Diagenode

MagMeDIP kit

135 publications found.

A Pre-Leukemic DNA Methylation Signature in Healthy Individuals at Higher Risk for Developing Myeloid Malignancy
Published: March, 2024

Abstract: Purpose: DNA methylation alterations are widespread in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), some of which appear to have evolved independently of somatic mutations in epigenetic regulators. While the presence of somatic...
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Neurofibromin 1 controls metabolic balance and Notch-dependent quiescence of murine juvenile myogenic progenitors
Published: February, 2024

Abstract: Patients affected by neurofibromatosis type 1 (NF1) frequently show muscle weakness with unknown etiology. Here we show that, in mice, Neurofibromin 1 (Nf1) is not required in muscle fibers, but specifically in early postnatal myogenic progenitors...
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Promoter DNA methylation patterns in oral, laryngeal and oropharyngeal anatomical regions are associated with tumor differentiation, nodal involvement and survival
Published: January, 2024

Abstract: Differentially methylated regions (DMRs) can be used as head and neck squamous cell carcinoma (HNSCC) diagnostic, prognostic and therapeutic targets in precision medicine workflows. DNA from 21 HNSCC and 10 healthy oral tissue samples was hybridiz...
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Cerebrospinal fluid methylome-based liquid biopsies for accuratemalignant brain neoplasm classification.
Published: August, 2023

Abstract: BACKGROUND: Resolving the differential diagnosis between brain metastases (BM), glioblastomas (GBM), and central nervous system lymphomas (CNSL) is an important dilemma for the clinical management of the main three intra-axial brain tumor types. C...
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Transgenerational endocrine disruptor effects of cadmium in zebrafish andcontribution of standing epigenetic variation to adaptation.
Published: August, 2023

Abstract: Evidence has emerged that environmentally-induced epigenetic changes can have long-lasting effects on gene transcription across generations. These recent findings highlight the need to investigate the transgenerational impacts of pollutants to ass...
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Differentiation block in acute myeloid leukemia regulated by intronicsequences of FTO
Published: August, 2023

Abstract: Iroquois transcription factor gene IRX3 is highly expressed in 20–30\% of acute myeloid leukemia (AML) and contributes to the pathognomonic differentiation block. Intron 8 FTO sequences ∼220kB downstream of I...
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Epigenetic modifier alpha-ketoglutarate modulates aberrant gene bodymethylation and hydroxymethylation marks in diabetic heart.
Published: April, 2023

Abstract: BACKGROUND: Diabetic cardiomyopathy (DCM) is a leading cause of death in diabetic patients. Hyperglycemic myocardial microenvironment significantly alters chromatin architecture and the transcriptome, resulting in aberrant activation of signaling ...
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Pre-diagnosis plasma cell-free DNA methylome profiling up to sevenyears prior to clinical detection reveals early signatures of breast cancer
Published: February, 2023

Abstract: Profiling of cell-free DNA (cfDNA) has been well demonstrated to be a potential non-invasive screening tool for early cancer detection. However, limited studies have investigated the detectability of cfDNA methylation markers that are predictive o...
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Cell-free multi-omics analysis reveals tumor status-informativesignatures in gastrointestinal cancer patients’ plasma
Published: February, 2023

Abstract: During cancer development, host’s tumorigenesis and immune signals are released to and informed by circulating molecules, like cell-free DNA (cfDNA) and RNA (cfRNA) in blood. However, these two kinds of molecules are still not systematically...
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Methylation and expression of glucocorticoid receptor exon-1 variants andFKBP5 in teenage suicide-completers.
Published: February, 2023

Abstract: A dysregulated hypothalamic-pituitary-adrenal (HPA) axis has repeatedly been demonstrated to play a fundamental role in psychiatric disorders and suicide, yet the mechanisms underlying this dysregulation are not clear. Decreased expression of the ...
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Bridging biological cfDNA features and machine learning approaches.
Published: February, 2023

Abstract: Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of ce...
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Gene body DNA hydroxymethylation restricts the magnitude oftranscriptional changes during aging.
Published: February, 2023

Abstract: DNA hydroxymethylation (5hmC) is the most abundant oxidative derivative of DNA methylation (5mC) and is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been ...
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Neonatal inflammation increases hippocampal KCC2 expression throughmethylation-mediated TGF-β1 downregulation leading to impairedhippocampal cognitive function and synaptic plasticity in adult mice.
Published: January, 2023

Abstract: The mechanisms by which neonatal inflammation leads to cognitive deficits in adulthood remain poorly understood. Inhibitory GABAergic synaptic transmission plays a vital role in controlling learning, memory and synaptic plasticity. Since early-lif...
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Impact of FecB Mutation on Ovarian DNA Methylome inSmall-Tail Han Sheep.
Published: January, 2023

Abstract: UNLABELLED: Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mec...
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Consistent DNA Hypomethylations in Prostate Cancer.
Published: December, 2022

Abstract: With approximately 1.4 million men annually diagnosed with prostate cancer (PCa) worldwide, PCa remains a dreaded threat to life and source of devastating morbidity. In recent decades, a significant decrease in age-specific PCa mortality has been ...
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Longitudinal monitoring of cell-free DNA methylation in ALK-positivenon-small cell lung cancer patients.
Published: December, 2022

