of RNA polymerase II transcription and is formed by the reversible association of the small Mediator (S-Mediator) and the kinase-module-harboring Cdk8. It is not known how the kinase module ...
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CTCF Regulates KSHV Latency Transcription by Nucleosome Displacement and RNA Polymerase Programming.
Published: November, 2012

Abstract: CTCF has been implicated in various aspects of viral and host chromatin organization and transcriptional control. We have previously shown that CTCF binds to a cluster of three sites in the first intron of the Kaposi's Sarcoma-Associated HerpesVir...
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Gene regulation by the lysine demethylase KDM4A in Drosophila.
Published: November, 2012

Abstract: Lysine methylation of histones is associated with both transcriptionally active chromatin and with silent chromatin, depending on what residue is modified. Histone methyltransferases and demethylases ensure that histone methylations are dynamic an...
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Post-replicative repair involves separase-dependent removal of the kleisin subunit of cohesin.
Published: November, 2012

Abstract: DNA double-strand break repair is critical for cell viability and involves highly coordinated pathways to restore DNA integrity at the lesion. An early event during homology-dependent repair is resection of the break to generate progressively long...
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Analysis of the peroxisome proliferator-activated receptor-beta/delta (PPARbeta/delta) cistrome reveals novel co-regulatory role of ATF4.
Published: November, 2012

Abstract: ABSTRACT: BACKGROUND: The present study coupled expression profiling with chromatin immunoprecipitation sequencing (ChIP-seq) to examine peroxisome proliferator-activated receptor-beta/delta (PPARbeta/delta)-dependent regulation of gene expression...
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Dual Role of Dextran Sulfate 5000 Da as Anti-Apoptotic and Pro-Autophagy Agent.
Published: November, 2012

Abstract: Dextran sulfate 5,000 Da (DS), a sulfated polysaccharide, has been used in recombinant mammalian cell cultures to prevent cell aggregation, thereby increasing cell viability. Previous studies using Chinese hamster ovary (CHO) suspension cultures h...
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Expression of Taurine Transporter (TauT) is Modulated by Heat Shock Factor 1 (HSF1) in Motor Neurons of ALS.
Published: November, 2012

Abstract: Amyotrophic lateral sclerosis (ALS) is a fatal neurological disorder characterized by progressive paralysis caused by the degeneration of motor neurons throughout the central nervous system. Mutations of the free radical scavenging enzyme Cu/Zn su...
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BTB-ZF factors recruit the E3 ligase cullin 3 to regulate lymphoid effector programs.
Published: November, 2012

Abstract: The differentiation of several T- and B-cell effector programs in the immune system is directed by signature transcription factors that induce rapid epigenetic remodelling. Here we report that promyelocytic leukaemia zinc finger (PLZF), the BTB-zi...
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Identification of p21 (CIP1/WAF1) as a direct target gene of HIC1 (hypermethylated in cancer 1).
Published: November, 2012

Abstract: The tumor suppressor gene HIC1 (Hypermethylated In Cancer 1) encodes a transcriptional repressor involved in the regulation of growth control and DNA damage response. We previously demonstrated that p57Kip2; a member of the CIP1/KIP family of CDK ...
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Limitations and possibilities of low cell number ChIP-seq.
Published: November, 2012

Abstract: ABSTRACT: BACKGROUND: Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting materi...
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Molecular characterization of transgene integration by next-generation sequencing in transgenic cattle.
Published: November, 2012

Abstract: As the number of transgenic livestock increases, reliable detection and molecular characterization of transgene integration sites and copy number are crucial not only for interpreting the relationship between the integration site and the specific ...
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Alterations in Cellular Energy Metabolism Associated with the Antiproliferative Effects of the ATM Inhibitor KU-55933 and with Metformin.
Published: November, 2012

Abstract: KU-55933 is a specific inhibitor of the kinase activity of the protein encoded by Ataxia telangiectasia mutated (ATM), an important tumor suppressor gene with key roles in DNA repair. Unexpectedly for an inhibitor of a tumor suppressor gene, KU-55...
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Reduced TOR signaling sustains hyphal development in Candida albicans by lowering Hog1 basal activity
Published: November, 2012

Abstract: Candida albicans is able to undergo reversible morphological changes between yeast and hyphal forms in response to environmental cues. This morphological plasticity is essential for its pathogenesis. Hyphal development requires two temporally link...
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Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted bornean elephant.
Published: November, 2012

Abstract: High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic informat...
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Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4.
Published: November, 2012

Abstract: Monomethylation of histone H3 on Lys 4 (H3K4me1) and acetylation of histone H3 on Lys 27 (H3K27ac) are histone modifications that are highly enriched over the body of actively transcribed genes and on enhancers. Although in yeast all H3K4 methylat...
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HMGA1 Reprograms Somatic Cells into Pluripotent Stem Cells by Inducing Stem Cell Transcriptional Networks.
Published: November, 2012

Abstract: BACKGROUND: Although recent studies have identified genes expressed in human embryonic stem cells (hESCs) that induce pluripotency, the molecular underpinnings of normal stem cell function remain poorly understood. The high mobility group A1 (HMGA...
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GADD45G Functions in Male Sex Determination by Promoting p38 Signaling and Sry Expression.
Published: November, 2012

Abstract: Male sex determination in mammals is induced by Sry, a gene whose regulation is poorly understood. Here we show that mice mutant for the stress-response gene Gadd45g display complete male-to-female sex reversal. Gadd45g and Sry have a strikingly s...
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Capturing native long-range contiguity by in situ library construction and optical sequencing.
Published: November, 2012

Abstract: The relatively short read lengths associated with the most cost-effective DNA sequencing technologies have limited their use in de novo genome assembly, structural variation detection, and haplotype-resolved genome sequencing. Consequently, there ...
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Timing of Transcriptional Quiescence during Gametogenesis Is Controlled by Global Histone H3K4 Demethylation.
Published: November, 2012

Abstract: Gametes are among the most highly specialized cells produced during development. Although gametogenesis culminates in transcriptional quiescence in plants and animals, regulatory mechanisms controlling this are unknown. Here, we confirm that gamet...
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Altered Binding Site Selection of P53 Transcription Cassettes by Hepatitis B Virus X Protein.
Published: November, 2012

Abstract: The key cellular regulator p53 is a common target of viral oncoproteins. However, the mechanism by which p53 transcription regulation is modulated by Hepatitis B virus X protein (HBx) - a transcription co-factor implicated in hepatitis B virus-ass...
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Dysregulation of REST-regulated coding and non-coding RNAs in a cellular model of Huntington's disease.
Published: November, 2012

Abstract: Huntingtin (Htt) protein interacts with many transcriptional regulators, with widespread disruption to the transcriptome in Huntington's disease (HD) brought about by altered interactions with the mutant Htt (muHtt) protein. Repressor Element-1 Si...
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Protein Group Modification and Synergy in the SUMO Pathway as Exemplified in DNA Repair.
Published: November, 2012

Abstract: Protein modification by SUMO affects a wide range of protein substrates. Surprisingly, although SUMO pathway mutants display strong phenotypes, the function of individual SUMO modifications is often enigmatic, and SUMOylation-defective mutants com...
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UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery.
Published: November, 2012

Abstract: piRNAs silence transposons during germline development. In Drosophila, transcripts from heterochromatic clusters are processed into primary piRNAs in the perinuclear nuage. The nuclear DEAD box protein UAP56 has been previously implicated in mRNA ...
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Polycomb Group Proteins Bind an engrailed PRE in Both the "ON" and "OFF" Transcriptional States of engrailed.
Published: November, 2012

Abstract: Polycomb group (PcG) and trithorax Group (trxG) proteins maintain the "OFF" and "ON" transcriptional states of HOX genes and other targets by modulation of chromatin structure. In Drosophila, PcG proteins are bound to DNA fragments called Polycomb...
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A Forward Genetic Screen Identifies Eukaryotic Translation Initiation Factor 3, Subunit H (eIF3h), as an Enhancer of Variegation in the Mouse.
Published: November, 2012

Abstract: We have used a forward genetic screen to identify genes required for transgene silencing in the mouse. Previously these genes were found using candidate-based sequencing, a slow and labor-intensive process. Recently, whole-exome deep sequencing ha...
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Systematic identification of functional residues in mammalian histone H2AX.
Published: October, 2012

Abstract: The histone variant H2AX is a principal component of chromatin involved in the detection, signaling and repair of DNA double-strand breaks (DSBs). H2AX is thought to operate primarily through its C-terminal S139 phosphorylation, which mediates the...
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Piccolo NuA4 catalyzed acetylation of nucleosomal histones: critical roles of an Esa1 Tudor/chromo barrel loop and an Epl1 Enhancer of Polycomb A (EPcA) basic region.
Published: October, 2012

Abstract: Piccolo NuA4 is an essential yeast histone acetyltransferase (HAT) complex that targets histones H4 and H2A in nucleosome substrates. While Piccolo NuA4's catalytic subunit Esa1 alone is unable to acetylate nucleosomal histones, its accessory subu...
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Regulation of Pluripotency and Self- Renewal of ESCs through Epigenetic- Threshold Modulation and mRNA Pruning.
Published: October, 2012

Abstract: Embryonic stem cell (ESC) pluripotency requires bivalent epigenetic modifications of key developmental genes regulated by various transcription factors and chromatin-modifying enzymes. How these factors coordinate with one another to maintain the ...
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High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum.
Published: October, 2012

Abstract: The transcriptional regulator GlxR has been characterised as a global hub within the gene-regulatory network of Corynebacterium glutamicum. Chromatin immunoprecipitation with a specific anti-GlxR antibody and subsequent high-throughput sequencing ...
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CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters.
Published: October, 2012

Abstract: One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two-thirds of genes, whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are ma...
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The H3K27 Demethylase JMJD3 Is Required for Maintenance of the Embryonic Respiratory Neuronal Network, Neonatal Breathing, and Survival.
Published: October, 2012

Abstract: JMJD3 (KDM6B) antagonizes Polycomb silencing by demethylating lysine 27 on histone H3. The interplay of methyltransferases and demethylases at this residue is thought to underlie critical cell fate transitions, and the dynamics of H3K27me3 during ...
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HIF1α is a central regulator of collagen hydroxylation and secretion under hypoxia during bone development
Published: October, 2012

Abstract: Collagen production is fundamental for the ontogeny and the phylogeny of all multicellular organisms. It depends on hydroxylation of proline residues, a reaction that uses molecular oxygen as a substrate. This dependency is expected to limit colla...
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Chromatin acetylation at transcription start sites and vitamin D receptor binding regions relates to effects of 1α,25-dihydroxyvitamin D3 and histone deacetylase inhibitors on gene expression.
Published: October, 2012

Abstract: The nuclear hormone 1α,25-dihydroxyvitamin D(3) (1α,25(OH)(2)D(3) or 1,25D) regulates its target genes via activation of the transcription factor vitamin D receptor (VDR) far more specifically than the chromatin modifier trichostatin A (TsA) via i...
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Distinct requirements for Sin3a in perinatal male gonocytes and differentiating spermatogonia.
Published: October, 2012

Abstract: Chromatin modifier Swi-independent 3a (SIN3A), together with associated histone deacetylases, influences gene expression during development and differentiation through a variety of transcription factors in a cell-specific manner. Sin3a is essentia...
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Periodontitis in established rheumatoid arthritis patients: a cross-sectional clinical, microbiological and serological study.
Published: October, 2012

Abstract: ABSTRACT: INTRODUCTION: The association between rheumatoid arthritis (RA) and periodontitis is suggested to be linked to the periodontal pathogen Porphyromonas gingivalis. Colonization of P. gingivalis in the oral cavity of RA patients has been sc...
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Histone variant macroH2A marks embryonic differentiation in vivo and acts as an epigenetic barrier to induced pluripotency.
Published: October, 2012

Abstract: How cell fate becomes restricted during somatic cell differentiation is a long lasting question in biology. Epigenetic mechanisms not present in pluripotent cells and acquired during embryonic development are expected to stabilise the differentiat...
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Epigenetic Regulation of Condensin-Mediated Genome Organization during the Cell Cycle and upon DNA Damage through Histone H3 Lysine 56 Acetylation.
Published: October, 2012

Abstract: Complex genome organizations participate in various nuclear processes including transcription, DNA replication, and repair. However, the mechanisms that generate and regulate these functional genome structures remain largely unknown. Here, we desc...
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Nucleolar accumulation of APE1 depends on charged lysine residues that undergo acetylation upon genotoxic stress and modulate its BER activity in cells.
Published: October, 2012

Abstract: Apurinic/apyrimidinic endonuclease 1 (APE1) is the main abasic endonuclease in the base excision repair (BER) pathway of DNA lesions caused by oxidation/alkylation in mammalian cells; within nucleoli it interacts with nucleophosmin and rRNA throug...
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MBD2 and multiple domains of CHD4 are required for transcriptional repression by Mi-2/NuRD complexes.
Published: October, 2012

Abstract: Mi-2/nucleosome remodeling and deacetylase (NuRD) chromatin remodeling complexes are important regulators of chromatin structure and DNA accessibility. We examined requirements for individual domains of chromodomain helicase DNA-binding protein 4 ...
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Human RNA Methyltransferase BCDIN3D Regulates MicroRNA Processing.
Published: October, 2012

Abstract: MicroRNAs (miRNAs) regulate key biological processes and their aberrant expression may lead to cancer. The primary transcript of canonical miRNAs is sequentially cleaved by the RNase III enzymes, Drosha and Dicer, which generate 5′ monophosphate e...
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MeDIP coupled with a promoter tiling array as a platform to investigate global DNA methylation patterns in AML cells.
Published: October, 2012

Abstract: Hypermethylation of CpGs in promoter regions and subsequent changes in gene expression are common features in acute myeloid leukemia (AML). Genome-wide studies of the methylome are not only useful to understand changes in DNA methylation and gene ...
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New partners in regulation of gene expression: the enhancer of trithorax and polycomb corto interacts with methylated ribosomal protein l12 via its chromodomain.
Published: October, 2012

Abstract: Chromodomains are found in many regulators of chromatin structure, and most of them recognize methylated lysines on histones. Here, we investigate the role of the Drosophila melanogaster protein Corto's chromodomain. The Enhancer of Trithorax and ...
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The Many Landscapes of Recombination in Drosophila melanogaster.
Published: October, 2012

Abstract: Recombination is a fundamental biological process with profound evolutionary implications. Theory predicts that recombination increases the effectiveness of selection in natural populations. Yet, direct tests of this prediction have been restricte...
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Oxidative stress-regulated lentiviral TK/GCV gene therapy for lung cancer treatment.
Published: October, 2012

Abstract: NRF2 is a transcription factor that regulates protection against a wide variety of toxic insults to cells, including cytotoxic cancer chemotherapeutic drugs. Many lung cancer cells harbor a mutation in either NRF2 or its inhibitor KEAP1 resulting ...
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FXR Controls the Tumor Suppressor NDRG2 and FXR Agonists Reduce Liver Tumor Growth and Metastasis in an Orthotopic Mouse Xenograft Model.
Published: October, 2012

Abstract: The farnesoid X receptor (FXR) is expressed predominantly in tissues exposed to high levels of bile acids and controls bile acid and lipid homeostasis. FXR(-/-) mice develop hepatocellular carcinoma (HCC) and show an increased prevalence for intes...
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Adhesion Regulates MAP Kinase/Ternary Complex Factor Exchange to Control a Proliferative Transcriptional Switch.
Published: October, 2012

Abstract: BACKGROUND: The ternary complex factors (TCFs; Elk1, Net, and Sap-1) are growth factor-responsive transcription cofactors of serum response factor (SRF) and are activated by MAP kinase (MAPK) phosphorylation to regulate immediate early gene transc...
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Initial Characterization of the Pf-Int Recombinase from the Malaria Parasite Plasmodium falciparum.
Published: October, 2012

Abstract: BACKGROUND: Genetic variation is an essential means of evolution and adaptation in many organisms in response to environmental change. Certain DNA alterations can be carried out by site-specific recombinases (SSRs) that fall into two families: the...
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Read length versus Depth of Coverage for Viral Quasispecies Reconstruction.
Published: October, 2012

Abstract: Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus popula...
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Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome.
Published: October, 2012

Abstract: ABSTRACT: BACKGROUND: Induction and promotion of liver cancer by exposure to non-genotoxic carcinogens coincides with epigenetic perturbations, including specific changes in DNA methylation. Here we investigate the genome-wide dynamics of 5-hydro...
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Regulation of delta-aminolevulinic Acid dehydratase by krüppel-like factor 1.
Published: October, 2012

Abstract: Krüppel-like factor 1(KLF1) is a hematopoietic-specific zinc finger transcription factor essential for erythroid gene expression. In concert with the transacting factor GATA1, KLF1 modulates the coordinate expression of the genes encoding the mult...
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A genome-wide signature of glucocorticoid receptor binding in neuronal PC12 cells.
Published: October, 2012

Abstract: ABSTRACT: BACKGROUND: Glucocorticoids, secreted by the adrenals in response to stress, profoundly affect structure and plasticity of neurons. Glucocorticoid action in neurons is mediated by glucocorticoid receptors (GR) that operate as transcripti...
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Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation.
Published: October, 2012

Abstract: The rate of meiotic crossing over (CO) varies considerably along chromosomes, leading to marked distortions between physical and genetic distances. The causes underlying this variation are being unraveled, and DNA sequence and chromatin states hav...
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The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine.
Published: October, 2012

Abstract: 5-Hydroxymethylcytosine (5hmC) is a newly discovered DNA base present at detectable levels in most mammalian cell types and tissues. It is generated by Tet-enzyme-mediated oxidation of 5-methylcytosine (5mC). 5hmC is important both because of its ...
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ChIP-exo Method for Identifying Genomic Location of DNA-Binding Proteins with Near-Single-Nucleotide Accuracy.
Published: October, 2012

Abstract: This unit describes the ChIP-exo methodology, which combines chromatin immunoprecipitation (ChIP) with lambda exonuclease digestion followed by high-throughput sequencing. ChIP-exo allows identification of a nearly complete set of the binding loca...
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Maize Unstable factor for orange1 Is Required for Maintaining Silencing Associated with Paramutation at the pericarp color1 and booster1 Loci.
Published: October, 2012

Abstract: To understand the molecular mechanisms underlying paramutation, we examined the role of Unstable factor for orange1 (Ufo1) in maintaining paramutation at the maize pericarp color1 (p1) and booster1 (b1) loci. Genetic tests revealed that the Ufo1-1...
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The histone demethylase PHF8 is essential for cytoskeleton dynamics.
Published: October, 2012

Abstract: PHF8 is a histone demethylase associated with X-linked mental retardation. It has been described as a transcriptional co-activator involved in cell cycle progression, but its physiological role is still poorly understood. Here we show that PHF8 co...
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Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline.
Published: October, 2012

Abstract: Mouse primordial germ cells (PGCs) erase global DNA methylation (5mC) as part of the comprehensive epigenetic reprogramming that occurs during PGC development. 5mC plays an important role in maintaining stable gene silencing and repression of tran...
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Draft Genome Sequence of Lactobacillus rossiae DSM 15814T.
Published: October, 2012

Abstract: The draft genome sequence of Lactobacillus rossiae DSM 15814(T) (CS1, ATCC BAA-88) was determined by a whole-genome shotgun approach. Reads were assembled to a 2.9-Mb draft version. RAST genome annotation evidenced 2,723 predicted coding sequences...
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Human-specific CpG "beacons" identify loci associated with human-specific traits and disease.
Published: October, 2012

Abstract: Regulatory change has long been hypothesized to drive the delineation of the human phenotype from other closely related primates. Here we provide evidence that CpG dinucleotides play a special role in this process. CpGs enable epigenome variabilit...
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FRUIT, a Scar-Free System for Targeted Chromosomal Mutagenesis, Epitope Tagging, and Promoter Replacement in Escherichia coli and Salmonella enterica
Published: September, 2012

Abstract: Recombineering is a widely-used approach to delete genes, introduce insertions and point mutations, and introduce epitope tags into bacterial chromosomes. Many recombineering methods have been described, for a wide range of bacterial species. Thes...
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A Quantitative Proteomic Workflow for Characterization of Frozen Clinical Biopsies: Laser Capture Microdissection Coupled with Label-Free Mass Spectrometry
Published: September, 2012

Abstract: This paper describes a simple, highly efficient and robust proteomic workflow for routine liquid-chromatography tandem mass spectrometry analysis of Laser Microdissection Pressure Catapulting (LMPC) isolates. Highly efficient protein recovery was ...
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PML promotes MHC class II gene expression by stabilizing the class II transactivator.
Published: September, 2012

Abstract: Promyelocytic leukemia (PML) nuclear bodies selectively associate with transcriptionally active genomic regions, including the gene-rich major histocompatibility (MHC) locus. In this paper, we have explored potential links between PML and interfer...
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Chromatin immunoprecipitation and microarray analysis reveal that TFIIB occupies the SL RNA gene promoter region in Trypanosoma brucei chromosomes
Published: September, 2012

Abstract: RNA polymerase II (RNAP-II) synthesizes the m7G-capped Spliced Leader (SL) RNA and most protein-coding mRNAs in trypanosomes. RNAP-II recruitment to DNA usually requires a set of transcription factors that make sequence-specific contacts near tran...
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TET1 Suppresses Cancer Invasion by Activating the Tissue Inhibitors of Metalloproteinases.
Published: September, 2012

Abstract: Tumor suppressor gene silencing through cytosine methylation contributes to cancer formation. Whether DNA demethylation enzymes counteract this oncogenic effect is unknown. Here, we show that TET1, a dioxygenase involved in cytosine demethylation,...
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Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile.
Published: September, 2012

Abstract: The catabolite control protein CcpA is a pleiotropic regulator that mediates the global transcriptional response to rapidly catabolizable carbohydrates, like glucose in Gram-positive bacteria. By whole transcriptome analyses, we characterized gluc...
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Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage.
Published: September, 2012

Abstract: Heart development is exquisitely sensitive to the precise temporal regulation of thousands of genes that govern developmental decisions during differentiation. However, we currently lack a detailed understanding of how chromatin and gene expressio...
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A GWAS sequence variant for platelet volume marks an alternative DNM3 promoter in megakaryocytes near a MEIS1 binding site.
Published: September, 2012

Abstract: We recently identified 68 genomic loci where common sequence variants are associated with platelet count and volume. Platelets are formed in the bone marrow by megakaryocytes, which are derived from hematopoietic stem cells by a process mainly con...
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Tet2 Facilitates the Derepression of Myeloid Target Genes during CEBPα-Induced Transdifferentiation of Pre-B Cells.
Published: September, 2012

Abstract: The methylcytosine hydroxylase Tet2 has been implicated in hematopoietic differentiation and the formation of myeloid malignancies when mutated. An ideal system to study the role of Tet2 in myelopoeisis is CEBPα-induced transdifferentiation of pre...
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A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development.
Published: September, 2012

Abstract: Directed differentiation of human embryonic stem cells (ESCs) into cardiovascular cells provides a model for studying molecular mechanisms of human cardiovascular development. Although it is known that chromatin modification patterns in ESCs diffe...
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Argonaute proteins couple chromatin silencing to alternative splicing.
Published: September, 2012

Abstract: Argonaute proteins play a major part in transcriptional gene silencing in many organisms, but their role in the nucleus of somatic mammalian cells remains elusive. Here, we have immunopurified human Argonaute-1 and Argonaute-2 (AGO1 and AGO2) chro...
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Salinomycin Induces Autophagy in Colon and Breast Cancer Cells with Concomitant Generation of Reactive Oxygen Species
Published: September, 2012

Abstract: Background Salinomycin is a polyether ionophore antibiotic that has recently been shown to induce cell death in human cancer cells displaying multiple mechanisms of drug resistance. The underlying mechanisms leading to cell death after salinomyci...
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A mechanistic basis for amplification differences between samples and between genome regions.
Published: September, 2012

Abstract: ABSTRACT: BACKGROUND: For many analytical methods the efficiency of DNA amplification varies across the genome and between samples. The most affected genome regions tend to correlate with high C + G content, however this relationship is complex an...
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A Snapshot of Histone Modifications within Transposable Elements in Drosophila Wild Type Strains.
Published: September, 2012

Abstract: Transposable elements (TEs) are a major source of genetic variability in genomes, creating genetic novelty and driving genome evolution. Analysis of sequenced genomes has revealed considerable diversity in TE families, copy number, and localizatio...
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Multigenerational epigenetic adaptation of the hepatic wound-healing response.
Published: September, 2012

Abstract: We investigated whether ancestral liver damage leads to heritable reprogramming of hepatic wound healing in male rats. We found that a history of liver damage corresponds with transmission of an epigenetic suppressive adaptation of the fibrogenic ...
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Mutant p53 is a transcriptional co-factor that binds to G-rich regulatory regions of active genes and generates transcriptional plasticity
Published: September, 2012

Abstract: The molecular mechanisms underlying mutant p53 (mutp53) “gain-of-function” (GOF) are still insufficiently understood, but there is evidence that mutp53 is a transcriptional regulator that is recruited by specialized transcription factors. Here we ...
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Genome-Wide Profiling of Peroxisome Proliferator-Activated Receptor γ in Primary Epididymal, Inguinal, and Brown Adipocytes Reveals Depot-Selective Binding Correlated with Gene Expression.
Published: September, 2012

Abstract: Peroxisome proliferator-activated receptor γ (PPARγ) is a master regulator of adipocyte differentiation and function. We and others have previously mapped PPARγ binding at a genome-wide level in murine and human adipocyte cell lines and in primary...
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Widespread plasticity in CTCF occupancy linked to DNA methylation.
Published: September, 2012

Abstract: CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have lon...
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BZLF1 Governs CpG-Methylated Chromatin of Epstein-Barr Virus Reversing Epigenetic Repression.
Published: September, 2012

Abstract: Epigenetic mechanisms are essential for the regulation of all genes in mammalian cells but transcriptional repression including DNA methylation are also major epigenetic mechanisms of defense inactivating potentially harmful pathogens. Epstein-Bar...
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PARP activation regulates the RNA-binding protein NONO in the DNA damage response to DNA double-strand breaks.
Published: August, 2012

Abstract: After the generation of DNA double-strand breaks (DSBs), poly(ADP-ribose) polymerase-1 (PARP-1) is one of the first proteins to be recruited and activated through its binding to the free DNA ends. Upon activation, PARP-1 uses NAD(+) to generate la...
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MutSβ and histone deacetylase complexes promote expansions of trinucleotide repeats in human cells.
Published: August, 2012

Abstract: Trinucleotide repeat (TNR) expansions cause at least 17 heritable neurological diseases, including Huntington's disease. Expansions are thought to arise from abnormal processing of TNR DNA by specific trans-acting proteins. For example, the DNA re...
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Prdm3 and Prdm16 are H3K9me1 Methyltransferases Required for Mammalian Heterochromatin Integrity.
Published: August, 2012

Abstract: Heterochromatin serves important functions, protecting genome integrity and stabilizing gene expression programs. Although the Suv39h methyltransferases (KMTs) are known to ensure pericentric H3K9me3 methylation, the mechanisms that initiate and m...
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Serine 192 in the tiny RS repeat of the adenoviral L4-33K splicing enhancer protein is essential for function and reorganization of the protein to the periphery of viral replication centers.
Published: August, 2012

Abstract: The adenovirus L4-33K protein is a key regulator involved in the temporal shift from early to late pattern of mRNA expression from the adenovirus major late transcription unit. L4-33K is a virus-encoded alternative splicing factor, which enhances ...
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Zinc finger transcription factor zDC is a negative regulator required to prevent activation of classical dendritic cells in the steady state.
Published: August, 2012

Abstract: Classical dendritic cells (cDCs) process and present antigens to T cells. Under steady-state conditions, antigen presentation by cDCs induces tolerance. In contrast, during infection or inflammation, cDCs become activated, express higher levels of...
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Genomic Profiling of a Human Organotypic Model of AEC Syndrome Reveals ZNF750 as an Essential Downstream Target of Mutant TP63.
Published: August, 2012

Abstract: The basis for impaired differentiation in TP63 mutant ankyloblepharon-ectodermal dysplasia-clefting (AEC) syndrome is unknown. Human epidermis harboring AEC TP63 mutants recapitulated this impairment, along with downregulation of differentiation a...
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Nuclear orphan receptor NR2F6 directly antagonizes NFAT and RORγt binding to the Il17a promoter.
Published: August, 2012

Abstract: Interleukin-17A (IL-17A) is the signature cytokine produced by Th17 CD4(+) T cells and has been tightly linked to autoimmune pathogenesis. In particular, the transcription factors NFAT and RORγt are known to activate Il17a transcription, although ...
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Genome-wide distribution of 5-formylcytosine in ES cells is associated with transcription and depends on thymine DNA glycosylase.
Published: August, 2012

Abstract: ABSTRACT: BACKGROUND: Methylation of cytosine in DNA (5mC) is an important epigenetic mark that is involved in the regulation of genome function. During early embryonic development in mammals, the methylation landscape is dynamically reprogrammed ...
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Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays.
Published: August, 2012

Abstract: Following the widespread use of genome-wide association studies (GWAS), focus is turning towards identification of causal variants rather than simply genetic markers of diseases and traits. As a step towards a high-throughput method to identify ge...
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The transcription factor Wilms tumor 1 confers resistance in myeloid leukemia cells against the proapoptotic therapeutic agent TRAIL by regulating the antiapoptotic protein Bcl-xL.
Published: August, 2012

Abstract: TRAIL is considered a promising cancer therapeutic agent due to its ability to induce apoptosis in a variety of cancer cells, while sparing normal cells. However, many human tumors including acute myeloid leukemia (AML) are partially or completely...
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Role of the HSP90-Associated Cochaperone p23 in Enhancing Activity of the Androgen Receptor and Significance for Prostate Cancer.
Published: August, 2012

Abstract: Prostate tumor growth initially depends on androgens, which act via the androgen receptor (AR). Despite androgen ablation therapy, tumors eventually progress to a castrate-resistant stage in which the AR remains active. The mechanisms are poorly u...
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Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA.
Published: August, 2012

Abstract: How different organs are formed from small sets of undifferentiated precursor cells is a key question in developmental biology. To understand the molecular mechanisms underlying organ specification in plants, we studied the function of the homeoti...
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Negative Regulation of Osteoclast Precursor Differentiation by CD11b and beta2 Integrin-BCL6 Signaling
Published: August, 2012

Abstract: Negative regulation of osteoclastogenesis is important for bone homeostasis and prevention of excessive bone resorption in inflammatory and other diseases. Mechanisms that directly suppress osteoclastogenesis are not well understood. In this study...
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Characterization of eight polymorphic loci for Maasai giraffe (Giraffa camelopardalis tippelskirchi) using non-invasive genetic samples
Published: August, 2012

Abstract: We used Illumina sequencing to develop eight novel microsatellite loci for Maasai giraffe (Giraffa camelopardalis tippelskirchi), and screened them using fecal DNA. Genetic diversity was assessed for 40 individuals from the Katavi National Park/Ru...
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KAP1/TRIM28: an inhibitor of IRF5 function in inflammatory macrophages
Published: August, 2012

Abstract: IRF5 plays a key role in the induction of pro-inflammatory cytokines, contributing to the plasticity and polarisation of macrophages to an M1 phenotype and initiation of a potent TH1-TH17 response. To better understand the means of IRF5 transcript...
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IRF-1 and miRNA126 Modulate VCAM-1 Expression in Response to a High Fat Meal.
Published: August, 2012

Abstract: Rationale: A high-fat diet accompanied by hypertriglyceridemia increases an individual's risk for developing atherosclerosis. An early event in this process is monocyte recruitment through binding to VCAM-1 upregulated on inflamed arterial endothe...
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Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion.
Published: August, 2012

Abstract: There is little quantitative information regarding how much splicing occurs co-transcriptionally in higher eukaryotes, and it remains unclear where precisely splicing occurs in the nucleus. Here we determine the global extent of co- and post-trans...
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Androgen Receptor Antagonism by Divalent Ethisterone Conjugates in Castrate-Resistant Prostate Cancer Cells.
Published: August, 2012

Abstract: Sustained treatment of prostate cancer with androgen receptor (AR) antagonists can evoke drug resistance, leading to castrate-resistant disease. Elevated activity of the AR is often associated with this highly aggressive disease state. Therefore, ...
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Erg and AP-1 as determinants of glucocorticoid response in acute lymphoblastic leukemia.
Published: August, 2012

Abstract: Glucocorticoids (GCs) are among the most widely prescribed medications in clinical practice. The beneficial effects of GCs in acute lymphoblastic leukemia (ALL) are based on their ability to induce apoptosis, but the underlying transcriptional mec...
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Selective targeting of the repressive transcription factors YY1 and cMyc to disrupt quiescent human immunodeficiency viruses.
Published: August, 2012

Abstract: Quiescent HIV-1 infection of resting CD4+ T cells is an obstacle to eradication of HIV-1 infection. These reservoirs are maintained, in part, by repressive complexes that bind to the HIV-1 long terminal repeat (LTR) and recruit histone deacetylase...
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DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons.
Published: August, 2012

Abstract: The plant-specific DNA-dependent RNA polymerase V (Pol V) evolved from Pol II to function in an RNA-directed DNA methylation pathway. Here, we have identified targets of Pol V in Arabidopsis thaliana on a genome-wide scale using ChIP-seq of NRPE1,...
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Generation of DNA single-strand displacement by compromised nucleotide excision repair.
Published: August, 2012

Abstract: Nucleotide excision repair (NER) is a precisely coordinated process essential to avoid DNA damage-induced cellular malfunction and mutagenesis. Here, we investigate the mechanistic details and effects of the NER machinery when it is compromised by...
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FM19G11 Favors Spinal Cord Injury Regeneration and Stem Cell Self-Renewal by Mitochondrial Uncoupling and Glucose Metabolism Induction.
Published: August, 2012

Abstract: Spinal cord injury is a major cause of paralysis with no currently effective therapies. Induction of self-renewal and proliferation of endogenous regenerative machinery with non-invasive and non-toxic therapies could constitute a real hope and an ...
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Defining the core Arabidopsis thaliana root microbiome.
Published: August, 2012

Abstract: Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) c...
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Carm1 Regulates Pax7 Transcriptional Activity through MLL1/2 Recruitment during Asymmetric Satellite Stem Cell Divisions.
Published: August, 2012

Abstract: In skeletal muscle, asymmetrically dividing satellite stem cells give rise to committed satellite cells that transcribe the myogenic determination factor Myf5, a Pax7-target gene. We identified the arginine methyltransferase Carm1 as a Pax7 intera...
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Functional Cooperation between Human Adenovirus Type 5 Early Region 4, Open Reading Frame 6 Protein, and Cellular Homeobox Protein HoxB7.
Published: August, 2012

Abstract: Human adenovirus type 5 (HAdV5) E4orf6 (early region 4 open reading frame 6 protein) is a multifunctional early viral protein promoting efficient replication and progeny production. E4orf6 complexes with E1B-55K to assemble cellular proteins into ...
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Epigenetic Silencing of Cd8 Genes by ThPOK-Mediated Deacetylation during CD4 T Cell Differentiation.
Published: August, 2012

Abstract: Intrathymic CD4/CD8 differentiation is a process that establishes the mutually exclusive expression profiles of the CD4 and CD8 T cell lineage. The RUNX3-mediated silencing of CD4 in CD8 lineage cells has been well documented; however, it is uncle...
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Chromatin Immunoprecipitation Analysis of Xenopus Embryos
Published: August, 2012

Abstract: Chromatin immunoprecipitation (ChIP) is a powerful technique to study epigenetic regulation and transcription factor binding events in the nucleus. It is based on immune-affinity capture of epitopes that have been cross-linked to genomic DNA in vi...
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TMPRSS2- Driven ERG Expression In Vivo Increases Self-Renewal and Maintains Expression in a Castration Resistant Subpopulation.
Published: July, 2012

