Diagenode

ChIP-qPCR

994 publications found.

Glucocorticoid receptor represses brain-derived neurotrophic factor expression in neuron-like cells
Published: April, 2017

Abstract: Brain-derived neurotrophic factor (BDNF) is involved in many functions such as neuronal growth, survival, synaptic plasticity and memorization. Altered expression levels are associated with many pathological situations such as depression, epilepsy...
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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-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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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 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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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Farnesoid X receptor directly regulates xenobiotic detoxification genes in the long-lived Little mice.
Published: September, 2013

Abstract: Activation of xenobiotic metabolism pathways has been linked to lifespan extension in different models of aging. However, the mechanisms underlying activation of xenobiotic genes remain largely unknown. Here we showed that although farnesoid X rec...
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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Expression of MUC17 Is Regulated by HIF1α-Mediated Hypoxic Responses and Requires a Methylation-Free Hypoxia Responsible Element in Pancreatic Cancer.
Published: September, 2012

Abstract: MUC17 is a type 1 membrane-bound glycoprotein that is mainly expressed in the digestive tract. Recent studies have demonstrated that the aberrant overexpression of MUC17 is correlated with the malignant potential of pancreatic ductal adenocarcinom...
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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Dataset integration identifies transcriptional regulation of microRNA genes by PPARγ in differentiating mouse 3T3-L1 adipocytes.
Published: February, 2012

Abstract: Peroxisome proliferator-activated receptor γ (PPARγ) is a key transcription factor in mammalian adipogenesis. Genome-wide approaches have identified thousands of PPARγ binding sites in mouse adipocytes and PPARγ upregulates hundreds of protein-cod...
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Hypermethylated in cancer 1 (HIC1) recruits polycomb repressive complex 2 (PRC2) to a subset of its target genes through interaction with human polycomb-like (hPCL) proteins.
Published: February, 2012

Abstract: HIC1 (Hypermethylated in Cancer 1) is a tumor suppressor gene epigenetically silenced or deleted in many human cancers. HIC1 is involved in regulatory loops modulating p53- and E2F1-dependent cell survival, growth control and stress responses. HIC...
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The composition and signaling of the IL-35 receptor are unconventional.
Published: February, 2012

Abstract: Interleukin 35 (IL-35) belongs to the IL-12 family of heterodimeric cytokines but has a distinct functional profile. IL-35 suppresses T cell proliferation and converts naive T cells into IL-35-producing induced regulatory T cells (iTr35 cells). He...
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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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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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The Spt5 C-terminal region recruits yeast 3’-RNA cleavage factor I
Published: January, 2012

Abstract: During transcription elongation, RNA polymerase (Pol) II binds the general elongation factor Spt5. Spt5 contains a repetitive C-terminal region (CTR) that is required for co-transcriptional recruitment of the Paf1 complex (44, 88). Here we report ...
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Transcriptional regulation of gene expression during osmotic stress responses by the mammalian target of rapamycin.
Published: January, 2012

Abstract: Although stress can suppress growth and proliferation, cells can induce adaptive responses that allow them to maintain these functions under stress. While numerous studies have focused on the inhibitory effects of stress on cell growth, less is kn...
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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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Histone deacetylase inhibitors sensitize glioblastoma cells to TRAIL-induced apoptosis by c-myc-mediated downregulation of cFLIP.
Published: January, 2012

Abstract: Glioblastoma is the most common primary brain tumor with a very poor prognosis, calling for novel treatment strategies. Here, we provide first evidence that histone deacetylase inhibitors (HDACI) prime glioblastoma cells for tumor necrosis factor-...
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Dual role of the ddx5/ddx17 RNA helicases in the control of the pro-migratory NFAT5 transcription factor.
Published: January, 2012

Abstract: Ddx5 and ddx17 are two highly related RNA helicases involved in both transcription and splicing. These proteins coactivate transcription factors involved in cancer such as the estrogen receptor alpha, p53 and beta-catenin. Ddx5 and ddx17 are part ...
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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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Activating transcription factor 4-dependent induction of FGF21 during amino acid deprivation.
Published: January, 2012