Abstract: BACKGROUND: DNA methylation (5-mC) signals in cell-free DNA (cfDNA) of cancer patients represent promising biomarkers for minimally invasive tumor detection. The high abundance of cancer-associated 5-mC alterations permits parallel and highly...
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Cell-free DNA methylation-defined prognostic subgroups in small celllung cancer identified by leukocyte methylation subtraction
Published: November, 2022

Abstract: Small cell lung cancer (SCLC) methylome is understudied. Here, we comprehensively profile SCLC using cell-free methylated DNA immunoprecipitation followed by sequencing (cfMeDIP-seq). Cell-free DNA (cfDNA) from plasma of 74 SCLC patients pre-treat...
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The cell-free DNA methylome captures distinctions between localized andmetastatic prostate tumors.
Published: October, 2022

Abstract: Metastatic prostate cancer remains a major clinical challenge and metastatic lesions are highly heterogeneous and difficult to biopsy. Liquid biopsy provides opportunities to gain insights into the underlying biology. Here, using the highly sensit...
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A SOX2-engineered epigenetic silencer factor represses the glioblastomagenetic program and restrains tumor development.
Published: August, 2022

Abstract: Current therapies remain unsatisfactory in preventing the recurrence of glioblastoma multiforme (GBM), which leads to poor patient survival. By rational engineering of the transcription factor SOX2, a key promoter of GBM malignancy, together with ...
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mTORC1 is required for epigenetic silencing during β-cell functionalmaturation.
Published: August, 2022

Abstract: OBJECTIVE: The mechanistic target of rapamycin comple×1 (mTORC1) is a key molecule that links nutrients, hormones, and growth factors to cell growth/function. Our previous studies have shown that mTORC1 is required for β-cell functional...
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Detection of ovarian cancer using plasma cell-free DNA methylomes.
Published: June, 2022

Abstract: BACKGROUND: Ovarian cancer (OC) is a highly lethal gynecologic cancer, and it is hard to diagnose at an early stage. Clinically, there are no ovarian cancer-specific markers for early detection. Here, we demonstrate the use of cell-free DNA (cfDNA...
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A genome-wide screen reveals new regulators of the 2-cell-like cell state
Published: June, 2022

Abstract: In mammals, only the zygote and blastomeres of the early embryo are fully totipotent. This totipotency is mirrored in vitro by mouse "2-cell-like cells" (2CLCs), which appear at low frequency in cultures of Embryonic Stem cells (ESCs). Because tot...
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Heat stress during grain filling regulates seed germination throughalterations of DNA methylation in barley (Hordeum vulgare L.).
Published: May, 2022

Abstract: KEY MESSAGE: Alterations in DNA methylation levels of ROS, GA and ABA related gene promoters cause transcriptional changes upon imbibition to induce seed germination in barley seeds exposed to heat stress during grain filling. Environmental change...
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Hexokinase 2 is a transcriptional target and a positive modulator ofAHR signalling.
Published: May, 2022

Abstract: The aryl hydrocarbon receptor (AHR) regulates the expression of numerous genes in response to activation by agonists including xenobiotics. Although it is well appreciated that environmental signals and cell intrinsic features may modulate this tr...
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Corticosterone induces discrete epigenetic signatures in the dorsal andventral hippocampus that depend upon sex and genotype: focus on methylatedNr3c1 gene.
Published: March, 2022

Abstract: The genomic effects of circulating glucocorticoids are particularly relevant in cortico-limbic structures, which express a high concentration of steroid hormone receptors. To date, no studies have investigated genomic differences in hippocampal su...
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Stella regulates the Development of Female Germline Stem Cells byModulating Chromatin Structure and DNA Methylation.
Published: January, 2022

Abstract: Female germline stem cells (FGSCs) have the ability to self-renew and differentiate into oocytes. , encoded by a maternal effect gene, plays an important role in oogenesis and early embryonic development. However, its function in FGSCs remains unc...
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Integrating SNPs-based genetic risk factor with blood epigenomicresponse of differentially arsenic-exposed rural subjects revealsdisease-associated signaling pathways.
Published: January, 2022

Abstract: Arsenic (As) contamination in groundwater is responsible for numerous adverse health outcomes among millions of people. Epigenetic alterations are among the most widely studied mechanisms of As toxicity. To understand how As exposure alters gene e...
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Examining age-dependent DNA methylation patterns and gene expression inthe male and female mouse hippocampus.
Published: December, 2021

Abstract: DNA methylation is a well-characterized epigenetic modification involved in numerous molecular and cellular functions. Methylation patterns have also been associated with aging mechanisms. However, how DNA methylation patterns change within key br...
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Dnmt1 has de novo activity targeted to transposable elements
Published: June, 2021

Abstract: DNA methylation plays a critical role during development, particularly in repressing retrotransposons. The mammalian methylation landscape is dependent on the combined activities of the canonical maintenance enzyme Dnmt1 and the de novo Dnmts, 3a ...
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Epigenetic Plasticity Enables CNS-Trafficking of EBV-infectedB Lymphocytes
Published: June, 2021

Abstract: Subpopulations of B-lymphocytes traffic to different sites and organs to provide diverse and tissue-specific functions. Here, we provide evidence that epigenetic differences confer a neuroinvasive phenotype. An EBV+ B cell lymphoma cell line (M14)...
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Alterations of DNA Methylation Caused by Cold Plasma Treatment Restore Delayed Germination of Heat-Stressed Rice (Oryza sativa L.) Seeds
Published: February, 2021