Abstract: Genomic rearrangements commonly occur in many types of cancers and often initiate or alter the progression of disease. Here we describe an in vivo mouse model that recapitulates the most frequent rearrangement in prostate cancer, the fusion of the...
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Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data.
Published: July, 2012

Abstract: The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction o...
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Retinoic acid receptors recognize the mouse genome through binding elements with diverse spacing and topology.
Published: July, 2012

Abstract: Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) and bind to RA response elements (RAREs) in the regulatory regions of their target genes. Although previous studies on limited sets of RA-regulated genes have defined c...
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ChAP-MS: A Method for Identification of Proteins and Histone Posttranslational Modifications at a Single Genomic Locus.
Published: July, 2012

Abstract: The field of epigenomics has been transformed by chromatin immunoprecipitation approaches that provide for the localization of a defined protein or posttranslationally modified protein to specific chromosomal sites. While these approaches have hel...
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Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy.
Published: July, 2012

Abstract: Despite antiretroviral therapy, proviral latency of human immunodeficiency virus type 1 (HIV-1) remains a principal obstacle to curing the infection. Inducing the expression of latent genomes within resting CD4(+) T cells is the primary strategy t...
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Expression of endogenous retroviruses is negatively regulated by the pluripotency marker Rex1/Zfp42.
Published: July, 2012

Abstract: Rex1/Zfp42 is a Yy1-related zinc-finger protein whose expression is frequently used to identify pluripotent stem cells. We show that depletion of Rex1 levels notably affected self-renewal of mouse embryonic stem (ES) cells in clonal assays, in the...
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Protein kinase CK2 inactivates PRH/Hhex using multiple mechanisms to de-repress VEGF-signalling genes and promote cell survival.
Published: July, 2012

Abstract: Protein kinase CK2 promotes cell survival and the activity of this kinase is elevated in several cancers including chronic myeloid leukaemia. We have shown previously that phosphorylation of the Proline-Rich Homeodomain protein (PRH/Hhex) by CK2 i...
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Curcumin induces human cathelicidin antimicrobial peptide gene expression through a vitamin D receptor-independent pathway.
Published: July, 2012

Abstract: The vitamin D receptor (VDR) mediates the pleiotropic biologic effects of 1α,25 dihydroxy-vitamin D(3). Recent in vitro studies suggested that curcumin and polyunsaturated fatty acids (PUFAs) also bind to VDR with low affinity. As potential ligand...
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Role of SUMOylation in full antiestrogenicity.
Published: July, 2012

Abstract: The selective estrogen receptor downregulator (SERD) fulvestrant can be used as second line treatment in patients relapsing after treatment with tamoxifen, a selective estrogen receptor modulator (SERM). Unlike tamoxifen, SERDs are devoid of parti...
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Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas.
Published: July, 2012

Abstract: Mutations in the genes encoding isocitrate dehydrogenase, IDH1 and IDH2, have been reported in gliomas, myeloid leukemias, chondrosarcomas and thyroid cancer. We discovered IDH1 and IDH2 mutations in 34 of 326 (10%) intrahepatic cholangiocarcinoma...
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Up-regulation of 2-oxoglutarate dehydrogenase as a stress response.
Published: July, 2012

Abstract: 2-Oxoglutarate dehydrogenase multienzyme complex (OGDHC) operates at a metabolic cross-road, mediating Ca(2+)- and ADP-dependent signals in mitochondria. Here, we test our hypothesis that OGDHC plays a major role in the neurotransmitter metabolism...
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Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels.
Published: July, 2012

Abstract: Messenger RNA levels in eukaryotes are controlled by multiple consecutive regulatory processes, which can be classified into two layers: primary transcriptional regulation at the chromosomal level and secondary, co- and post-transcriptional regula...
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A Key Role for Chd1 in Histone H3 Dynamics at the 3′ Ends of Long Genes in Yeast
Published: July, 2012

Abstract: Chd proteins are ATP–dependent chromatin remodeling enzymes implicated in biological functions from transcriptional elongation to control of pluripotency. Previous studies of the Chd1 subclass of these proteins have implicated them in diverse role...
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Genome-wide Analysis Reveals Extensive Functional Interaction between DNA Replication Initiation and Transcription in the Genome of Trypanosoma brucei
Published: July, 2012

Abstract: Identification of replication initiation sites, termed origins, is a crucial step in understanding genome transmission in any organism. Transcription of the Trypanosoma brucei genome is highly unusual, with each chromosome comprising a few discret...
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Ecdysone Induced Gene Expression Is Associated with Acetylation of Histone H3 Lysine 23 in Drosophila melanogaster
Published: July, 2012

Abstract: Posttranslational modification of histones regulates transcription but the exact role that acetylation of specific lysine residues plays in biological processes in vivo is still not clearly understood. To assess the contribution of different histo...
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Glucocorticoids Modulate the mTOR Pathway in the Hippocampus: Differential Effects Depending on Stress History.
Published: July, 2012

Abstract: Glucocorticoid (GC) hormones, released by the adrenals in response to stress, are key regulators of neuronal plasticity. In the brain, the hippocampus is a major target of GC, with abundant expression of the GC receptor. GC differentially affect t...
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The transcription factor Lyl-1 regulates lymphoid specification and the maintenance of early T lineage progenitors.
Published: July, 2012

Abstract: Thymopoiesis depends on the recruitment and expansion of bone marrow-derived progenitor populations; tight regulation of these processes is required for maintenance of the homeostasis of the T lineage. Lyl-1, a transcription factor that regulates ...
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SATB1-mediated Functional Packaging of Chromatin into Loops.
Published: July, 2012

Abstract: Mammalian genomes are organized into multiple layers of higher-order chromatin structure, and in this organization chromatin looping is a striking and crucial feature that brings together distal genomic loci into close spatial proximity. Such thre...
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An investigation of the affinities, specificity and kinetics involved in the interaction between the Yin Yang 1 transcription factor and DNA.
Published: July, 2012

Abstract: Human transcription factor Yin Yang 1 (YY1) is a four-zinc-finger protein that regulates a large number of genes with different biological functions in processes such as development, carcinogenesis and B-cell maturation. The natural binding sites ...
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Histone H2B monoubiquitination is required to reach maximal transcript levels of circadian clock genes in Arabidopsis
Published: July, 2012

Abstract: Previously, we had identified HISTONE MONOUBIQUITINATION1 (HUB1) as an unconventional ubiquitin E3 ligase that was not involved in protein degradation but in histone H2B modification implicated in transcription activation in plants. HUB1-mediated ...
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Lipocalin 2 (LCN2), the TNF-like receptor TWEAKR and its ligand TWEAK act downstream of NFAT1 to regulate breast cancer cell invasion.
Published: July, 2012

Abstract: NFAT1 is a transcription factor that elicits breast carcinoma cells to become invasive, contributing thus to formation of metastasis. The molecular mechanisms by which NFAT1 operates in this respect are still poorly known. Here, we report that NFA...
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The human CST complex is a terminator of telomerase activity.
Published: July, 2012

Abstract: The lengths of human telomeres, which protect chromosome ends from degradation and end fusions, are crucial determinants of cell lifespan. During embryogenesis and in cancer, the telomerase enzyme counteracts telomeric DNA shortening. As shown in ...
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Aberrant expression of IFN-γ in Th2 cells from Th2 LCR-deficient mice.
Published: July, 2012

Abstract: The Th2 locus control region (LCR) has been shown to be a crucial cis-acting element for Th2 cytokine expression and Th2 cell differentiation. To study the role of Th2 LCR in ifng locus regulation, we examined the expression of IFN-γ in Th2 cells ...
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XPG and XPF Endonucleases Trigger Chromatin Looping and DNA Demethylation for Accurate Expression of Activated Genes.
Published: July, 2012

Abstract: Nucleotide excision repair factors, initially characterized as part of DNA repair, have been shown to participate in the transcriptional process in the absence of genotoxic attack. However, their molecular function when recruited at the promoters ...
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Occludin is a direct target of thyroid transcription factor-1 (TTF-1/NKX2-1).
Published: July, 2012

Abstract: The thyroid transcription factor 1 gene (TTF-1 or NKX2-1) is essential to lung development; however, it is also a critical factor in lung cancer. TTF-1 is amplified in lung cancers, suggesting that it is a gain-of-function lung oncogene. Conversel...
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Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors.
Published: July, 2012

Abstract: The transcription factors Foxa1 and Foxa2 promote the specification of midbrain dopaminergic (mDA) neurons and the floor plate. Whether their role is direct has remained unclear as they also regulate the expression of Shh, which has similar roles....
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Quantitative single-molecule microscopy reveals that CENP-A(Cnp1) deposition occurs during G2 in fission yeast.
Published: July, 2012

Abstract: The inheritance of the histone H3 variant CENP-A in nucleosomes at centromeres following DNA replication is mediated by an epigenetic mechanism. To understand the process of epigenetic inheritance, or propagation of histones and histone variants, ...
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Transcription termination between polo and snap, two closely spaced tandem genes of D. melanogaster.
Published: July, 2012

Abstract: Transcription termination of RNA polymerase II between closely spaced genes is an important, though poorly understood, mechanism. This is true, in particular, in the Drosophila genome, where approximately 52% of tandem genes are separated by less ...
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Live cell monitoring of periodic gene expression in synchronous human cells identifies forkhead genes involved in cell cycle control
Published: June, 2012

Abstract: We developed a system to monitor periodic luciferase activity from cell cycle-regulated promoters in synchronous cells. Reporters were driven by a minimal human E2F1 promoter with peak expression in G1/S, or a basal promoter with six Forkhead DNA ...
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Cohesins Repress KSHV Immediate Early Gene Transcription During Latency.
Published: June, 2012

Abstract: Chromatin-organizing factors, like CTCF and cohesins, have been implicated in the control of complex viral regulatory programs. We investigated the role of CTCF and cohesin in the control of the latent to lytic switch for Kaposi's Sarcoma-Associat...
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Neurog2 Simultaneously Activates and Represses Alternative Gene Expression Programs in the Developing Neocortex.
Published: June, 2012

Abstract: Progenitor cells undergo a series of stable identity transitions on their way to becoming fully differentiated cells with unique identities. Each cellular transition requires that new sets of genes are expressed, while alternative genetic programs...
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Cdc28 kinase activity regulates the basal transcription machinery at a subset of genes.
Published: June, 2012

Abstract: The cyclin-dependent kinase Cdc28 is the master regulator of the cell cycle in Saccharomyces cerevisiae. Cdc28 initiates the cell cycle by activating cell-cycle-specific transcription factors that switch on a transcriptional program during late G1...
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Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae).
Published: June, 2012

Abstract: ABSTRACT: BACKGROUND: Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating 'noisy' data with misleadi...
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ZRF1 controls oncogene-induced senescence through the INK4-ARF locus.
Published: June, 2012

Abstract: The reactivation of the INK4-ARF locus, which is epigenetically repressed by Polycomb proteins in healthy cells, is a hallmark of senescence. One mechanism of reactivating Polycomb-silenced genes is mediated by the epigenetic factor ZRF1, which as...
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Fluorescence-based phenotypic selection allows forward genetic screens in haploid human cells.
Published: June, 2012

Abstract: The isolation of haploid cell lines has recently allowed the power of forward genetic screens to be applied to mammalian cells. The interest in applying this powerful genetic approach to a mammalian system is only tempered by the limited utility o...
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Histone demethylase Kdm4b functions as a co-factor of C/EBPβ to promote mitotic clonal expansion during differentiation of 3T3-L1 preadipocytes.
Published: June, 2012

Abstract: CCAAT/enhancer-binding protein (C/EBP) β is required for both mitotic clonal expansion (MCE) and terminal adipocyte differentiation of 3T3-L1 preadipocytes. Although the role of C/EBPβ in terminal adipocyte differentiation is well defined, its mec...
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The Saccharomyces cerevisiae Hot1p regulated gene YHR087W (HGI1) has a role in translation upon high glucose concentration stress.
Published: June, 2012

Abstract: ABSTRACT: BACKGROUND: While growing in natural environments yeasts can be affected by osmotic stress provoked by high glucose concentrations. The response to this adverse condition requires the HOG pathway and involves transcriptional and posttran...
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Bovine polledness - an autosomal dominant trait with allelic heterogeneity.
Published: June, 2012

Abstract: The persistent horns are an important trait of speciation for the family Bovidae with complex morphogenesis taking place briefly after birth. The polledness is highly favourable in modern cattle breeding systems but serious animal welfare issues u...
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Topoisomerase II is required for the production of long Pol II gene transcripts in yeast.
Published: June, 2012

Abstract: The extent to which the DNA relaxation activities of eukaryotic topoisomerases (topo I and topo II) are redundant during gene transcription is unclear. Although both enzymes can often substitute for each other in vivo, studies in vitro had reveale...
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A Cell Cycle Role for the Epigenetic Factor CTCF-L/BORIS.
Published: June, 2012

Abstract: CTCF is a ubiquitous epigenetic regulator that has been proposed as a master keeper of chromatin organisation. CTCF-like, or BORIS, is thought to antagonise CTCF and has been found in normal testis, ovary and a large variety of tumour cells. The c...
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The CACCC-binding protein KLF3/BKLF represses a subset of KLF1/EKLF target genes and is required for proper erythroid maturation in vivo.
Published: June, 2012

Abstract: The CACCC-box binding protein Erythroid Krüppel-like Factor (EKLF/KLF1) is a master regulator that directs the expression of many important erythroid genes. We have previously shown that EKLF drives transcription of a second Klf, Basic Krüppel-lik...
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Extensive promoter hypermethylation and hypomethylation is associated with aberrant microRNA expression in chronic lymphocytic leukemia.
Published: June, 2012

Abstract: Dysregulated microRNA (miRNA) expression contributes to the pathogenesis of hematopoietic malignancies, including chronic lymphocytic leukemia (CLL). However, an understanding of the mechanisms that cause aberrant miRNA transcriptional control is ...
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Defective mitochondrial morphology and bioenergetic function in mice lacking the transcription factor YY1 in skeletal muscle
Published: June, 2012

Abstract: Formation, distribution and maintenance of functional mitochondria are achieved through dynamic processes that strictly depend on transcription of nuclear genes encoding for mitochondrial proteins. A large number of these mitochondrial genes conta...
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Targeted re-sequencing of the allohexaploid wheat exome.
Published: June, 2012

Abstract: Bread wheat, Triticum aestivum, is an allohexaploid composed of the three distinct ancestral genomes, A, B and D. The polyploid nature of the wheat genome together with its large size has limited our ability to generate the significant amount of s...
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GSK3-SCF(FBXW7) targets JunB for degradation in G2 to preserve chromatid cohesion before anaphase.
Published: June, 2012

Abstract: JunB, an activator protein-1 (AP-1) transcription factor component, acts either as a tumor suppressor or as an oncogene depending on the cell context. In particular, JunB is strongly upregulated in anaplastic lymphoma kinase (ALK)-positive anaplas...
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Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation.
Published: June, 2012

Abstract: In female (XX) mammals, one of the two X chromosomes is inactivated to ensure an equal dose of X-linked genes with males (XY). X-chromosome inactivation in eutherian mammals is mediated by the non-coding RNA Xist. Xist is not found in metatherians...
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PGC-1β regulates mouse carnitine-acylcarnitine translocase through estrogen-related receptor α
Published: June, 2012

Abstract: Carnitine/acylcarnitine translocase (CACT) is a mitochondrial-membrane carrier proteins that mediates the transport of acylcarnitines into the mitochondrial matrix for their oxidation by the mitochondrial fatty acid-oxidation pathway. CACT deficie...
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Phosphorylated and small ubiquitin-like modifier protein-deficient progesterone receptors drive proliferative gene signatures during breast cancer progression.
Published: June, 2012

Abstract: ABSTRACT: INTRODUCTION: Progesterone receptors (PR) are emerging as important breast cancer drivers. Phosphorylation events common to breast cancer cells impact PR transcriptional activity, in part by direct phosphorylation. PR-B but not PR-A isof...
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Cardioprotective mIGF-1/SIRT1 signaling induces hypertension, leukocytosis and fear response in mice.
Published: June, 2012

Abstract: Locally acting insulin growth factor isoform (mIGF-1) and the NAD+-dependent protein deacetylase SIRT1 are implicated in life and health span. Heart failure is associated with aging and is a major cause of death. mIGF-1 protects the heart from oxi...
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Functional characterization of the promoter region of the human EVI1 gene in acute myeloid leukemia: RUNX1 and ELK1 directly regulate its transcription.
Published: June, 2012

Abstract: The EVI1 gene (3q26) codes for a transcription factor with important roles in normal hematopoiesis and leukemogenesis. High expression of EVI1 is a negative prognostic indicator of survival in acute myeloid leukemia (AML) irrespective of the prese...
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Whole-Exome Sequencing and High Throughput Genotyping Identified KCNJ11 as the Thirteenth MODY Gene.
Published: June, 2012

Abstract: BACKGROUND: Maturity-onset of the young (MODY) is a clinically heterogeneous form of diabetes characterized by an autosomal-dominant mode of inheritance, an onset before the age of 25 years, and a primary defect in the pancreatic beta-cell functio...
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RNA Polymerase II Pausing Downstream of Core Histone Genes Is Different from Genes Producing Polyadenylated Transcripts.
Published: June, 2012

Abstract: Recent genome-wide chromatin immunoprecipitation coupled high throughput sequencing (ChIP-seq) analyses performed in various eukaryotic organisms, analysed RNA Polymerase II (Pol II) pausing around the transcription start sites of genes. In this s...
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Transcriptional networks driving enhancer function in the CFTR gene.
Published: June, 2012

Abstract: A critical cis-regulatory element for the cystic fibrosis transmembrane conductance regulator (CFTR) gene is located in intron 11, 100 kb distal to the promoter, with which it interacts. This sequence contains an intestine-selective enhancer and a...
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GSK3 Temporally Regulates Neurogenin 2 Proneural Activity in the Neocortex.
Published: June, 2012

Abstract: The neocortex is comprised of six neuronal layers that are generated in a defined temporal sequence. While extrinsic and intrinsic cues are known to regulate the sequential production of neocortical neurons, how these factors interact and function...
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Developmentally non-redundant SET domain proteins SUVH2 and SUVH9 are required for transcriptional gene silencing in Arabidopsis thaliana.
Published: June, 2012

Abstract: In plants, RNA-directed DNA methylation (RdDM) and related transcriptional gene silencing (TGS) involve members of the suppressor of variegation 3-9-homologous (SUVH) group of putative histone methyltransferases. Utilizing a reverse genetic approa...
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Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.
Published: June, 2012

Abstract: DNA cytosine methylation regulates gene expression in mammals. In bacteria, its role in gene expression and genome architecture is less understood. Here we perform high-throughput sequencing of bisulfite-treated genomic DNA from Escherichia coli K...
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SUMO-targeted ubiquitin E3 ligase RNF4 is required for the response of human cells to DNA damage.
Published: June, 2012

Abstract: Here we demonstrate that RNF4, a highly conserved small ubiquitin-like modifier (SUMO)-targeted ubiquitin E3 ligase, plays a critical role in the response of mammalian cells to DNA damage. Human cells in which RNF4 expression was ablated by siRNA ...
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FOXO1 in the ventromedial hypothalamus regulates energy balance.
Published: June, 2012

Abstract: The transcription factor FOXO1 plays a central role in metabolic homeostasis by regulating leptin and insulin activity in many cell types, including neurons. However, the neurons mediating these effects and the identity of the molecular targets th...
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Histone H2B Ubiquitylation Promotes Activity of the Intact Set1 Histone Methyltransferase Complex in Fission Yeast.
Published: June, 2012

Abstract: The methylation of histone H3 at lysine 4 (H3K4me) is critical for the formation of transcriptionally active chromatin in eukaryotes. In yeast, Drosophila, and some human cell lines, H3K4me is globally stimulated by the monoubiquitylation of histo...
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Preferential Genome Targeting of the CBP Co-Activator by Rel and Smad Proteins in Early Drosophila melanogaster Embryos.
Published: June, 2012

Abstract: CBP and the related p300 protein are widely used transcriptional co-activators in metazoans that interact with multiple transcription factors. Whether CBP/p300 occupies the genome equally with all factors or preferentially binds together with some...
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Multiple Histone Methyl and Acetyltransferase Complex Components Bind the HLA-DRA Gene.
Published: May, 2012

Abstract: Major histocompatibility complex class II (MHC-II) genes are fundamental components that contribute to adaptive immune responses. While characterization of the chromatin features at the core promoter region of these genes has been studied, the sco...
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Serum Response Factor and cAMP Response Element Binding Protein Are Both Required for Cocaine Induction of {Delta}FosB.
Published: May, 2012

Abstract: The molecular mechanism underlying induction by cocaine of ΔFosB, a transcription factor important for addiction, remains unknown. Here, we demonstrate a necessary role for two transcription factors, cAMP response element binding protein (CREB) an...
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Genome-Wide Characterization of Menin-Dependent H3K4me3 Reveals a Specific Role for Menin in the Regulation of Genes Implicated in MEN1-Like Tumors.
Published: May, 2012

Abstract: Inactivating mutations in the MEN1 gene predisposing to the multiple endocrine neoplasia type 1 (MEN1) syndrome can also cause sporadic pancreatic endocrine tumors. MEN1 encodes menin, a subunit of MLL1/MLL2-containing histone methyltransferase co...
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Myb-binding protein 1a (Mybbp1a) regulates levels and processing of Pre-ribosomal RNA.
Published: May, 2012

Abstract: Ribosomal RNA gene transcription, co-transcriptional processing and ribosome biogenesis are highly coordinated processes that are tightly regulated during cell growth. In this study, we discovered that Mybbp1a is associated with both the RNA Polym...
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Mus81-Mms4 function as a single heterodimer to cleave nicked intermediates in recombinational DNA repair.
Published: May, 2012

Abstract: The formation of crossovers is a fundamental genetic process. The XPF-family endonuclease, Mus81-Mms4 (Eme1), contributes significantly to crossing-over in eukaryotes. A key question is whether Mus81-Mms4 can process Holliday junctions that contai...
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The aryl hydrocarbon receptor ligands 2,3,7,8-tetrachlorodibenzo-p-dioxin and 3-methylcholanthrene regulate distinct genetic networks.
Published: May, 2012

Abstract: The two estrogen receptor isoforms ERα and ERβ mediate biological effects of estrogens, but are also targets for endocrine disruptive chemicals (EDCs), compounds that interfere with hormonal signaling. 3-Methylcholanthrene (3-MC) and dioxin (TCDD)...
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Functional Genomic Methods to Study Estrogen Receptor Activity.
Published: May, 2012

Abstract: Estrogen Receptor (ER) is a nuclear receptor that mediates the actions of estrogen and tamoxifen. ER is expressed in a major fraction of human breast cancers. Recently, genomic maps for estrogen- and tamoxifen-ER have been published. Interestingly...
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Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.
Published: May, 2012

Abstract: The generation of distinctive cell types that form different tissues and organs requires precise, temporal and spatial control of gene expression. This depends on specific cis-regulatory elements distributed in the non-coding DNA surrounding their...
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Evolution of Burkholderia pseudomallei in Recurrent Melioidosis.
Published: May, 2012

Abstract: Burkholderia pseudomallei, the etiologic agent of human melioidosis, is capable of causing severe acute infection with overwhelming septicemia leading to death. A high rate of recurrent disease occurs in adult patients, most often due to recrudesc...
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The Stat6-regulated KRAB domain zinc finger protein Zfp157 regulates the balance of lineages in mammary glands and compensates for loss of Gata-3.
Published: May, 2012

Abstract: Lineage commitment studies in mammary glands have focused on identifying cell populations that display stem or progenitor properties. However, the mechanisms that control cell fate have been incompletely explored. Herein we show that zinc finger p...
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The angiogenesis suppressor gene AKAP12 is under the epigenetic control of HDAC7 in endothelial cells.
Published: May, 2012

Abstract: Histone deacetylases (HDACs) are a family of 18 enzymes that deacetylate lysine residues of both histone and nonhistone proteins and to a large extent govern the process of angiogenesis. Previous studies have shown that specific inhibition of HDAC...
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HIF1A induces expression of the WASF3 metastasis-associated gene under hypoxic conditions.
Published: May, 2012

Abstract: The WASF3 (WAVE3) gene is an important mediator of cell motility, invasion and metastasis and is expressed at high levels in some advanced stage tumors. In our survey of breast cancer cells, we now demonstrate that exposure to hypoxic conditions i...
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The linker histone plays a dual role during gametogenesis in S. cerevisiae.
Published: May, 2012

Abstract: The differentiation of gametes involves dramatic changes to chromatin, affecting transcription, meiosis, and cell morphology. Sporulation in S. cerevisiae shares many chromatin features with spermatogenesis, including a ten-fold compaction of the ...
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BIM promoter directly targeted by EBNA3C in polycomb-mediated repression by EBV.
Published: May, 2012

Abstract: Detailed analyses of the chromatin around the BIM promoter has revealed that latent Epstein-Barr virus (EBV) triggers the recruitment of polycomb repressive complex 2 (PRC2) core subunits and the trimethylation of histone H3 lysine 27 (H3K27me3) a...
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Glucose-Dependent Regulation of NR2F2 Promoter and Influence of SNP-rs3743462 on Whole Body Insulin Sensitivity.
Published: May, 2012

Abstract: BACKGROUND: The Nuclear Receptor 2F2 (NR2F2/COUP-TFII) heterozygous knockout mice display low basal insulinemia and enhanced insulin sensitivity. We previously established that insulin represses NR2F2 gene expression in pancreatic β-cells. The cis...
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Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO.
Published: May, 2012

Abstract: The molecular role of corepressors is poorly understood. Here, we studied the transcriptional function of the corepressor SMRT during terminal adipogenesis. Genome-wide DNA-binding profiling revealed that this corepressor is predominantly located ...
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A Long ncRNA Links Copy Number Variation to a Polycomb/Trithorax Epigenetic Switch in FSHD Muscular Dystrophy.
Published: May, 2012

Abstract: Repetitive sequences account for more than 50% of the human genome. Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal-dominant disease associated with reduction in the copy number of the D4Z4 repeat mapping to 4q35. By an unknown mecha...
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The histone demethylase Kdm3a is essential to progression through differentiation.
Published: May, 2012

Abstract: Histone demethylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity by still poorly understood mechanisms. Here, we examined the role of histone demethylase K...
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Hsp90 globally targets paused RNA polymerase to regulate gene expression in response to environmental stimuli.
Published: May, 2012

Abstract: The molecular chaperone Heat shock protein 90 (Hsp90) promotes the maturation of several important proteins and plays a key role in development, cancer progression, and evolutionary diversification. By mapping chromatin-binding sites of Hsp90 at h...
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Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation.
Published: May, 2012

Abstract: The p63 transcription factor (TP63) is critical in development, growth and differentiation of stratifying epithelia. This is highlighted by the severity of congenital abnormalities caused by TP63 mutations in humans, the dramatic phenotypes in kno...
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RBE controls microRNA164 expression to effect floral organogenesis.
Published: May, 2012

Abstract: The establishment and maintenance of organ boundaries are vital for animal and plant development. In the Arabidopsis flower, three microRNA164 genes (MIR164a, b and c) regulate the expression of CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, which encode ...
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Differential Modulation of the Oligodendrocyte Transcriptome by Sonic Hedgehog and Bone Morphogenetic Protein 4 via Opposing Effects on Histone Acetylation.
Published: May, 2012

Abstract: Differentiation of oligodendrocyte progenitor cells (OPCs) into mature oligodendrocytes is regulated by the interplay between extrinsic signals and intrinsic epigenetic determinants. In this study, we analyze the effect that the extracellular liga...
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The Flk1-cre Mediated Deletion of ETV2 Defines Its Narrow Temporal Requirement During Embryonic Hematopoietic Development.
Published: May, 2012

Abstract: During embryonic development, the emergence of hematopoiesis and vasculogenesis is tightly associated, with many transcription factors implicated in both developmental processes. Among those factors, ETV2 acts at the top of the hierarchy and contr...
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High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation.
Published: May, 2012

Abstract: Chromatin immunoprecipitation (ChIP) is an assay for interrogating protein-DNA interactions that is increasingly being used for drug target discovery and screening applications. Currently the complexity of the protocol and the amount of hands-on t...
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Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster.
Published: May, 2012

Abstract: Differentiation is accompanied by extensive epigenomic reprogramming, leading to the repression of stemness factors and the transcriptional maintenance of activated lineage-specific genes. Here we use the mammalian Hoxa cluster of developmental ge...
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Genome-wide search reveals the existence of a limited number of thyroid hormone receptor alpha target genes in cerebellar neurons.
Published: May, 2012

Abstract: Thyroid hormone (T3) has a major influence on cerebellum post-natal development. The major phenotypic landmark of exposure to low levels of T3 during development (hypothyroidism) in the cerebellum is the retarded inward migration of the most numer...
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piRNA-mediated transgenerational inheritance of an acquired trait.
Published: May, 2012

Abstract: The maintenance of genome integrity is an essential trait to the successful transmission of genetic information. In animal germ cells, piRNAs guide PIWI proteins to silence transposable elements (TEs) in order to maintain genome integrity. In inse...
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Disruption of RAB40AL function leads to Martin-Probst syndrome, a rare X-linked multisystem neurodevelopmental human disorder.
Published: May, 2012

Abstract: Background and aim Martin-Probst syndrome (MPS) is a rare X-linked disorder characterised by deafness, cognitive impairment, short stature and distinct craniofacial dysmorphisms, among other features. The authors sought to identify the causative m...
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Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing.
Published: May, 2012

Abstract: Increasing evidence suggests that chromatin modifications have important roles in modulating constitutive or alternative splicing. Here we demonstrate that the PWWP domain of the chromatin-associated protein Psip1/Ledgf can specifically recognize ...
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Characterization of glomerular diseases using proteomic analysis of laser capture microdissected glomeruli.
Published: May, 2012

Abstract: The application of molecular techniques to characterize clinical kidney biopsies has the potential to provide insights into glomerular diseases that cannot be revealed by traditional renal pathology. The present work is a proof-of-concept approach...
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SOX7 regulates the expression of VE-cadherin in the haemogenic endothelium at the onset of haematopoietic development.
Published: May, 2012

Abstract: At early stages of vertebrate ontogeny, blood and endothelial cells develop from a common mesodermal progenitor, the haemangioblast. Upon haematopoietic commitment, the haemangioblast generates blood precursors through populations of endothelial c...
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Kdm2b promotes induced pluripotent stem cell generation by facilitating gene activation early in reprogramming.
Published: May, 2012

Abstract: Transcription-factor-directed reprogramming from somatic cells to induced pluripotent stem cells (iPSCs) is by nature an epigenetic process of cell fate change. Previous studies have demonstrated that this inefficient process can be facilitated by...
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Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.
Published: May, 2012

Abstract: This protocol describes the batch isolation of tissue-specific chromatin for immunoprecipitation (BiTS-ChIP) for analysis of histone modifications, transcription factor binding, or polymerase occupancy within the context of a multicellular organis...
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Can soy phytoestrogens decrease DNA methylation in BRCA1 and BRCA2 oncosuppressor genes in breast cancer?
Published: May, 2012

Abstract: Although soy phytoestrogens have been postulated to exert a protective effect against breast cancer, the attendant mechanisms, in particular epigenetics underpinnings, have remained elusive. We investigated the putative effects on DNA methylation ...
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Antiproliferative Effects of DNA Methyltransferase 3B Depletion Are Not Associated with DNA Demethylation.
Published: May, 2012

Abstract: Silencing of genes by hypermethylation contributes to cancer progression and has been shown to occur with increased frequency at specific genomic loci. However, the precise mechanisms underlying the establishment and maintenance of aberrant methyl...
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LINT, a Novel dL(3)mbt-Containing Complex, Represses Malignant Brain Tumour Signature Genes.
Published: May, 2012

Abstract: Mutations in the l(3)mbt tumour suppressor result in overproliferation of Drosophila larval brains. Recently, the derepression of different gene classes in l(3)mbt mutants was shown to be causal for transformation. However, the molecular mechanism...
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Dynamic deposition of histone variant h3.3 accompanies developmental remodeling of the Arabidopsis transcriptome.
Published: May, 2012

Abstract: In animals, replication-coupled histone H3.1 can be distinguished from replication-independent histone H3.3. H3.3 variants are enriched at active genes and their promoters. Furthermore, H3.3 is specifically incorporated upon gene activation. Histo...
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Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant.
Published: May, 2012

Abstract: Genetically identical cells grown in the same culture display striking cell-to-cell heterogeneity in gene expression and other traits. A crucial challenge is to understand how much of this heterogeneity reflects the noise tolerance of a robust sys...
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Transient neonatal diabetes mellitus gene Zac1 impairs insulin secretion in mice through Rasgrf1.
Published: April, 2012

Abstract: Biallelic expression of the imprinted gene ZAC1/PLAGL1 underlies ∼60% of all cases of transient neonatal diabetes mellitus (TNDM) which present with low perinatal insulin secretion. Molecular targets of ZAC1 misexpression in pancreatic β-cells are...
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The SEC family of RNA Polymerase II elongation factors: gene target specificity and transcriptional output.
Published: April, 2012

Abstract: The elongation stage of transcription is highly regulated in metazoans. We previously purified the AFF1/AFF4-containing Super Elongation Complex (SEC) as a major regulator of development and cancer pathogenesis. Here, we report the biochemical iso...
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iASPP inhibits p53-independent apoptosis by inhibiting transcriptional activity of p63/p73 on promoters of proapoptotic genes.
Published: April, 2012

Abstract: The ability to induce apoptosis is the most important tumor-suppression function of p53. Inhibitory member of apoptosis-stimulating protein of p53 family (iASPP) is an apoptotic-specific regulator of p53. iASPP suppresses apoptosis by inhibiting t...
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Bloom's Syndrome and PICH Helicases Cooperate with Topoisomerase IIα in Centromere Disjunction before Anaphase.
Published: April, 2012

Abstract: Centromeres are specialized chromosome domains that control chromosome segregation during mitosis, but little is known about the mechanisms underlying the maintenance of their integrity. Centromeric ultrafine anaphase bridges are physiological DNA...
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Dendritic Cells Activated by IFN-γ/STAT1 Express IL-31 Receptor and Release Proinflammatory Mediators upon IL-31 Treatment.
Published: April, 2012

Abstract: IL-31 is a T cell-derived cytokine that signals via a heterodimeric receptor composed of IL-31Rα and oncostatin M receptor β. Although several studies have aimed to investigate IL-31-mediated effects, the biological functions of this cytokine are ...
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Uncovering cis-regulatory sequence requirements for context specific transcription factor binding.
Published: April, 2012

Abstract: The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between d...
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Genome Wide Analysis Of Pax8 Binding Provides New Insights Into Thyroid Functions.
Published: April, 2012

Abstract: ABSTRACT: BACKGROUND: The transcription factor Pax8 is essential for the differentiation of thyroid cells. However, there are few data on genes transcriptionally regulated by Pax8 other than thyroid-related genes. To better understand the role of ...
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Global analysis of the regulon of the transcriptional repressor LexA, a key component of the SOS response in Mycobacterium tuberculosis.
Published: April, 2012

Abstract: The DNA damage response is crucial for bacterial survival. The transcriptional repressor LexA is a key component of the SOS response, the main mechanism for the regulation of DNA repair genes in many bacteria. In contrast, in mycobacteria gene ind...
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Performance comparison of benchtop high-throughput sequencing platforms.
Published: April, 2012

Abstract: Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can gen...
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A novel reporter system for bacterial and mammalian cells based on the non-ribosomal peptide indigoidine.
Published: April, 2012

Abstract: The biosynthesis of non-ribosomal peptides, many of which have pharmaceutical activities, is an evolutionary privilege of microorganisms. Capitalizing on the universal set of the Streptomyces lavendulae non-ribosomal peptide synthase BpsA and the ...
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Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm.
Published: April, 2012

Abstract: Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selecti...
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Preparation and use of Xenopus egg extracts to study DNA replication and chromatin associated proteins.
Published: April, 2012

