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62 publications found.

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...
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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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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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