Abstract: In rice (Oryza sativa L.), seeds exposed to heat stress during grain filling exhibit delayed germination because of DNA methylation levels at promoters of abscisic acid (ABA, a germination-inhibiting hormone) catabolism genes and α-amylase (...
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Prenatal Stress Leads to the Altered Maturation of Corticostriatal SynapticPlasticity and Related Behavioral Impairments Through EpigeneticModifications of Dopamine D2 Receptor in Mice.
Published: January, 2021

Abstract: Prenatal stress (PRS) had a long-term adverse effect on motor behaviors. Corticostriatal synaptic plasticity, a cellular basis for motor controlling, has been proven to participate in the pathogenesis of many behavior disorders. Based on the repor...
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Comparative genome-wide methylation analysis of longissimus dorsi musclesin Yorkshire and Wannanhua pigs.
Published: December, 2020

Abstract: DNA methylation was one of the earliest discovered epigenetic modifications in vertebrates, and is an important epigenetic mechanism involved in the expression of genes in many biological processes, including muscle growth and development. Its eff...
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Mechanism of delayed seed germination caused by high temperature duringgrain filling in rice (Oryza sativa L.).
Published: October, 2020

Abstract: High temperature during grain filling considerably reduces yield and quality in rice (Oryza sativa L.); however, how high temperature affects seed germination of the next generation is not yet well understood. Here, we report that seeds from plant...
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Network integration and modelling of dynamic drug responses at multi-omicslevels.
Published: October, 2020

Abstract: Uncovering cellular responses from heterogeneous genomic data is crucial for molecular medicine in particular for drug safety. This can be realized by integrating the molecular activities in networks of interacting proteins. As proof-of-concept we...
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Frataxin gene editing rescues Friedreich's ataxia pathology in dorsal rootganglia organoid-derived sensory neurons.
Published: August, 2020

Abstract: Friedreich's ataxia (FRDA) is an autosomal-recessive neurodegenerative and cardiac disorder which occurs when transcription of the FXN gene is silenced due to an excessive expansion of GAA repeats into its first intron. Herein, we generate dorsal ...
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Integrated analysis of DNA methylation profile of HLA-G gene andimaging in coronary heart disease: Pilot study.
Published: August, 2020

Abstract: AIMS: Immune endothelial inflammation, underlying coronary heart disease (CHD) related phenotypes, could provide new insight into the pathobiology of the disease. We investigated DNA methylation level of the unique CpG island of HLA-G gene in CHD ...
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Comparative DNA methylome analysis of estrus ewes reveals the complexregulatory pathways of sheep fecundity.
Published: August, 2020

Abstract: BACKGROUND/AIMS: Sheep are important livestock with variant ovulation rate and fertility. Dorset sheep is a typical breed with low prolificacy, whereas Small Tail Han sheep with FecB mutation (HanBB) have hyperprolificacy. Our previous studies hav...
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Methylation in pericytes after acute injury promotes chronic kidneydisease.
Published: August, 2020

Abstract: The origin and fate of renal myofibroblasts is not clear after acute kidney injury (AKI). Here, we demonstrate that myofibroblasts were activated from quiescent pericytes (qPericytes) and the cell numbers increased after ischemia/reperfusion injur...
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Integrated epigenetic biomarkers in circulating cell-free DNA as a robust classifier for pancreatic cancer.
Published: July, 2020

Abstract: BACKGROUND: The high lethal rate of pancreatic cancer is partly due to a lack of efficient biomarkers for screening and early diagnosis. We attempted to develop effective and noninvasive methods using 5-methylcytosine (5mC) and 5-hydroxymethylcyto...
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Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes.
Published: June, 2020

Abstract: Definitive diagnosis of intracranial tumors relies on tissue specimens obtained by invasive surgery. Noninvasive diagnostic approaches provide an opportunity to avoid surgery and mitigate unnecessary risk to patients. In the present study, we show...
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Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes.
Published: June, 2020

Abstract: Improving early cancer detection has the potential to substantially reduce cancer-related mortality. Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) is a highly sensitive assay capable of detecting early-s...
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DNA methylation enzymes and PRC1 restrict B-cell Epstein-Barr virus oncoprotein expression.
Published: May, 2020

Abstract: To accomplish the remarkable task of lifelong infection, the Epstein-Barr virus (EBV) switches between four viral genome latency and lytic programmes to navigate the B-cell compartment and evade immune responses. The transforming programme, consis...
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Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro differentiation of a putative hepatocyte progenitor.
Published: May, 2020

Abstract: A basic question linked to differential patterns of gene expression is how cells reach different fates despite using the same DNA template. Since 5-hydroxymethylcytosine (5hmC) emerged as an intermediate metabolite in active DNA demethylation, the...
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TET-Mediated Hypermethylation Primes SDH-Deficient Cells for HIF2α-Driven Mesenchymal Transition.
Published: March, 2020

Abstract: Loss-of-function mutations in the SDHB subunit of succinate dehydrogenase predispose patients to aggressive tumors characterized by pseudohypoxic and hypermethylator phenotypes. The mechanisms leading to DNA hypermethylation and its cont...
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Genome-wide DNA Methylation Analysis of Mantle Edge and Mantle Central from Pearl Oyster Pinctada fucata martensii.
Published: March, 2020