Abstract: The use of cell-free extracts prepared from eggs of the South African clawed toad, Xenopus laevis, has led to many important discoveries in cell cycle research. These egg extracts recapitulate the key nuclear transitions of the eukaryotic cell cyc...
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Developmental silencing of the AtTERT gene is associated with increased H3K27me3 loading and maintenance of its euchromatic environment.
Published: April, 2012

Abstract: Telomerase, an enzyme responsible for the maintenance of linear chromosome ends, is precisely regulated during plant development. In animals, involvement of the epigenetic state of the telomerase reverse transcriptase (TERT) gene in the complex re...
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A dual role of linker histone H1.4 Lys 34 acetylation in transcriptional activation.
Published: April, 2012

Abstract: The linker histone H1 is a key player in chromatin organization, yet our understanding of the regulation of H1 functions by post-translational modifications is very limited. We provide here the first functional characterization of H1 acetylation. ...
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Breast Cancer Cells Induce Stromal Fibroblasts to Secrete ADAMTS1 for Cancer Invasion through an Epigenetic Change.
Published: April, 2012

Abstract: Microenvironment plays an important role in cancer development. We have reported that the cancer-associated stromal cells exhibit phenotypic and functional changes compared to stromal cells neighboring to normal tissues. However, the molecular mec...
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HDAC1 Regulates Fear Extinction in Mice.
Published: April, 2012

Abstract: Histone acetylation has been implicated with the pathogenesis of neuropsychiatric disorders and targeting histone deacetylases (HDACs) using HDAC inhibitors was shown to be neuroprotective and to initiate neuroregenerative processes. However, litt...
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Miz1 Is a Critical Repressor of cdkn1a during Skin Tumorigenesis.
Published: April, 2012

Abstract: The transcription factor Miz1 forms repressive DNA-binding complexes with the Myc, Gfi-1 and Bcl-6 oncoproteins. Known target genes of these complexes encode the cyclin-dependent kinase inhibitors (CKIs) cdkn2b (p15(Ink4)), cdkn1a (p21(Cip1)), and...
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Kruppel-like factor 15 regulates skeletal muscle lipid flux and exercise adaptation.
Published: April, 2012

Abstract: The ability of skeletal muscle to enhance lipid utilization during exercise is a form of metabolic plasticity essential for survival. Conversely, metabolic inflexibility in muscle can cause organ dysfunction and disease. Although the transcription...
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Yin Yang 1 Deficiency in Skeletal Muscle Protects against Rapamycin-Induced Diabetic-like Symptoms through Activation of Insulin/IGF Signaling.
Published: April, 2012

Abstract: Rapamycin and its derivatives are mTOR inhibitors used in tissue transplantation and cancer therapy. A percentage of patients treated with these inhibitors develop diabetic-like symptoms, but the molecular mechanisms are unknown. We show here that...
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Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding.
Published: April, 2012

Abstract: Oncidium is an important ornamental plant but the study of its functional genomics is difficult. Erycina pusilla is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period,...
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The RNA-Binding Protein Human Antigen R Controls Global Changes in Gene Expression during Schwann Cell Development.
Published: April, 2012

Abstract: An important prerequisite to myelination in peripheral nerves is the establishment of one-to-one relationships between axons and Schwann cells. This patterning event depends on immature Schwann cell proliferation, apoptosis, and morphogenesis, whi...
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Fast Homozygosity Mapping and Identification of a Zebrafish ENU-Induced Mutation by Whole-Genome Sequencing.
Published: April, 2012

Abstract: Forward genetics using zebrafish is a powerful tool for studying vertebrate development through large-scale mutagenesis. Nonetheless, the identification of the molecular lesion is still laborious and involves time-consuming genetic mapping. Here, ...
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Characterization of endolysin from a Salmonella Typhimurium-infecting bacteriophage SPN1S.
Published: April, 2012

Abstract: The full genome sequence of bacteriophage SPN1S, which infects Salmonella, contains genes that encode homologues of holin, endolysin and Rz/Rz1-like accessory proteins, which are 4 phage lysis proteins. The ability of these proteins to lyse Escher...
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A hindbrain-repressive Wnt3a/Meis3/Tsh1 circuit promotes neuronal differentiation and coordinates tissue maturation.
Published: April, 2012

Abstract: During development, early inducing programs must later be counterbalanced for coordinated tissue maturation. In Xenopus laevis embryos, activation of the Meis3 transcription factor by a mesodermal Wnt3a signal lies at the core of the hindbrain dev...
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Rev-erbα and Rev-erbβ coordinately protect the circadian clock and normal metabolic function.
Published: April, 2012

Abstract: The nuclear receptor Rev-erbα regulates circadian rhythm and metabolism, but its effects are modest and it has been considered to be a secondary regulator of the cell-autonomous clock. Here we report that depletion of Rev-erbα together with closel...
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UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair.
Published: April, 2012

Abstract: Transcription-coupled nucleotide-excision repair (TC-NER) is a subpathway of NER that efficiently removes the highly toxic RNA polymerase II blocking lesions in DNA. Defective TC-NER gives rise to the human disorders Cockayne syndrome and UV-sensi...
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A GATA Transcription Factor Recruits Hda1 in Response to Reduced Tor1 Signaling to Establish a Hyphal Chromatin State in Candida albicans.
Published: April, 2012

Abstract: Candida albicans is an important opportunistic fungal pathogen of immunocompromised individuals. One critical virulence attribute is its morphogenetic plasticity. Hyphal development requires two temporally linked changes in promoter chromatin, whi...
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Frequent aberrant expression of the human ether à go-go (hEAG1) potassium channel in head and neck cancer: pathobiological mechanisms and clinical implications.
Published: March, 2012

Abstract: Compelling evidence indicates that the human ether-à-go-go voltage-gated potassium channels (hEAG1) may represent new valuable membrane therapeutic targets and diagnostic/prognostic biomarkers in various cancers. This study is the first to investi...
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ErbB2-Driven Breast Cancer Cell Invasion Depends on a Complex Signaling Network Activating Myeloid Zinc Finger-1-Dependent Cathepsin B Expression.
Published: March, 2012

Abstract: Aberrant ErbB2 receptor tyrosine kinase activation in breast cancer is strongly linked to an invasive disease. The molecular basis of ErbB2-driven invasion is largely unknown. We show that cysteine cathepsins B and L are elevated in ErbB2 positive...
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A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli.
Published: March, 2012

Abstract: ABSTRACT: BACKGROUND: Recombinant protein production is a process of great industrial interest, with products that range from pharmaceuticals to biofuels. Since high level production of recombinant protein imposes significant stress in the host or...
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Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.
Published: March, 2012

Abstract: Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here we present sequential ChIP-bisulfite-sequen...
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The lhx2 transcription factor controls thalamocortical axonal guidance by specific regulation of robo1 and robo2 receptors.
Published: March, 2012

Abstract: The assembly of neural circuits is dependent upon the generation of specific neuronal subtypes, each subtype displaying unique properties that direct the formation of selective connections with appropriate target cells. Actions of transcription fa...
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Inflammasome-Activated Caspase 7 Cleaves PARP1 to Enhance the Expression of a Subset of NF-κB Target Genes.
Published: March, 2012

Abstract: Caspase 1 is part of the inflammasome, which is assembled upon pathogen recognition, while caspases 3 and/or 7 are mediators of apoptotic and nonapoptotic functions. PARP1 cleavage is a hallmark of apoptosis yet not essential, suggesting it has an...
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DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees.
Published: March, 2012

Abstract: In honey bees (Apis mellifera), the development of a larva into either a queen or worker depends on differential feeding with royal jelly and involves epigenomic modifications by DNA methyltransferases. To understand the role of DNA methylation in...
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Analysis of Chromatin Dynamics during Glucocorticoid Receptor Activation.
Published: March, 2012

Abstract: Steroid hormone receptors initiate a genetic program tightly regulated by the chromatin environment of the responsive regions. Using the glucocorticoid receptor (GR) as a model factor for transcriptional initiation, we classified chromatin structu...
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A dual Role for the dREAM/MMB complex in the regulation of differentiation-specific E2F/RB target genes.
Published: March, 2012

Abstract: E2F and RB proteins regulate the expression of genes involved in cell cycle progression, apoptosis, differentiation, and development. Recent studies indicate that they function as part of an evolutionary conserved multi-protein complex, termed dRE...
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DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation.
Published: March, 2012

Abstract: Alternative messenger RNA splicing is the main reason that vast mammalian proteomic complexity can be achieved with a limited number of genes. Splicing is physically and functionally coupled to transcription, and is greatly affected by the rate of...
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Low-Dose Cd Induces Hepatic Gene Hypermethylation, along with the Persistent Reduction of Cell Death and Increase of Cell Proliferation in Rats and Mice.
Published: March, 2012

Abstract: BACKGROUND: Cadmium (Cd) is classified as a human carcinogen probably associated with epigenetic changes. DNA methylation is one of epigenetic mechanisms by which cells control gene expression. Therefore, the present study genome-widely screened t...
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Deconstruction of the SS18-SSX fusion oncoprotein complex: insights into disease etiology and therapeutics.
Published: March, 2012

Abstract: Synovial sarcoma is a translocation-associated sarcoma where the underlying chromosomal event generates SS18-SSX fusion transcripts. In vitro and in vivo studies have shown that the SS18-SSX fusion oncoprotein is both necessary and sufficient to s...
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Genetic and Epigenetic Determinants of Neurogenesis and Myogenesis.
Published: March, 2012

Abstract: The regulatory networks of differentiation programs have been partly characterized; however, the molecular mechanisms of lineage-specific gene regulation by highly similar transcription factors remain largely unknown. Here we compare the genome-wi...
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Mammalian HCA66 protein is required for both ribosome synthesis and centriole duplication.
Published: March, 2012

Abstract: Ribosome production, one of the most energy-consuming biosynthetic activities in living cells, is adjusted to growth conditions and coordinated with the cell cycle. Connections between ribosome synthesis and cell cycle progression have been descri...
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Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana.
Published: March, 2012

Abstract: Nucleosomes package eukaryotic DNA and are composed of four different histone proteins, designated H3, H4, H2A, and H2B. Histone H3 has two main variants, H3.1 and H3.3, which show different genomic localization patterns in animals. We profiled H3...
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DLK2 is a transcriptional target of KLF4 in the early stages of adipogenesis.
Published: March, 2012

Abstract: The epidermal growth factor-like protein DLK2, highly homologous to DLK1, has been identified as a modulator of adipogenesis in vitro. Knocking down Dlk2 expression prevents adipogenesis of 3T3-L1 cells but enhances that of the mesenchymal cell li...
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Proteome analysis of Acetobacter pasteurianus during acetic acid fermentation.
Published: March, 2012

Abstract: Acetic acid bacteria (AAB) are Gram-negative, strictly aerobic microorganisms that show a unique resistance to ethanol (EtOH) and acetic acid (AcH). Members of the Acetobacter and Gluconacetobacter genera are capable of transforming EtOH into AcH ...
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Identification and characterization of ToRC, a novel ISWI-containing ATP-dependent chromatin assembly complex.
Published: March, 2012

Abstract: SNF2-like motor proteins, such as ISWI, cooperate with histone chaperones in the assembly and remodeling of chromatin. Here we describe a novel, evolutionarily conserved, ISWI-containing complex termed ToRC (Toutatis-containing chromatin remodelin...
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Genome-wide evaluation of histone methylation changes associated with leaf senescence in Arabidopsis.
Published: March, 2012

Abstract: Leaf senescence is the orderly dismantling of older tissue that allows recycling of nutrients to developing portions of the plant and is accompanied by major changes in gene expression. Histone modifications correlate to levels of gene expression,...
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Resveratrol Inhibits KSHV Reactivation by Lowering the Levels of Cellular EGR-1.
Published: March, 2012

Abstract: In the field of herpesvirus research, the exact molecular mechanism by which such viruses reactivate from latency remains elusive. Kaposi's sarcoma-associated herpesvirus (KSHV) primarily exists in a latent state, while only 1-3% of cells support ...
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CBX4-mediated SUMO modification regulates BMI1 recruitment at sites of DNA damage.
Published: March, 2012

Abstract: Polycomb group (PcG) proteins are involved in epigenetic silencing where they function as major determinants of cell identity, stem cell pluripotency and the epigenetic gene silencing involved in cancer development. Recently numerous PcG proteins,...
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Methylome analysis using MeDIP-seq with low DNA concentrations.
Published: March, 2012

Abstract: DNA methylation is an epigenetic mark that has a crucial role in many biological processes. To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome-wide analysis should be embraced. This in turn requires a t...
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Integrated epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells.
Published: March, 2012

Abstract: Epigenetic regulation of gene expression is commonly altered in human cancer. We have observed alterations of DNA methylation and microRNA expression that reflect the biology of bladder cancer. This common disease arises by distinct pathways with ...
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Chromatin-modifying enzymes as modulators of reprogramming.
Published: March, 2012

Abstract: Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling. Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic states of cells befor...
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Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells.
Published: March, 2012

Abstract: The generation of induced pluripotent stem cells (iPSCs) often results in aberrant epigenetic silencing of the imprinted Dlk1-Dio3 gene cluster, compromising the ability to generate entirely iPSC-derived adult mice ('all-iPSC mice'). Here, we show...
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Mutually exclusive binding of telomerase RNA and DNA by ku alters telomerase recruitment model.
Published: March, 2012

Abstract: In Saccharomyces cerevisiae, the Ku heterodimer contributes to telomere maintenance as a component of telomeric chromatin and as an accessory subunit of telomerase. How Ku binding to double-stranded DNA (dsDNA) and to telomerase RNA (TLC1) promote...
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Mapping and Functional Characterisation of a CTCF-Dependent Insulator Element at the 3' Border of the Murine Scl Transcriptional Domain.
Published: March, 2012

Abstract: The Scl gene encodes a transcription factor essential for haematopoietic development. Scl transcription is regulated by a panel of cis-elements spread over 55 kb with the most distal 3' element being located downstream of the neighbouring gene Map...
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RYBP Represses Endogenous Retroviruses and Preimplantation- and Germ Line-Specific Genes in Mouse Embryonic Stem Cells.
Published: March, 2012

Abstract: Polycomb repressive complexes (PRCs) are important chromatin regulators of embryonic stem (ES) cell function. RYBP binds Polycomb H2A monoubiquitin ligases Ring1A and Ring1B and has been suggested to assist PRC localization to their targets. Moreo...
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Pdgfrα and Flk1 are direct target genes of Mixl1 in differentiating embryonic stem cells.
Published: March, 2012

Abstract: The Mixl1 homeodomain protein plays a key role in mesendoderm patterning during embryogenesis, but its target genes remain to be identified. We compared gene expression in differentiating heterozygous Mixl1(GFP/w) and homozygous null Mixl1(GFP/Hyg...
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The rs3743205 SNP Is Important for the Regulation of the Dyslexia Candidate Gene DYX1C1 by Estrogen Receptor β and DNA Methylation.
Published: March, 2012

Abstract: Estrogen is involved in numerous physiological processes such as growth, differentiation, and function of the male and female reproductive tissues. In the developing brain, estrogen signaling has been linked to cognitive functions, such as learnin...
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EZH2 couples pancreatic regeneration to neoplastic progression.
Published: March, 2012

Abstract: Although the polycomb group protein Enhancer of Zeste Homolog 2 (EZH2) is well recognized for its role as a key regulator of cell differentiation, its involvement in tissue regeneration is largely unknown. Here we show that EZH2 is up-regulated fo...
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Widespread site-dependent buffering of human regulatory polymorphism.
Published: March, 2012

Abstract: The average individual is expected to harbor thousands of variants within non-coding genomic regions involved in gene regulation. However, it is currently not possible to interpret reliably the functional consequences of genetic variation within a...
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Small-molecule-induced DNA damage identifies alternative DNA structures in human genes.
Published: March, 2012

Abstract: Guanine-rich DNA sequences that can adopt non-Watson-Crick structures in vitro are prevalent in the human genome. Whether such structures normally exist in mammalian cells has, however, been the subject of active research for decades. Here we show...
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RNA Profiling and Chromatin Immunoprecipitation-Sequencing Reveal that PTF1a Stabilizes Pancreas Progenitor Identity via the Control of MNX1/HLXB9 and a Network of Other Transcription Factors.
Published: March, 2012

Abstract: Pancreas development is initiated by the specification and expansion of a small group of endodermal cells. Several transcription factors are crucial for progenitor maintenance and expansion, but their interactions and the downstream targets mediat...
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Dynamic MicroRNA Gene Transcription and Processing during T Cell Development.
Published: February, 2012

Abstract: By disrupting microRNA (miRNA) biogenesis, we previously showed that this pathway is critical for the differentiation and function of T cells. Although various cloning studies have shown that many miRNAs are expressed during T cell development, an...
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Transcriptional induction of salt-inducible kinase 1 by transforming growth factor β leads to negative regulation of type I receptor signaling in cooperation with the Smurf2 ubiquitin ligase.
Published: February, 2012

Abstract: Transforming growth factor β (TGFβ)1 regulates many physiological processes and requires control mechanisms to safeguard proper and timely action. We have previously described how negative regulation of TGFβ signaling is controlled by the serine/t...
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Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing.
Published: February, 2012

Abstract: Fetal chromosomal abnormalities are the most common reasons for invasive prenatal testing. Currently, G-band karyotyping and several molecular genetic methods have been established for diagnosis of chromosomal abnormalities. Although these testing...
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Human Histone Acetyltransferase 1 Protein Preferentially Acetylates H4 Histone Molecules in H3.1-H4 over H3.3-H4.
Published: February, 2012

Abstract: In mammalian cells, canonical histone H3 (H3.1) and H3 variant (H3.3) differ by five amino acids and are assembled, along with histone H4, into nucleosomes via distinct nucleosome assembly pathways. H3.1-H4 molecules are assembled by histone chape...
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Transcriptional Activation of the Adenoviral Genome Is Mediated by Capsid Protein VI
Published: February, 2012

Abstract: Gene expression of DNA viruses requires nuclear import of the viral genome. Human Adenoviruses (Ads), like most DNA viruses, encode factors within early transcription units promoting their own gene expression and counteracting cellular antiviral d...
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3T3 Cell Lines Stably Expressing Pax6 or Pax6(5a) – A New Tool Used for Identification of Common and Isoform Specific Target Genes
Published: February, 2012

Abstract: Pax6 and Pax6(5a) are two isoforms of the evolutionary conserved Pax6 gene often co-expressed in specific stochiometric relationship in the brain and the eye during development. The Pax6(5a) protein differs from Pax6 by having a 14 amino acid inse...
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Dual-Mode Modulation of Smad Signaling by Smad-Interacting Protein Sip1 Is Required for Myelination in the Central Nervous System
Published: February, 2012

Abstract: Myelination by oligodendrocytes in the central nervous system (CNS) is essential for proper brain function, yet the molecular determinants that control this process remain poorly understood. The basic helix-loop-helix transcription factors Olig1 a...
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Circadian rhythms govern cardiac repolarization and arrhythmogenesis
Published: February, 2012

Abstract: Sudden cardiac death exhibits diurnal variation in both acquired and hereditary forms of heart disease1,2, but the molecular basis of this variation is unknown. A common mechanism that underlies susceptibility to ventricular arrhythmias is abnorma...
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Polycomb repressive complex 2-dependent and -independent functions of Jarid2 in transcriptional regulation in Drosophila.
Published: February, 2012

Abstract: Jarid2 was recently identified as an important component of the mammalian Polycomb Repressive Complex 2 (PRC2), where it has a major effect on PRC2 recruitment in mouse embryonic stem cells. Although Jarid2 is conserved in Drosophila, it has not p...
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Two Cellular Protein Kinases, DNA-PK and PKA, Phosphorylate the Adenoviral L4-33K Protein and Have Opposite Effects on L1 Alternative RNA Splicing
Published: February, 2012

Abstract: Accumulation of the complex set of alternatively processed mRNA from the adenovirus major late transcription unit (MLTU) is subjected to a temporal regulation involving both changes in poly (A) site choice and alternative 39 splice site usage. We ...
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Kinetics of DNA methylation inheritance by the Dnmt1-including complexes during the cell cycle.
Published: February, 2012

Abstract: ABSTRACT: BACKGROUND: The clonal transmission of lineage-specific DNA methylation patterns in a mammalian genome during the cellular division is a crucial biological process controlled by the DNA methyltransferase Dnmt1, mainly. To investigate pos...
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The Receptor Tyrosine Kinase EphA2 Is a Direct Target Gene of Hypermethylated in Cancer 1 (HIC1).
Published: February, 2012

Abstract: The tumor suppressor gene hypermethylated in cancer 1 (HIC1), which encodes a transcriptional repressor, is epigenetically silenced in many human tumors. Here, we show that ectopic expression of HIC1 in the highly malignant MDA-MB-231 breast cance...
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The transcription factor Erg controls endothelial cell quiescence by repressing the activity of nuclear factor (NF)-κB p65.
Published: February, 2012

Abstract: The interaction of transcription factors with specific DNA sequences is critical for activation of gene expression programmes. In endothelial cells (EC), the transcription factor NFκB is important in the switch from quiescence to activation, and i...
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Opposing Functions of the ETS Factor Family Define Shh Spatial Expression in Limb Buds and Underlie Polydactyly
Published: February, 2012

Abstract: Sonic hedgehog (Shh) expression during limb development is crucial for specifying the identity and number of digits. The spatial pattern of Shh expression is restricted to a region called the zone of polarizing activity (ZPA), and this expression ...
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Anticheckpoint pathways at telomeres in yeast
Published: February, 2012

Abstract: Telomeres hide (or ‘cap’) chromosome ends from DNA-damage surveillance mechanisms that arrest the cell cycle and promote repair, but the checkpoint status of telomeres is not well understood. Here we characterize the response in Saccharomyces cere...
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RHBDF2 mutations are associated with tylosis, a familial esophageal cancer syndrome.
Published: February, 2012

Abstract: Tylosis esophageal cancer (TOC) is an autosomal-dominant syndrome characterized by palmoplantar keratoderma, oral precursor lesions, and a high lifetime risk of esophageal cancer. We have previously localized the TOC locus to a small genomic inter...
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A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq.
Published: February, 2012

Abstract: Deciphering the structure of gene regulatory networks across the tree of life remains one of the major challenges in postgenomic biology. We present a novel ChIP-seq workflow for the archaea using the model organism Halobacterium salinarum sp. NRC...
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Research Resource: The Pdx1 Cistrome of Pancreatic Islets.
Published: February, 2012

Abstract: The homeodomain transcription factor pancreas duodenal homeobox 1 (Pdx1, also known as insulin promoter factor 1) is a master regulator of pancreas development, as mice or humans lacking Pdx1 function are a pancreatic. Importantly, heterozygous mu...
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RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3.
Published: February, 2012

Abstract: Polycomb-repressive complex 1 (PRC1) has a central role in the regulation of heritable gene silencing during differentiation and development. PRC1 recruitment is generally attributed to interaction of the chromodomain of the core protein Polycomb ...
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High-throughput molecular diagnosis of von Willebrand diseaseby next generation sequencing methods.
Published: February, 2012

Abstract: Genetic analysis of von Willebrand disease by von Willebrand factor gene sequencing has not yet become routine practice. Nevertheless, the prospects for molecular diagnosis have changed dramatically in recent years with the unveiling of next-gener...
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Three-dimensional folding and functional organization principles of the Drosophila genome.
Published: February, 2012

Abstract: Chromosomes are the physical realization of genetic information and thus form the basis for its readout and propagation. Here we present a high-resolution chromosomal contact map derived from a modified genome-wide chromosome conformation capture ...
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Serial translocation by means of circular intermediates underlies colour sidedness in cattle.
Published: February, 2012

Abstract: Colour sidedness is a dominantly inherited phenotype of cattle characterized by the polarization of pigmented sectors on the flanks, snout and ear tips. It is also referred to as 'lineback' or 'witrik' (which means white back), as colour-sided ani...
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Polychlorinated biphenyls affect histone modification pattern in early development of rats: a role for androgen receptor-dependent modulation?
Published: February, 2012

Abstract: BACKGROUND: The epigenome represents an important target of environmental pollution. Early-life exposure to polychlorinated biphenyls (PCBs) modifies sex steroid enzymes and receptor transcription patterns. Steroid receptors, such as androgen rece...
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Connexin 43 reverses malignant phenotypes of glioma stem cells by modulating E-cadherin.
Published: February, 2012

Abstract: Malfunctioned gap junctional intercellular communication (GJIC) has been thought associated with malignant transformation of normal cells. However, the role of GJIC-related proteins such as connexins in sustaining the malignant behavior of cancer ...
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Nucleolar proteins with altered expression in leukemic cell lines.
Published: February, 2012

Abstract: The function of the nucleolus is intimately connected to cell proliferation, division and growth. Many cancer cells have enlarged nucleoli, and several nucleolar proteins have been linked to tumorigenesis. In order to find proteins whose expressio...
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Conserved molecular interactions within the HBO1 acetyltransferase complexes regulate cell proliferation.
Published: February, 2012

Abstract: Acetyltransferase complexes of the MYST family with distinct substrate specificities and functions maintain a conserved association with different ING tumor suppressor proteins. ING complexes containing the HBO1 acetylase are a major source of his...
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Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.
Published: February, 2012

Abstract: While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic ...
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Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
Published: February, 2012

Abstract: Chromatin modifications are associated with many aspects of gene expression, yet their role in cellular transitions during development remains elusive. Here, we use a new approach to obtain cell type-specific information on chromatin state and RNA...
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Epigenetic regulation of the latency-associated region of Marek's disease virus in tumor-derived T-cell lines and primary lymphoma.
Published: February, 2012

Abstract: Meq is the major Marek's disease virus (MDV)-encoded oncoprotein and is essential for T-cell lymphomagenesis. Meq and several noncoding RNAs, including three microRNA (MiR) clusters, are expressed from the repeats of the MDV genome during latent i...
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Histone deacetylase 6 (HDAC6) is an essential modifier of glucocorticoid-induced hepatic gluconeogenesis.
Published: February, 2012

Abstract: In the current study, we investigated the importance of histone deacetylase (HDAC)6 for glucocorticoid receptor-mediated effects on glucose metabolism and its potential as a therapeutic target for the prevention of glucocorticoid-induced diabetes....
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Translocation capture sequencing: a method for high throughput mapping of chromosomal rearrangements.
Published: January, 2012

Abstract: Chromosomal translocations require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are involved in producing leukemias, lymphomas and sarcomas. Translocations are frequent, clonal and ...
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Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages.
Published: January, 2012

Abstract: ABSTRACT: BACKGROUND: The liver X receptors (LXRs) are oxysterol sensing nuclear receptors with multiple effects on metabolism and immune cells. However, the complete genome-wide cistrome of LXR in cells of human origin has not yet been provided. ...
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Histone deacetylase 1 is required for Carbamazepine-induced CYP3A4 expression.
Published: January, 2012

Abstract: Carbamazepine (CBZ) is a commonly prescribed antiepileptic drug. Adverse effects and drug-drug interaction are the two major concerns for its clinic application. CBZ is mainly metabolized by cytochrome P450 (CYP) 3A4, a strong inducer of CYP3A4 as...
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Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.
Published: January, 2012

Abstract: ABSTRACT: BACKGROUND: DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylatio...
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A novel retinoblastoma therapy from genomic and epigenetic analyses
Published: January, 2012

Abstract: Retinoblastoma is an aggressive childhood cancer of the developing retina that is initiated by the biallelic loss of RB1. Tumours progress very quickly following RB1 inactivation but the underlying mechanism is not known. Here we show that the ret...
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Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia.
Published: January, 2012

Abstract: T cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling. In this study we report the presence of loss-of-function mutations and deletions of the EZH2 and SUZ12 g...
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Nonoverlapping functions of the Polycomb group Cbx family of proteins in embryonic stem cells.
Published: January, 2012

Abstract: Polycomb group proteins are essential regulators of cell fate decisions during embryogenesis. In mammals, at least five different Cbx proteins (Cbx2, Cbx4, Cbx6, Cbx7, and Cbx8) are known to associate with the core Polycomb repressive complex 1 (P...
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RAD tag sequencing as a source of SNP markers in Cynara cardunculus L.
Published: January, 2012

Abstract: ABSTRACT: BACKGROUND: The globe artichoke (Cynara cardunculus L. var. scolymus) genome is relatively poorly explored, especially compared to those of the other major Asteraceae crops sunflower and lettuce. No SNP markers are in the public domain....
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dSet1 is the main H3K4 di- and tri-methyltransferase throughout Drosophila development.
Published: January, 2012

Abstract: In eukaryotes, the post-translational addition of methyl groups to histone H3 lysine 4 (H3K4) plays key roles in maintenance and establishment of appropriate gene expression patterns and chromatin states. We report here that an essential locus wit...
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The cytokine temporal profile in rat cortex after controlled cortical impact.
Published: January, 2012

Abstract: Cerebral inflammatory responses may initiate secondary cascades following traumatic brain injury (TBI). Changes in the expression of both cytokines and chemokines may activate, regulate, and recruit innate and adaptive immune cells associated with...
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Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity.
Published: December, 2011

Abstract: The TET family of FE(II) and 2-oxoglutarate-dependent enzymes (Tet1/2/3) promote DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which they further oxidize into 5-formylcytosine and 5-carboxylcytosine. Tet1 is r...
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High-Mobility Group A1 Protein: A New Coregulator of Peroxisome Proliferator-Activated Receptor-γ-Mediated Transrepression in the Vasculature.
Published: December, 2011

Abstract: Rationale:The nuclear receptor peroxisome proliferator-activated receptor-γ (PPARγ) is an important regulator of gene transcription in vascular cells and mediates the vascular protection observed with antidiabetic glitazones.Objective:To determine...
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The little elongation complex regulates small nuclear RNA transcription.
Published: December, 2011

Abstract: Eleven-nineteen lysine-rich leukemia (ELL) participates in the super elongation complex (SEC) with the RNA polymerase II (Pol II) CTD kinase P-TEFb. SEC is a key regulator in the expression of HOX genes in mixed lineage leukemia (MLL)-based hemato...
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Adaptation to P element transposon invasion in Drosophila melanogaster.
Published: December, 2011

Abstract: Transposons evolve rapidly and can mobilize and trigger genetic instability. Piwi-interacting RNAs (piRNAs) silence these genome pathogens, but it is unclear how the piRNA pathway adapts to invasion of new transposons. In Drosophila, piRNAs are en...
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Caenorhabditis elegans Heterochromatin Protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism.
Published: December, 2011

Abstract: ABSTRACT: BACKGROUND: Heterochromatin protein 1 (HP1) family proteins have a well-characterized role in heterochromatin packaging and gene regulation. Their function in organismal development, however, is less well understood. Here we used genome...
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Characterization of a proximal Sp1 response element in the mouse Dlk2 gene promoter.
Published: December, 2011

Abstract: ABSTRACT: BACKGROUND: DLK2 is an EGF-like membrane protein, closely related to DLK1, which is involved in adipogenesis. Both proteins interact with the NOTCH1 receptor and are able to modulate its activation. The expression of the gene Dlk2 is co...
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A small molecule differentiation inducer increases insulin production by pancreatic β cells.
Published: December, 2011

Abstract: New drugs for preserving and restoring pancreatic β-cell function are critically needed for the worldwide epidemic of type 2 diabetes and the cure for type 1 diabetes. We previously identified a family of neurogenic 3,5-disubstituted isoxazoles (I...
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Second order regulator Collier directly controls intercalary-specific segment polarity gene expression.
Published: December, 2011

Abstract: In Drosophila, trunk metamerization is established by a cascade of segmentation gene activities: the gap genes, the pair rule genes, and the segment polarity genes. In the anterior head, metamerization requires also gap-like genes and segment pola...
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Regulation of cell growth by Notch signaling and its differential requirement in normal vs. tumor-forming stem cells in Drosophila.
Published: December, 2011

Abstract: Cancer stem cells (CSCs) are postulated to be a small subset of tumor cells with tumor-initiating ability that shares features with normal tissue-specific stem cells. The origin of CSCs and the mechanisms underlying their genesis are poorly unders...
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cAMP response element-binding protein is a primary hub of activity-driven neuronal gene expression.
Published: December, 2011

Abstract: Long-lasting forms of neuronal plasticity require de novo gene expression, but relatively little is known about the events that occur genome-wide in response to activity in a neuronal network. Here, we unveil the gene expression programs initiated...
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The Chromatin Binding Protein HMGN1 Regulates the Expression of Methyl CpG Binding Protein 2 (MECP2) and Affects the Behavior of Mice.
Published: December, 2011

Abstract: High Mobility Group N1 protein (HMGN1), a nucleosomal binding protein that affects the structure and function of chromatin, is encoded by a gene located on chromosome 21, and is overexpressed in Down syndrome, one of the most prevalent genomic dis...
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Genome-wide profiling of LXR, RXR and PPARα in mouse liver reveals extensive sharing of binding sites.
Published: December, 2011

Abstract: The liver X receptors (LXRs) are nuclear receptors that form permissive heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism in the liver. We have recently shown that RXR agonist-induced hypertriglyceridemia...
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Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA.
Published: December, 2011

Abstract: Across vertebrate genomes methylation of cytosine residues within the context of CpG dinucleotides is a pervasive epigenetic mark that can impact gene expression and has been implicated in various developmental and disease-associated processes. Se...
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Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution.
Published: December, 2011

Abstract: Chromatin immunoprecipitation (ChIP-chip and ChIP-seq) assays identify where proteins bind throughout a genome. However, DNA contamination and DNA fragmentation heterogeneity produce false positives (erroneous calls) and imprecision in mapping. Co...
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A distinct mechanism for coactivator versus corepressor function by histone methyltransferase G9a in transcriptional regulation.
Published: December, 2011

Abstract: Histone methyltransferase G9a has been understood primarily as a corepressor of gene expression, but we showed previously that G9a positively regulates nuclear receptor-mediated transcription in reporter gene assays. Here, we show that endogenous ...
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Notch Activation of Jagged1 Contributes to the Assembly of the Arterial Wall
Published: December, 2011

Abstract: BACKGROUND: Notch signaling in vascular smooth muscle precursors is required for smooth muscle differentiation. Jagged1 expression on endothelium activates Notch in vascular smooth muscle precursors including those of neural crest origin to initi...
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NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression.
Published: December, 2011

Abstract: Pluripotent cells possess the ability to differentiate into any cell type. Commitment to differentiate into specific lineages requires strict control of gene expression to coordinate the downregulation of lineage inappropriate genes while enabling...
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DNA methylation regulates the expression of CXCL12 in rheumatoid arthritis synovial fibroblasts.
Published: December, 2011

Abstract: In the search for specific genes regulated by DNA methylation in rheumatoid arthritis (RA), we investigated the expression of CXCL12 in synovial fibroblasts (SFs) and the methylation status of its promoter and determined its contribution to the ex...
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A simple method for the parallel deep sequencing of full influenza A genomes.
Published: December, 2011

Abstract: Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this p...
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Etsrp/Etv2 Is Directly Regulated by Foxc1a/b in the Zebrafish Angioblast.
Published: December, 2011

Abstract: Rationale:Endothelial cells are developmentally derived from angioblasts specified in the mesodermal germ cell layer. The transcription factor etsrp/etv2 is at the top of the known genetic hierarchy for angioblast development. The transcriptional ...
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Novel insights into the regulation of antioxidant-response-element-mediated gene expression by electrophiles: induction of the transcriptional repressor BACH1 by Nrf2.
Published: December, 2011

Abstract: A central mechanism in cellular defence against oxidative or electrophilic stress is mediated by transcriptional induction of genes via the ARE (antioxidant-response element), a cis-acting sequence present in the regulatory regions of genes involv...
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Role of farnesoid X receptor (FXR) in the process of differentiation of bone marrow stromal cells into osteoblasts.
Published: December, 2011

Abstract: Bone tissue contains bile acids which accumulate from serum and which can be released in large amounts in the bone microenvironment during bone resorption. However, the direct effects of bile acids on bone cells remain largely unexplored. Bile aci...
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Notch1 binds and induces degradation of Snail in hepatocellular carcinoma.
Published: November, 2011