Abstract: Nutrient deprivation or starvation frequently correlates with amino acid limitation. Amino acid starvation initiates a signal transduction cascade starting with the activation of the kinase GCN2 phosphorylation of eukaryotic initiation factor 2, 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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The prosensory function of sox2 in the chicken inner ear relies on the direct regulation of atoh1.
Published: January, 2012

Abstract: The proneural gene Atoh1 is crucial for the development of inner ear hair cells and it requires the function of the transcription factor Sox2 through yet unknown mechanisms. In the present work, we used the chicken embryo and HEK293T cells to expl...
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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Genome-wide analysis of target genes regulated by HoxB4 in hematopoietic stem and progenitor cells developing from embryonic stem cells.
Published: April, 2011

Abstract: Forced expression of the transcription factor HoxB4 has been shown to enhance the self-renewal capacity of mouse bone marrow hematopoietic stem cells (HSCs) and confer a long-term repopulating capacity to yolk sac and embryonic stem (ES) cell-deri...
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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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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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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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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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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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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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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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TNFR1 is essential for CD40, but not for lipopolysaccharide-induced sickness behavior and clock gene dysregulation.
Published: March, 2011

Abstract: Autoimmune and infectious diseases are associated with behavioral changes referred to as sickness behavior syndrome (SBS). In autoimmunity, the generation of anti-self T lymphocytes and autoantibodies critically involves binding of CD40 ligand on ...
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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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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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DNA methylation and histone H3-K9 modifications contribute to MUC17 expression.
Published: February, 2011

Abstract: MUC17 glycoprotein is a membrane-associated mucin that is mainly expressed in the digestive tract. It has been suggested that MUC17 expression is correlated with the malignancy potential of pancreatic ductal adenocarcinomas (PDACs). In the present...
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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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Control of chromatin structure by spt6: different consequences in coding and regulatory regions.
Published: February, 2011

Abstract: Spt6 is a highly conserved factor required for normal transcription and chromatin structure. To gain new insights into the roles of Spt6, we measured nucleosome occupancy along Saccharomyces cerevisiae chromosome III in an spt6 mutant. We found th...
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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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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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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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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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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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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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Herpes simplex virus induces the marked up-regulation of the zinc finger transcriptional factor INSM1, which modulates the expression and localization of the immediate early protein ICP0.
Published: January, 2011

Abstract: BACKGROUND: Herpes simplex viruses (HSVs) rapidly shut off macromolecular synthesis in host cells. In contrast, global microarray analyses have shown that HSV infection markedly up-regulates a number of host cell genes that may play important role...
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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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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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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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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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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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ZEB1 limits adenoviral infectability by transcriptionally repressing the coxsackie virus and adenovirus receptor.
Published: January, 2011

Abstract: BACKGROUND: We have previously reported that RAS-MEK (Cancer Res. 2003 May 1;63(9):2088-95) and TGF-β (Cancer Res. 2006 Feb 1;66(3):1648-57) signaling negatively regulate coxsackie virus and adenovirus receptor (CAR) cell-surface expression and ad...
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Epigenetic regulation of miR-212 expression in lung cancer.
Published: January, 2011

Abstract: Many studies have shown that microRNA expression in cancer may be regulated by epigenetic events. Recently, we found that in lung cancer miR-212 was strongly down-regulated. However, mechanisms involved in the regulation of miR-212 expression are ...
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Control of flowering and cell fate by LIF2, an RNA binding partner of the polycomb complex component LHP1.
Published: January, 2011

Abstract: Polycomb Repressive Complexes (PRC) modulate the epigenetic status of key cell fate and developmental regulators in eukaryotes. The chromo domain protein like heterochromatin protein1 (LHP1) is a subunit of a plant PRC1-like complex in Arabidopsis...
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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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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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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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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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Cell cycle-dependent accumulation of histone H3.3 and euchromatic histone modifications in pericentromeric heterochromatin in response to a decrease in DNA methylation levels.
Published: October, 2010