Abstract: DNA methylation is a type of epigenetic modification that alters gene expression without changing the DNA sequence and mediates some cases of phenotypic plasticity. In this study, we identified six DNA methyltransferase (DNMT) genes and two&n...
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Preterm birth is associated with epigenetic programming of transgenerational hypertension in mice.
Published: January, 2020

Abstract: Renal and cardiovascular complications of prematurity are well established, notably the development of hypertension in adulthood. However, the underlying molecular mechanisms remain poorly understood. Our objective was to investigate the impact of...
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Alteration in global DNA methylation status following preconditioning injury influences axon growth competence of the sensory neurons.
Published: January, 2020

Abstract: Preconditioning peripheral nerve injury primes the sensory neurons in the dorsal root ganglia (DRGs) to acquire axon regeneration competence. Transcription of a large set of regeneration-associated-genes (RAGs) contributes to the enhanced intrinsi...
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Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.
Published: November, 2019

Abstract: Cranial radiotherapy in children has detrimental effects on cognition, mood, and social competence in young cancer survivors. Treatments harnessing hippocampal neurogenesis are currently of great relevance in this context. Lithium, a well-known mo...
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Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA.
Published: August, 2019

Abstract: Circulating cell-free DNA (cfDNA) comprises small DNA fragments derived from normal and tumor tissue that are released into the bloodstream. Recently, methylation profiling of cfDNA as a liquid biopsy tool has been gaining prominence due to the pr...
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Human mitochondrial DNA is extensively methylated in a non-CpG context
Published: August, 2019

Abstract: Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global a...
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Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants.
Published: August, 2019

Abstract: Brown algae have convergently evolved plant-like body plans and reproductive cycles, which in plants are controlled by differential DNA methylation. Here we provide the first single-base methylome profiles of haploid gametophytes and diploid sporo...
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Genome-wide methylation in alcohol use disorder subjects: implications for an epigenetic regulation of the cortico-limbic glucocorticoid receptors (NR3C1).
Published: June, 2019

Abstract: Environmental factors, including substance abuse and stress, cause long-lasting changes in the regulation of gene expression in the brain via epigenetic mechanisms, such as DNA methylation. We examined genome-wide DNA methylation patterns in the p...
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DNA methylation of the Tacr2 gene in a CUMS model of depression.
Published: June, 2019

Abstract: Tacr2, the gene encoding the NK2 receptor, belongs to G protein-coupled receptors. Accumulating evidence has indicated that the tachykinin receptors may contribute to the pathophysiology of depression. During the last decade, some studies have sho...
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The methylation pattern of DNA and complex correlations with gene expressions during TuMV infection in Chinese cabbage
Published: May, 2019

Abstract: Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most important economic crops. However, its yield and quality can be severely threatened by Turnip mosaic virus (TuMV). Emerging evidence indicates that epigenetic mechanisms, especi...
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Epigenetic Alterations in Juvenile Spondyloarthritis Patients: a Preliminary Study of Selected Genes Promoter Methylation and Silencing
Published: May, 2019

Abstract: Juvenile spondyloarthritis (jSpA) is a complex disease with both genetic and environmental factors contributing to etiology. Multiple studies have shown that epigenetic mechanisms could link the environment and gene expression and thus provide a p...
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Epigenetic control of the angiotensin-converting enzyme in endothelial cells during inflammation.
Published: May, 2019

Abstract: The angiotensin-converting enzyme (ACE) plays a central role in the renin-angiotensin system, which is involved in the regulation of blood pressure. Alterations in ACE expression or activity are associated with various pathological phenotypes, par...
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Genome-wide DNA methylation profiles in Tibetan and Yorkshire pigs under high-altitude hypoxia.
Published: April, 2019

Abstract: Background: Tibetan pigs, which inhabit the Tibetan Plateau, exhibit distinct phenotypic and physiological characteristics from those of lowland pigs and have adapted well to the extreme conditions at high altitude. However, the genetic and epigen...
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Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis.
Published: April, 2019

Abstract: Dynamic changes in DNA (hydroxy-)methylation are fundamental for stem cell differentiation. However, the signature of these epigenetic marks in specific cell types during corticogenesis is unknown. Moreover, site-specific manipulation of cytosine ...
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DMSO induces drastic changes in human cellular processes and epigenetic landscape in vitro.
Published: March, 2019

Abstract: Though clinical trials for medical applications of dimethyl sulfoxide (DMSO) reported toxicity in the 1960s, later, the FDA classified DMSO in the safest solvent category. DMSO became widely used in many biomedical fields and biological effects we...
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Evidence of association of circulating epigenetic-sensitive biomarkers with suspected coronary heart disease evaluated by Cardiac Computed Tomography.
Published: January, 2019

Abstract: Circulating biomarkers available in clinical practice do not allow to stratify patients with coronary heart disease (CHD) prior the onset of a clinically relevant event. We evaluated the methylation status of specific genomic segments and gene exp...
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LncRNA Dnmt3aos regulates Dnmt3a expression leading to aberrant DNA methylation in macrophage polarization
Published: January, 2019

Abstract: Long non-coding RNAs (lncRNAs) play key roles in various biological processes. However, the roles of lncRNAs in macrophage polarization remain largely unexplored. In this study, thousands of lncRNAs were identified that are differentially expresse...
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Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia.
Published: January, 2019