Abstract: BACKGROUND: Hepatocellular carcinoma (HCC) is a common, highly invasive malignant tumor associated with a high mortality rate. We previously reported that the aberrant expression of Snail via activation of reactive oxygen species contributes to th...
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Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing.
Published: November, 2011

Abstract: Next Generation Sequencing (NGS) technologies are gaining importance in the routine clinical diagnostic setting. It is thus desirable to simplify the workflow for high-throughput diagnostics. Fragmentation of DNA is a crucial step for preparation ...
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Distinct Epigenomic Features in End-Stage Failing Human Hearts
Published: November, 2011

Abstract: Background—The epigenome refers to marks on the genome, including DNA methylation and histone modifications, that regulate the expression of underlying genes. A consistent profile of gene expression changes in end-stage cardiomyopathy led us to hy...
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Generation and characterization of rat and mouse monoclonal antibodies specific for MeCP2 and their use in X-inactivation studies.
Published: November, 2011

Abstract: Methyl CpG binding protein 2 (MeCP2) binds DNA, and has a preference for methylated CpGs and, hence, in cells, it accumulates in heterochromatin. Even though it is expressed ubiquitously MeCP2 is particularly important during neuronal maturation. ...
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Expression profile of the sphingosine kinase signalling system in the lung of patients with chronic obstructive pulmonary disease.
Published: November, 2011

Abstract: AIMS: Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide. Despite its importance, treatment methods are limited and restricted to symptomatic care, highlighting the urgent need for new treatment options. Tissue dama...
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Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions.
Published: November, 2011

Abstract: Long noncoding RNAs (lncRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retriev...
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Human tRNA genes function as chromatin insulators
Published: November, 2011

Abstract: nsulators help separate active chromatin domains from silenced ones. In yeast, gene promoters act as insulators to block the spread of Sir and HP1 mediated silencing while in metazoans most insulators are multipartite autonomous entities. tDNAs ar...
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The forkhead transcription factor FOXK2 promotes AP-1-mediated transcriptional regulation.
Published: November, 2011

Abstract: The transcriptional control circuitry in eukaryotic cells is complex and is orchestrated by combinatorially acting transcription factors. Forkhead transcription factors often function in concert with heterotypic transcription factors to specify di...
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FOG-1 and GATA-1 act sequentially to specify definitive megakaryocytic and erythroid progenitors.
Published: November, 2011

Abstract: The transcription factors that control lineage specification of haematopoietic stem cells (HSCs) have been well described for the myeloid and lymphoid lineages, whereas transcriptional control of erythroid (E) and megakaryocytic (Mk) fate is less ...
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YY1 associates with the macrosatellite DXZ4 on the inactive X chromosome and binds with CTCF to a hypomethylated form in some male carcinomas.
Published: November, 2011

Abstract: DXZ4 is an X-linked macrosatellite composed of 12-100 tandemly arranged 3-kb repeat units. In females, it adopts opposite chromatin arrangements at the two alleles in response to X-chromosome inactivation. In males and on the active X chromosome, ...
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Rapid mapping and identification of mutations in Caenorhabditis elegans by restriction site-associated DNA mapping and genomic interval pull-down sequencing.
Published: November, 2011

Abstract: Forward genetic screens provide a powerful approach for inferring gene function on the basis of the phenotypes associated with mutated genes. However, determining the causal mutation by traditional mapping and candidate gene sequencing is often th...
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Osteocalcin gene expression is regulated by wild-type p53.
Published: November, 2011

Abstract: The tumor-suppressor p53 is a transcription factor that regulates a number of genes in the process of cell-cycle inhibition, apoptosis, and DNA damage. Recent studies have revealed a crucial role for p53 in bone remodeling. In our previous studies...
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Down-Regulation of the Histone Methyltransferase EZH2 Contributes to the Epigenetic Programming of Decidualizing Human Endometrial Stromal Cells.
Published: November, 2011

Abstract: Differentiation of human endometrial stromal cells (HESC) into decidual cells represents a highly coordinated process essential for embryo implantation. We show that decidualizing HESC down-regulate the histone methyltransferase enhancer of Zeste ...
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Pharmacodynamics of curcumin as DNA hypomethylation agent in restoring the expression of Nrf2 via promoter CpGs demethylation.
Published: November, 2011

Abstract: Prostate cancer (PCa) is one of the most deadly malignancies among men in the United States. Although localized prostate cancer can be effectively treated via surgery or radiation, metastatic disease is usually lethal. Recent evidence suggests tha...
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Low-dose paclitaxel ameliorates fibrosis in the remnant kidney model by down-regulating miR-192.
Published: November, 2011

Abstract: Transforming growth factor (TGF)-β has been shown to play a central role in the development of tubulointerstitial fibrosis, which can be corrected via treatment with paclitaxel. The biology of microRNA (miR) can be modulated by paclitaxel. We hypo...
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The draft genome and transcriptome of Cannabis sativa.
Published: October, 2011

Abstract: ABSTRACT: BACKGROUND: Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including...
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Tumor suppressor protein p53 recruits human Sin3B/HDAC1 complex for down-regulation of its target promoters in response to genotoxic stress.
Published: October, 2011

Abstract: Master regulator protein p53, popularly known as the "guardian of genome" is the hub for regulation of diverse cellular pathways. Depending on the cell type and severity of DNA damage, p53 protein mediates cell cycle arrest or apoptosis, besides a...
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The oxidized thiol proteome in fission yeast--optimization of an ICAT-based method to identify H2O2-oxidized proteins.
Published: October, 2011

Abstract: Major intracellular disulfide formation is prevented in the cytosol by potent reducing systems. However, protein thiols can be oxidized as a consequence of redox-mediated physiological reactions or due to the unwanted toxicity of reactive oxygen s...
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Androgen receptor and nutrient signaling pathways coordinate the demand for increased amino acid transport during prostate cancer progression.
Published: October, 2011

Abstract: L-type amino acid transporters such as LAT1 and LAT3 mediate the uptake of essential amino acids. Here we report that prostate cancer cells coordinate the expression of LAT1 and LAT3 to maintain sufficient levels of leucine needed for mTORC1 signa...
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R432 is a key residue for the multiple functions of Ndt80p in Candida albicans.
Published: October, 2011

Abstract: Ndt80p is an important transcription modulator to various stress-response genes in Candida albicans, the most common human fungal pathogen in systemic infections. We found that Ndt80p directly regulated its target genes, such as YHB1, via the mid-...
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Maternal cannabis use alters ventral striatal dopamine D2 gene regulation in the offspring.
Published: October, 2011

Abstract: BACKGROUND: Prenatal cannabis exposure has been linked to addiction vulnerability, but the neurobiology underlying this risk is unknown. METHODS: Striatal dopamine and opioid-related genes were studied in human fetal subjects exposed to cannabis (...
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Transcriptional signatures of regulatory and toxic responses to benzo-[a]-pyrene exposure.
Published: October, 2011

Abstract: ABSTRACT: BACKGROUND: Small molecule ligands often have multiple effects on the transcriptional program of a cell: they trigger a receptor specific response and additional, indirect responses ("side effects"). Distinguishing those responses is im...
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Mutations in CSTA, encoding Cystatin A, underlie exfoliative ichthyosis and reveal a role for this protease inhibitor in cell-cell adhesion.
Published: October, 2011

Abstract: Autosomal-recessive exfoliative ichthyosis presents shortly after birth as dry, scaly skin over most of the body with coarse peeling of nonerythematous skin on the palms and soles, which is exacerbated by excessive moisture and minor trauma. Using...
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CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.
Published: October, 2011

Abstract: Alternative splicing of pre-messenger RNA is a key feature of transcriptome expansion in eukaryotic cells, yet its regulation is poorly understood. Spliceosome assembly occurs co-transcriptionally, raising the possibility that DNA structure may di...
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NF-κB controls energy homeostasis and metabolic adaptation by upregulating mitochondrial respiration.
Published: October, 2011

Abstract: Cell proliferation is a metabolically demanding process. It requires active reprogramming of cellular bioenergetic pathways towards glucose metabolism to support anabolic growth. NF-κB/Rel transcription factors coordinate many of the signals that ...
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Size-dependent cytotoxicity of amorphous silica nanoparticles in human hepatoma HepG2 cells.
Published: October, 2011

Abstract: The purpose of this study is to compare the potential cytotoxicity induced by amorphous silica particles with different sizes. The effects of one fine particle (498 nm) and three nanoparticles (68, 43, and 19 nm) on cultured human hepatoma (HepG2)...
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Specific regulatory motifs predict glucocorticoid responsiveness of hippocampal gene expression.
Published: October, 2011

Abstract: The glucocorticoid receptor (GR) is an ubiquitously expressed ligand-activated transcription factor that mediates effects of cortisol in relation to adaptation to stress. In the brain, GR affects the hippocampus to modulate memory processes throug...
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Separation-of-function mutation in HPC2, a member of the HIR complex in S. cerevisiae, results in derepression of the histone genes but does not confer cryptic TATA phenotypes.
Published: October, 2011

Abstract: The HIR complex, which is comprised of the four proteins Hir1, Hir2, Hir3 and Hpc2, was first characterized as a repressor of three of the four histone gene loci in Saccharomyces cerevisiae. Using a bioinformatical approach, previous studies have ...
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Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe.
Published: October, 2011

Abstract: Spt6 is a conserved factor, critically required for several transcription- and chromatin-related processes. We now show that Spt6 and its binding partner, Iws1, are required for heterochromatic silencing in Schizosaccharomyces pombe. Our studies d...
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Large-scale methylation domains mark a functional subset of neuronally expressed genes.
Published: October, 2011

Abstract: DNA methylation is essential for embryonic and neuronal differentiation, but the function of most genomic DNA methylation marks is poorly understood. Generally the human genome is highly methylated (>70%) except for CpG islands and gene promoters....
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Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.
Published: October, 2011

Abstract: We applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quanti...
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Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes.
Published: September, 2011

Abstract: Chromosomal rearrangements, including translocations, require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are frequently involved in producing leukemias, lymphomas and sarcomas. De...
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A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines
Published: September, 2011

Abstract: Mass spectrometry-based proteomics increasingly relies on relative or absolute quantification. In relative quantification, stable isotope based methods often allow mixing at early stages of sample preparation, whereas for absolute quantification t...
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DNA-end capping by the budding yeast transcription factor and subtelomeric binding protein Tbf1
Published: September, 2011

Abstract: Telomere repeats in budding yeast are maintained at a constant average length and protected (‘capped’), in part, by mechanisms involving the TG13 repeat-binding protein Rap1. However, metazoan telomere repeats (T2AG3) can be maintained in yeast t...
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An evolutionarily conserved kernel of gata5, gata6, otx2 and prdm1a operates in the formation of endoderm in zebrafish.
Published: September, 2011

Abstract: An evolutionarily conserved subcircuit (kernel) dedicated to a specific developmental function is found at the top of the gene regulatory networks (GRNs) hierarchy. Here we comprehensively demonstrate that a pan-deuterostome endoderm specification...
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Studying RNA–Protein Interactions In Vivo By RNA Immunoprecipitation
Published: September, 2011

Abstract: The crucial roles played by RNA-binding proteins in all aspects of RNA metabolism, particularly in the regulation of transcription, have become increasingly evident. Moreover, other factors that do not directly interact with RNA molecules can neve...
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Reciprocal repression between Sox3 and snail transcription factors defines embryonic territories at gastrulation.
Published: September, 2011

Abstract: In developing amniote embryos, the first epithelial-to-mesenchymal transition (EMT) occurs at gastrulation, when a subset of epiblast cells moves to the primitive streak and undergoes EMT to internalize and generate the mesoderm and the endoderm. ...
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Glutathione-S-transferase pi 1(GSTP1) gene silencing in prostate cancer cells is reversed by the histone deacetylase inhibitor depsipeptide.
Published: September, 2011

Abstract: Gene silencing by epigenetic mechanisms is frequent in prostate cancer (PCA). The link between DNA hypermethylation and histone modifications is not completely understood. We chose the GSTP1 gene which is silenced by hypermethylation to analyze th...
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BRCA1 tumour suppression occurs via heterochromatin-mediated silencing.
Published: September, 2011

Abstract: Mutations in the tumour suppressor gene BRCA1 lead to breast and/or ovarian cancer. Here we show that loss of Brca1 in mice results in transcriptional de-repression of the tandemly repeated satellite DNA. Brca1 deficiency is accompanied by a reduc...
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Interaction of Arabidopsis DET1 with CCA1 and LHY in mediating transcriptional repression in the plant circadian clock.
Published: September, 2011

Abstract: The COP10-DET1-DDB1 (CDD) complex is an evolutionarily conserved protein complex discovered for its role in the repression of photomorphogenesis in Arabidopsis. It is important in many cellular and developmental processes in both plants and animal...
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Diverse roles of RNA polymerase II-associated factor 1 complex in different subpathways of nucleotide excision repair.
Published: September, 2011

Abstract: Transcription-coupled repair (TCR) and global genomic repair (GGR) are two pathways of nucleotide excision repair (NER). In Saccharomyces cerevisiae, Rad26 is important but not absolutely required for TCR. Rpb4, a nonessential RNA polymerase II (P...
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Regulation of human epidermal stem cell proliferation and senescence requires polycomb- dependent and -independent functions of Cbx4.
Published: September, 2011

Abstract: Human epidermal stem cells transit from a slow cycling to an actively proliferating state to contribute to homeostasis. Both stem cell states differ in their cell cycle profiles but must remain guarded from differentiation and senescence. Here we ...
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Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage.
Published: September, 2011

Abstract: Using mouse skin, where bountiful reservoirs of synchronized hair follicle stem cells (HF-SCs) fuel cycles of regeneration, we explore how adult SCs remodel chromatin in response to activating cues. By profiling global mRNA and chromatin changes i...
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The transcription factor FOXM1 is a cellular target of the natural product thiostrepton.
Published: September, 2011

Abstract: Transcription factors are proteins that bind specifically to defined DNA sequences to promote gene expression. Targeting transcription factors with small molecules to modulate the expression of certain genes has been notoriously difficult to achie...
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Disruption of the histone acetyltransferase MYST4 leads to a Noonan syndrome-like phenotype and hyperactivated MAPK signaling in humans and mice.
Published: September, 2011

Abstract: Epigenetic regulation of gene expression, through covalent modification of histones, is a key process controlling growth and development. Accordingly, the transcription factors regulating these processes are important targets of genetic diseases. ...
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Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features.
Published: September, 2011

Abstract: In metazoans, thousands of DNA replication origins (Oris) are activated at each cell cycle. Their genomic organization and their genetic nature remain elusive. Here, we characterized Oris by nascent strand (NS) purification and a genome-wide analy...
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Improved quantitative and qualitative production of single-domain intrabodies mediated by the co-expression of Erv1p sulfhydryl oxidase.
Published: September, 2011

Abstract: Camelidae single domain antibodies (VHHs) have structural and binding features that render them suitable alternatives to conventional IgG antibodies. VHHs are usually easier to produce as recombinant proteins than other antibody fragments. However...
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Smad3-mediated upregulation of miR-21 promotes renal fibrosis.
Published: September, 2011

Abstract: TGF-β/Smad signaling plays a role in fibrogenesis, but therapies targeting TGF-β are ineffective in treating renal fibrosis. Here, we explored the therapeutic potential of targeting TGF-β-induced microRNA in the progression of renal fibrosis. Micr...
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PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters.
Published: September, 2011

Abstract: PROMoter uPstream Transcripts (PROMPTs) were identified as a new class of human RNAs, which are heterologous in length and produced only upstream of the promoters of active protein-coding genes. Here, we show that PROMPTs carry 3'-adenosine tails ...
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High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences.
Published: September, 2011

Abstract: To investigate the demographic history of human populations from the Caucasus and surrounding regions, we used high-throughput sequencing to generate 147 complete mtDNA genome sequences from random samples of individuals from three groups from the...
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Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast.
Published: August, 2011

Abstract: ABSTRACT: BACKGROUND: The generation of mature mRNAs involves interconnected processes, including transcription by RNA polymerase II (Pol II), modification of histones, and processing of pre-mRNAs through capping, intron splicing, and polyadenyla...
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Anthracyclines induce the accumulation of mutant p53 through E2F1-dependent and -independent mechanisms.
Published: August, 2011

Abstract: Mutant p53 frequently accumulates in cancer cells and promotes tumor cell invasion, as part of its gain of function. Its accumulation is partially due to enhanced stability, but little is known about how the mRNA levels of mutant p53 can be regula...
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A cytoplasmic negative regulator isoform of ATF7 impairs ATF7 and ATF2 phosphorylation and transcriptional activity.
Published: August, 2011

Abstract: Alternative splicing and post-translational modifications are processes that give rise to the complexity of the proteome. The nuclear ATF7 and ATF2 (activating transcription factor) are structurally homologous leucine zipper transcription factors ...
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SIRT6 is required for maintenance of telomere position effect in human cells.
Published: August, 2011

Abstract: In Saccharomyces cerevisiae, the repressive chromatin environment at telomeres gives rise to telomere position effect (TPE), the epigenetic silencing of telomere-proximal genes. Chromatin-modifying factors that control TPE in yeast have been exten...
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Exome sequencing identifies a DYNC1H1 mutation in a large pedigree with dominant axonal Charcot-Marie-Tooth disease.
Published: August, 2011

Abstract: Charcot-Marie-Tooth disease is characterized by length-dependent axonal degeneration with distal sensory loss and weakness, deep-tendon-reflex abnormalities, and skeletal deformities. It is caused by mutations in more than 40 genes. We investigate...
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The tumour antigen PRAME is a subunit of a Cul2 ubiquitin ligase and associates with active NFY promoters.
Published: August, 2011

Abstract: The human tumour antigen PRAME (preferentially expressed antigen of melanoma) is frequently overexpressed in tumours. High PRAME levels correlate with poor clinical outcome of several cancers, but the mechanisms by which PRAME could be involved in...
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The X-inactivation trans-activator Rnf12 is negatively regulated by pluripotency factors in embryonic stem cells.
Published: August, 2011

Abstract: X-inactivation, the molecular mechanism enabling dosage compensation in mammals, is tightly controlled during mouse early embryogenesis. In the morula, X-inactivation is imprinted with exclusive silencing of the paternally inherited X-chromosome. ...
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EVI1-mediated down regulation of MIR449A is essential for the survival of EVI1 positive leukaemic cells.
Published: August, 2011

Abstract: Chromosomal rearrangements involving the MECOM (MDS1 and EVI1 complex) locus are recurrent genetic events in myeloid leukaemia and are associated with poor prognosis. In this study, we assessed the role of MECOM locus protein EVI1 in the transcrip...
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Polycomb eviction as a new distant enhancer function.
Published: August, 2011

Abstract: Remote distal enhancers may be located tens or thousands of kilobases away from their promoters. How they control gene expression is still poorly understood. Here, we analyze the influence of a remote enhancer on the balance between repression (Po...
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Long-range epigenetic silencing associates with deregulation of Ikaros targets in colorectal cancer cells.
Published: August, 2011

Abstract: Transcription factors are common targets of epigenetic inactivation in human cancer. Promoter hypermethylation and subsequent silencing of transcription factors can lead to further deregulation of their targets. In this study, we explored the pote...
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Systematic bias in high-throughput sequencing data and its correction by BEADS.
Published: August, 2011

Abstract: Genomic sequences obtained through high-throughput sequencing are not uniformly distributed across the genome. For example, sequencing data of total genomic DNA show significant, yet unexpected enrichments on promoters and exons. This systematic b...
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Histone tails regulate DNA methylation by allosterically activating de novo methyltransferase.
Published: August, 2011

Abstract: Cytosine methylation of genomic DNA controls gene expression and maintains genome stability. How a specific DNA sequence is targeted for methylation by a methyltransferase is largely unknown. Here, we show that histone H3 tails lacking lysine 4 (K...
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Analysis of HP1α regulation in human breast cancer cells.
Published: August, 2011

Abstract: The three mammalian HP1 proteins, HP1α/CBX5, HP1β/CBX1, and HPγ/CBX3, are involved in chromatin packing and gene regulation. The HP1α protein is down-regulated in invasive compared to non-invasive breast cancer cells and HP1α is a suppressor of ce...
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Coordination of KSHV latent and lytic gene control by CTCF-cohesin mediated chromosome conformation.
Published: August, 2011

Abstract: Herpesvirus persistence requires a dynamic balance between latent and lytic cycle gene expression, but how this balance is maintained remains enigmatic. We have previously shown that the Kaposi's Sarcoma-Associated Herpesvirus (KSHV) major latency...
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Gcn5 facilitates Pol II progression, rather than recruitment to nucleosome-depleted stress promoters, in Schizosaccharomyces pombe.
Published: August, 2011

Abstract: In the fission yeast, the MAP kinase Sty1 and the transcription factor Atf1 regulate up to 400 genes in response to environmental signals, and both proteins have been shown to bind to their promoters in a stress-dependent manner. In a genetic sear...
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Methyl-binding domain protein 2-dependent proliferation and survival of breast cancer cells.
Published: August, 2011

Abstract: Methyl cytosine binding domain protein 2 (MBD2) has been shown to bind to and mediate repression of methylated tumor suppressor genes in cancer cells, where repatterning of CpG methylation and associated gene silencing is common. We have investiga...
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msl2 mRNA is bound by free nuclear MSL complex in Drosophila melanogaster.
Published: August, 2011

Abstract: In Drosophila, the global increase in transcription from the male X chromosome to compensate for its monosomy is mediated by the male-specific lethal (MSL) complex consisting of five proteins and two non-coding RNAs, roX1 and roX2. After an initia...
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Reciprocal regulation of human immunodeficiency virus-1 gene expression and replication by heat shock proteins 40 and 70.
Published: July, 2011

Abstract: Cellular heat shock proteins (Hsps) are induced upon heat shock, UV irradiation and microbial or viral infection. They are also known to be involved in apoptosis and immune response in addition to their chaperone function. Although some literature...
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Regulation of adipocyte differentiation by the zinc finger protein ZNF638.
Published: July, 2011

Abstract: Zinc finger proteins constitute the largest family of transcription regulators in eukaryotes. These factors are involved in diverse processes in many tissues, including development and differentiation. We report here the characterization of the zi...
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Negative regulation of HIV-1 transcription by a heterodimeric NF-κB1/p50 and C-terminally truncated STAT5 complex.
Published: July, 2011

Abstract: Signal transducers and activator of transcription (STAT) proteins are often constitutively activated in leukocytes of HIV-1(+) individuals, which frequently show a dominant expression of a C-terminally truncated isoform of STAT5 (STAT5Δ). STAT5Δ c...
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Rtt107 is required for recruitment of the SMC5/6 complex to DNA double strand breaks.
Published: July, 2011

Abstract: Genome integrity is maintained by a network of DNA damage response pathways, including checkpoints and DNA repair processes. In Saccharomyces cerevisiae, the BRCT domain-containing protein Rtt107/Esc4 is required for the restart of DNA replication...
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Defective GATA-3 expression in Th2 LCR-deficient mice.
Published: July, 2011

Abstract: Th2 cell differentiation is critically influenced by transcription factor GATA-3 and by various cis-acting elements including enhancers, silencers and a locus control region (LCR) in the Th2 cytokine locus. Th2 LCR-deficient Th2 cells completely l...
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Transcription factors KLF1 and KLF2 positively regulate embryonic and fetal beta-globin genes through direct promoter binding.
Published: July, 2011

Abstract: Krüppel-like factors (KLFs) control cell differentiation and embryonic development. KLF1 (erythroid Krüppel-like factor) plays essential roles in embryonic and adult erythropoiesis. KLF2 is a positive regulator of the mouse and human embryonic β-g...
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Cap2-HAP complex is a critical transcriptional regulator that has dual but contrasting roles in regulation of iron homeostasis in Candida albicans.
Published: July, 2011

Abstract: Iron homeostasis is highly regulated in organisms across evolutionary time scale as iron is essential for various cellular processes. In a computational screen, we identified the Yap/bZIP domain family in Candida clade genomes. Cap2/Hap43 is essen...
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Hyperexpansion of GAA repeats affects post-initiation steps of FXN transcription in Friedreich's ataxia.
Published: July, 2011

Abstract: Friedreich's ataxia (FRDA) is caused by biallelic expansion of GAA repeats leading to the transcriptional silencing of the frataxin (FXN) gene. The exact molecular mechanism of inhibition of FXN expression is unclear. Herein, we analyze the effect...
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Human mediator subunit MED26 functions as a docking site for transcription elongation factors.
Published: July, 2011

Abstract: Promoter-proximal pausing by initiated RNA polymerase II (Pol II) and regulated release of paused polymerase into productive elongation has emerged as a major mechanism of transcription activation. Reactivation of paused Pol II correlates with rec...
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Transcription factor T-bet represses expression of the inhibitory receptor PD-1 and sustains virus-specific CD8+ T cell responses during chronic infection.
Published: July, 2011

Abstract: T cell exhaustion has a major role in failure to control chronic infection. High expression of inhibitory receptors, including PD-1, and the inability to sustain functional T cell responses contribute to exhaustion. However, the transcriptional co...
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Cell type-specific DNA methylation at intragenic CpG islands in the immune system.
Published: July, 2011

Abstract: Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, ∼50% of all CGIs are remote from annotated promoters but, nevertheless, o...
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Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters.
Published: July, 2011

Abstract: Transcription of long noncoding RNAs (lncRNAs) within gene regulatory elements can modulate gene activity in response to external stimuli, but the scope and functions of such activity are not known. Here we use an ultrahigh-density array that tile...
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H3K9 histone acetylation predicts pluripotency and reprogramming capacity of ES cells
Published: July, 2011

Abstract: The pluripotent genome is characterized by unique epigenetic features and a decondensed chromatin conformation. However, the relationship between epigenetic regulation and pluripotency is not altogether clear. Here, using an enhanced MEF/ESC fusio...
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Hyphal development in Candida albicans requires two temporally linked changes in promoter chromatin for initiation and maintenance.
Published: July, 2011

Abstract: Phenotypic plasticity is common in development. For Candida albicans, the most common cause of invasive fungal infections in humans, morphological plasticity is its defining feature and is critical for its pathogenesis. Unlike other fungal pathoge...
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Association of Rex-1 to target genes supports its interaction with Polycomb function.
Published: July, 2011

Abstract: Rex-1/Zfp42 displays a remarkably restricted pattern of expression in preimplantation embryos, primary spermatocytes, and undifferentiated mouse embryonic stem (ES) cells and is frequently used as a marker gene for pluripotent stem cells. To under...
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SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data.
Published: June, 2011

Abstract: BACKGROUND: The popularity of massively parallel exome and transcriptome sequencing projects demands new data mining tools with a comprehensive set of features to support a wide range of analysis tasks. RESULTS: SeqGene, a new data mining tool, su...
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DNA methylation status predicts cell type-specific enhancer activity
Published: June, 2011

Abstract: Cell-selective glucocorticoid receptor (GR) binding to distal regulatory elements is associated with cell type-specific regions of locally accessible chromatin. These regions can either pre-exist in chromatin (pre-programmed) or be induced by the ...
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Occupancy of chromatin organizers in the Epstein-Barr virus genome.
Published: June, 2011

Abstract: The human CCCTC-binding factor, CTCF, regulates transcription of the double-stranded DNA genomes of herpesviruses. The architectural complex cohesin and RNA Polymerase II also contribute to this organization. We profiled the occupancy of CTCF, coh...
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Mutations in ZBTB24 are associated with immunodeficiency, centromeric instability, and facial anomalies syndrome type 2.
Published: June, 2011

Abstract: Autosomal-recessive immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is mainly characterized by recurrent, often fatal, respiratory and gastrointestinal infections. About 50% of patients carry mutations in the DNA met...
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Human teneurin-1 is a direct target of the homeobox transcription factor EMX2 at a novel alternate promoter.
Published: June, 2011

Abstract: BACKGROUND: Teneurin-1 is a member of a family of type II transmembrane proteins conserved from C.elegans to vertebrates. Teneurin expression in vertebrates is best studied in mouse and chicken, where the four members teneurin-1 to -4 are predomin...
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Maps of open chromatin guide the functional follow-up of genome-wide association signals: application to hematological traits.
Published: June, 2011

Abstract: Turning genetic discoveries identified in genome-wide association (GWA) studies into biological mechanisms is an important challenge in human genetics. Many GWA signals map outside exons, suggesting that the associated variants may lie within regu...
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Coxsackie and adenovirus receptor is a target and a mediator of estrogen action in breast cancer.
Published: June, 2011

Abstract: The involvement of the coxsackie and adenovirus receptor (CAR), an adhesion molecule known to be the main determinant of adenovirus transduction of the cells, in cancer is currently under investigation. Recent reports suggest that CAR levels are e...
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Enhancer of Zeste 2 (EZH2) is up-regulated in malignant gliomas and in glioma stem-like cells.
Published: June, 2011

Abstract: AIMS: Proteins of the Polycomb repressive complex 2 (PRC2) are epigenetic gene silencers and are involved in tumour development. Their oncogenic function might be associated with their role in stem cell maintenance. The histone methyltransferase E...
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A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma.
Published: June, 2011

Abstract: MYCN is a major driver of neuroblastoma tumorigenesis and MYCN amplification is the worst prognostic indicator of aggressive NB. To identify potentially therapeutic tumor suppressor microRNAs for aggressive NB, we utilized a conditional MYCN syste...
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How chromatin is remodelled during DNA repair of UV-induced DNA damage in Saccharomyces cerevisiae.
Published: June, 2011

Abstract: Global genome nucleotide excision repair removes DNA damage from transcriptionally silent regions of the genome. Relatively little is known about the molecular events that initiate and regulate this process in the context of chromatin. We've shown...
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Dynamic chromatin localization of Sirt6 shapes stress- and aging-related transcriptional networks.
Published: June, 2011

Abstract: The sirtuin Sirt6 is a NAD-dependent histone deacetylase that is implicated in gene regulation and lifespan control. Sirt6 can interact with the stress-responsive transcription factor NF-κB and regulate some NF-κB target genes, but the full scope ...
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Mediator influences telomeric silencing and cellular life span.
Published: June, 2011

Abstract: The Mediator complex is required for the regulated transcription of nearly all RNA polymerase II-dependent genes. Here we demonstrate a new role for Mediator which appears to be separate from its function as a transcriptional coactivator. Mediator...
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Human imprinted retrogenes exhibit non-canonical imprint chromatin signatures and reside in non-imprinted host genes.
Published: June, 2011

Abstract: Imprinted retrotransposed genes share a common genomic organization including a promoter-associated differentially methylated region (DMR) and a position within the intron of a multi-exonic 'host' gene. In the mouse, at least one transcript of the...
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Circumventing heterozygosity: sequencing the amplified genome of a single haploid Drosophila melanogaster embryo.
Published: June, 2011

Abstract: Heterozygosity is a major challenge to efficient, high-quality genomic assembly and to the full genomic survey of polymorphism and divergence. In Drosophila melanogaster lines derived from equatorial populations are particularly resistant to inbre...
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Pre-TCR signaling and CD8 gene bivalent chromatin resolution during thymocyte development.
Published: June, 2011

Abstract: The CD8 gene is silent in CD4(-)CD8(-) double-negative thymocytes, expressed in CD4(+)CD8(+) double-positive cells, and silenced in cells committing to the CD4(+) single-positive (SP) lineage, remaining active in the CD8(+) SP lineage. In this stu...
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Reversible epigenetic fingerprint-mediated glutathione-S-transferase P1 gene silencing in human leukemia cell lines.
Published: June, 2011

Abstract: Glutathione-S-transferase P1 (GSTP1) gene is commonly silenced by CpG island promoter hypermethylation in prostate, breast, and liver cancers. However, mechanisms leading to GSTP1 repression by promoter hypermethylation in leukemia and its relatio...
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Analysis of the GAD1 promoter: trans-acting factors and DNA methylation converge on the 5' untranslated region.
Published: June, 2011

Abstract: GAD67 corresponds to one of two enzymes that decarboxylates glutamate to produce γ-aminobutyric acid, the main inhibitory neurotransmitter in the mammalian central nervous system, hence defining the cellular phenotype of a diverse set of inhibitor...
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Differential nuclear localisation and promoter occupancy play a role in glucocorticoid receptor ligand-specific transcriptional responses.
Published: May, 2011

Abstract: The glucocorticoid receptor (GR) is a ligand-activated transcription factor for which a number of endogenous and synthetic ligands exist. A key question in steroid receptor biology is how different ligands elicit different maximal transcriptional ...
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Arginine and glutamate-rich 1 (ARGLU1) interacts with mediator subunit 1 (MED1) and is required for estrogen receptor-mediated gene transcription and breast cancer cell growth.
Published: May, 2011

Abstract: Estrogen receptor is a nuclear receptor superfamily member of transcriptional activators that regulate gene expression by recruiting diverese transcriptional coregulators. The Mediator complex is a central transcriptional coactivator complex that ...
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RNF20 inhibits TFIIS-facilitated transcriptional elongation to suppress pro-oncogenic gene expression.
Published: May, 2011

Abstract: hBRE1/RNF20 is the major E3 ubiquitin ligase for histone H2B. RNF20 depletion causes a global reduction of monoubiquitylated H2B (H2Bub) levels and augments the expression of growth-promoting, pro-oncogenic genes. Those genes reside preferentially...
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Cohesin mediates chromatin interactions that regulate mammalian β-globin expression.
Published: May, 2011

Abstract: The β-globin locus undergoes dynamic chromatin interaction changes in differentiating erythroid cells that are thought to be important for proper globin gene expression. However, the underlying mechanisms are unclear. The CCCTC-binding factor, CTC...
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Caenorhabditis elegans chromatin-associated proteins SET-2 and ASH-2 are differentially required for histone H3 Lys 4 methylation in embryos and adult germ cells.
Published: May, 2011

Abstract: Methylation of histone H3 lysine 4 (H3K4me), a mark associated with gene activation, is mediated by SET1 and the related mixed lineage leukemia (MLL) histone methyltransferases (HMTs) across species. Mammals contain seven H3K4 HMTs, Set1A, Set1B, ...
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AP-2c regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription
Published: May, 2011

Abstract: Oestrogen receptor α (ERα) is key player in the progression of breast cancer. Recently, the cistrome and interactome of ERα were mapped in breast cancer cells, revealing the importance of spatial organization in oestrogen-mediated transcription. H...
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Mapping and analysis of chromatin state dynamics in nine human cell types.
Published: May, 2011

Abstract: Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cell...
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Requirement for Dot1l in murine postnatal hematopoiesis and leukemogenesis by MLL translocation.
Published: May, 2011

Abstract: Disruptor of telomeric silencing 1-like (Dot1l) is a histone 3 lysine 79 methyltransferase. Studies of constitutive Dot1l knockout mice show that Dot1l is essential for embryonic development and prenatal hematopoiesis. DOT1L also interacts with tr...
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LIF, a Novel STAT5-Regulated Gene, Is Aberrantly Expressed in Myeloproliferative Neoplasms.
Published: May, 2011

Abstract: A search for genes potentially regulated by STAT5 identified leukemia inhibitory factor (LIF) as a good candidate. Using various experimental approaches, we have validated LIF as a direct transcriptional target of STAT5 in myeloid cell lines: STAT...
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Histone H3K4 trimethylation by MLL3 as part of ASCOM complex is critical for NR activation of bile acid transporter genes and is downregulated in cholestasis.
Published: May, 2011

Abstract: The nuclear receptor Farnesoid x receptor (FXR) is a critical regulator of multiple genes involved in bile acid homeostasis. The coactivators attracted to promoters of FXR target genes and epigenetic modifications that occur after ligand binding t...
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Epigenetic profile of the euchromatic region of human Y chromosome.
Published: May, 2011

Abstract: The genome of a multi-cellular organism acquires various functional capabilities in different cell types by means of distinct chromatin modifications and packaging states. Acquired during early development, the cell type-specific epigenotype is ma...
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NF-kB and c-Jun induce the expression of the oncogenic miR-221 and miR-222 in prostate carcinoma and glioblastoma cells.
Published: May, 2011