Abstract: In mammals, DNA methylation is an important epigenetic mark that is associated with gene silencing, particularly in constitutive heterochromatin. However, the effect of DNA methylation on other epigenetic properties of chromatin is controversial. ...
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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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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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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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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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The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny.
Published: September, 2010

Abstract: Methylation of histone H3K36 in higher eukaryotes is mediated by multiple methyltransferases. Set2-related H3K36 methyltransferases are targeted to genes by association with RNA Polymerase II and are involved in preventing aberrant transcription i...
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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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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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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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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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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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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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Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping.
Published: June, 2010

Abstract: The current concept of epigenetic repression is based on one repressor unit corresponding to one silent gene. This notion, however, cannot adequately explain concurrent silencing of multiple loci observed in large chromosome regions. The long-rang...
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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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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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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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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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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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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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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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Autonomous silencing of the imprinted Cdkn1c gene in stem cells
Published: April, 2010

Abstract: Parent-of-origin specific expression of imprinted genes relies on the differential DNA methylation of specific genomic regions. Differentially methylated regions (DMRs) acquire DNA methylation either during gametogenesis (primary DMR) or after fer...
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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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Distinct factors control histone variant H3.3 localization at specific genomic regions.
Published: March, 2010

Abstract: The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc-finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic s...
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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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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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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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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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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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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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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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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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CTCF prevents the epigenetic drift of EBV latency promoter Qp.
Published: January, 2010

Abstract: The establishment and maintenance of Epstein-Barr Virus (EBV) latent infection requires distinct viral gene expression programs. These gene expression programs, termed latency types, are determined largely by promoter selection, and controlled thr...
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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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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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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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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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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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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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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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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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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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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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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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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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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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Genistein induces adipogenesis but inhibits leptin induction in human synovial fibroblasts.
Published: July, 2009

Abstract: It was shown recently that synovial fibroblast transformation into adipocytes reduced the expression of interleukin-6 (IL-6) and IL-8. However, the synovial fibroblast adipogenesis was inhibited in inflammatory conditions induced by the tumor necr...
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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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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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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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Gfi1 integrates progenitor versus granulocytic transcriptional programming.
Published: May, 2009

Abstract: In patients with severe congenital neutropenia (SCN) and mice with growth factor independent-1 (Gfi1) loss of function, arrested myeloid progenitors accumulate, whereas terminal granulopoiesis is blocked. One might assume that Gfi-null progenitors...
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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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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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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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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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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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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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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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Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.
Published: October, 2008

Abstract: In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 genes. To gain insight int...
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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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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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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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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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Gene transactivation without direct DNA binding defines a novel gain-of-function for PML-RARalpha.
Published: February, 2008

Abstract: PML-RARalpha is the causative oncogene in 5% to 10% of the cases of acute myeloid leukemia. At physiological concentrations of retinoic acid, PML-RARalpha silences RARalpha target genes, blocking differentiation of the cells. At high concentration...
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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Fragrant Unsaturated Aldehydes Elicit Activation of the Keap1=Nrf2 System Leading to the Upregulation of Thioredoxin Expression and Protection Against Oxidative Stress

Abstract: Thioredoxin, a key molecule in redox regulation, and many redox enzymes are regulated through the antioxidant responsive element (ARE). To search for antioxidative constituents, we screened extracts from vegetables and found that the extracts of P...
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  • "Molecular Biosystems" Conference on Eukaryotic Gene Regulation and Functional Genomics
    Puerto Varas, Región de Los Lagos, Chile
    Sep 23-Sep 26, 2017
  • The 76th Annual Meeting of the Japanese Cancer Association
    Tokyo, Japan
    Sep 28-Sep 30, 2017
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