Abstract: BACKGROUND: Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot...
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Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues.
Published: January, 2019

Abstract: This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex li...
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Sensitive tumour detection and classification using plasma cell-free DNA methylomes.
Published: November, 2018

Abstract: The use of liquid biopsies for cancer detection and management is rapidly gaining prominence. Current methods for the detection of circulating tumour DNA involve sequencing somatic mutations using cell-free DNA, but the sensitivity of these method...
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Genome-wide analysis of DNA methylation to identify genes and pathways associated with male sterility in soybean
Published: September, 2018

Abstract: DNA methylation is an epigenetic modification, which is important for gene expression regulation. Although genome-wide DNA methylation studies have been reported in several plant species, the difference in the methylation pattern between the cytop...
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Folic acid supplementation alters the DNA methylation profile and improves insulin resistance in high-fat-diet-fed mice.
Published: September, 2018

Abstract: Folic acid (FA) supplementation may protect from obesity and insulin resistance, the effects and mechanism of FA on chronic high-fat-diet-induced obesity-related metabolic disorders are not well elucidated. We adopted a genome-wide approach to dir...
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Embryonic germ cell extracts erase imprinted genes and improve the efficiency of induced pluripotent stem cells.
Published: July, 2018

Abstract: Patient-specific induced pluripotent stem cells (iPSCs) have the potential to be useful in the treatment of human diseases. While prior studies have reported multiple methods to generate iPSCs, DNA methylation continues to limit the totipotency an...
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Molecular Signatures of Regression of the Canine Transmissible Venereal Tumor.
Published: April, 2018

Abstract: The canine transmissible venereal tumor (CTVT) is a clonally transmissible cancer that regresses spontaneously or after treatment with vincristine, but we know little about the regression mechanisms. We performed global transcriptional, methylatio...
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Copper induces expression and methylation changes of early development genes in Crassostrea gigas embryos.
Published: March, 2018

Abstract: Copper contamination is widespread along coastal areas and exerts adverse effects on marine organisms such as mollusks. In the Pacific oyster, copper induces severe developmental abnormalities during early life stages; however, the underlying mole...
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Aberrant methylated key genes of methyl group metabolism within the molecular etiology of urothelial carcinogenesis.
Published: February, 2018

Abstract: Urothelial carcinoma (UC), the most common cancer of the urinary bladder causes severe morbidity and mortality, e.g. about 40.000 deaths in the EU annually, and incurs considerable costs for the health system due to the need for prolonged treatmen...
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Integrative omics data analyses of repeated dose toxicity of valproic acid in vitro reveal new mechanisms of steatosis induction
Published: January, 2018

Abstract: Valproic acid (VPA) is a very potent anti-cancer and neuro-protective drug probably by its HDAC inhibiting properties, which may cause steatosis in the liver. The present study investigates the effect of repetitive VPA treatment of primary human h...
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Copper induces expression and methylation changes of early development genes in Crassostrea gigas embryos
Published: January, 2018

Abstract: Copper contamination is widespread along coastal areas and exerts adverse effects on marine organisms such as mollusks. In the Pacific oyster, copper induces severe developmental abnormalities during early life stages; however, the underlying mole...
Read more »

Genome-wide analysis of day/night DNA methylation differences in Populus nigra.
Published: January, 2018

Abstract: DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understo...
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Obligatory and facilitative allelic variation in the DNA methylome within common disease-associated loci
Published: January, 2018

Abstract: Integrating epigenetic data with genome-wide association study (GWAS) results can reveal disease mechanisms. The genome sequence itself also shapes the epigenome, with CpG density and transcription factor binding sites (TFBSs) strongly e...
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Epigenetic alterations in TRAMP mice: epigenome DNA methylation profiling using MeDIP-seq.
Published: January, 2018

Abstract: Purpose: We investigated the genomic DNA methylation profile of prostate cancer in transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model and to analyze the crosstalk among targeted genes and the related functional pathways. Methods:...
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Analysis of DNA methylome and transcriptome profiling following Gibberellin A3 (GA3) foliar application in Nicotiana tabacum L.
Published: January, 2018

Abstract: The present work investigated a comprehensive genome-wide landscape of DNA methylome and its relationship with transcriptome upon gibberellin A3 (GA3) foliar application under practical field conditions in solanaceae model, Nicotiana tabacum L. Me...
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Data on novel DNA methylation changes induced by valproic acid in human hepatocytes
Published: November, 2017

Abstract: Valproic acid (VPA) is a widely prescribed antiepileptic drug in the world. Despite its pharmacological importance, it may cause liver toxicity and steatosis. However the exact mechanism of the steatosis formation is unknown. The data presented in...
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Nuclear and Mitochondrial DNA Methylation Patterns Induced by Valproic Acid in Human Hepatocytes
Published: October, 2017

Abstract: Valproic acid (VPA) is one of the most widely prescribed antiepileptic drugs in the world. Despite its pharmacological importance, it may cause liver toxicity and steatosis through mitochondrial dysfunction. The aim of this study is to further inv...
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Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos
Published: October, 2017

Abstract: Tibetan chickens have unique adaptations to the extreme high-altitude environment that they inhabit. Epigenetic DNA methylation affects many biological processes, including hypoxic adaptation; however, the regulatory genes for DNA methylation in h...
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Emerging Role of One-Carbon Metabolism and DNA Methylation Enrichment on δ-Containing GABAA Receptor Expression in the Cerebellum of Subjects with Alcohol Use Disorders (AUD
Published: August, 2017