Abstract: MicroRNAs (miRNAs) are potent negative regulators of gene expression involved in all aspects of cell biology. They finely modulate virtually all physiological pathways in metazoans, and are deeply implicated in all main pathologies, among which ca...
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Functional analysis of KAP1 genomic recruitment.
Published: May, 2011

Abstract: TRIM28 (KAP1) is upregulated in many cancers and has been implicated in both transcriptional activation and repression. Using chromatin immunoprecipitation and sequencing, we show that KAP1 binding sites fall into several categories, specifically,...
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JAG2 induction in hypoxic tumor cells alters Notch signaling and enhances endothelial cell tube formation.
Published: May, 2011

Abstract: Several studies have revealed links between hypoxia and activation of Notch in solid tumors. While most reports have focused on intracellular domain of the Notch1 receptor (icN1) stabilization by direct interaction with HIF proteins, little attent...
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Mechanism of 1α,25-dihydroxyvitamin D(3)-dependent repression of interleukin-12B.
Published: May, 2011

Abstract: Interleukin 12 (IL-12) is a heterodimeric, pro-inflammatory cytokine that plays a central role in activation and differentiation of CD4(+) T cells into interferon-γ secreting T-helper type 1 cells. IL-12B, a gene encoding the larger subunit of act...
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Aryl hydrocarbon receptor ligands of widely different toxic equivalency factors induce similar histone marks in target gene chromatin.
Published: May, 2011

Abstract: Posttranslational histone modifications are a critical regulatory mechanism of gene transcription. Previous studies from our laboratory have shown that contingent on binding to its cognate promoter motifs in the Cyp1a1 gene, activation of the aryl...
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The histone demethylase JARID1A regulates progesterone receptor expression.
Published: May, 2011

Abstract: Transcriptional control of the progesterone receptor gene by estrogen is a complex mechanism. It involves estrogen receptor α which uses several enzymes that locally modify histone tails as cofactors. Using MCF-7 cells as a model, we found that Ju...
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Selective genomic targeting by FRA-2/FOSL2 transcription factor: regulation of the Rgs4 gene is mediated by a variant activator protein 1 (AP-1) promoter sequence/CREB-binding protein (CBP) mechanism.
Published: April, 2011

Abstract: FRA-2/FOSL2 is a basic region-leucine zipper motif transcription factor that is widely expressed in mammalian tissues. The functional repertoire of this factor is unclear, partly due to a lack of knowledge of genomic sequences that are targeted. H...
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Chromatin-modifying agents promote the ex vivo production of functional human erythroid progenitor cells.
Published: April, 2011

Abstract: Presently, blood transfusion products (TPs) are composed of terminally differentiated cells with a finite life span. We have developed an ex vivo-generated TP composed of erythroid progenitor cells (EPCs) and precursors cells. Several histone deac...
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Widespread negative response elements mediate direct repression by agonist-liganded glucocorticoid receptor.
Published: April, 2011

Abstract: The glucocorticoid (GC) receptor (GR), when liganded to GC, activates transcription through direct binding to simple (+)GRE DNA binding sequences (DBS). GC-induced direct repression via GR binding to complex "negative" GREs (nGREs) has been report...
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Coordinated cancer germline antigen promoter and global DNA hypomethylation in ovarian cancer: association with the BORIS/CTCF expression ratio and advanced stage.
Published: April, 2011

Abstract: PURPOSE: Cancer germline (CG) antigens are frequently expressed and hypomethylated in epithelial ovarian cancer (EOC), but the relationship of this phenomenon to global DNA hypomethylation is unknown. In addition, the potential mechanisms leading ...
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Tumour evolution inferred by single-cell sequencing.
Published: April, 2011

Abstract: Genomic analysis provides insights into the role of copy number variation in disease, but most methods are not designed to resolve mixed populations of cells. In tumours, where genetic heterogeneity is common, very important information may be los...
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TLE3 is a dual-function transcriptional coregulator of adipogenesis.
Published: April, 2011

Abstract: PPARγ and Wnt signaling are central positive and negative regulators of adipogenesis, respectively. Here we identify the groucho family member TLE3 as a transcriptional integrator of the PPARγ and Wnt pathways. TLE3 is a direct target of PPARγ tha...
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Replication stress induces 53BP1-containing OPT domains in G1 cells.
Published: April, 2011

Abstract: Chromosomal deletions and rearrangements in tumors are often associated with common fragile sites, which are specific genomic loci prone to gaps and breaks in metaphase chromosomes. Common fragile sites appear to arise through incomplete DNA repli...
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Tracing the domestication of a biofilm-forming bacterium.
Published: April, 2011

Abstract: Over the course of more than a century of laboratory experimentation, Bacillus subtilis has become "domesticated," losing its ability to carry out many behaviors characteristic of its wild ancestors. One such characteristic is the ability to form ...
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New role for granulocyte colony-stimulating factor-induced extracellular signal-regulated kinase 1/2 in histone modification and retinoic acid receptor α recruitment to gene promoters: relevance to acute promyelocytic leukemia cell differentiation.
Published: April, 2011

Abstract: The induction of the granulocytic differentiation of leukemic cells by all-trans retinoic acid (RA) has been a major breakthrough in terms of survival for acute promyelocytic leukemia (APL) patients. Here we highlight the synergism and the underly...
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Regulation of mouse embryonic stem cell self-renewal by a Yes-YAP-TEAD2 signaling pathway downstream of LIF.
Published: April, 2011

Abstract: The cytoplasmic tyrosine kinase Yes has previously been shown to have an important role in maintaining mouse and human embryonic stem (ES) self-renewal through an unknown pathway downstream of leukemia inhibitory factor (LIF) and one or more facto...
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The chromodomains of CHD1 are critical for enzymatic activity but less important for chromatin localization.
Published: April, 2011

Abstract: The molecular motor protein CHD1 has been implicated in the regulation of transcription and in the transcription-independent genome-wide incorporation of H3.3 into paternal chromatin in Drosophila melanogaster. A key feature of CHD1 is the presenc...
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Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers.
Published: April, 2011

Abstract: Transcription factors (TFs) bind specifically to discrete regions of mammalian genomes called cis-regulatory elements. Among those are enhancers, which play key roles in regulation of gene expression during development and differentiation. Despite...
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HDAC-mediated deacetylation of NF-κB is critical for Schwann cell myelination.
Published: April, 2011

Abstract: Schwann cell myelination is tightly regulated by timely expression of key transcriptional regulators that respond to specific environmental cues, but the molecular mechanisms underlying such a process are poorly understood. We found that the acety...
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The Bin3 RNA methyltransferase is required for repression of caudal translation in the Drosophila embryo.
Published: April, 2011

Abstract: Bin3 was first identified as a Bicoid-interacting protein in a yeast two-hybrid screen. In human cells, a Bin3 ortholog (BCDIN3) methylates the 5' end of 7SK RNA, but its role in vivo is unknown. Here, we show that in Drosophila, Bin3 is important...
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Psm3 acetylation on conserved lysine residues is dispensable for viability in fission yeast but contributes to Eso1-mediated sister chromatid cohesion by antagonizing Wpl1.
Published: April, 2011

Abstract: In budding yeast and humans, cohesion establishment during S phase requires the acetyltransferase Eco1/Esco1-2, which acetylates the cohesin subunit Smc3 on two conserved lysine residues. Whether Smc3 is the sole Eco1/Esco1-2 effector and how Smc3...
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Heterochromatin formation in bistable chromatin domains controls the epigenetic repression of clonally variant Plasmodium falciparum genes linked to erythrocyte invasion.
Published: April, 2011

Abstract: Clonally variant gene expression is a common survival strategy used by many pathogens, including the malaria parasite Plasmodium falciparum. Among the genes that show variant expression in this parasite are several members of small gene families l...
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Recombineering, transfection, Western, IP and ChIP methods for protein tagging via gene targeting or BAC transgenesis.
Published: April, 2011

Abstract: Protein tagging offers many advantages for proteomic and regulomic research. Ideally, protein tagging is equivalent to having a high affinity antibody for every chosen protein. However, these advantages are compromised if the tagged protein is ove...
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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.
Published: March, 2011

Abstract: Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosoph...
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Biparental inheritance of chromosomal abnormalities in male twins with non-syndromic mental retardation.
Published: March, 2011

Abstract: In a monozygotic twin couple with mental retardation (MR), we identified a maternally inherited inversion and a paternally inherited translocation: 46,XY,inv(10)(p11.2q21.2)mat,t(9;18)(p22;q21.1)pat. The maternally inherited inv(10) was a benign v...
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Direct recruitment of ERK cascade components to inducible genes is regulated by heterogeneous nuclear ribonucleoprotein (hnRNP) K.
Published: March, 2011

Abstract: Components of the ERK cascade are recruited to genes, but it remains unknown how they are regulated at these sites. The RNA-binding protein heterogeneous nuclear ribonucleoprotein (hnRNP) K interacts with kinases and is found along genes including...
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Regulation of the PMP22 gene through an intronic enhancer.
Published: March, 2011

Abstract: Successful myelination of the peripheral nervous system depends upon induction of major protein components of myelin, such as peripheral myelin protein 22 (PMP22). Myelin stability is also sensitive to levels of PMP22, as a 1.4 Mb duplication on h...
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The multifunctional Ccr4-Not complex directly promotes transcription elongation.
Published: March, 2011

Abstract: The Ccr4-Not complex has been implicated in the control of multiple steps of mRNA metabolism; however, its functions in transcription remain ambiguous. The discovery that Ccr4/Pop2 is the major cytoplasmic mRNA deadenylase and the detection of Not...
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Role for miR-204 in human pulmonary arterial hypertension.
Published: March, 2011

Abstract: Pulmonary arterial hypertension (PAH) is characterized by enhanced proliferation and reduced apoptosis of pulmonary artery smooth muscle cells (PASMCs). Because microRNAs have been recently implicated in the regulation of cell proliferation and ap...
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Cutting edge: persistently open chromatin at effector gene loci in resting memory CD8+ T cells independent of transcriptional status.
Published: March, 2011

Abstract: Memory CD8(+) T cells are characterized by more rapid and robust effector function upon infection compared with naive T cells, but factors governing effector gene responsiveness are incompletely understood. We sought to understand transcriptional ...
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Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons.
Published: March, 2011

Abstract: Pre-messenger RNAs (pre-mRNAs) maturation is initiated cotranscriptionally. It is therefore conceivable that chromatin-borne information participates in alternative splicing. Here we find that elevated levels of trimethylation of histone H3 on Lys...
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Ah receptor antagonism inhibits constitutive and cytokine inducible IL6 production in head and neck tumor cell lines.
Published: March, 2011

Abstract: There is increasing evidence that the aryl hydrocarbon receptor (AHR) plays a role in tumor progression through numerous mechanisms. We have previously shown that, in certain cancer cell lines that are typically nonresponsive to cytokine-mediated ...
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Prolyl hydroxylase 3 (PHD3) is essential for hypoxic regulation of neutrophilic inflammation in humans and mice.
Published: March, 2011

Abstract: The regulation of neutrophil lifespan by induction of apoptosis is critical for maintaining an effective host response and preventing excessive inflammation. The hypoxia-inducible factor (HIF) oxygen-sensing pathway has a major effect on the susce...
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SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing.
Published: March, 2011

Abstract: The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the product...
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EpiChIP: gene-by-gene quantification of epigenetic modification levels.
Published: March, 2011

Abstract: The combination of chromatin immunoprecipitation with next-generation sequencing technology (ChIP-seq) is a powerful and increasingly popular method for mapping protein-DNA interactions in a genome-wide fashion. The conventional way of analyzing t...
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DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria.
Published: March, 2011

Abstract: Mitochondrial DNA (mtDNA) has been reported to contain 5-methylcytosine (5mC) at CpG dinucleotides, as in the nuclear genome, but neither the mechanism generating mtDNA methylation nor its functional significance is known. We now report the presen...
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High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Published: March, 2011

Abstract: Regulation of gene transcription in diverse cell types is determined largely by varied sets of cis-elements where transcription factors bind. Here we demonstrate that data from a single high-throughput DNase I hypersensitivity assay can delineate ...
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Synergism between DNA methylation and macroH2A1 occupancy in epigenetic silencing of the tumor suppressor gene p16(CDKN2A).
Published: March, 2011

Abstract: Promoter hypermethylation and heterochromatinization is a frequent event leading to gene inactivation and tumorigenesis. At the molecular level, inactivation of tumor suppressor genes in cancer has many similarities to the inactive X chromosome in...
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Role for cohesin in the formation of a heterochromatic domain at fission yeast subtelomeres.
Published: March, 2011

Abstract: Increasing evidence implicates cohesin in the control of gene expression. Here we report the first analysis of cohesin-dependent gene regulation in fission yeast. Global expression profiling of the mis4-367 cohesin loader mutant identified a small...
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Estrogen receptor α-mediated transcription induces cell cycle-dependent DNA double-strand breaks.
Published: March, 2011

Abstract: Prolonged exposure to estrogen increases breast cancer risk. Estrogen is known to induce chromosomal aberrations, yet the mechanisms by which estrogen promotes genomic instability are not fully understood. Here, we show that exposure of MCF-7 cell...
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A critical role for the protein phosphatase 2A B'α regulatory subunit in dephosphorylation of sphingosine kinase 1.
Published: March, 2011

Abstract: Sphingosine kinase 1 (SK1) is an important regulator of cellular signalling that has gained recent attention as a potential target for anti-cancer therapies. SK1 activity, subcellular localization and oncogenic function are regulated by phosphoryl...
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Involvement of placental growth factor in Wallerian degeneration.
Published: March, 2011

Abstract: Wallerian degeneration (WD) is an inflammatory process of nerve degeneration, which occurs more rapidly in the peripheral nervous system compared with the central nervous system, resulting, respectively in successful and aborted axon regeneration....
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Aurora kinase B activity is modulated by thyroid hormone during transcriptional activation of pituitary genes.
Published: March, 2011

Abstract: Covalent histone modifications clearly play an essential role in ligand-dependent transcriptional regulation by nuclear receptors. One of the predominant mechanisms used by nuclear receptors to activate or repress target-gene transcription is the ...
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H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation.
Published: March, 2011

Abstract: Methylation of histone H3 lysine 4 (H3K4me) is an evolutionarily conserved modification whose role in the regulation of gene expression has been extensively studied. In contrast, the function of H3K4 acetylation (H3K4ac) has received little attent...
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Stress induces parallel changes in corticotrophin-releasing hormone (CRH) Transcription and nuclear translocation of transducer of regulated cAMP response element-binding activity 2 in hypothalamic CRH neurones.
Published: March, 2011

Abstract: Recent studies in vitro have shown that the cAMP response element-binding (CREB) co-activator, transducer of regulated CREB activity (TORC), is required for transcriptional activation of the corticotrophin-releasing hormone (CRH) gene. To determin...
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Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability.
Published: February, 2011

Abstract: Thymine DNA glycosylase (TDG) is a member of the uracil DNA glycosylase (UDG) superfamily of DNA repair enzymes. Owing to its ability to excise thymine when mispaired with guanine, it was proposed to act against the mutability of 5-methylcytosine ...
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miRNA-132 orchestrates chromatin remodeling and translational control of the circadian clock.
Published: February, 2011

Abstract: Mammalian circadian rhythms are synchronized to the external time by daily resetting of the suprachiasmatic nucleus (SCN) in response to light. As the master circadian pacemaker, the SCN coordinates the timing of diverse cellular oscillators in mu...
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Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.
Published: February, 2011

Abstract: The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further...
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Mitogen-activated protein kinases ERK 1/2- and p38-GATA4 pathways mediate the Ang II-induced activation of FGF2 gene in neonatal rat cardiomyocytes.
Published: February, 2011

Abstract: Several genes, including fibroblast growth factor 2 (FGF2), are up-regulated in the hypertrophic heart. However, the molecular mechanisms responsible for the angiotensin II (Ang II)-induced activation of FGF2 in cardiomyocyte hypertrophy are large...
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9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response.
Published: February, 2011

Abstract: Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) in the 9p21 gene desert associated with coronary artery disease (CAD) and type 2 diabetes. Despite evidence for a role of the associated interval in neighbourin...
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The antiprogestin Lonaprisan inhibits breast cancer cell proliferation by inducing p21 expression.
Published: February, 2011

Abstract: The ovarian steroid hormone progesterone is essential for normal mammary gland physiology but may also play a role in breast cancer. Highly potent and selective antiprogestins may therefore represent a new treatment option for this disease. Here w...
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Clustering heterochromatin: Sir3 promotes telomere clustering independently of silencing in yeast.
Published: February, 2011

Abstract: A general feature of the nucleus is the organization of repetitive deoxyribonucleic acid sequences in clusters concentrating silencing factors. In budding yeast, we investigated how telomeres cluster in perinuclear foci associated with the silenci...
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ΔNp63α is an oncogene that targets chromatin remodeler Lsh to drive skin stem cell proliferation and tumorigenesis.
Published: February, 2011

Abstract: The p53 homolog p63 is essential for development, yet its role in cancer is not clear. We discovered that p63 deficiency evokes the tumor-suppressive mechanism of cellular senescence, causing a striking absence of stratified epithelia such as the ...
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Analysis of Histone Exchange during Chromatin Purification.
Published: February, 2011

Abstract: Central to the study of chromosome biology are techniques that permit the purification of small chromatin sections for analysis of associated DNA and proteins, including histones. Chromatin purification protocols vary greatly in the extent of chem...
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Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection.
Published: February, 2011

Abstract: Screening large numbers of target regions in multiple DNA samples for sequence variation is an important application of next-generation sequencing but an efficient method to enrich the samples in parallel has yet to be reported. We describe an adv...
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Rapid and reversible light-mediated chromatin modifications of Arabidopsis phytochrome A locus.
Published: February, 2011

Abstract: Recent genome-wide surveys showed that acetylation of H3K9 and H3K27 is correlated with gene activation during deetiolation of Arabidopsis thaliana seedlings, but less is known regarding changes in the histone status of repressed genes. Phytochrom...
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A human pathology-related mutation prevents import of an aminoacyl-tRNA synthetase into mitochondria.
Published: February, 2011

Abstract: Mutations in the nuclear gene coding for the mitochondrial aspartyl-tRNA synthetase, a key enzyme for mitochondrial translation, are correlated with leukoencephalopathy. A Ser⁴⁵ to Gly⁴⁵ mutation is located in the predicted targeting signal of the...
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Expression of P. falciparum var genes involves exchange of the histone variant H2A.Z at the promoter.
Published: February, 2011

Abstract: Plasmodium falciparum employs antigenic variation to evade the human immune response by switching the expression of different variant surface antigens encoded by the var gene family. Epigenetic mechanisms including histone modifications and sub-nu...
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Rescue of gene expression by modified REST decoy oligonucleotides in a cellular model of Huntington's disease.
Published: February, 2011

Abstract: Transcriptional dysfunction is a prominent hallmark of Huntington's disease (HD). Several transcription factors have been implicated in the aetiology of HD progression and one of the most prominent is repressor element 1 (RE1) silencing transcript...
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Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin.
Published: February, 2011

Abstract: Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in different cell types using ChIP-array analysis of histone modifica...
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Facultative heterochromatin formation at the IL-1 beta promoter in LPS tolerance and sepsis.
Published: February, 2011

Abstract: The clinical phenotype in sepsis that is observed as LPS tolerance is determined by silencing of pro-inflammatory genes like IL-1 beta (IL-1β). This study shows that facultative heterochromatin (fHC) silences IL-1β expression during sepsis, where ...
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Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation.
Published: February, 2011

Abstract: LONG HYPOCOTYL 5 (HY5) is a basic leucine zipper transcription factor (TF) that functions downstream of multiple families of photoreceptors. Mutations in the HY5 gene cause a myriad of aberrant phenotypes in Arabidopsis, including elongated hypoco...
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Comprehensive analysis of DNA-methylation in mammalian tissues using MeDIP-chip.
Published: February, 2011

Abstract: Genome-wide mapping of epigenetic changes is essential for understanding the mechanisms involved in gene regulation during cell differentiation and embryonic development. DNA-methylation is one of these key epigenetic marks that is directly linked...
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Recombineering BAC transgenes for protein tagging.
Published: February, 2011

Abstract: Protein tagging offers many advantages for proteomic and regulomic research, particularly due to the use of generic and highly sensitive methods that can be applied with reasonable throughput. Ideally, protein tagging is equivalent to having a hig...
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Cell cycle regulated expression of NCoR might control cyclic expression of androgen responsive genes in an immortalized prostate cell line.
Published: January, 2011

Abstract: In this work we have studied the mechanisms of regulation of expression of androgen receptor (AR) target genes. We have used an immortalized non-tumorigenic prostate cell line RWPE-1-AR(tag) constitutively expressing an exogenous AR as a model. We...
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Chromatin Immunoprecipitation (ChIP): Revisiting the Efficacy of Sample Preparation, Sonication, Quantification of Sheared DNA, and Analysis via PCR.
Published: January, 2011

Abstract: The "quantitative" ChIP, a tool commonly used to study protein-DNA interactions in cells and tissue, is a difficult assay often plagued with technical error. We present, herein, the process required to merge multiple protocols into a quick, reliab...
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Identification and characterisation of a novel adhesin Ifp in Yersinia pseudotuberculosis.
Published: January, 2011

Abstract: BACKGROUND: In order to identify new virulence determinants in Y. pseudotuberculosis a comparison between its genome and that of Yersinia pestis was undertaken. This reveals dozens of pseudogenes in Y. pestis, which are still putatively functional...
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Local de novo assembly of RAD paired-end contigs using short sequencing reads.
Published: January, 2011

Abstract: Despite the power of massively parallel sequencing platforms, a drawback is the short length of the sequence reads produced. We demonstrate that short reads can be locally assembled into longer contigs using paired-end sequencing of restriction-si...
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Characterisation of genome-wide PLZF/RARA target genes.
Published: January, 2011

Abstract: The PLZF/RARA fusion protein generated by the t(11;17)(q23;q21) translocation in acute promyelocytic leukaemia (APL) is believed to act as an oncogenic transcriptional regulator recruiting epigenetic factors to genes important for its transforming...
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Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.
Published: January, 2011

Abstract: Targeted sequencing is a cost-efficient way to obtain answers to biological questions in many projects, but the choice of the enrichment method to use can be difficult. In this study we compared two hybridization methods for target enrichment for ...
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The Saccharomyces cerevisiae histone chaperone Rtt106 mediates the cell cycle recruitment of SWI/SNF and RSC to the HIR-dependent histone genes.
Published: January, 2011

Abstract: BACKGROUND: In Saccharomyces cerevisiae, three out of the four histone gene pairs (HTA1-HTB1, HHT1-HHF1, and HHT2-HHF2) are regulated by the HIR co-repressor complex. The histone chaperone Rtt106 has recently been shown to be present at these hist...
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ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.
Published: January, 2011

Abstract: BACKGROUND: Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone m...
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Dot1 binding induces chromatin rearrangements by histone methylation-dependent and -independent mechanisms.
Published: January, 2011

Abstract: UNLABELLED: BACKGROUND: Methylation of histone H3 lysine 79 (H3K79) by Dot1 is highly conserved among species and has been associated with both gene repression and activation. To eliminate indirect effects and examine the direct consequences of D...
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Affinity-based enrichment strategies to assay methyl-CpG binding activity and DNA methylation in early Xenopus embryos.
Published: January, 2011

Abstract: UNLABELLED: ABSTRACT: BACKGROUND: DNA methylation is a widespread epigenetic modification in vertebrate genomes. Genomic sites of DNA methylation can be bound by methyl-CpG-binding domain proteins (MBDs) and specific zinc finger proteins, which ca...
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Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice.
Published: January, 2011

Abstract: Evidence suggests that epigenetic perturbations are involved in the adverse effects associated with some drugs and toxicants, including certain classes of non-genotoxic carcinogens. Such epigenetic changes (altered DNA methylation and covalent his...
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Role of p53 serine 46 in p53 target gene regulation.
Published: January, 2011

Abstract: The tumor suppressor p53 plays a crucial role in cellular growth control inducing a plethora of different response pathways. The molecular mechanisms that discriminate between the distinct p53-responses have remained largely elusive. Here, we have...
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Phosphorylation of the MBF repressor Yox1p by the DNA replication checkpoint keeps the G1/S cell-cycle transcriptional program active.
Published: January, 2011

Abstract: BACKGROUND: In fission yeast Schizosaccharomyces pombe G1/S cell-cycle regulated transcription depends upon MBF. A negative feedback loop involving Nrm1p and Yox1p bound to MBF leads to transcriptional repression as cells exit G1 phase. However, a...
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Effects of nickel treatment on H3K4 trimethylation and gene expression.
Published: January, 2011

Abstract: Occupational exposure to nickel compounds has been associated with lung and nasal cancers. We have previously shown that exposure of the human lung adenocarcinoma A549 cells to NiCl(2) for 24 hr significantly increased global levels of trimethylat...
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Enhanced chromatin accessibility and recruitment of JUNB mediate the sustained IL-4 expression in NFAT1 deficient T helper 2 cells.
Published: January, 2011

Abstract: Nuclear factor of activated T cells (NFAT) is a family of transcription factors composed of five proteins. Among them, NFAT1 is a predominant NFAT protein in CD4(+) T cells. NFAT1 positively regulates transcription of a large number of inducible c...
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Necdin, a Negative Growth Regulator, Is a Novel STAT3 Target Gene Down-Regulated in Human Cancer.
Published: January, 2011

Abstract: Cytokine and growth factor signaling pathways involving STAT3 are frequently constitutively activated in many human primary tumors, and are known for the transcriptional role they play in controlling cell growth and cell cycle progression. However...
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RNA sequencing reveals two major classes of gene expression levels in metazoan cells.
Published: January, 2011

Abstract: The expression level of a gene is often used as a proxy for determining whether the protein or RNA product is functional in a cell or tissue. Therefore, it is of fundamental importance to understand the global distribution of gene expression level...
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Wnt/β-catenin signaling pathway is a direct enhancer of thyroid transcription factor-1 in human papillary thyroid carcinoma cells.
Published: January, 2011

Abstract: The Wnt/β-catenin signaling pathway is involved in the normal development of thyroid gland, but its disregulation provokes the appearance of several types of cancers, including papillary thyroid carcinomas (PTC) which are the most common thyroid t...
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Identification of novel SNPs in glioblastoma using targeted resequencing.
Published: January, 2011

Abstract: High-throughput sequencing opens avenues to find genetic variations that may be indicative of an increased risk for certain diseases. Linking these genomic data to other "omics" approaches bears the potential to deepen our understanding of pathoge...
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Sleep Loss Reduces the DNA-Binding of BMAL1, CLOCK, and NPAS2 to Specific Clock Genes in the Mouse Cerebral Cortex.
Published: January, 2011

Abstract: We have previously demonstrated that clock genes contribute to the homeostatic aspect of sleep regulation. Indeed, mutations in some clock genes modify the markers of sleep homeostasis and an increase in homeostatic sleep drive alters clock gene e...
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Pluripotency factor binding and Tsix expression act synergistically to repress Xist in undifferentiated embryonic stem cells.
Published: January, 2011

Abstract: UNLABELLED: ABSTRACT: BACKGROUND: Expression of Xist, the master regulator of X chromosome inactivation, is extinguished in pluripotent cells, a process that has been linked to programmed X chromosome reactivation. The key pluripotency transcripti...
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Convergence of miRNA Expression Profiling, α-Synuclein Interacton and GWAS in Parkinson's Disease.
Published: January, 2011

Abstract: miRNAs were recently implicated in the pathogenesis of numerous diseases, including neurological disorders such as Parkinson's disease (PD). miRNAs are abundant in the nervous system, essential for efficient brain function and play important roles...
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MLL-AF9 and MLL-ENL alter the dynamic association of transcriptional regulators with genes critical for leukemia.
Published: January, 2011

Abstract: OBJECTIVE: The aim of this study was to better understand how mixed lineage leukemia (MLL) fusion proteins deregulate the expression of genes critical for leukemia. MATERIALS AND METHODS: The transforming domain of one of the most common MLL fusio...
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Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays.
Published: January, 2011

Abstract: UNLABELLED: ABSTRACT: BACKGROUND: The processes that compose expression of a given gene are far more complex than previously thought presenting unprecedented conceptual and mechanistic challenges that require development of new tools. Chromatin st...
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Global analysis of DNA methylation by methyl-capture sequencing reveals epigenetic control of Cisplatin resistance in ovarian cancer cell.
Published: January, 2011

Abstract: Cisplatin resistance is one of the major reasons leading to the high death rate of ovarian cancer. Methyl-Capture sequencing (MethylCap-seq), which combines precipitation of methylated DNA by recombinant methyl-CpG binding domain of MBD2 protein w...
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Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine.
Published: January, 2011

Abstract: In contrast to 5-methylcytosine (5-mC), which has been studied extensively, little is known about 5-hydroxymethylcytosine (5-hmC), a recently identified epigenetic modification present in substantial amounts in certain mammalian cell types. Here w...
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Direct recruitment of insulin receptor and ERK signaling cascade to insulin-inducible gene loci.
Published: January, 2011

Abstract: OBJECTIVE: Insulin receptor (IR) translocates to the nucleus, but its recruitment to gene loci has not been demonstrated. Here, we tested the hypothesis that IR and its downstream mitogenic transducers are corecruited to two prototypic insulin-ind...
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Phosphatidylinositol 3-kinase (PI3K) signaling via glycogen synthase kinase-3 (Gsk-3) regulates DNA methylation of imprinted loci.
Published: December, 2010

Abstract: Glycogen synthase kinase-3 (Gsk-3) isoforms, Gsk-3α and Gsk-3β, are constitutively active, largely inhibitory kinases involved in signal transduction. Underscoring their biological significance, altered Gsk-3 activity has been implicated in diabet...
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H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3.
Published: December, 2010

Abstract: Epigenetic regulatory mechanisms and their enzymes are promising targets for malaria therapeutic intervention; however, the epigenetic component of gene expression in P. falciparum is poorly understood. Dynamic or stable association of epigenetic ...
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Hdac1 and Hdac2 act redundantly to control p63 and p53 functions in epidermal progenitor cells.
Published: December, 2010

Abstract: Epidermal and hair follicle development from surface ectodermal progenitor cells requires coordinated changes in gene expression. Histone deacetylases alter gene expression programs through modification of chromatin and transcription factors. We f...
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ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes.
Published: December, 2010

Abstract: Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type. Thus, cell fate is mainly determined by cell type-specific silencing of transcription factor...
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Targets and dynamics of promoter DNA methylation during early mouse development.
Published: December, 2010

Abstract: DNA methylation is extensively reprogrammed during the early phases of mammalian development, yet genomic targets of this process are largely unknown. We optimized methylated DNA immunoprecipitation for low numbers of cells and profiled DNA methyl...
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Quality control and single nucleotide resolution analysis of methylated DNA immunoprecipitation products.
Published: December, 2010

Abstract: DNA methylation patterns are altered in many diseases, and their analysis has become of great interest. Methylated DNA immunoprecipitation (MeDIP) is a simple method to enrich the methylated fraction of the genome. However, it has been difficult t...
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Multiplexed DNA sequence capture of mitochondrial genomes using PCR products.
Published: November, 2010

Abstract: BACKGROUND: To utilize the power of high-throughput sequencers, target enrichment methods have been developed. The majority of these require reagents and equipment that are only available from commercial vendors and are not suitable for the target...
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Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root.
Published: November, 2010

Abstract: The balance between cellular proliferation and differentiation is a key aspect of development in multicellular organisms. Using high-resolution expression data from the Arabidopsis root, we identified a transcription factor, UPBEAT1 (UPB1), that r...
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Transcription factor IIS impacts UV-inhibited transcription.
Published: November, 2010

Abstract: Inhibition of transcription elongation can cause severe developmental and neurological abnormalities notably manifested by the rare recessive progeroid disorder Cockayne syndrome (CS). DNA alterations can cause permanent blocks to an elongating RN...
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Loss of H3 K79 trimethylation leads to suppression of Rtt107-dependent DNA damage sensitivity through the translesion synthesis pathway.
Published: November, 2010

Abstract: Genomic integrity is maintained by the coordinated interaction of many DNA damage response pathways, including checkpoints, DNA repair processes, and cell cycle restart. In Saccharomyces cerevisiae, the BRCA1 C-terminal domain-containing protein R...
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Whole-genome DNA methylation profiling using MethylCap-seq.
Published: November, 2010

Abstract: MethylCap-seq is a robust procedure for genome-wide profiling of DNA methylation. The approach consists of the capture of methylated DNA using the MBD domain of MeCP2, and subsequent next-generation sequencing of eluted DNA. Elution of the capture...
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High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.
Published: November, 2010

Abstract: The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regi...
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Glucocorticoid receptor regulates overlapping and differential gene subsets in developing and adult skin.
Published: November, 2010

Abstract: We have previously shown that the glucocorticoid receptor (GR) is required for skin homeostasis and epidermal barrier competence. To understand the transcriptional program by which GR regulates skin development, we performed a microarray analysis ...
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Transcriptional profiling by deep sequencing identifies differences in mRNA transcript abundance in in vivo-derived versus in vitro-cultured porcine blastocyst stage embryos.
Published: November, 2010

Abstract: In vitro embryo culture systems promote development at rates lower than in vivo systems. The goal of this project was to discover transcripts that may be responsible for a decrease of embryo competency in blastocyst-stage embryos cultured in vitro...
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The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells.
Published: November, 2010

Abstract: The initiation of DNA synthesis is governed by the licensing of replication origins, which consists of assembling a pre-replication complex (pre-RC) on origins during late M- and G1-phases. In metazoans, functional replication origins do not show ...
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Nucleosome-interacting proteins regulated by DNA and histone methylation.
Published: October, 2010

Abstract: Modifications on histones or on DNA recruit proteins that regulate chromatin function. Here, we use nucleosomes methylated on DNA and on histone H3 in an affinity assay, in conjunction with a SILAC-based proteomic analysis, to identify "crosstalk"...
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Promoter-exon relationship of H3 lysine 9, 27, 36 and 79 methylation on pluripotency-associated genes.
Published: October, 2010

Abstract: Evidence links pluripotency to a gene regulatory network organized by the transcription factors Oct4, Nanog and Sox2. Expression of these genes is controlled by epigenetic modifications on regulatory regions. However, little is known on profiles o...
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ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours.
Published: October, 2010

Abstract: Gastrointestinal stromal tumour (GIST) is the most common human sarcoma and is primarily defined by activating mutations in the KIT or PDGFRA receptor tyrosine kinases. KIT is highly expressed in interstitial cells of Cajal (ICCs)-the presumed cel...
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Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators.
Published: October, 2010

Abstract: Combinatorial transcription factor (TF) interactions control cellular phenotypes and, therefore, underpin stem cell formation, maintenance, and differentiation. Here, we report the genome-wide binding patterns and combinatorial interactions for te...
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Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
Published: October, 2010

Abstract: Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing...
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Lysine-specific demethylase 1 regulates the embryonic transcriptome and CoREST stability.
Published: October, 2010

Abstract: Lysine-specific demethylase 1 (LSD1), which demethylates mono- and dimethylated histone H3-Lys4 as part of a complex including CoREST and histone deacetylases (HDACs), is essential for embryonic development in the mouse beyond embryonic day 6.5 (e...
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Transcriptional regulation of lipid homeostasis in mycobacteria.
Published: October, 2010

Abstract: Mycolic acids are major components of the cell envelope of mycobacteria, such as Mycobacterium tuberculosis, and play an important role in its architecture, impermeability and interaction with the environment. Synthesis of mycolic acids is carried...
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Quantitative comparison of genome-wide DNA methylation mapping technologies.
Published: October, 2010

Abstract: DNA methylation plays a key role in regulating eukaryotic gene expression. Although mitotically heritable and stable over time, patterns of DNA methylation frequently change in response to cell differentiation, disease and environmental influences...
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DNA methylation and Yin Yang-1 repress adenosine A2A receptor levels in human brain.
Published: October, 2010