Abstract: Background Cerebellum is an area of the brain particularly sensitive to the effects of acute and chronic alcohol consumption. Alcohol exposure decreases cerebellar Purkinje cell output by increasing GABA release from Golgi cells onto extrasyn...
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Coordinate Regulation of TET2 and EBNA2 Control DNA Methylation State of Latent Epstein-Barr Virus
Published: August, 2017

Abstract: Epstein-Barr Virus (EBV) latency and its associated carcinogenesis are regulated by dynamic changes in DNA methylation of both virus and host genomes. We show here that the Ten-Eleven Translocation 2 (TET2) gene, implicated in hydroxymethylation a...
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Intracellular adenosine regulates epigenetic programming in endothelial cells to promote angiogenesis
Published: July, 2017

Abstract: The nucleoside adenosine is a potent regulator of vascular homeostasis, but it remains unclear how expression or function of the adenosine-metabolizing enzyme adenosine kinase (ADK) and the intracellular adenosine levels influence angiogenesis. We...
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Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b
Published: July, 2017

Abstract: Background Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances th...
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Dynamics of DNA methylomes underlie oyster development
Published: June, 2017

Abstract: DNA methylation is a critical epigenetic regulator of development in mammals and social insects, but its significance in development outside these groups is not understood. Here we investigated the genome-wide dynamics of DNA methylation in a moll...
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MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination
Published: May, 2017

Abstract: Background DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embry...
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Protective vaccination and blood-stage malaria modify DNA methylation of gene promoters in the liver of Balb/c mice.
Published: May, 2017

Abstract: Epigenetic mechanisms such as DNA methylation are increasingly recognized to be critical for vaccination efficacy and outcome of different infectious diseases, but corresponding information is scarcely available for host defense against malaria. I...
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Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia
Published: March, 2017

Abstract: We conducted a comparative study of multiplexed affinity enrichment sequence methodologies (MBD-seq and MeDIP-seq) in a rodent model of schizophrenia, induced by in utero methylazoxymethanol acetate (MAM) exposure. We also examined related gene ex...
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Overexpression of LINE-1 Retrotransposons in Autism Brain
Published: February, 2017

Abstract: Long interspersed nuclear elements-1 (LINE-1 or L1) are mobile DNA sequences that are capable of duplication and insertion (retrotransposition) within the genome. Recently, retrotransposition of L1 was shown to occur within human brain leading to ...
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Integrative "-Omics" Analysis in Primary Human Hepatocytes Unravels Persistent Mechanisms of Cyclosporine A-Induced Cholestasis
Published: December, 2016

Abstract: Cyclosporine A (CsA) is an undecapeptide with strong immunosuppressant activities and is used a lot after organ transplantation. Furthermore, it may induce cholestasis in the liver. In general, the drug-induced cholestasis (DIC) pathway includes g...
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Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples
Published: December, 2016

Abstract: We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Br...
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Genome-wide DNA promoter methylation and transcriptome analysis in human adipose tissue unravels novel candidate genes for obesity
Published: November, 2016

Abstract: Objective/methods DNA methylation plays an important role in obesity and related metabolic complications. We examined genome-wide DNA promoter methylation along with mRNA profiles in paired samples of human subcutaneous adipose tissue (SAT) and o...
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Novel regional age-associated DNA methylation changes within human common disease-associated loci
Published: September, 2016

Abstract: BACKGROUND: Advancing age progressively impacts on risk and severity of chronic disease. It also modifies the epigenome, with changes in DNA methylation, due to both random drift and variation within specific functional loci. RESULTS: In a di...
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Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing
Published: September, 2016

Abstract: Gene silencing is instrumental to interrogate gene function and holds promise for therapeutic applications. Here, we repurpose the endogenous retroviruses' silencing machinery of embryonic stem cells to stably silence three highly expressed g...
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Trichloroethylene-Induced DNA Methylation Changes in Male F344 Rat Liver
Published: September, 2016

Abstract: Trichloroethylene (TCE), a common environmental contaminant, causes hepatocellular carcinoma in mice but not in rats. To understand the mechanisms of the species-specific hepatocarcinogenecity of TCE, we examined the methylation status of DNA in t...
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Dynamic Interplay between the Transcriptome and Methylome in Response to Oxidative and Alkylating Stress
Published: August, 2016

Abstract: In recent years, it has been shown that free radicals not only react directly with DNA but also regulate epigenetic processes such as DNA methylation, which may be relevant within the context of, for example, tumorigenesis. However, how these free...
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Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis
Published: June, 2016

Abstract: We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. MATERIALS & METHODS: The DNA methylation status of liver and stomach tissues was profiled using fou...
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Aflatoxin B1 induces persistent epigenomic effects in primary human hepatocytes associated with hepatocellular carcinoma
Published: May, 2016

Abstract: Chronic exposure to aflatoxin B1 (AFB1) has, in certain regions in the world, been strongly associated with hepatocellular carcinoma (HCC) development. AFB1 is a very potent hepatotoxic and carcinogenic mycotoxin which is frequently reported as a ...
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Paternal B Vitamin Intake Is a Determinant of Growth, Hepatic Lipid Metabolism and Intestinal Tumor Volume in Female Apc1638N Mouse Offspring
Published: March, 2016