Abstract: Adenosine A(2A) receptors (A(2A) Rs) are G-protein coupled receptors that stimulate adenylyl cyclase activity. The most A(2A) Rs-enriched brain region is the striatum, in which A(2A) Rs are largely restricted to GABAergic neurons of the indirect p...
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A chromatin-remodeling protein is a component of fission yeast mediator.
Published: September, 2010

Abstract: The multiprotein Mediator complex is an important regulator of RNA polymerase II-dependent genes in eukaryotic cells. In contrast to the situation in many other eukaryotes, the conserved Med15 protein is not a stable component of Mediator isolated...
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Distinct epigenetic domains separated by a CTCF bound insulator between the tandem genes, BLU and RASSF1A.
Published: September, 2010

Abstract: BACKGROUND: Tumor suppressor gene (TSG) RASSF1A and candidate TSG BLU are two tandem head-to-tail genes located at 3p21.3. We hypothesized that there may be a concordance on their gene expression and promoter methylation status. If not, then there...
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HAATI survivors replace canonical telomeres with blocks of generic heterochromatin.
Published: September, 2010

Abstract: The notion that telomeres are essential for chromosome linearity stems from the existence of two chief dangers: inappropriate DNA damage response (DDR) reactions that mistake natural chromosome ends for double-strand DNA breaks (DSBs), and the pro...
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SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation.
Published: September, 2010

Abstract: Special AT-rich binding protein 1 (SATB1) is a global chromatin organizer and a transcription factor regulated by interleukin-4 (IL-4) during the early T helper 2 (Th2) cell differentiation. Here we show that SATB1 controls multiple IL-4 target ge...
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Chromatin remodeling is required for gene reactivation after decitabine-mediated DNA hypomethylation.
Published: September, 2010

Abstract: The DNA hypomethylating drug decitabine (DAC) reactivates silenced gene expression in cancer and is approved for the treatment of the myelodysplastic syndrome. Gene reactivation after DAC is variable and incompletely understood. Here, we establish...
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Transcriptional profiling of day 12 porcine embryonic disc and trophectoderm samples using ultra-deep sequencing technologies.
Published: September, 2010

Abstract: cDNA derived from trophectoderm (TE) and embryonic disc (ED) of a single day 12 porcine embryo was subjected to next-generation sequencing using the Illumina platform. The short sequencing reads from triplicate sequencing runs were aligned to a cu...
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Demonstrating polymorphic miRNA-mediated gene regulation in vivo: application to the g+6223G->A mutation of Texel sheep.
Published: September, 2010

Abstract: We herein describe the development of a biochemical method to evaluate the effect of single nucleotide polymorphisms (SNPs) in target genes on their regulation by microRNAs in vivo. The method is based on the detection of allelic imbalance in RNAs...
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Cellular and pharmacological selectivity of the peroxisome proliferator-activated receptor-beta/delta antagonist GSK3787.
Published: September, 2010

Abstract: The availability of high-affinity agonists for peroxisome proliferator-activated receptor-beta/delta (PPARbeta/delta) has led to significant advances in our understanding of the functional role of PPARbeta/delta. In this study, a new PPARbeta/delt...
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DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas.
Published: August, 2010

Abstract: Aberrant DNA methylation commonly occurs in cancer cells where it has been implicated in the epigenetic silencing of tumor suppressor genes. Additional roles for DNA methylation, such as transcriptional activation, have been predicted but have yet...
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Iron regulatory proteins secure mitochondrial iron sufficiency and function.
Published: August, 2010

Abstract: Mitochondria supply cells with ATP, heme, and iron sulfur clusters (ISC), and mitochondrial energy metabolism involves both heme- and ISC-dependent enzymes. Here, we show that mitochondrial iron supply and function require iron regulatory proteins...
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The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors.
Published: August, 2010

Abstract: In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio...
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Genome-wide mapping of histone H4 serine-1 phosphorylation during sporulation in Saccharomyces cerevisiae.
Published: August, 2010

Abstract: We previously showed that histone H4 serine-1 phosphorylation (H4S1ph) is evolutionarily conserved during gametogenesis, and contributes to post-meiotic nuclear compaction and to full completion of sporulation in the yeast Saccharomyces cerevisiae...
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Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.
Published: August, 2010

Abstract: Heterozygous mutations in p63 are associated with split hand/foot malformations (SHFM), orofacial clefting, and ectodermal abnormalities. Elucidation of the p63 gene network that includes target genes and regulatory elements may reveal new genes f...
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The repressing function of the oncoprotein BCL-3 requires CtBP, while its polyubiquitination and degradation involve the E3 ligase TBLR1.
Published: August, 2010

Abstract: The nuclear and oncogenic BCL-3 protein activates or represses gene transcription when bound to NF-kappaB proteins p50 and p52, yet the molecules that specifically interact with BCL-3 and drive BCL-3-mediated effects on gene expression remain larg...
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Differential regulation of HIC1 target genes by CtBP and NuRD, via an acetylation/SUMOylation switch, in quiescent versus proliferating cells.
Published: August, 2010

Abstract: The tumor suppressor gene HIC1 encodes a transcriptional repressor involved in regulatory loops modulating P53-dependent and E2F1-dependent cell survival, growth control, and stress responses. Despite its importance, few HIC1 corepressors and targ...
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miR-192 mediates TGF-beta/Smad3-driven renal fibrosis.
Published: August, 2010

Abstract: TGF-beta/Smad3 promotes renal fibrosis, but the mechanisms that regulate profibrotic genes remain unclear. We hypothesized that miR-192, a microRNA expressed in the kidney may mediate renal fibrosis in a Smad3-dependent manner. Microarray and real...
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The down-regulation of the human MYC gene by the nuclear hormone 1alpha,25-dihydroxyvitamin D3 is associated with cycling of corepressors and histone deacetylases.
Published: July, 2010

Abstract: MYC is a pleiotropic transcription factor that coordinates the expression of diverse programs that are together necessary for the growth and expansion of somatic cells. The nuclear hormone 1alpha,25-dihydroxyvitamin D(3) down-regulates MYC express...
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Terminal osseous dysplasia is caused by a single recurrent mutation in the FLNA gene.
Published: July, 2010

Abstract: Terminal osseous dysplasia (TOD) is an X-linked dominant male-lethal disease characterized by skeletal dysplasia of the limbs, pigmentary defects of the skin, and recurrent digital fibroma with onset in female infancy. After performing X-exome cap...
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Conserved role of intragenic DNA methylation in regulating alternative promoters.
Published: July, 2010

Abstract: Although it is known that the methylation of DNA in 5' promoters suppresses gene expression, the role of DNA methylation in gene bodies is unclear. In mammals, tissue- and cell type-specific methylation is present in a small percentage of 5' CpG i...
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Novel trans-tail regulation of H2B ubiquitylation and H3K4 methylation by the N terminus of histone H2A.
Published: July, 2010

Abstract: Chromatin is regulated by cross talk among different histone modifications, which can occur between residues within the same tail or different tails in the nucleosome. The latter is referred to as trans-tail regulation, and the best-characterized ...
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Loss of Rb proteins causes genomic instability in the absence of mitogenic signaling.
Published: July, 2010

Abstract: Loss of G1/S control is a hallmark of cancer, and is often caused by inactivation of the retinoblastoma pathway. However, mouse embryonic fibroblasts lacking the retinoblastoma genes RB1, p107, and p130 (TKO MEFs) are still subject to cell cycle c...
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Aryl hydrocarbon receptor and NF-E2-related factor 2 are key regulators of human MRP4 expression.
Published: July, 2010

Abstract: Multidrug resistance protein 4 (MRP4; ABCC4) is an ATP binding cassette transporter that facilitates the excretion of bile salt conjugates and other conjugated steroids in hepatocytes and renal proximal tubule epithelium. MRP4/Mrp4 undergoes adapt...
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The impact of intragenic CpG content on gene expression.
Published: July, 2010

Abstract: The development of vaccine components or recombinant therapeutics critically depends on sustained expression of the corresponding transgene. This study aimed to determine the contribution of intragenic CpG content to expression efficiency in trans...
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Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize.
Published: July, 2010

Abstract: High-copy transposons have been effectively exploited as mutagens in a variety of organisms. However, their utility for phenotype-driven forward genetics has been hampered by the difficulty of identifying the specific insertions responsible for ph...
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The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots.
Published: July, 2010

Abstract: Global population increases and climate change underscore the need for better comprehension of how plants acquire and process nutrients such as iron. Using cell type-specific transcriptional profiling, we identified a pericycle-specific iron defic...
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Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming.
Published: June, 2010

Abstract: Dissecting the molecular mechanisms by which T helper (Th) cells differentiate to effector Th2 cells is important for understanding the pathogenesis of immune-mediated diseases, such as asthma and allergy. Because the STAT6 transcription factor is...
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A gene-specific requirement of RNA polymerase II CTD phosphorylation for sexual differentiation in S. pombe.
Published: June, 2010

Abstract: BACKGROUND: The switch from cellular proliferation to differentiation occurs to a large extent through specific programs of gene expression. In fission yeast, the master regulator of sexual differentiation, ste11, is induced by environmental condi...
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Vertebrate homologue of Drosophila GAGA factor.
Published: June, 2010

Abstract: Polycomb group (PcG) and trithorax group (trxG) proteins are chromatin-mediated regulators of a number of developmentally important genes including the homeotic genes. In Drosophila melanogaster, one of the trxG members, Trithorax like (Trl), enco...
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A simple method for gene expression and chromatin profiling of individual cell types within a tissue.
Published: June, 2010

Abstract: Understanding the production and function of specialized cells during development requires the isolation of individual cell types for analysis, but this is currently a major technical challenge. Here we describe a method for cell type-specific RNA...
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Regulation of cyclin B2 expression and cell cycle G2/m transition by menin.
Published: June, 2010

Abstract: Multiple endocrine neoplasia type 1 (MEN1) results from mutations in tumor suppressor gene Men1, which encodes nuclear protein menin. Menin up-regulates certain cyclin-dependent kinase inhibitors through increasing histone H3 lysine 4 (H3K4) methy...
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Th2 LCR is essential for regulation of Th2 cytokine genes and for pathogenesis of allergic asthma.
Published: June, 2010

Abstract: Previous studies have shown that Th2 cytokine genes on mouse chromosome 11 are coordinately regulated by the Th2 locus control region (LCR). To examine the in vivo function of Th2 LCR, we generated CD4-specific Th2 LCR-deficient (cLCR KO) mice usi...
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A murine ESC-like state facilitates transgenesis and homologous recombination in human pluripotent stem cells.
Published: June, 2010

Abstract: Murine pluripotent stem cells can exist in two functionally distinct states, LIF-dependent embryonic stem cells (ESCs) and bFGF-dependent epiblast stem cells (EpiSCs). However, human pluripotent cells so far seemed to assume only an epiblast-like ...
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Promoter demethylation and chromatin remodeling by green tea polyphenols leads to re-expression of GSTP1 in human prostate cancer cells.
Published: June, 2010

Abstract: Epigenetic silencing of gluthathione-S-transferase pi (GSTP1) is recognized as being a molecular hallmark of human prostate cancer. We investigated the effects of green tea polyphenols (GTPs) on GSTP1 re-expression and further elucidated its mecha...
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CDKL5 is a brain MeCP2 target gene regulated by DNA methylation.
Published: June, 2010

Abstract: Rett syndrome and its "early-onset seizure" variant are severe neurodevelopmental disorders associated with mutations within the MECP2 and the CDKL5 genes. Antidepressants and drugs of abuse induce the expression of the epigenetic factor MeCP2, th...
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Illumina sequencing library preparation for highly multiplexed target capture and sequencing.
Published: June, 2010

Abstract: The large amount of DNA sequence data generated by high-throughput sequencing technologies often allows multiple samples to be sequenced in parallel on a single sequencing run. This is particularly true if subsets of the genome are studied rather ...
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Accumulation of piRNAs in the chromatoid bodies purified by a novel isolation protocol.
Published: May, 2010

Abstract: Haploid male germ cells are featured by an intriguing cytoplasmic cloud-like structure that has been named as chromatoid body (CB) on the basis of its staining properties and appearance under a microscope. Notwithstanding its early discovery in th...
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Altered histone acetylation is associated with age-dependent memory impairment in mice.
Published: May, 2010

Abstract: As the human life span increases, the number of people suffering from cognitive decline is rising dramatically. The mechanisms underlying age-associated memory impairment are, however, not understood. Here we show that memory disturbances in the a...
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FOXO3A as a key molecule for all-trans retinoic acid-induced granulocytic differentiation and apoptosis in acute promyelocytic leukemia.
Published: May, 2010

Abstract: All-trans retinoic acid (ATRA) induces granulocytic differentiation and apoptosis in acute promyelocytic leukemia (APL) cells, although the detailed mechanisms are not fully understood. We investigated ATRA-induced cellular responses mediated by t...
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Cooperation between the transcription factors p63 and IRF6 is essential to prevent cleft palate in mice.
Published: May, 2010

Abstract: Cleft palate is a common congenital disorder that affects up to 1 in 2,500 live human births and results in considerable morbidity to affected individuals and their families. The etiology of cleft palate is complex, with both genetic and environme...
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Repression of transcriptional activity of C/EBPalpha by E2F-dimerization partner complexes.
Published: May, 2010

Abstract: The transcription factor CCAAT/enhancer-binding protein alpha (C/EBPalpha) coordinates proliferation arrest and the differentiation of myeloid progenitors, adipocytes, hepatocytes, keratinocytes, and cells of the lung and placenta. C/EBPalpha tran...
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Profiling of promoter occupancy by PPARalpha in human hepatoma cells via ChIP-chip analysis.
Published: May, 2010

Abstract: The transcription factor peroxisome proliferator-activated receptor alpha (PPARalpha) is an important regulator of hepatic lipid metabolism. While PPARalpha is known to activate transcription of numerous genes, no comprehensive picture of PPARalph...
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Drosophila RB proteins repress differentiation-specific genes via two different mechanisms.
Published: May, 2010

Abstract: The RB and E2F proteins play important roles in the regulation of cell division, cell death, and development by controlling the expression of genes involved in these processes. The mechanisms of repression by the retinoblastoma protein (pRB) have ...
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Cooperation of NFkappaB and CREB to induce synergistic IL-6 expression in astrocytes.
Published: May, 2010

Abstract: Astrocytes are critical players in the innate immune response of the central nervous system. Upon encountering proinflammatory stimuli, astrocytes produce a plethora of inflammatory mediators. Here, we have investigated how beta(2)-adrenergic rece...
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Massively parallel sequencing, a new method for detecting adventitious agents.
Published: May, 2010

Abstract: There has been an upsurge of interest in developing new veterinary and human vaccines and, in turn, this has involved the development of new mammalian and insect cell substrates. Excluding adventitious agents from these cells can be problematic, p...
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Regulation of Epstein-Barr virus OriP replication by poly(ADP-ribose) polymerase 1.
Published: May, 2010

Abstract: Poly(ADP-ribose) polymerase (PARP) is an abundant, chromatin-associated, NAD-dependent enzyme that functions in multiple chromosomal processes, including DNA replication and chromatin remodeling. The Epstein-Barr virus (EBV) origin of plasmid repl...
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Hypoxia-inducible factor-2 is a novel regulator of aberrant CXCL12 expression in multiple myeloma plasma cells.
Published: May, 2010

Abstract: BACKGROUND: Multiple myeloma is an incurable malignancy of bone marrow plasma cells. Progression of multiple myeloma is accompanied by an increase in bone marrow angiogenesis. Studies from our laboratory suggest a role for the CXCL12 chemokine in ...
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Inhibitor of kappaB kinase beta regulates redox homeostasis by controlling the constitutive levels of glutathione.
Published: May, 2010

Abstract: Cytokine-activated inhibitor of kappaB kinase beta (IKKbeta) is a key mediator of immune and inflammatory responses, but recent studies suggest that IKKbeta is also required for tissue homeostasis in physiopathological processes. Here we report a ...
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Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs.
Published: May, 2010

Abstract: Luminal-like breast tumor cells express estrogen receptor alpha (ERalpha), a member of the nuclear receptor family of ligand-activated transcription factors that controls their proliferation, survival, and functional status. To identify the molecu...
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The in vivo pattern of binding of RAG1 and RAG2 to antigen receptor loci.
Published: April, 2010

Abstract: The critical initial step in V(D)J recombination, binding of RAG1 and RAG2 to recombination signal sequences flanking antigen receptor V, D, and J gene segments, has not previously been characterized in vivo. Here, we demonstrate that RAG protein ...
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NER factors are recruited to active promoters and facilitate chromatin modification for transcription in the absence of exogenous genotoxic attack.
Published: April, 2010

Abstract: Upon gene activation, we found that RNA polymerase II transcription machinery assembles sequentially with the nucleotide excision repair (NER) factors at the promoter. This recruitment occurs in absence of exogenous genotoxic attack, is sensitive ...
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Orchestration of floral initiation by APETALA1.
Published: April, 2010

Abstract: The MADS-domain transcription factor APETALA1 (AP1) is a key regulator of Arabidopsis flower development. To understand the molecular mechanisms underlying AP1 function, we identified its target genes during floral initiation using a combination o...
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A chromodomain switch mediated by histone H3 Lys 4 acetylation regulates heterochromatin assembly.
Published: April, 2010

Abstract: Chromodomain proteins (Chp1/Chp2/Swi6/Clr4) bind to methylated H3K9 (H3K9me) and regulate pericentric heterochromatin in fission yeast. Chp1 and Clr4 (H3K9-HMT), bind transcriptionally active heterochromatin, whereas Chp2/Swi6 (HP1 homologs) are r...
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Targeted high throughput sequencing of a cancer-related exome subset by specific sequence capture with a fully automated microarray platform.
Published: April, 2010

Abstract: Sequence capture methods for targeted next generation sequencing promise to massively reduce cost of genomics projects compared to untargeted sequencing. However, evaluated capture methods specifically dedicated to biologically relevant genomic re...
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Long intronic GAA repeats causing Friedreich ataxia impede transcription elongation.
Published: April, 2010

Abstract: Friedreich ataxia is a degenerative disease caused by deficiency of the protein frataxin (FXN). An intronic expansion of GAA triplets in the FXN-encoding gene, FXN, causes gene silencing and thus reduced FXN protein levels. Although it is widely a...
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Regulation of photoreceptor gene expression by the retinal homeobox (Rx) gene product.
Published: March, 2010

Abstract: The retinal homeobox (Rx) gene product is essential for eye development. However little is known about its molecular function. It has been demonstrated that Rx binds to photoreceptor conserved element (PCE-1), a highly conserved element found in t...
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DNA methylation regulates adenosine A(2A) receptor cell surface expression levels.
Published: March, 2010

Abstract: Adenosine A(2A) receptors (A(2A)Rs) appear to play important roles in inflammation and in certain diseases of the nervous system. Pharmacological modulation of A(2A)Rs is particularly useful in Parkinson's disease and has been tested in schizophre...
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Splicing factor Spf30 assists exosome-mediated gene silencing in fission yeast.
Published: March, 2010

Abstract: Heterochromatin assembly in fission yeast relies on the processing of cognate noncoding RNAs by both the RNA interference and the exosome degradation pathways. Recent evidence indicates that splicing factors facilitate the cotranscriptional proces...
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Dr1 (NC2) is present at tRNA genes and represses their transcription in human cells.
Published: March, 2010

Abstract: Dr1 (also known as NC2beta) was identified as a repressor of RNA polymerase (pol) II transcription. It was subsequently shown to inhibit pol III transcription when expressed at high levels in vitro or in yeast cells. However, endogenous Dr1 was no...
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Bone morphogenetic protein-7 inhibits proximal tubular epithelial cell Smad3 signaling via increased SnoN expression.
Published: March, 2010

Abstract: Bone morphogenetic protein-7 (BMP-7) improves outcome in animal models of fibrotic renal disease by opposing transforming growth factor beta1 (TGF-beta)-dependent fibrosis. However, the underlying mechanisms remain obscure. Here, we studied the ef...
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Viral induction of the zinc finger antiviral protein is IRF3-dependent but NF-kappaB-independent.
Published: February, 2010

Abstract: The zinc finger antiviral protein (ZAP) is an interferon-stimulated gene that restricts the replication of retroviruses, alphaviruses, and filoviruses. Relatively little is known, however, regarding the detailed mechanism of ZAP induction during v...
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The lysyl oxidases LOX and LOXL2 are necessary and sufficient to repress E-cadherin in hypoxia: insights into cellular transformation processes mediated by HIF-1.
Published: February, 2010

Abstract: Hypoxia has been shown to promote tumor metastasis and lead to therapy resistance. Recent work has demonstrated that hypoxia represses E-cadherin expression, a hallmark of epithelial to mesenchymal transition, which is believed to amplify tumor ag...
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Targets of the Tal1 transcription factor in erythrocytes: E2 ubiquitin conjugase regulation by Tal1.
Published: February, 2010

Abstract: The Tal1 transcription factor is essential for the development of the hematopoietic system and plays a role during definitive erythropoiesis in the adult. Despite the importance of Tal1 in erythropoiesis, only a small number of erythroid different...
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AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.
Published: February, 2010

Abstract: Transcriptome profiling has become a routine tool in biology. For Arabidopsis (Arabidopsis thaliana), the Affymetrix ATH1 expression array is most commonly used, but it lacks about one-third of all annotated genes present in the reference strain. ...
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Antiinflammatory properties of a plant-derived nonsteroidal, dissociated glucocorticoid receptor modulator in experimental autoimmune encephalomyelitis.
Published: February, 2010

Abstract: Compound A (CpdA), a plant-derived phenyl aziridine precursor, was recently characterized as a fully dissociated nonsteroidal antiinflammatory agent, acting via activation of the glucocorticoid receptor, thereby down-modulating nuclear factor-kapp...
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Human papillomavirus type 8 E2 protein unravels JunB/Fra-1 as an activator of the beta4-integrin gene in human keratinocytes.
Published: February, 2010

Abstract: The papillomavirus life cycle parallels keratinocyte differentiation in stratifying epithelia. We have previously shown that the human papillomavirus type 8 (HPV8) E2 protein downregulates beta4-integrin expression in normal human keratinocytes, w...
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Potential role of estrogen in regulation of the insulin-like growth factor2-H19 locus in the rat testis.
Published: January, 2010

Abstract: The selective estrogen receptor modulator, tamoxifen, has been shown to reduce DNA methylation at Insulin-like growth factor 2/H19 differentially methylated region (Igf2/H19 DMR) in the spermatozoa of the Holtzman rats. Since imprint at this locus...
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Epigenetic chromatin states uniquely define the developmental plasticity of murine hematopoietic stem cells.
Published: January, 2010

Abstract: Heritable epigenetic signatures are proposed to serve as an important regulatory mechanism in lineage fate determination. To investigate this, we profiled chromatin modifications in murine hematopoietic stem cells, lineage-restricted progenitors, ...
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Early-life experience reduces excitation to stress-responsive hypothalamic neurons and reprograms the expression of corticotropin-releasing hormone.
Published: January, 2010

Abstract: Increased sensory input from maternal care attenuates neuroendocrine and behavioral responses to stress long term and results in a lifelong phenotype of resilience to depression and improved cognitive function. Whereas the mechanisms of this clini...
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Activation of Cdc6 by MyoD is associated with the expansion of quiescent myogenic satellite cells.
Published: January, 2010

Abstract: MyoD is a transcriptional factor that is required for the differentiation of muscle stem cells (satellite cells). In this study, we describe a previously unknown function for MyoD in regulating a gene (Cdc6) that is vital to endowing chromatin wit...
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Unlocking short read sequencing for metagenomics.
Published: January, 2010

Abstract: BACKGROUND: Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved. METHODOLOGY/PR...
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Polycomb target genes are silenced in multiple myeloma.
Published: January, 2010

Abstract: Multiple myeloma (MM) is a genetically heterogeneous disease, which to date remains fatal. Finding a common mechanism for initiation and progression of MM continues to be challenging. By means of integrative genomics, we identified an underexpress...
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A comprehensive map of insulator elements for the Drosophila genome.
Published: January, 2010

Abstract: Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries. A thorough understanding of their location and function is necessary to address the complexities of metazoan gene regulat...
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Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.
Published: January, 2010

Abstract: Next-generation sequencing is revolutionizing the identification of transcription factor binding sites throughout the human genome. However, the bioinformatics analysis of large datasets collected using chromatin immunoprecipitation and high-throu...
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Differential DNA methylation correlates with differential expression of angiogenic factors in human heart failure.
Published: January, 2010

Abstract: Epigenetic mechanisms such as microRNA and histone modification are crucially responsible for dysregulated gene expression in heart failure. In contrast, the role of DNA methylation, another well-characterized epigenetic mark, is unknown. In order...
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Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.
Published: January, 2010

Abstract: We characterize and extend a highly efficient method for constructing shotgun fragment libraries in which transposase catalyzes in vitro DNA fragmentation and adaptor incorporation simultaneously. We apply this method to sequencing a human genome ...
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A Method to Study the Epigenetic Chromatin States of Rare Hematopoietic Stem and Progenitor Cells; MiniChIP-Chip.
Published: January, 2010

Abstract: Dynamic chromatin structure is a fundamental property of gene transcriptional regulation, and has emerged as a critical modulator of physiological processes during cellular differentiation and development. Analysis of chromatin structure using mo...
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The epigenetic landscape of latent Kaposi sarcoma-associated herpesvirus genomes.
Published: January, 2010

Abstract: Herpesvirus latency is generally thought to be governed by epigenetic modifications, but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood. Here, we report a comprehensive spatial and temporal analysis o...
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The core binding factor CBF negatively regulates skeletal muscle terminal differentiation.
Published: January, 2010

Abstract: BACKGROUND: Core Binding Factor or CBF is a transcription factor composed of two subunits, Runx1/AML-1 and CBF beta or CBFbeta. CBF was originally described as a regulator of hematopoiesis. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that CBF is ...
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The Runx transcriptional co-activator, CBFbeta, is essential for invasion of breast cancer cells.
Published: January, 2010

Abstract: BACKGROUND: The transcription factor Runx2 has an established role in cancers that metastasize to bone. In metastatic breast cancer cells Runx2 is overexpressed and contributes to the invasive capacity of the cells by regulating the expression of ...
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A paucity of heterochromatin at functional human neocentromeres.
Published: January, 2010

Abstract: BACKGROUND: Centromeres are responsible for the proper segregation of replicated chromatids during cell division. Neocentromeres are fully functional ectopic human centromeres that form on low-copy DNA sequences and permit analysis of centromere s...
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An NF-kappaB-dependent role for JunB in the induction of proinflammatory cytokines in LPS-activated bone marrow-derived dendritic cells.
Published: January, 2010

Abstract: BACKGROUND: Dendritic cells (DCs) play a key role in the induction of adaptive and memory immune responses. Upon encounter with pathogens, they undergo a complex maturation process and migrate toward lymphoid organs where they stimulate immune eff...
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Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis.
Published: January, 2010

Abstract: BACKGROUND: Increasing evidence demonstrates that stem cells maintain their identities by a unique transcription network and chromatin structure. Opposing epigenetic modifications H3K27 me3 and H3K4 me3 have been proposed to label differentiation-...
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Retinoic acid protects human breast cancer cells against etoposide-induced apoptosis by NF-kappaB-dependent but cIAP2-independent mechanisms.
Published: January, 2010

Abstract: BACKGROUND: Retinoids, through their cognate nuclear receptors, exert potent effects on cell growth, differentiation and apoptosis, and have significant promise for cancer therapy and chemoprevention. These ligands can determine the ultimate fate ...
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Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated.
Published: January, 2010

Abstract: BACKGROUND: DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predic...
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Acetylation of p65 at lysine 314 is important for late NF-kappaB-dependent gene expression.
Published: January, 2010

Abstract: BACKGROUND: NF-kappaB regulates the expression of a large number of target genes involved in the immune and inflammatory response, apoptosis, cell proliferation, differentiation and survival. We have earlier reported that p65, a subunit of NF-kapp...
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Antagonism of aryl hydrocarbon receptor signaling by 6,2',4'-trimethoxyflavone.
Published: January, 2010

Abstract: The aryl hydrocarbon receptor (AHR) is regarded as an important homeostatic transcriptional regulator within physiological and pathophysiological processes, including xenobiotic metabolism, endocrine function, immunity, and cancer. Agonist activat...
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Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA.
Published: January, 2010

Abstract: BACKGROUND: DNA methylation contributes to the regulation of gene expression during development and cellular differentiation. The recently developed Methylated DNA ImmunoPrecipitation (MeDIP) assay allows a comprehensive analysis of this epigeneti...
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Downstream targets of methyl CpG binding protein 2 and their abnormal expression in the frontal cortex of the human Rett syndrome brain.
Published: January, 2010

Abstract: BACKGROUND: The Rett Syndrome (RTT) brain displays regional histopathology and volumetric reduction, with frontal cortex showing such abnormalities, whereas the occipital cortex is relatively less affected. RESULTS: Using microarrays and quantitat...
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Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing.
Published: January, 2010

Abstract: Many disease-associated variants identified by genome-wide association (GWA) studies are expected to regulate gene expression. Allele-specific expression (ASE) quantifies transcription from both haplotypes using individuals heterozygous at tested ...
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Global regulator SATB1 recruits beta-catenin and regulates T(H)2 differentiation in Wnt-dependent manner.
Published: January, 2010

Abstract: In vertebrates, the conserved Wnt signalling cascade promotes the stabilization and nuclear accumulation of beta-catenin, which then associates with the lymphoid enhancer factor/T cell factor proteins (LEF/TCFs) to activate target genes. Wnt/beta ...
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Halogenated imidazole derivatives block RNA polymerase II elongation along mitogen inducible genes.
Published: January, 2010

Abstract: BACKGROUND: Aberrant activation of protein kinases is one of the essential oncogenic driving forces inherent to the process of tumorigenesis. The protein kinase CK2 plays an important role in diverse biological processes, including cell growth and...
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Novel snail1 target proteins in human colon cancer identified by proteomic analysis.
Published: January, 2010

Abstract: BACKGROUND: The transcription factor Snail1 induces epithelial-to-mesenchymal transition (EMT), a process responsible for the acquisition of invasiveness during tumorigenesis. Several transcriptomic studies have reported Snail1-regulated genes in ...
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Nrf2 expression is regulated by epigenetic mechanisms in prostate cancer of TRAMP mice.
Published: January, 2010

Abstract: Nuclear factor-erythroid 2 p45-related factor 2 (Nrf2) is a transcription factor which regulates the expression of many cytoprotective genes. In the present study, we found that the expression of Nrf2 was suppressed in prostate tumor of the Transg...
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Nuclear myosin 1 is in complex with mature rRNA transcripts and associates with the nuclear pore basket.
Published: January, 2010

Abstract: In rRNA biogenesis, nuclear myosin 1 (NM1) and actin synergize to activate rRNA gene transcription. Evidence that actin is in preribosomal subunits and NM1 may control rRNA biogenesis post-transcriptionally prompted us to investigate whether NM1 a...
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Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene.
Published: January, 2010

Abstract: Glucocorticoids act in part via glucocorticoid receptor binding to hormone response elements (HREs), but their direct target genes in vivo are still largely unknown. We developed the criterion that genomic occurrence of paired HREs at an inter-HRE...
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Molecular and evolutionary characteristics of the fraction of human alpha satellite DNA associated with CENP-A at the centromeres of chromosomes 1, 5, 19, and 21.
Published: January, 2010

Abstract: BACKGROUND: The mode of evolution of the highly homogeneous Higher-Order-Repeat-containing alpha satellite arrays is still subject to discussion. This is also true of the CENP-A associated repeats where the centromere is formed. RESULTS: In this p...
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Cytotoxic effect and apoptosis induction by silver nanoparticles in HeLa cells.
Published: December, 2009

Abstract: Nanosilver has well-known antibacterial properties, and is widely used in daily life as various medical and general products. In comparison with silver ion, there is serious lacking of information concerning the biological effects of nanoAg. In th...
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Muscle inactivation of mTOR causes metabolic and dystrophin defects leading to severe myopathy.
Published: December, 2009

Abstract: Mammalian target of rapamycin (mTOR) is a key regulator of cell growth that associates with raptor and rictor to form the mTOR complex 1 (mTORC1) and mTORC2, respectively. Raptor is required for oxidative muscle integrity, whereas rictor is dispen...
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Oct4 and LIF/Stat3 additively induce Krüppel factors to sustain embryonic stem cell self-renewal.
Published: December, 2009

Abstract: Embryonic stem cell (ESC) pluripotency is dependent on an intrinsic gene regulatory network centered on Oct4. Propagation of the pluripotent state is stimulated by the cytokine leukemia inhibitory factor (LIF) acting through the transcriptional re...
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Dissection of Rad9 BRCT domain function in the mitotic checkpoint response to telomere uncapping.
Published: December, 2009

Abstract: In Saccharomyces cerevisiae, destabilizing telomeres, via inactivation of telomeric repeat binding factor Cdc13, induces a cell cycle checkpoint that arrests cells at the metaphase to anaphase transition--much like the response to an unrepaired DN...
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Histone H1 binding is inhibited by histone variant H3.3
Published: December, 2009

Abstract: Linker histones are involved in the formation of higher-order chromatin structure and the regulation of specific genes, yet it remains unclear what their principal binding determinants are. We generated a genome-wide high-resolution binding map fo...
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Cag3 is a novel essential component of the Helicobacter pylori Cag type IV secretion system outer membrane subcomplex.
Published: December, 2009

Abstract: Helicobacter pylori strains harboring the cag pathogenicity island (PAI) have been associated with more severe gastric disease in infected humans. The cag PAI encodes a type IV secretion (T4S) system required for CagA translocation into host cells...
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Simultaneous quantitative analysis of N-acylethanolamides in clinical samples.
Published: December, 2009

Abstract: A simple and rapid analytical method is described for the simultaneous quantitative analysis of three different N-acylethanolamides in human biological samples: anandamide (AEA), oleoylethanolamide (OEA), and palmitoylethanolamide (PEA). The metho...
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CpG-island promoters drive transcription of human telomeres.
Published: December, 2009

Abstract: The longstanding dogma that telomeres, the heterochromatic extremities of linear eukaryotic chromosomes, are transcriptionally silent was overturned by the discovery that DNA-dependent RNA polymerase II (RNAPII) transcribes telomeric DNA into telo...
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Dynamic DNA methylation programs persistent adverse effects of early-life stress.
Published: December, 2009

Abstract: Adverse early life events can induce long-lasting changes in physiology and behavior. We found that early-life stress (ELS) in mice caused enduring hypersecretion of corticosterone and alterations in passive stress coping and memory. This phenotyp...
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Set2-dependent K36 methylation is regulated by novel intratail interactions within H3.
Published: December, 2009

Abstract: Posttranslational modifications to histones have been studied extensively, but the requirement for the residues within the tails for different stages of transcription is less clear. Using RNR3 as a model, we found that the residues within the N te...
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ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth.
Published: December, 2009

Abstract: A single nucleotide substitution in intron 3 of IGF2 in pigs abrogates a binding site for a repressor and leads to a 3-fold up-regulation of IGF2 in skeletal muscle. The mutation has major effects on muscle growth, size of the heart, and fat depos...
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Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy.
Published: November, 2009

Abstract: GATA factors interact with simple DNA motifs (WGATAR) to regulate critical processes, including hematopoiesis, but very few WGATAR motifs are occupied in genomes. Given the rudimentary knowledge of mechanisms underlying this restriction and how GA...
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Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms' tumor.
Published: November, 2009

Abstract: Wilms' tumour (WT) is a pediatric tumor of the kidney that arises via failure of the fetal developmental program. The absence of identifiable mutations in the majority of WTs suggests the frequent involvement of epigenetic aberrations in WT. We th...
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Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II.
Published: November, 2009

Abstract: A common landmark of activated genes is the presence of trimethylation on lysine 4 of histone H3 (H3K4) at promoter regions. Set1/COMPASS was the founding member and is the only H3K4 methylase in Saccharomyces cerevisiae; however, in mammals, at l...
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Sp1 mediate hypoxia induced ephrinB2 expression via a hypoxia-inducible factor independent mechanism.
Published: October, 2009

Abstract: Environmental factors are instrumental in maintaining a healthy vasculature. Oxygen tension is higher in arteries than in veins and thus has the potential to be an instructive signal in arterial/venous specification. EphrinB2 is specifically expre...
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The NF-kappaB factor RelB and histone H3 lysine methyltransferase G9a directly interact to generate epigenetic silencing in endotoxin tolerance.
Published: October, 2009

Abstract: The interplay of transcription factors, histone modifiers, and DNA modification can alter chromatin structure that epigenetically controls gene transcription. During severe systemic inflammatory (SSI), the generation of facultative heterochromatin...
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JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin.
Published: October, 2009

Abstract: Activation of Janus kinase 2 (JAK2) by chromosomal translocations or point mutations is a frequent event in haematological malignancies. JAK2 is a non-receptor tyrosine kinase that regulates several cellular processes by inducing cytoplasmic signa...
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INTS3 controls the hSSB1-mediated DNA damage response.
Published: October, 2009

Abstract: Human SSB1 (single-stranded binding protein 1 [hSSB1]) was recently identified as a part of the ataxia telangiectasia mutated (ATM) signaling pathway. To investigate hSSB1 function, we performed tandem affinity purifications of hSSB1 mutants mimic...
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Smad3 is required for normal follicular follicle-stimulating hormone responsiveness in the mouse.
Published: October, 2009

Abstract: Follicle-stimulating hormone (FSH) is the major regulator of folliculogenesis, but other factors modulate its action, including members of the transforming growth factor (TGF) beta family. The intersection of signal transduction pathways that inte...
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Foxa1 and Foxa2 function both upstream of and cooperatively with Lmx1a and Lmx1b in a feedforward loop promoting mesodiencephalic dopaminergic neuron development.
Published: September, 2009

Abstract: Mesodiencephalic dopaminergic neurons control voluntary movement and reward based behaviours. Their dysfunction can lead to neurological disorders, including Parkinson's disease. These neurons are thought to arise from progenitors in the floor pla...
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Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation.
Published: September, 2009

Abstract: To identify regulators involved in determining the differential pattern of H3K79 methylation by Dot1, we screened the entire yeast gene deletion collection by GPS for genes required for normal levels of H3K79 di- but not trimethylation. We identif...
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p57Kip2 is a repressor of Mash1 activity and neuronal differentiation in neural stem cells.
Published: September, 2009

Abstract: Mammalian central nervous system (CNS) development is a highly organized process involving the precise and coordinated timing of cell-cycle exit, differentiation, survival, and migration. These events require proper expression of pro-neuronal gene...
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Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors.
Published: September, 2009

Abstract: Epigenetic processes are the main conductors of phenotypic variation in eukaryotes. The malaria parasite Plasmodium falciparum employs antigenic variation of the major surface antigen PfEMP1, encoded by 60 var genes, to evade acquired immune respo...
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Functional connection between deimination and deacetylation of histones.
Published: September, 2009

Abstract: Histone methylation plays key roles in regulating chromatin structure and function. The recent identification of enzymes that antagonize or remove histone methylation offers new opportunities to appreciate histone methylation plasticity in the reg...
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Three-dimensional structure of the two-peptide bacteriocin plantaricin JK.
Published: September, 2009

Abstract: The three-dimensional structures of the two peptides, PlnJ and PlnK, that constitutes the two-peptide bacteriocin plantaricin JK have been solved in water/TFE and water/DPC-micellar solutions using nuclear magnetic resonance (NMR) spectroscopy. Pl...
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Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing.
Published: September, 2009

Abstract: The lack of efficient high-throughput methods for enrichment of specific sequences from genomic DNA represents a key bottleneck in exploiting the enormous potential of next-generation sequencers. Such methods would allow for a systematic and targe...
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Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex.
Published: September, 2009

Abstract: The Saccharomyces cerevisiae kinase Bur1 is involved in coupling transcription elongation to chromatin modification, but not all important Bur1 targets in the elongation complex are known. Using a chemical genetics strategy wherein Bur1 kinase was...
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The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.
Published: September, 2009

Abstract: We present the first Korean individual genome sequence (SJK) and analysis results. The diploid genome of a Korean male was sequenced to 28.95-fold redundancy using the Illumina paired-end sequencing method. SJK covered 99.9% of the NCBI human refe...
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Transcription independent insulation at TFIIIC-dependent insulators.
Published: September, 2009

Abstract: Chromatin insulators separate active from repressed chromatin domains. In yeast the RNA pol III transcription machinery bound to tRNA genes function with histone acetylases and chromatin remodelers to restrict the spread of heterochromatin. Our re...
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The multiple endocrine neoplasia type 1 (MEN1) tumor suppressor regulates peroxisome proliferator-activated receptor gamma-dependent adipocyte differentiation.
Published: September, 2009

Abstract: Menin, the product of the MEN1 (multiple endocrine neoplasia type 1) tumor suppressor gene, is involved in activation of gene transcription as part of an MLL1 (mixed-lineage leukemia 1)/MLL2 (KMT2A/B)-containing protein complex which harbors methy...
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Characterization of glucocorticoid receptor and hepatocyte nuclear factor 4alpha (HNF4alpha) binding to the hnf4alpha gene in the liver.
Published: September, 2009

Abstract: Hepatocyte nuclear factor 4alpha (HNF4alpha) plays a crucial role in hepatocyte differentiation, liver organogenesis and regulation of liver functions. In mouse liver, HNF4alpha is expressed from two promoters, P1 and P2, the latter being very wea...
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Ultradian hormone stimulation induces glucocorticoid receptor-mediated pulses of gene transcription.
Published: September, 2009

Abstract: Studies on glucocorticoid receptor (GR) action typically assess gene responses by long-term stimulation with synthetic hormones. As corticosteroids are released from adrenal glands in a circadian and high-frequency (ultradian) mode, such treatment...
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ID1 promotes expansion and survival of primary erythroid cells and is a target of JAK2V617F-STAT5 signaling.
Published: August, 2009

Abstract: The discovery of JAK2V617F as an acquired mutation in the majority of patients with myeloproliferative disorders (MPDs) and the key role of the JAK2-STAT5 signaling cascade in normal hematopoiesis has focused attention on the downstream transcript...
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Targeting of EZH2 to a defined genomic site is sufficient for recruitment of Dnmt3a but not de novo DNA methylation
Published: August, 2009

Abstract: Polycomb-mediated gene silencing and DNA methylation underlie many epigenetic processes important in normal development as well as in cancer. An interaction between EZH2 of the Polycomb repressive complex 2 (PRC2), which trimethyl- ates lysine 27 ...
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HIC1 interacts with a specific subunit of SWI/SNF complexes, ARID1A/BAF250A.
Published: August, 2009

Abstract: HIC1, a tumor suppressor gene epigenetically silenced in many human cancers encodes a transcriptional repressor involved in regulatory loops modulating p53-dependent and E2F1-dependent cell survival and stress responses. HIC1 is also implicated in...
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Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation.
Published: August, 2009

Abstract: Transcription is a sophisticated multi-step process in which RNA polymerase II (Pol II) transcribes a DNA template into RNA in concert with a broad array of transcription initiation, elongation, capping, termination, and histone modifying factors....
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BRG1 increases transcription of proinflammatory genes in renal ischemia.
Published: August, 2009

Abstract: Acute kidney injury stimulates renal production of inflammatory mediators, including TNF-alpha and monocyte chemoattractant protein 1 (MCP-1). These responses reflect, in part, injury-induced transcription of proinflammatory genes by proximal tubu...
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CpG methylation controls reactivation of HIV from latency.
Published: August, 2009

Abstract: DNA methylation of retroviral promoters and enhancers localized in the provirus 5' long terminal repeat (LTR) is considered to be a mechanism of transcriptional suppression that allows retroviruses to evade host immune responses and antiretroviral...
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Cutting edge: SWI/SNF mediates antisense Igh transcription and locus-wide accessibility in B cell precursors.
Published: August, 2009

Abstract: The stepwise process of Ag receptor gene assembly, termed V(D)J recombination, is coordinated during lymphocyte development by sweeping changes in chromatin that permit or deny access to a single recombinase enzyme. We now show that switching/sucr...
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Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation.
Published: August, 2009

Abstract: The Drosophila melanogaster male-specific lethal (MSL) complex binds the single male X chromosome to upregulate gene expression to equal that from the two female X chromosomes. However, it has been puzzling that approximately 25% of transcribed ge...
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Endoplasmic reticulum stress regulates adipocyte resistin expression.
Published: August, 2009

Abstract: OBJECTIVE: Resistin is a secreted polypeptide that impairs glucose metabolism and, in rodents, is derived exclusively from adipocytes. In murine obesity, resistin circulates at elevated levels but its gene expression in adipose tissue is paradoxic...
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p38 Mitogen-activated protein kinase- and HuR-dependent stabilization of p21(Cip1) mRNA mediates the G(1)/S checkpoint.
Published: August, 2009

Abstract: Activation of p38 mitogen-activated protein kinase (MAPK) plays an important role in the G(2)/M cell cycle arrest induced by DNA damage, but little is known about the role of this signaling pathway in the G(1)/S transition. Upregulation of the cyc...
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Regulon-specific control of transcription elongation across the yeast genome.
Published: August, 2009

Abstract: Transcription elongation by RNA polymerase II was often considered an invariant non-regulated process. However, genome-wide studies have shown that transcriptional pausing during elongation is a frequent phenomenon in tightly-regulated metazoan ge...
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Snail2 cooperates with Snail1 in the repression of vitamin D receptor in colon cancer.
Published: August, 2009

Abstract: Vitamin D receptor (VDR) mediates the antitumoral action of the active vitamin D metabolite 1alpha,25-dihydroxyvitamin D(3) (1,25(OH)(2)D(3)). VDR expression is lost during colon cancer progression causing unresponsiveness to 1,25(OH)(2)D(3) and i...
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SWI/SNF and Asf1p cooperate to displace histones during induction of the saccharomyces cerevisiae HO promoter.
Published: August, 2009

Abstract: Regulation of the Saccharomyces cerevisiae HO promoter has been shown to require the recruitment of chromatin-modifying and -remodeling enzymes. Despite this, relatively little is known about what changes to chromatin structure occur during the co...
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The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.
Published: August, 2009

Abstract: The regulation of the G1- to S-phase transition is critical for cell-cycle progression. This transition is driven by a transient transcriptional wave regulated by transcription factor complexes termed MBF/SBF in yeast and E2F-DP in mammals. Here w...
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Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).
Published: July, 2009

Abstract: The binding of sequence-specific regulatory factors and the recruitment of chromatin remodeling activities cause nucleosomes to be evicted from chromatin in eukaryotic cells. Traditionally, these active sites have been identified experimentally th...
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Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection.
Published: July, 2009

Abstract: To exploit contemporary sequencing technologies for targeted genetic analyses, we developed a hybridization enrichment strategy for DNA capture that uses PCR products as subgenomic traps. We applied this strategy to 115 kilobases of the human geno...
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Histone methylation regulator PTIP is required for PPARgamma and C/EBPalpha expression and adipogenesis.
Published: July, 2009

Abstract: PPARgamma and C/EBPalpha cooperate to control preadipocyte differentiation (adipogenesis). However, the factors that regulate PPARgamma and C/EBPalpha expression during adipogenesis remain largely unclear. Here, we show PTIP, a protein that associ...
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Global analysis of DNA methylation and transcription of human repetitive sequences
Published: July, 2009

Abstract: Half of the human genome consists of repetitive DNA sequences. Recent studies in various organisms highlight the role of chromatin regulation of repetitive DNA in gene regulation as well as in maintainance of chromosomes and genome integrity. Henc...
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CRTC2 (TORC2) contributes to the transcriptional response to fasting in the liver but is not required for the maintenance of glucose homeostasis.
Published: July, 2009

Abstract: The liver contributes to glucose homeostasis by promoting either storage or production of glucose, depending on the physiological state. The cAMP response element-binding protein (CREB) is a principal regulator of genes involved in coordinating th...
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Improved Protocols for Illumina Sequencing
Published: July, 2009

Abstract: In this unit, we describe a set of improvements we have made to the standard Illumina protocols to make the sequencing process more reliable in a high-throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and ...
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The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells.
Published: July, 2009

Abstract: CD6 is a lymphocyte surface receptor involved in lymphocyte activation and differentiation processes that is constitutively expressed on developing and mature T cells and on the B1a cells. To define the molecular basis for the tissue-specific expr...
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Metabolic intermediates selectively stimulate transcription factor interaction and modulate phosphate and purine pathways.
Published: June, 2009

Abstract: Cells use strategic metabolites to sense the metabolome and accordingly modulate gene expression. Here, we show that the purine and phosphate pathways are positively regulated by the metabolic intermediate AICAR (5'-phosphoribosyl-5-amino-4-imidaz...
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Phosphorylation of histone H3 Thr-45 is linked to apoptosis.
Published: June, 2009

Abstract: Numerous post-translational modifications have been identified in histones. Most of these occur within the histone tails, but a few have been identified within the histone core sequences. Histone core post-translational modifications have the pote...
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Tumor vasculature is regulated by PHD2-mediated angiogenesis and bone marrow-derived cell recruitment.
Published: June, 2009

Abstract: Sustained angiogenesis, through either local sprouting (angiogenesis) or the recruitment of bone marrow-derived cells (BMDCs) (vasculogenesis), is essential to the development of a tumor. How BMDCs are recruited to the tumor and their contribution...
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A novel mechanism of antagonism between ATP-dependent chromatin remodeling complexes regulates RNR3 expression.
Published: June, 2009

Abstract: Gene expression depends upon the antagonistic actions of chromatin remodeling complexes. While this has been studied extensively for the enzymes that covalently modify the tails of histones, the mechanism of how ATP-dependent remodeling complexes ...
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The Dot1 histone methyltransferase and the Rad9 checkpoint adaptor contribute to cohesin-dependent double-strand break repair by sister chromatid recombination in Saccharomyces cerevisiae.
Published: June, 2009

Abstract: Genomic integrity is threatened by multiple sources of DNA damage. DNA double-strand breaks (DSBs) are among the most dangerous types of DNA lesions and can be generated by endogenous or exogenous agents, but they can arise also during DNA replica...
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Magnet-guided transduction of mammalian cells and mice using engineered magnetic lentiviral particles.
Published: May, 2009

Abstract: Targeted delivery of therapeutic transgenes into specific cells remains a highly relevant challenge for tissue engineering and future gene-based therapies. We have designed streptavidin-pseudotyped lentiviral particles which upon coupling with bio...
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Characterization of the murine Ephrin-B2 promoter.
Published: May, 2009

Abstract: Eph/ephrin signaling is pivotal in prenatal angiogenesis. Although their role in these processes has been extensively studied the mechanisms controlling eph/ephrin expression is not fully understood. To better understand the transcriptional regula...
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The PRC1 Polycomb group complex interacts with PLZF/RARA to mediate leukemic transformation.
Published: May, 2009

Abstract: Ectopic repression of retinoic acid (RA) receptor target genes by PML/RARA and PLZF/RARA fusion proteins through aberrant recruitment of nuclear corepressor complexes drives cellular transformation and acute promyelocytic leukemia (APL) developmen...
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A comprehensive analysis of recruitment and transactivation potential of K-Rta and K-bZIP during reactivation of Kaposi's sarcoma-associated herpesvirus.
Published: April, 2009

Abstract: Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi's sarcoma. K-Rta and K-bZIP are two major viral transcription factors that control reactivation of this virus. Here we report a genome-wide analysis of transcriptional...
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Dynamic Histone H1 Isotype 4 Methylation and Demethylation by Histone Lysine Methyltransferase G9a/KMT1C and the Jumonji Domain-containing JMJD2/KDM4 Proteins.
Published: March, 2009

Abstract: The linker histone H1 generally participates in the establishment of chromatin structure. However, of the seven somatic H1 isotypes in humans some are also implicated in the regulation of local gene expression. Histone H1 isotype 4 (H1.4) represse...
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Cyclical chromatin looping and transcription factor association on the regulatory regions of the p21 (CDKN1A) gene in response to 1alpha,25-dihydroxyvitamin D3.
Published: March, 2009

Abstract: The nuclear receptor vitamin D receptor (VDR) is known to associate with three vitamin D response element (VDREs)-containing regions within the CDKN1A (p21) gene region. Here we show in MDA-MB453 breast cancer cells that the natural VDR ligand 1al...
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A PP2A regulatory subunit regulates C. elegans insulin/IGF-1 signaling by modulating AKT-1 phosphorylation.
Published: March, 2009

Abstract: The C. elegans insulin/IGF-1 signaling (IIS) cascade plays a central role in regulating life span, dauer, metabolism, and stress. The major regulatory control of IIS is through phosphorylation of its components by serine/threonine-specific protein...
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The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer.
Published: March, 2009

Abstract: The natural history of cancers associated with virus exposure is intriguing, since only a minority of human tissues infected with these viruses inevitably progress to cancer. However, the molecular reasons why the infection is controlled or instea...
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Genome-wide regulon and crystal structure of BlaI (Rv1846c) from Mycobacterium tuberculosis.
Published: March, 2009

Abstract: Comparative genomics with Staphylococcus aureus suggested the existence of a regulatory system governing beta-lactamase (BlaC) production in Mycobacterium tuberculosis. The crystal structure of Rv1846c, a winged helix regulator of previously unkno...
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Differential chromatin marking of introns and expressed exons by H3K36me3.
Published: March, 2009

Abstract: Variation in patterns of methylations of histone tails reflects and modulates chromatin structure and function. To provide a framework for the analysis of chromatin function in Caenorhabditis elegans, we generated a genome-wide map of histone H3 t...
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Temporal regulation of Ath5 gene expression during eye development.
Published: February, 2009

Abstract: During central nervous system development the timing of progenitor differentiation must be precisely controlled to generate the proper number and complement of neuronal cell types. Proneural basic helix-loop-helix (bHLH) transcription factors play...
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Intestinal hypoxia-inducible transcription factors are essential for iron absorption following iron deficiency.
Published: February, 2009

Abstract: Iron deficiency and iron overload are among the most prevalent nutritional disorders worldwide. Duodenal cytochrome b (DcytB) and divalent metal transporter 1 (DMT1) are regulators of iron absorption. Their expression is increased during high syst...
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The reelin and GAD67 promoters are activated by epigenetic drugs that facilitate the disruption of local repressor complexes.
Published: February, 2009

Abstract: The epigenetic down-regulation of genes is emerging as a possible underlying mechanism of the GABAergic neuron dysfunction in schizophrenia. For example, evidence has been presented to show that the promoters associated with reelin and GAD67 are d...
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Nuclear factor-kappaB binds to the Epstein-Barr Virus LMP1 promoter and upregulates its expression.
Published: February, 2009

Abstract: The latent membrane protein 1 (LMP1) oncogene carried by Epstein-Barr virus (EBV) is essential for transformation and maintenance of EBV-immortalized B cells in vitro, and it is expressed in most EBV-associated tumor types. The activation of the N...
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Survival motor neuron gene 2 silencing by DNA methylation correlates with spinal muscular atrophy disease severity and can be bypassed by histone deacetylase inhibition.
Published: January, 2009

Abstract: Spinal muscular atrophy (SMA), a common neuromuscular disorder, is caused by homozygous absence of the survival motor neuron gene 1 (SMN1), while the disease severity is mainly influenced by the number of SMN2 gene copies. This correlation is not ...
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SIRT6 links histone H3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span.
Published: January, 2009

Abstract: Members of the sirtuin (SIRT) family of NAD-dependent deacetylases promote longevity in multiple organisms. Deficiency of mammalian SIRT6 leads to shortened life span and an aging-like phenotype in mice, but the underlying molecular mechanisms are...
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Distinct differences in chromatin structure at subtelomeric X and Y' elements in budding yeast.
Published: January, 2009

Abstract: In Saccharomyces cerevisiae, all ends of telomeric DNA contain telomeric repeats of (TG(1-3)), but the number and position of subtelomeric X and Y' repeat elements vary. Using chromatin immunoprecipitation and genome-wide analyses, we here demonst...
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Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing.
Published: January, 2009

Abstract: Complementary techniques that deepen information content and minimize reagent costs are required to realize the full potential of massively parallel sequencing. Here, we describe a resequencing approach that directs focus to genomic regions of hig...
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Cell-free circulating DNA: diagnostic value in patients with testicular germ cell cancer.
Published: January, 2009

Abstract: PURPOSE: Increased levels of cell-free circulating DNA have been described in various malignancies as a diagnostic and prognostic biomarker. We analyzed the significance of cell-free DNA in patients with testicular cancer. MATERIALS AND METHODS: C...
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TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation.
Published: January, 2009

Abstract: BACKGROUND: The re-replication inhibitor Geminin binds to several transcription factors including homeodomain proteins, and to members of the polycomb and the SWI/SNF complexes. RESULTS: Here we describe the TATA-binding protein-like factor-intera...
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Methylated DNA immunoprecipitation and microarray-based analysis: detection of DNA methylation in breast cancer cell lines.
Published: January, 2009

Abstract: The methylated DNA immunoprecipitation microarray (MeDIP-chip) is a genome-wide, high-resolution approach to detect DNA methylation in whole genome or CpG (cytosine base followed by a guanine base) islands. The method utilizes anti-methylcytosine ...
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The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis.
Published: January, 2009

Abstract: BACKGROUND: SET-domain proteins are histone lysine (K) methyltransferases (HMTase) implicated in defining transcriptionally permissive or repressive chromatin. The Arabidopsis ASH1 HOMOLOG 2 (ASHH2) protein (also called SDG8, EFS and CCR1) has bee...
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Approaches to determine expression of inflammatory cytokines.
Published: January, 2009

Abstract: There is an increasing awareness of the role of inflammation in cancer. Immune responses can limit the growth of some tumors, but paradoxically, may promote the growth of others. Cytokines are critical mediators of both the innate and the adaptive...
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Cooperation between NRF-2 and YY-1 transcription factors is essential for triggering the expression of the PREPL-C2ORF34 bidirectional gene pair.
Published: January, 2009

Abstract: BACKGROUND: Many mammalian genes are organized as bidirectional (head-to-head) gene pairs with the two genes separated only by less than 1 kb. The transcriptional regulation of these bidirectional gene pairs remains largely unclear, but a few stud...
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Core promoter acetylation is not required for high transcription from the phosphoenolpyruvate carboxylase promoter in maize.
Published: January, 2009

Abstract: BACKGROUND: Acetylation of promoter nucleosomes is tightly correlated and mechanistically linked to gene activity. However, transcription is not necessary for promoter acetylation. It seems, therefore, that external and endogenous stimuli control ...
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Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing.
Published: January, 2009

Abstract: BACKGROUND: The emergence of next-generation sequencing technology presents tremendous opportunities to accelerate the discovery of rare variants or mutations that underlie human genetic disorders. Although the complete sequencing of the affected ...
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Monodispersity of recombinant Cre recombinase correlates with its effectiveness in vivo.
Published: January, 2009

Abstract: BACKGROUND: Cre recombinase is a common reagent used for the in vivo on/off switching of the expression of target genes flanked by loxP sites. In particular, recombinant TAT-Cre fusion constructs purified from bacteria have been used to promote th...
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Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae.
Published: January, 2009

Abstract: BACKGROUND: Methylation of lysine 79 on histone H3 by Dot1 is required for maintenance of heterochromatin structure in yeast and humans. However, this histone modification occurs predominantly in euchromatin. Thus, Dot1 affects silencing by indire...
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Sox17 promotes cell cycle progression and inhibits TGF-beta/Smad3 signaling to initiate progenitor cell behavior in the respiratory epithelium.
Published: January, 2009

Abstract: The Sry-related high mobility group box transcription factor Sox17 is required for diverse developmental processes including endoderm formation, vascular development, and fetal hematopoietic stem cell maintenance. Expression of Sox17 in mature res...
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The protein tyrosine phosphatase receptor type R gene is an early and frequent target of silencing in human colorectal tumorigenesis.
Published: January, 2009

Abstract: BACKGROUND: Tumor development in the human colon is commonly accompanied by epigenetic changes, such as DNA methylation and chromatin modifications. These alterations result in significant, inheritable changes in gene expression that contribute to...
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BEAF regulates cell-cycle genes through the controlled deposition of H3K9 methylation marks into its conserved dual-core binding sites.
Published: December, 2008

Abstract: Chromatin insulators/boundary elements share the ability to insulate a transgene from its chromosomal context by blocking promiscuous enhancer-promoter interactions and heterochromatin spreading. Several insulating factors target different DNA con...
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p53-Responsive micrornas 192 and 215 are capable of inducing cell cycle arrest.
Published: December, 2008

Abstract: microRNAs provide a novel layer of regulation for gene expression by interfering with the stability and/or translation of specific target mRNAs. Overall levels of microRNAs are frequently down-regulated in cancer cells, and reducing general microR...
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Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies.
Published: December, 2008

Abstract: High-throughput, microarray-based chromatin immunoprecipitation (ChIP-chip) technology allows in vivo elucidation of transcriptional networks. However this complex is not yet readily accessible, in part because its many parameters have not been sy...
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The LPS-induced transcriptional upregulation of the chicken lysozyme locus involves CTCF eviction and noncoding RNA transcription.
Published: October, 2008

Abstract: Transcription of the lysozyme gene is rapidly induced by proinflammatory stimuli such as treatment with bacterial lipopolysaccharide (LPS). Here we show that this induction involves both the relief of repression mediated by the enhancer-blocking p...
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Pax5 and linker histone H1 coordinate DNA methylation and histone modifications in the 3' regulatory region of the immunoglobulin heavy chain locus.
Published: October, 2008

Abstract: The 3' regulatory region (3' RR) of the murine immunoglobulin heavy chain (IgH) locus contains multiple DNase I-hypersensitive (hs) sites. Proximal sites hs3A, hs1.2, and hs3B are located in an extensive palindromic region and together with hs4 ar...
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Novel isoenzyme of 2-oxoglutarate dehydrogenase is identified in brain, but not in heart.
Published: October, 2008

Abstract: 2-Oxoglutarate dehydrogenase (OGDH) is the first and rate-limiting component of the multienzyme OGDH complex (OGDHC) whose malfunction is associated with neurodegeneration. The essential role of this complex in the degradation of glucose and gluta...
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Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex.
Published: September, 2008

Abstract: Yeast RNA polymerase (Pol) II consists of a 10-subunit core enzyme and the Rpb4/7 subcomplex, which is dispensable for catalytic activity and dissociates in vitro. To investigate whether Rpb4/7 is an integral part of DNA-associated Pol II in vivo,...
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Postmitotic Nkx2-1 controls the migration of telencephalic interneurons by direct repression of guidance receptors.
Published: September, 2008

Abstract: The homeodomain transcription factor Nkx2-1 plays key roles in the developing telencephalon, where it regulates the identity of progenitor cells in the medial ganglionic eminence (MGE) and mediates the specification of several classes of GABAergic...
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Regulation of DNA methylation activity through Dnmt3L promoter methylation by Dnmt3 enzymes in embryonic development.
Published: September, 2008

Abstract: The genomic DNA is methylated by de novo methyltransferases Dnmt3a and Dnmt3b during early embryonic development. The establishment of appropriate methylation patterns depends on a fine regulation of the methyltransferase activity. The activity of...
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Stem cell-specific epigenetic priming and B cell-specific transcriptional activation at the mouse Cd19 locus.
Published: September, 2008

Abstract: Low-level expression of multiple lineage-specific genes is a hallmark of hematopoietic stem cells (HSCs). HSCs predominantly express genes specific for the myeloid or megakaryocytic-erythroid lineages, whereas the transcription of lymphoid specifi...
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SUMO-modified Sp3 represses transcription by provoking local heterochromatic gene silencing.
Published: September, 2008

Abstract: Modification of many transcription factors including Sp3 and steroidogenic factor 1 with the small ubiquitin-like modifier (SUMO) is associated with transcriptional repression. Here, we show that SUMOylation of transcription factors bound to DNA p...
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The histone demethylase KDM5b/JARID1b plays a role in cell fate decisions by blocking terminal differentiation.
Published: September, 2008

Abstract: The histone demethylase lysine demethylase 5b (KDM5b) specifically demethylates lysine 4 of histone H3 (meH3K4), thereby repressing gene transcription. KDM5b regulates cell cycle control genes in cancer and is expressed in the early epiblast. This...
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BACH1 is a specific repressor of HMOX1 that is inactivated by arsenite.
Published: August, 2008

Abstract: Intracellular heme is a redox active molecule that can be detrimental to cells at high concentrations or under oxidizing conditions. To prevent accumulation, the inducible enzyme heme oxygenase-1 (HMOX1) catalyzes degradation of heme. In the absen...
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Transcriptional regulation of autocrine IL-6 expression in multiple myeloma cells.
Published: August, 2008

Abstract: Multiple myeloma (MM) is an as to date incurable hematopoietic malignancy. The importance of Interleukin-6 (IL-6) as an autocrine growth factor for MM cells is widely accepted, yet very little is known about the mechanisms at the basis of deregula...
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Regulation of p53 target gene expression by peptidylarginine deiminase 4.
Published: August, 2008

Abstract: Histone Arg methylation has been correlated with transcriptional activation of p53 target genes. However, whether this modification is reversed to repress the expression of p53 target genes is unclear. Here, we report that peptidylarginine deimina...
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Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci.
Published: July, 2008

Abstract: To efficiently transcribe genes, RNA Polymerase II (Pol II) must overcome barriers imposed by nucleosomes and higher-order chromatin structure. Many genes, including Drosophila melanogaster Hsp70, undergo changes in chromatin structure upon activa...
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Nucleotide excision repair driven by the dissociation of CAK from TFIIH.
Published: July, 2008

Abstract: The transcription/DNA repair factor TFIIH is organized into a core that associates with the CDK-activating kinase (CAK) complex. Using chromatin immunoprecipitation, we have followed the composition of TFIIH over time after UV irradiation of repai...
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Recruitment of CREB1 and histone deacetylase 2 (HDAC2) to the mouse Ltbp-1 promoter regulates its constitutive expression in a dioxin receptor-dependent manner.
Published: June, 2008

Abstract: Latent TGFbeta-binding protein 1 (LTBP-1) is a key regulator of TGFbeta targeting and activation in the extracellular matrix. LTBP-1 is recognized as a major docking molecule to localize, and possibly to activate, TGFbeta in the extracellular matr...
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Role of STAT3 in glucocorticoid-induced expression of the human IL-10 gene.
Published: June, 2008

Abstract: In the present report we have determined the molecular mechanisms, which govern the expression of the human IL-10 gene when induced by the glucocorticoid Methyl-Prednisolone (MP). Treatment of cells with MP at 10(-6) M will readily induce IL-10 in...
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A link between RNA metabolism and silencing affecting Arabidopsis development.
Published: June, 2008

Abstract: MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are abundant endogenous small RNAs (smRNAs) that control transcript expression through posttranscriptional gene silencing. Here, we show that concomitant loss of XRN4/EIN5, a 5'-3' exoribonucl...
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Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila.
Published: May, 2008

Abstract: Dosage compensation, mediated by the MSL complex, regulates X-chromosomal gene expression in Drosophila. Here we report that the histone H4 lysine 16 (H4K16) specific histone acetyltransferase MOF displays differential binding behavior depending o...
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Modulation of RNA polymerase assembly dynamics in transcriptional regulation.
Published: May, 2008

Abstract: The interaction of transcription factors with target genes is highly dynamic. Whether the dynamic nature of these interactions is merely an intrinsic property of transcription factors or serves a regulatory role is unknown. Here we have used singl...
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Dorsal interacting protein 3 potentiates activation by Drosophila Rel homology domain proteins.
Published: May, 2008

Abstract: Dorsal interacting protein 3 (Dip3) contains a MADF DNA-binding domain and a BESS protein interaction domain. The Dip3 BESS domain was previously shown to bind to the Dorsal Rel homology domain. We show here that Dip3 also binds to the Relish Rel ...
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Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
Published: May, 2008

Abstract: Deciphering the multiple layers of epigenetic regulation that control transcription is critical to understanding how plants develop and respond to their environment. Using sequencing-by-synthesis technology we directly sequenced the cytosine methy...
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Dispersibility and stability improvement of unfunctionalized nanotubes in amide solvents by polymer wrapping
Published: May, 2008

Abstract: Improvement on the stability and loading of unfunctionalized single wall carbon nanotubes (SWNTs) in amide solvents is necessary to enhance the performances of SWNT-polymer composites used for optical applications (e.g., as non-linear saturable ab...
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Formation of composite organic thin film transistors with nanotubes and nanowires
Published: May, 2008

Abstract: Plastic electronics is a rapidly expanding topic, much of which has been focused on organic semiconductors. However, it is also of interest to find viable ways to integrate nanomaterials, such as silicon nanowires (SiNWs) and carbon nanotubes (CNT...
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Optical trapping of carbon nanotubes
Published: May, 2008

Abstract: Optical trapping is a new tool for the manipulation and deposition of single wall carbon nanotube (SWNT) bundles. We present a study on optical trapping and manipulation of SWNT bundles in different environments, aimed at understanding the trappin...
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Cell cycle association of the retinoblastoma protein Rb and the histone demethylase LSD1 with the Epstein-Barr virus latency promoter Cp.
Published: April, 2008

Abstract: The Epstein-Barr virus C promoter (Cp) regulates the major multicistronic transcript encoding the EBNA-LP, 1, 2, and 3 genes required for B-cell proliferation during latency. The growth-transforming potential of these viral genes suggests that the...
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SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin.
Published: March, 2008

Abstract: The Sir2 deacetylase regulates chromatin silencing and lifespan in Saccharomyces cerevisiae. In mice, deficiency for the Sir2 family member SIRT6 leads to a shortened lifespan and a premature ageing-like phenotype. However, the molecular mechanism...
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Global transcription regulation by DNA topoisomerase I in exponentially growing Saccharomyces cerevisiae cells: activation of telomere-proximal genes by TOP1 deletion.
Published: March, 2008

Abstract: To establish the cellular functions of DNA topoisomerase I-B (Top1p) at a global level, we have determined the expression profiles and histone modification patterns affected by TOP1 gene deletion (DeltaTOP1) in Saccharomyces cerevisiae. In exponen...
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Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification.
Published: March, 2008

Abstract: Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is a powerful technique to detect in vivo protein-DNA interactions. Due to low yields, ChIP assays of transcription factors generally require amplification of immunoprecipitat...
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Poising of Escherichia coli RNA polymerase and its release from the sigma 38 C-terminal tail for osmY transcription.
Published: February, 2008

Abstract: Bacteria must adapt their transcription to overcome the osmotic stress associated with the gastrointestinal tract of their host. This requires the sigma 38 (rpoS) form of RNA polymerase. Here, chromatin immunoprecipitation experiments show that ac...
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MicroChIP--a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies.
Published: February, 2008

Abstract: Chromatin immunoprecipitation (ChIP) is a powerful technique for studying protein-DNA interactions. Drawbacks of current ChIP assays however are a requirement for large cell numbers, which limits applicability of ChIP to rare cell samples, and/or ...
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Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation.
Published: December, 2007

Abstract: Transcription activation causes dramatic changes in a gene's compaction and macromolecular associations and, in some cases, triggers the translocation of the gene to a nuclear substructure. Here, we evaluate the location, movement, and transcripti...
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Interplay of chromatin modifiers on a short basic patch of histone H4 tail defines the boundary of telomeric heterochromatin.
Published: December, 2007

Abstract: Dot1 (Disruptor of telomeric silencing-1) is a histone H3 lysine 79 methyltransferase that contributes to the establishment of heterochromatin boundary and has been linked to transcription elongation. We found that histone H4 N-terminal domain, un...
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Differential regulation of NAB corepressor genes in Schwann cells.
Published: December, 2007