Abstract: Background The importance of maternal nutrition to offspring health and risk of disease is well established. Emerging evidence suggests paternal diet may affect offspring health as well. Objective In the current study we sought to determine whe...
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Regulation of miR-200c/141 expression by intergenic DNA-looping and transcriptional read-through
Published: January, 2016

Abstract: The miR-200 family members have been implicated in stress responses and ovarian tumorigenesis. Here, we find that miR-200c/141 transcription is intimately linked to the transcription of the proximal upstream gene PTPN6 (SHP1) in all physiological ...
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Maternal immune activation induces GAD1 and GAD2 promoter remodeling in the offspring prefrontal cortex
Published: December, 2015

Abstract: Maternal infection during pregnancy increases the risk of neurodevelopmental disorders in the offspring. In addition to its influence on other neuronal systems, this early-life environmental adversity has been shown to negatively affect cortical &...
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DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip
Published: December, 2015

Abstract: AIMS: To compare the performance of four sequence-based and one microarray methods for DNA methylation profiling. METHODS: DNA from two cell lines were profiled by reduced representation bisulfite sequencing, methyl capture sequencing (SS-Met...
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Evidence for Epigenetic Regulation of Pro-Inflammatory Cytokines, Interleukin-12 and Interferon Gamma, in Peripheral Blood Mononuclear Cells from PTSD Patients
Published: November, 2015

Abstract: While Post Traumatic Stress Disorder (PTSD) is associated with immune dysfunction, the underlying mechanisms remain unclear. Studies suggest a role for involvement of epigenetic mechanisms and microRNAs (miRNAs). Here, we examined genome-wide hist...
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High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases
Published: September, 2015

Abstract: BACKGROUND: Childhood stress leads to increased risk of many adult diseases, such as major depression and cardiovascular disease. Studies show that adults with experienced childhood stress have specific epigenetic changes, but to understand the...
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Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo
Published: July, 2015

Abstract: BACKGROUND: Atherosclerosis is a heterogeneously distributed disease of arteries in which the endothelium plays an important central role. Spatial transcriptome profiling of endothelium in pre-lesional arteries has demonstrated differential phe...
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Genome-wide analysis of DNA methylation in photoperiod- and thermo-sensitive male sterile rice Peiai 64S.
Published: February, 2015

Abstract: BACKGROUND: Epigenetic modifications play important roles in the regulation of plant development. DNA methylation is an important epigenetic modification that dynamically regulates gene expression during developmental processes. However, little st...
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The Dynamics of DNA Methylation in Maize Roots under Pb Stress.
Published: December, 2014

Abstract: Plants adapt to adverse conditions through a series of physiological, cellular, and molecular processes, culminating in stress tolerance. However, little is known about the associated regulatory mechanisms at the epigenetic level in maize under le...
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Involvement of microRNA-24 and DNA Methylation in Resistance of Nasopharyngeal Carcinoma to Ionizing Radiation.
Published: October, 2014

Abstract: Nasopharyngeal carcinoma (NPC) is a malignant tumor originating in the epithelium. Radiotherapy is the standard therapy, but tumor resistance to this treatment reduces the 5-year patient survival rate dramatically. Studies are urgently needed to e...
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Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets.
Published: September, 2014

Abstract: BACKGROUND: Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or abnormalities in cloned animals, but the underlying mechanism of the abnormal phenotype in ...
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Genome-wide analysis of DNA methylation in UVB- and DMBA/TPA-induced mouse skin cancer models.
Published: September, 2014

Abstract: AIMS: Ultraviolet irradiation and carcinogens have been reported to induce epigenetic alterations, which potentially contribute to the development of skin cancer. We aimed to study the genome-wide DNA methylation profiles of skin cancers induced b...
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Genome-wide analysis of DNA methylation patterns in horse
Published: July, 2014

Abstract: Background DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data a...
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Apigenin reactivates Nrf2 anti-oxidative stress signaling in mouse skin epidermal JB6 P + cells through epigenetics modifications.
Published: July, 2014

Abstract: Nrf2 is a crucial transcription factor that controls a critical anti-oxidative stress defense system and is implicated in skin homeostasis. Apigenin (API), a potent cancer chemopreventive agent, protects against skin carcinogenesis and elicits mul...
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Impact of MLL5 expression on decitabine efficacy and DNA methylation in acute myeloid leukemia.
Published: June, 2014

Abstract: Hypomethylating agents are widely used in patients with myelodysplastic syndromes and unfit patients with acute myeloid leukemia. However, it is not well understood why only some patients respond to hypomethylating agents. We found previously that...
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Impacts of TCDD and MeHg on DNA methylation in zebrafish (Danio rerio) across two generations.
Published: May, 2014

Abstract: This study aimed to investigate whether dioxin (TCDD) and methylmercury (MeHg) pose a threat to offspring of fish exposed to elevated concentrations of these chemicals via epigenetic-based mechanisms. Adult female zebrafish were fed diets added ei...
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Do ABO blood group antigens hamper the therapeutic efficacy of mesenchymal stromal cells?
Published: January, 2014

Abstract: Investigation into predictors for treatment outcome is essential to improve the clinical efficacy of therapeutic multipotent mesenchymal stromal cells (MSCs). We therefore studied the possible harmful impact of immunogenic ABO blood groups antigen...
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Differential methylation of the TRPA1 promoter in pain sensitivity.
Published: January, 2014