Abstract: BACKGROUND: Myelination of peripheral nerves by Schwann cells requires not only the Egr2/Krox-20 transactivator, but also the NGFI-A/Egr-binding (NAB) corepressors, which modulate activity of Egr2. Previous work has shown that axon-dependent expre...
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CHD8 associates with human Staf and contributes to efficient U6 RNA polymerase III transcription.
Published: December, 2007

Abstract: Chromatin remodeling and histone modification are essential for eukaryotic transcription regulation, but little is known about chromatin-modifying activities acting on RNA polymerase III (Pol III)-transcribed genes. The human U6 small nuclear RNA ...
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The transcription factor snail mediates epithelial to mesenchymal transitions by repression of estrogen receptor-alpha.
Published: December, 2007

Abstract: The estrogen receptor (ER)-alpha (ESR1) is a key regulatory molecule in mammary epithelial cell development. Loss of ER-alpha in breast cancer is correlated with poor prognosis, increased recurrence after treatment, and an elevated incidence of me...
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Molecular basis for estrogen receptor alpha deficiency in BRCA1-linked breast cancer.
Published: November, 2007

Abstract: BACKGROUND: BRCA1-mutant breast tumors are typically estrogen receptor alpha (ER alpha) negative, whereas most sporadic tumors express wild-type BRCA1 and are ER alpha positive. We examined a possible mechanism for the observed ER alpha-negative p...
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Analysis of transcription, chromatin dynamics and epigenetic changes in neural genes.
Published: November, 2007

Abstract: The ways in which gene transcription is investigated have undergone radical change since the turn of the millennium. Piece-meal approaches focussed upon model genes have increasingly been complemented by genome-wide approaches that allow interroga...
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The JmjC domain protein Epe1 prevents unregulated assembly and disassembly of heterochromatin
Published: October, 2007

Abstract: Heterochromatin normally has prescribed chromosomal positions and must not encroach on adjacent regions. We demonstrate that the fission yeast protein Epe1 stabilises silent chromatin, preventing the oscillation of heterochromatin domains. Epe1 lo...
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Heme oxygenase-1 induction by NRF2 requires inactivation of the transcriptional repressor BACH1.
Published: October, 2007

Abstract: Oxidative stress activates the transcription factor NRF2, which in turn binds cis-acting antioxidant response element (ARE) enhancers and induces expression of protective antioxidant genes. In contrast, the transcriptional repressor BACH1 binds AR...
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Chromium cross-links histone deacetylase 1-DNA methyltransferase 1 complexes to chromatin, inhibiting histone-remodeling marks critical for transcriptional activation.
Published: October, 2007

Abstract: Transcriptional regulation of gene expression requires posttranslational modification of histone proteins, which, in concert with chromatin-remodeling factors, modulate chromatin structure. Exposure to environmental agents may interfere with speci...
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Protein arginine-methyltransferase-dependent oncogenesis.
Published: October, 2007

Abstract: Enzymes that mediate reversible epigenetic modifications have not only been recognized as key in regulating gene expression and oncogenesis, but also provide potential targets for molecular therapy. Although the methylation of arginine 3 of histon...
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Redundancy of chromatin remodeling pathways for the induction of the yeast PHO5 promoter in vivo.
Published: September, 2007

Abstract: Induction of the yeast PHO5 and PHO8 genes leads to a prominent chromatin transition at their promoter regions as a prerequisite for transcription activation. Although induction of PHO8 is strictly dependent on Snf2 and Gcn5, there is no chromatin...
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Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus.
Published: August, 2007

Abstract: MLL-containing complexes methylate histone H3 at lysine 4 (H3K4) and have been implicated in the regulation of transcription. However, it is unclear how MLL complexes are targeted to specific gene loci. Here, we show that the MLL2 complex associat...
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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
Published: August, 2007

Abstract: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generate...
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NuA4-directed chromatin transactions throughout the Saccharomyces cerevisiae genome.
Published: August, 2007

Abstract: Two of the major histone acetyltransferases in Saccharomyces cerevisiae are NuA4 and SAGA, which acetylate histones H4 and H3, respectively. Acetylated H3 and H4 tails have been implicated in binding bromodomain proteins, including Bdf1. Bdf1 inte...
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MTERF3 is a negative regulator of mammalian mtDNA transcription.
Published: July, 2007

Abstract: Regulation of mammalian mtDNA gene expression is critical for altering oxidative phosphorylation capacity in response to physiological demands and disease processes. The basal machinery for initiation of mtDNA transcription has been molecularly de...
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HDAC1 bound to the Cyp1a1 promoter blocks histone acetylation associated with Ah receptor-mediated trans-activation.
Published: July, 2007

Abstract: Metabolic bioactivation of polycyclic aromatic hydrocarbons, such as the environmental procarcinogen benzo[a]pyrene, is catalyzed by a cytochrome P450 monooxygenase encoded by the substrate-inducible Cyp1a1 gene. Cyp1a1 induction requires trans-ac...
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E2F activation of S phase promoters via association with HCF-1 and the MLL family of histone H3K4 methyltransferases.
Published: July, 2007

Abstract: E2F transcriptional regulators control human-cell proliferation by repressing and activating the transcription of genes required for cell-cycle progression, particularly the S phase. E2F proteins repress transcription in association with retinobla...
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Plasticity of fission yeast CENP-A chromatin driven by relative levels of histone H3 and H4.
Published: July, 2007

Abstract: The histone H3 variant CENP-A assembles into chromatin exclusively at centromeres. The process of CENP-A chromatin assembly is epigenetically regulated. Fission yeast centromeres are composed of a central kinetochore domain on which CENP-A chromat...
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RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena.
Published: June, 2007

Abstract: Methylated H3K27 is an important mark for Polycomb group (PcG) protein-mediated transcriptional gene silencing (TGS) in multicellular eukaryotes. Here a Drosophila E(z) homolog, EZL1, is characterized in the ciliated protozoan Tetrahymena thermoph...
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Notch activation stimulates transient and selective binding of Su(H)/CSL to target enhancers.
Published: June, 2007

Abstract: The CSL [CBF1/Su(H)/Lag2] proteins [Su(H) in Drosophila] are implicated in repression and activation of Notch target loci. Prevailing models imply a static association of these DNA-binding transcription factors with their target enhancers. Our ana...
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CHD4/Mi-2beta activity is required for the positioning of the mesoderm/neuroectoderm boundary in Xenopus.
Published: April, 2007

Abstract: Experiments in Xenopus have illustrated the importance of extracellular morphogens for embryonic gene regulation in vertebrates. Much less is known about how induction leads to the correct positioning of boundaries; for example, between germ layer...
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Ubiquitylation of histone H2B controls RNA polymerase II transcription elongation independently of histone H3 methylation.
Published: April, 2007

Abstract: Transcription by RNA polymerase II (polII) is accompanied by dramatic changes in chromatin structure. Numerous enzymatic activities contribute to these changes, including ATP-dependent nucleosome remodeling enzymes and histone modifying enzymes. R...
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Carbon nanotube polymer composites for photonic devices
Published: March, 2007

Abstract: We report the fabrication of high optical quality single wall carbon nanotube polyvinyl alcohol composites and their application in nanotube based photonic devices. These show a broad absorption of semiconductor tubes centred at ˜1.55 μm, the spec...
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An unmethylated 3' promoter-proximal region is required for efficient transcription initiation.
Published: February, 2007

Abstract: The promoter regions of approximately 40% of genes in the human genome are embedded in CpG islands, CpG-rich regions that frequently extend on the order of one kb 3' of the transcription start site (TSS) region. CpGs 3' of the TSS of actively tran...
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Genetic unmasking of an epigenetically silenced microRNA in human cancer cells.
Published: February, 2007

Abstract: The mechanisms underlying microRNA (miRNA) disruption in human disease are poorly understood. In cancer cells, the transcriptional silencing of tumor suppressor genes by CpG island promoter hypermethylation has emerged as a common hallmark. We won...
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H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability.
Published: January, 2007

Abstract: Investigations aimed at identifying regulators of nuclear architecture in Drosophila demonstrated that cells lacking H3K9 methylation and RNA interference (RNAi) pathway components displayed disorganized nucleoli, ribosomal DNA (rDNA) and satellit...
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Epigenetic regulation of histone H3 serine 10 phosphorylation status by HCF-1 proteins in C. elegans and mammalian cells.
Published: January, 2007

Abstract: BACKGROUND: The human herpes simplex virus (HSV) host cell factor HCF-1 is a transcriptional coregulator that associates with both histone methyl- and acetyltransferases, and a histone deacetylase and regulates cell proliferation and division. In ...
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JunB is required for endothelial cell morphogenesis by regulating core-binding factor beta.
Published: December, 2006

Abstract: The molecular mechanism triggering the organization of endothelial cells (ECs) in multicellular tubules is mechanistically still poorly understood. We demonstrate that cell-autonomous endothelial functions of the AP-1 subunit JunB are required for...
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Protein interactions within the Set1 complex and their roles in the regulation of histone 3 lysine 4 methylation.
Published: November, 2006

Abstract: Set1 is the catalytic subunit and the central component of the evolutionarily conserved Set1 complex (Set1C) that methylates histone 3 lysine 4 (H3K4). Here we have determined protein/protein interactions within the complex and related the substru...
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Tsix-mediated epigenetic switch of a CTCF-flanked region of the Xist promoter determines the Xist transcription program.
Published: October, 2006

Abstract: Initiation of X inactivation depends on the coordinated expression of the sense/antisense pair Xist/Tsix. We show here that a precisely defined Xist promoter region flanked by CTCF is maintained by Tsix in a heterochromatic-like state in undiffere...
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Architecture of a polycomb nucleoprotein complex.
Published: October, 2006

Abstract: Polycomb group (PcG) epigenetic silencing proteins act through cis-acting DNA sequences, named Polycomb response elements (PREs). Within PREs, Pleiohomeotic (PHO) binding sites and juxtaposed Pc binding elements (PBEs) function as an integrated DN...
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A profile of methyl-CpG binding domain protein occupancy of hypermethylated promoter CpG islands of tumor suppressor genes in human cancer.
Published: September, 2006

Abstract: Methyl-CpG binding domain (MBD) proteins have been shown to couple DNA methylation to transcriptional repression. This biological property suggests a role for MBD proteins in the silencing of tumor suppressor genes that are hypermethylated at thei...
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Influenza virus inhibits RNA polymerase II elongation.
Published: July, 2006

Abstract: The influenza virus RNA-dependent RNA polymerase interacts with the serine-5 phosphorylated carboxy-terminal domain (CTD) of the large subunit of RNA polymerase II (Pol II). It was proposed that this interaction allows the viral RNA polymerase to ...
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Menin links estrogen receptor activation to histone H3K4 trimethylation.
Published: May, 2006

Abstract: The product of the multiple endocrine neoplasia type 1 (MEN1) tumor suppressor gene, menin, is an integral component of MLL1/MLL2 histone methyltransferase complexes specific for Lys4 of histone H3 (H3K4). We show that menin is a transcriptional c...
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The Polycomb group protein EZH2 directly controls DNA methylation.
Published: February, 2006

Abstract: The establishment and maintenance of epigenetic gene silencing is fundamental to cell determination and function. The essential epigenetic systems involved in heritable repression of gene activity are the Polycomb group (PcG) proteins and the DNA ...
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The benzamide MS-275 is a potent, long-lasting brain region-selective inhibitor of histone deacetylases
Published: January, 2006

Abstract: The association of the histone deacetylase (HDAC) inhibitor valproate (VPA) with atypical antipsychotics has become a frequent treatment strategy for schizophrenia and bipolar disorder. Because the VPA doses administered are elevated, one cannot a...
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Role of Dot1-dependent histone H3 methylation in G1 and S phase DNA damage checkpoint functions of Rad9.
Published: October, 2005

Abstract: We screened radiation-sensitive yeast mutants for DNA damage checkpoint defects and identified Dot1, the conserved histone H3 Lys 79 methyltransferase. DOT1 deletion mutants (dot1Delta) are G1 and intra-S phase checkpoint defective after ionizing ...
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Defective CD3gamma gene transcription is associated with NFATc2 overexpression in the lymphocytic variant of hypereosinophilic syndrome.
Published: October, 2005

Abstract: OBJECTIVE: Determine the molecular defects underlying the CD3(-)CD4(+) T-cell phenotype and persistence of this clonal population in patients with hypereosinophilic syndrome. PATIENTS AND METHODS: Patients in this study suffer from the lymphocytic...
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Improving Chromatin Immunoprecipitation (ChIP) by Suppression of Method-Induced DNA-Damage Signaling.

Abstract: Genomic DNA is always associated with proteins that modulate the accessibility of the genetic information. This chromatin is the essential structure in which all nuclear activity from regulation to replication, transcription, and repair takes plac...
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Post-mortem genetic analysis in juvenile cases of sudden cardiac death

Abstract: Background The reason behind a sudden death of a young individual remains unknown in up to 50% of postmortem cases. Pathogenic mutations in genes encoding heart proteins are known to cause sudden cardiac death. Objective The aim of our study was...
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β-Catenin is essential for ethanol metabolism and protection against alcohol-mediated liver steatosis in mice

Abstract: The liver plays a central role in ethanol metabolism, and oxidative stress is implicated in alcohol-mediated liver injury. β-Catenin regulates hepatic metabolic zonation and adaptive response to oxidative stress. We hypothesized that β-catenin reg...
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Gel-based and gel-free proteomic analysis of Nicotiana tabacum trichomes identifies proteins involved in secondary metabolism and in the (a)biotic stress response

Abstract: Nicotiana tabacum leaves are covered by trichomes involved in the secretion of large amounts of secondary metabolites, some of which play a major role in plant defense. However, little is known about the metabolic pathways that operate in these st...
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Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications

Abstract: The dynamic modification of DNA and histones plays a key role in transcriptional regulation through - altering the packaging of DNA and modifying the nucleosome surface. These chromatin states, also referred to as the epigenome, are distinctive fo...
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Location Analysis and Expression Profiling Using Next-Generation Sequencing for Research in Neurodegenerative Diseases

Abstract: Neurodegenerative diseases carry a huge burden in terms of human suffering and economic cost. In spite of advances in the field of neurology, there is still no effective cure. A combination of novel genomic approaches and techniques such as chroma...
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Experimental Study on Malignant Transformation of Human Bronchial Epithelial Cells Induced by Glycidyl Methacrylate and Analysis on its Methylation

Abstract: Objective To establish the model of human bronchial epithelial cells(16HBE) malignant transformation induced by glycidyl methacrylate(GMA) and define the different methylation genes at different stages. Methods DNA was extracted at different 16...
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A novel method for the genome-wide high resolution analysis of DNA damage.

Abstract: DNA damage occurs via endogenous and exogenous genotoxic agents and compromises a genome's integrity. Knowing where damage occurs within a genome is crucial to understanding the repair mechanisms which protect this integrity. This paper describes ...
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Oxyphil Cell Metaplasia in the Parathyroids Is Characterized by Somatic Mitochondrial DNA Mutations in NADH Dehydrogenase Genes and Cytochrome c Oxidase Activity–Impairing Genes

Abstract: Oxyphil cell transformation of epithelial cells due to the accumulation of mitochondria occurs often during cellular aging. To understand the pathogenic mechanisms, we studied mitochondrial DNA (mtDNA) alterations in the three cell types of the pa...
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Foxa1 and Foxa2 positively and negatively regulate Shh signalling to specify ventral midbrain progenitor identity.

Abstract: Foxa2, a member of the Foxa family of forkhead/winged helix family of transcription factors, has previously been shown to be an upstream positive regulator of Shh expression in many different tissues. Recent studies also strongly suggest that Foxa...
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AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay

Abstract: DNA methylation is an epigenetic mark linking DNA sequence and transcription regulation, and therefore plays an important role in phenotypic plasticity. The ideal whole genome methylation (methylome) assay should be accurate, affordable, high-thro...
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Alterations of the RRAS and ERCC1 Genes at 19q13 in Gemistocytic Astrocytomas.

Abstract: Gemistocytic astrocytoma (World Health Organization grade II) is a rare variant of diffuse astrocytoma that is characterized by the presence of neoplastic gemistocytes and has a significantly less favorable prognosis. Other than frequent TP53 muta...
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Low dose effects of dichlorodiphenyltrichloroethane (DDT) on gene transcription and DNA methylation in the hypothalamus of young male rats: implication of hormesis-like effects.

Abstract: To verify the relationship between oxidative stress and DNA methylation in the young brain, dichlorodiphenyltrichloroethane (DDT) was administered by gavage to male young rats at doses of 0, 0.006, 0.06, 0.6, 6, and 60 mg/kg/day for a period of 4 ...
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Atypical Regulation of Virulence-Associated Functions by a Diffusible Signal Factor in Xanthomonas oryzae pv. oryzae

Abstract: In Xanthomonas oryzae pv. oryzae, the bacterial blight pathogen of rice, a secreted fatty acid signaling molecule known as diffusible signal factor (DSF) is required for virulence and growth on low-iron medium. To identify other virulence-associat...
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Monitoring the effects of chromatin remodelers on long-range interactions in vivo.

Abstract: In metazoans transcriptional enhancers and their more complex relatives, locus control regions, are often located at great linear distances from their target genes. In addition, these elements frequently activate different members of gene families...
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Genome-wide epigenetic analysis of human pluripotent stem cells by ChIP and ChIP-Seq.

Abstract: Chromatin immunoprecipitation (ChIP) is used to evaluate the interaction of proteins and genomic DNA. In eukaryotic cells, the DNA is highly compacted with the evolutionarily conserved histone proteins (which together with DNA form the nucleosome)...
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Epigenetic-Mediated Downregulation of μ-Protocadherin in Colorectal Tumours

Abstract: Carcinogenesis involves altered cellular interaction and tissue morphology that partly arise from aberrant expression of cadherins. Mucin-like protocadherin is implicated in intercellular adhesion and its expression was found decreased in colorect...
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Genetic Screens for Floral Mutants in Arabidopsis thaliana: Enhancers and Suppressors

Abstract: The flower is a hallmark feature that has contributed to the evolutionary success of land plants. Diverse mutagenic agents have been employed as a tool to genetically perturb flower development and identify genes involved in floral patterning and ...
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Cell type-specific affinity purification of nuclei for chromatin profiling in whole animals.

Abstract: Analyzing cell differentiation during development in a complex organism requires the analysis of expression and chromatin profiles in individual cell types. Our laboratory has developed a simple and generally applicable strategy to purify specific...
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Biochemical fractionation of membrane receptors in the nucleus.

Abstract: Fractionation of cytoplasmic and nuclear proteins is a well-recognized biochemical technique to detect the intracellular distribution and expression level of proteins of interest. In the last decade, accumulating evidence shows that various types ...
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Waking up Streptomyces Secondary Metabolism by Constitutive Expression of Activators or Genetic Disruption of Repressors.

Abstract: Streptomycete bacteria are renowned as a prolific source of natural products with diverse biological activities. Production of these metabolites is often subject to transcriptional regulation: the biosynthetic genes remain silent until the require...
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Genome-wide binding of transcription factors in inv(16) acute myeloid leukemia

Abstract: The inv(16) translocation is associated with 5% of AML cases and gives rise to expression of the oncofusion protein CBFβ-MYH11. Although different molecular mechanisms for the oncogenic activity of this fusion protein have been proposed these were...
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Studying Histone Modifications and Their Genomic Functions by Employing Chromatin Immunoprecipitation and Immunoblotting

Abstract: Histones are one of the most abundant and highly conserved proteins in eukaryotes. Apart from serving as structural entities for orderly compaction of genomes, they play an instrumental role in the regulation of many important biological processes...
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Transcriptional regulation of epidermal barrier formation.

Abstract: The mammalian epidermis is a self-renewing stratified squamous epithelium. Its basal cell layer contains proliferating keratinocytes that exit the cell cycle when they move into the suprabasal compartment. These cells activate a gene differentiati...
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Mapping protein-DNA interactions using ChIP-sequencing.

Abstract: Chromatin immunoprecipitation (ChIP) allows enrichment of genomic regions which are associated with specific transcription factors, histone modifications, and indeed any other epitopes which are present on chromatin. The original ChIP methods used...
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Exome sequencing reveals new insights into the progression of abdominal aortic aneurysm.

Abstract: BACKGROUND: Abdominal aortic aneurysm (AAA) is a multi-factorial disease and its underlying pathogenesis remains poorly understood. AIM: We aim to search for the underlying etiology of AAA using whole exome sequencing and gene expression analysi...
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Liver X receptor regulates hepatic nuclear O-GlcNAc signaling and carbohydrate responsive element-binding protein activity.

Abstract: Liver X receptor (LXR)α and LXRβ play key roles in hepatic de novo lipogenesis through their regulation of lipogenic genes, including sterol regulatory element-binding protein (SREBP)-1c and carbohydrate responsive element-binding protein (ChREBP)...
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SNP Discovery and Genotyping for Evolutionary Genetics Using RAD Sequencing

Abstract: Next-generation sequencing technologies are revolutionizing the field of evolutionary biology, opening the possibility for genetic analysis at scales not previously possible. Research in population genetics, quantitative trait mapping, comparative...
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Comparison of protein precipitation methods for various rat brain structures prior to proteomic analysis

Abstract: Sample preparation is a fundamental step in proteomic methodologies. The quality of the results from a proteomic experiment is dependent on the nature of the sample and the properties of the proteins. In this study, various pre-treatment methods w...
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Clinical and public health research using methylated DNA immunoprecipitation (MeDIP) A comparison of commercially available kits to examine differential DNA methylation across the genome

Abstract: The methylated DNA immunoprecipitation method (MeDIP) is a genome-wide, high-resolution approach that detects DNA methylation with oligonucleotide tiling arrays or high throughput sequencing platforms. A simplified highthroughput MeDIP assay will ...
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High-throughput whole-genome sequencing of E14 mouse embryonic stem cells

Abstract: Mouse E14 embryonic stem cells (ESCs) are the most used ESC line, often employed for genome-wide studies involving next generation sequencing analysis [1 – 5] . More than 2 × 10 E9 sequences made on Illumina platform derivedfromthegenomeofE14embry...
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Deletion of the de novo DNA methyltransferase Dnmt3a promotes lung tumor progression.

Abstract: Alterations in DNA methylation have been associated with genome-wide hypomethylation and regional de novo methylation in numerous cancers. De novo methylation is mediated by the de novo methyltransferases Dnmt3a and 3b, but only Dnmt3b has been im...
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Step-by-step preparation of proteins for mass spectrometric analysis.

Abstract: Nowadays, identification of proteins from biological samples by mass spectrometry is widely used. In principle there are two scenarios. Proteins are pre-fractionated in some way, e.g. by gel electrophoresis or are analyzed as complex mixture (shot...
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In Vivo ChIP for the Analysis of Microdissected Tissue Samples

Abstract: The development of chromatin immunoprecipitation assays (ChIP) as a tool to examine the interactions between nuclear proteins and DNA has enhanced essentially our understanding of the dynamic association of transcription factors and chromatin modi...
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Endosperm-specific chromatin profiling by fluorescence-activated nuclei sorting and ChIP-on-chip.

Abstract: Cell-type-specific analysis of gene expression and chromatin profiling requires the isolation of discrete cell populations from complex pools. However, until now this most critical step has been labor intensive and technical challenging. Here, we ...
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Isolation of integrin-based adhesion complexes.

Abstract: The integration of cells with their extracellular environment is facilitated by cell surface adhesion receptors, such as integrins, which play important roles in both normal development and the onset of pathologies. Engagement of integrins with th...
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Fatty acids regulate perilipin5 in muscle by activating PPARδ

Abstract: The surface of lipid droplets (LDs) in various cell types is coated with perilipin proteins encoded by the Plin genes. Perilipins regulate LD metabolism by selectively recruiting lipases and other proteins to LDs. We have studied the expression of...
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Analysis of Histone Posttranslational Modifications from Nucleolus-Associated Chromatin by Mass Spectrometry

Abstract: Chromatin is unevenly distributed within the eukaryote nucleus and it contributes to the formation of morphologically and functionally distinct substructures, called chromatin domains and nuclear bodies. Here we describe an approach to assess spec...
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Analysis of Chromatin Composition of Repetitive Sequences: The ChIP-Chop Assay

Abstract: Chromatin immunoprecipitation (ChIP) is a powerful method that allows to probe specific protein-DNA interactions in vivo and to estimate the occupancy of proteins at specific sites of the genome. However, the traditional ChIP assay is not able to ...
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ChIP for Hox proteins from Drosophila imaginal discs.

Abstract: Chromatin immunoprecipitation (ChIP) is a technique that reveals in vivo location of a protein bound to DNA. ChIP coupled with DNA microarrays (ChIP-chip) or next-generation sequencing (ChIP-seq) allows for identification of binding sites of trans...
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Transcription by the multifunctional RNA polymerase I in Trypanosoma brucei functions independently of RPB7.

Abstract: Trypanosoma brucei has a multifunctional RNA polymerase (pol) I that transcribes ribosomal gene units (RRNA) and units encoding its major cell surface proteins variant surface glycoprotein (VSG) and procyclin. Previous analysis of tandem affinity-...
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Methylation analysis by microarray.

Abstract: Differential methylation hybridization (DMH) is a high-throughput DNA methylation screening tool that utilizes methylation-sensitive restriction enzymes to profile methylated fragments by hybridizing them to a CpG island microarray. This array con...
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Chromatin immunoprecipitation analysis in filamentous fungi.

Abstract: Chromatin immunoprecipitation (ChIP) is used to map the interaction between proteins and DNA at a specific genomic locus in the living cell. The protein-DNA complexes are stabilized already in vivo by reversible crosslinking and the DNA is sheared...
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Library preparation and data analysis packages for rapid genome sequencing.

Abstract: High-throughput sequencing (HTS) has quickly become a valuable tool for comparative genetics and genomics and is now regularly carried out in laboratories that are not connected to large sequencing centers. Here we describe an updated version of o...
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ChIP-exonuclease in mammalian cells (Prot 66)

Abstract: ChIP - exonuclease (ChIP - exo) is a high resolution method of genome - wide mapping of DNA - associated proteins that outperforms ChIP - seq by all parameters . We adap ted this method created by Fran k Pugh and Ho Sung Rhee from SOLiD to the Ill...
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Analysis of in vivo transcription factor recruitment by chromatin immunoprecipitation of mouse embryonic kidney.

Abstract: Chromatin immunoprecipitation (ChIP) is a powerful technique for examining transcription factor recruitment to chromatin, or histone modifications, at the level of specific genomic sequences. As such, it provides an invaluable tool for elucidating...
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Analyzing the Global Chromatin Structure of Keratinocytes by MNase-Seq.

Abstract: Eukaryotic DNA is wrapped around histone octamers, known as nucleosomes, in an orderly fashion that provides the primary structure of chromatin organization. The compaction of DNA into nucleosomal repeats not only allows the tight packaging of the...
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Chromatin immunoprecipitation to identify global targets of WRKY transcription factor family members involved in plant immunity.

Abstract: The completion of the alfalfa, Arabidopsis, papaya, poplar, and rice genome sequences along with ongoing sequencing projects of various crop species, offers an excellent opportunity to study gene expression at the whole genome level and to unravel...
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Short-read DNA Sequencing Yields Microsatellite Markers for Rheum

Abstract: Identifying and evaluating genetic diversity of culinary rhubarb (Rheum ×rhababarum) cultivars using morphological characteristics is challenging given the existence of synonyms and nomenclatural inconsistencies. Some cultivars with similar names ...
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Chromatin Immunoprecipitation

Abstract: Chromatin plays important functions in regulating many biological processes, including DNA transcription, replication, and repair. The use of chromatin immunoprecipitation (ChIP) assays has contributed enor- mously to identify interactions between...
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Broad spectrum microarray for fingerprint-based bacterial species identification.

Abstract: BACKGROUND: Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays ar...
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Soluble adenylyl cyclase in vascular endothelium: gene expression control of epithelial sodium channel-α, Na+/K+-ATPase-α/β, and mineralocorticoid receptor.

Abstract: The Ca(2+)- and bicarbonate-activated soluble adenylyl cyclase (sAC) has been identified recently as an important mediator of aldosterone signaling in the kidney. Nuclear sAC has been reported to stimulate cAMP response element-binding protein 1 p...
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FoxK2 is required for cellular proliferation and survival

Abstract: FoxK2 is a forkhead transcription factor expressed ubiquitously in the developing murine central nervous system. Here we investigated the role of FoxK2 in vitro and focused on proliferation and cellular survival. Knockdown of FoxK2 results in a de...
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Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution

Abstract: Laboratory microcosm experiments using protists as model organisms have a long tradition and are widely used to investigate general concepts in population biology, community ecology and evolutionary biology. Many variables of interest are meas...
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Age-related brain expression and regulation of the chemokine CCL4/MIP-1β in APP/PS1 double-transgenic mice.

Abstract: The detrimental effect of activation of the chemokine CCL4/MIP-1β on neuronal integrity in patients with HIV-associated dementia has directed attention to the potential role of CCL4 expression and regulation in Alzheimer disease. Here, we show tha...
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Loss of Sirt1 Promotes Prostatic Intraepithelial Neoplasia, Reduces Mitophagy, and Delays Park2 Translocation to Mitochondria

Abstract: Prostatic intraepithelial neoplasia is a precursor to prostate cancer. Herein, deletion of the NAD+-dependent histone deacetylase Sirt1 induced histological features of prostatic intraepithelial neoplasia at 7 months of age; these features were as...
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Detection of DNA methylation by MeDIP and MBDCap assays: an overview of techniques.

Abstract: DNA methylation has been characterized as the representative example of epigenetic modifications and implicated in numerous biological processes, such as genomic imprinting and X chromosome inactivation. It primarily occurs at CpG dinucleotides in...
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Mapping replication origin sequences in eukaryotic chromosomes.

Abstract: Recent advances in genome-sequencing technology have led to the complete mapping of DNA replication initiation sites in the human genome. This thorough origin mapping facilitates understanding of the relationship between replication initiation eve...
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ChIP-seq profiling of the active chromatin marker H3K4me3 and PPARγ, CEBPα and LXR target genes in human SGBS adipocytes

Abstract: Transcription factors (TFs) represent key factors to establish a cellular phenotype. It is known that several TFs could play a role in disease, yet less is known so far how their targets overlap. We focused here on identifying the most highly indu...
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Intracellular MMP-2 Activity in Skeletal Muscle Is Associated With Type II Fibers.

Abstract: Matrix metalloproteinase 2 (MMP-2) is a proteolytic enzyme implicated in motility, differentiation, and regeneration of skeletal muscle fibers through processing of extracellular substrates. Although MMP-2 has been found to be localized intracellu...
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Chromatin Immunoprecipitation in Mouse Hippocampal Cells and Tissues

Abstract: Chromatin immunoprecipitation (ChIP) has been developed for studying protein-DNA interactions and has been extensively used for mapping the localization of posttranslationally modified histones, histone variants, transcription factors, or chromati...
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Epigenome profiling of specific plant cell types using a streamlined INTACT protocol and ChIP-seq

Abstract: Plants consist of many functionally specialized cell types, each with its own unique epigenome, transcriptome, and proteome. Characterization of these cell type-specific properties is essential to understanding cell fate specification and the resp...
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Nucleophosmin 1 cooperates with the methyltransferase DOT1L toregulate H3K79me2 levels and DNA satellites expression atperi-nucleolar heterochromatin

Abstract: The histone methyltransferase DOT1L catalyzes methylation of H3K79 and it is highly conserved in mammals. DOT1L plays a functional role in several biological processes including cell cycle regulation, DNA repair, RNA splicing and gene expression, ...
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A method for measuring fatty acid oxidation in C. elegans

Abstract: The nematode C. elegans has during the past decade proven to be a valuable model organism to identify and examine molecular mechanisms regulating lipid storage and metabolism. While the primary approach has been to identify genes and pathways conf...
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Consistency of metagenomic assignment programs in simulated and real data.

Abstract: BACKGROUND: Metagenomics is the genomic study of uncultured environmental samples, which has been greatly facilitated by the advent of shotgun-sequencing technologies. One of the main focuses of metagenomics is the discovery of previously uncultur...
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TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator.

Abstract: BACKGROUND: Hypoxia induces the epithelial-mesenchymal transition, EMT, to promote cancer metastasis. In addition to transcriptional regulation mediated by hypoxia-inducible factors, HIFs, other epigenetic mechanisms of gene regulation, such as hi...
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Quantitative Proteomics Identifies Activation of Hallmark Pathways of Cancer in Patient Melanoma

Abstract: Molecular pathways regulating melanoma initiation and progression are potential targets of therapeutic development for this aggressive cancer. Identification and molecular analysis of these pathways in patients has been primarily restricted to tar...
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BET protein inhibition sensitizes glioblastoma cells to temozolomidetreatment by attenuating MGMT expression

Abstract: Bromodomain and extra-terminal tail (BET) proteins have been identified as potential epigenetic targets in cancer, including glioblastoma. These epigenetic modifiers link the histone code to gene transcription that can be disrupted with small mole...
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Effect of hypoxia on the expression of αB-crystallin in head and neck squamous cell carcinoma.

Abstract: BACKGROUND: The presence of hypoxia in head and neck squamous cell carcinoma (HNSCC) is associated with therapeutic resistance and increased risk of metastasis formation. αB-crystallin (HspB5) is a small heat shock protein, which is also associate...
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Methylated DNA Immunoprecipitation (MeDIP) from Low Amounts of Cells.

Abstract: Methylated DNA immunoprecipitation (MeDIP) is an immunocapturing approach for unbiased enrichment of DNA that is methylated on cytosines. The principle is that genomic DNA is randomly sheared by sonication and immunoprecipitated with an antibody t...
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Identification of Novel Long Noncoding RNAs Associated with TGF-β/Smad3-Mediated Renal Inflammation and Fibrosis by RNA Sequencing.

Abstract: We have previously shown that transforming growth factor-β/Smad3-dependent miRNAs play a critical role in renal inflammation and fibrosis. However, off-target effects of miRNAs limit their therapeutic application. Recently, emerging roles of long ...
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Chromatin Immunoprecipitation to Characterize the Epigenetic Profiles of Imprinted Domains

Abstract: Imprinted genes are marked by parental allele speci fi c DNA methylation and histone modi fi cations which regulate their monoallelic expression. Chromatin immunoprecipitation (ChIP) is the technique of choice to characterize the histones associat...
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Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506-binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population.

Abstract: Cervical cancer is a major health concern among women in Latin America due to its high incidence and mortality. Therefore, the discovery of molecular markers for cervical cancer screening and triage is imperative. The aim of this study was to use ...
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Diagnostic applications of next generation sequencing: working towards quality standards

Abstract: Over the past 6 years, next generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. Al...
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An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment

Abstract: The role of DNA sequence in determining chromatin state is incompletely understood.We have previously demonstrated that large chromosomal segments from human cells recapitulate their native chromatin state in mouse cells, but the relative contribu...
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Analysis of sDMA modifications of PIWI proteins.

Abstract: Arginine methylation is an important posttranslational protein modification that modulates protein function for a wide range of biological processes. PIWI proteins, a subclade of the Argonaute family proteins, contain evolutionarily conserved symm...
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ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos.

Abstract: This protocol describes a method to detect in vivo associations between proteins and DNA in developing Drosophila embryos. It combines formaldehyde crosslinking and immunoprecipitation of protein-bound sequences with genome-wide analysis using mic...
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Genome-wide mapping of Painting of fourth on Drosophila melanogaster salivary gland polytene chromosomes

Abstract: The protein Painting of fourth (POF) in Drosophila melanogaster specifically targets and stimulates expression output from the heterochromatic 4th chromosome, thereby representing an autosome specific protein [ [1] and [2]]. Despite the high speci...
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Enrichment of Methylated DNA by Methyl-CpG Immunoprecipitation.

Abstract: Normal DNA methylation is an epigenetic modification required for proper development. Aberrant DNA methylation, in contrast, is frequently observed in many different malignancies including leukemias and lymphomas. Global DNA methylation profiling ...
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