Abstract: Chronic pain is a global public health problem, but the underlying molecular mechanisms are not fully understood. Here we examine genome-wide DNA methylation, first in 50 identical twins discordant for heat pain sensitivity and then in 50 further ...
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Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells.
Published: August, 2013

Abstract: DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germ line, and may be mediated by Tet (ten eleven t...
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DNA unmethylome profiling by covalent capture of CpG sites.
Published: July, 2013

Abstract: Dynamic patterns of cytosine-5 methylation and successive hydroxylation are part of epigenetic regulation in eukaryotes, including humans, which contributes to normal phenotypic variation and disease risk. Here we present an approach for the mappi...
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Constitutional trisomy 8 mosaicism as a model for epigenetic studies of aneuploidy.
Published: July, 2013

Abstract: BACKGROUND: To investigate epigenetic patterns associated with aneuploidy we used constitutional trisomy 8 mosaicism (CT8M) as a model, enabling analyses of single cell clones, harboring either trisomy or disomy 8, from the same patient; this circ...
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Methyl donor supplementation blocks the adverse effects of maternal high fat diet on offspring physiology.
Published: May, 2013

Abstract: Maternal consumption of a high fat diet during pregnancy increases the offspring risk for obesity. Using a mouse model, we have previously shown that maternal consumption of a high fat (60%) diet leads to global and gene specific decreases in DNA ...
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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 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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T cell receptor stimulation-induced epigenetic changes and foxp3 expression are independent and complementary events required for treg cell development.
Published: November, 2012

Abstract: The transcription factor Foxp3 is essential for the development of regulatory T (Treg) cells, yet its expression is insufficient for establishing the Treg cell lineage. Here we showed that Treg cell development was achieved by the combination of t...
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Can soy phytoestrogens decrease DNA methylation in BRCA1 and BRCA2 oncosuppressor genes in breast cancer?
Published: May, 2012

Abstract: Although soy phytoestrogens have been postulated to exert a protective effect against breast cancer, the attendant mechanisms, in particular epigenetics underpinnings, have remained elusive. We investigated the putative effects on DNA methylation ...
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Methylome analysis using MeDIP-seq with low DNA concentrations.
Published: March, 2012

Abstract: DNA methylation is an epigenetic mark that has a crucial role in many biological processes. To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome-wide analysis should be embraced. This in turn requires a t...
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Gene expression and epigenetic changes by furan in rat liver.
Published: November, 2011

Abstract: Furan, a widely used industrial compound, has been found in a number of heated food items. Furan is carcinogenic to rats and mice, but the mechanism behind its carcinogenic effect is still not well understood. In this study, we tested the hypothes...
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Activation of group II metabotropic glutamate receptors promotes DNA demethylation in the mouse brain.
Published: July, 2011

Abstract: Activation of group II metabotropic glutamate receptors (mGlu2 and -3 receptors) has shown a potential antipsychotic activity, yet the underlying mechanism is only partially known. Altered epigenetic mechanisms contribute to the pathogenesis of sc...
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Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis.
Published: January, 2011

Abstract: BACKGROUND: DNA methylation is an epigenetic mechanism associated with regulation of gene expression and it is modulated during chemical carcinogenesis. The zebrafish is increasingly employed as a human disease model; however there is a lack of in...
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Whole genome DNA methylation analysis based on high throughput sequencing technology.
Published: November, 2010

Abstract: There are numerous approaches to decipher a whole genome DNA methylation profile ("methylome"), each varying in cost, throughput and resolution. The gold standard of these methods, whole genome bisulfite-sequencing (BS-seq), involves treatment of ...
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Low doses of the carcinogen furan alter cell cycle and apoptosis gene expression in rat liver independent of DNA methylation.
Published: November, 2010

Abstract: BACKGROUND: Evidence of potent rodent carcinogenicity via an unclear mechanism suggests that furan in various foods [leading to an intake of up to 3.5 microg/kg body weight (bw)/day] may present a potential risk to human health. OBJECTIVES: We tes...
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Clinical and public health research using methylated DNA immunoprecipitation (MeDIP) A comparison of commercially available kits to examine differential DNA methylation across the genome

Abstract: The methylated DNA immunoprecipitation method (MeDIP) is a genome-wide, high-resolution approach that detects DNA methylation with oligonucleotide tiling arrays or high throughput sequencing platforms. A simplified highthroughput MeDIP assay will ...
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Deletion of the de novo DNA methyltransferase Dnmt3a promotes lung tumor progression.

Abstract: Alterations in DNA methylation have been associated with genome-wide hypomethylation and regional de novo methylation in numerous cancers. De novo methylation is mediated by the de novo methyltransferases Dnmt3a and 3b, but only Dnmt3b has been im...
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Prenatal diagnosis of 21 trisomy by quantification of methylated fetal DNA in maternal blood: study on 10 pregnancies

Abstract: Background. The Down syndrome is a severe disease without pathogenic therapy. The only possibility to reduce the consequences of disease is prenatal screening and diagnosis. The gold standard in prenatal diagnosis is the conventional banding cytog...
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Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506-binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population.

Abstract: Cervical cancer is a major health concern among women in Latin America due to its high incidence and mortality. Therefore, the discovery of molecular markers for cervical cancer screening and triage is imperative. The aim of this study was to use ...
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