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MethylCap

38 publications found.

Antioxydation And Cell Migration Genes Are Identified as Potential Therapeutic Targets in Basal-Like and BRCA1 Mutated Breast Cancer Cell Lines
Published: January, 2018
Abstract: Basal-like breast cancers are among the most aggressive cancers and effective targeted therapies are still missing. In order to identify new therapeutic targets, we performed Methyl-Seq and RNA-Seq of 10 breast cancer cell lines with different phe...
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Methylome analysis of extreme chemoresponsive patients identifies novel markers of platinum sensitivity in high-grade serous ovarian cancer
Published: June, 2017
Abstract: BACKGROUND: Despite an early response to platinum-based chemotherapy in advanced stage high-grade serous ovarian cancer (HGSOC), the majority of patients will relapse with drug-resistant disease. Aberrant epigenetic alterations like DNA methyla...
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ALDH1A3 is epigenetically regulated during melanocyte transformation and is a target for melanoma treatment
Published: June, 2017
Abstract: Despite the promising targeted and immune-based interventions in melanoma treatment, long-lasting responses are limited. Melanoma cells present an aberrant redox state that leads to the production of toxic aldehydes that must be converted into les...
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Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos
Published: April, 2017
Abstract: BACKGROUND: Infertility in dairy cattle is a concern where reduced fertilization rates and high embryonic loss are contributing factors. Studies of the paternal contribution to reproductive performance are limited. However, recent discoveries h...
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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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Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans.
Published: February, 2017
Abstract: In humans, DNA methylation at specific CpG sites can be used to estimate the 'epigenetic clock', a biomarker of aging and health. The mechanisms that regulate the aging epigenome and level of conservation are not entirely clear. We performed affin...
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Epigenetic sampling effects: nephrectomy modifies the clear cell renal cell cancer methylome
Published: January, 2017
Abstract: Purpose Currently, it is unclear to what extent sampling procedures affect the epigenome. Here, this phenomenon was evaluated by studying the impact of artery ligation on DNA methylation in clear cell renal cancer. Methods DNA methylation...
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Determinants of orofacial clefting II: Effects of 5-Aza-2′-deoxycytidine on gene methylation during development of the first branchial arch
Published: January, 2017
Abstract: Defects in development of the secondary palate, which arise from the embryonic first branchial arch (1-BA), can cause cleft palate (CP). Administration of 5-Aza-2′-deoxycytidine (AzaD), a demethylating agent, to pregnant mice on gestational ...
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Comparative DNA Methylation and Gene Expression Analysis Identifies Novel Genes for Structural Congenital Heart Diseases
Published: August, 2016
Abstract: Aims For the majority of congenital heart diseases (CHDs), the full complexity of the causative molecular network, which is driven by genetic, epigenetic and environmental factors, is yet to be elucidated. Epigenetic alterations are suggested to...
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Molecular and epigenetic features of melanomas and tumor immune microenvironment linked to durable remission to ipilimumab - based immunotherapy in metastatic patients
Published: August, 2016
Abstract: Background Ipilimumab (Ipi) improves the survival of advanced melanoma patients with an incremental long-term benefit in 10–15 % of patients. A tumor signature that correlates with this survival benefit could help optimizing individu...
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Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells
Published: July, 2016
Abstract: Background Germline stem cells play an essential role in establishing the fertility of an organism. Although extensively characterized, the regulatory mechanisms that govern the fundamental properties of mammalian female germline stem cells rem...
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RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis
Published: July, 2016
Abstract: Oral and oropharyngeal squamous cell carcinoma (OOSCC) have a low survival rate, mainly due to metastasis to the regional lymph nodes. For optimal treatment of these metastases, a neck dissection is required; however, inaccurate detection methods ...
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Genic DNA methylation drives codon bias in stony corals
Published: May, 2016
Abstract: Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein coding sequences is particularly puzzling, because methylat...
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Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Published: March, 2016
Abstract: Background Despite the significant global loss of DNA hydroxymethylation marks in prostate cancer tissues, the locus-specific role of hydroxymethylation in prostate tumorigenesis is unknown. We characterized hydroxymethylation and methylation m...
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A genome-wide search for eigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq
Published: February, 2016
Abstract: Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the zebra finch genome, a model organism in neuroscience, as well as id...
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DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
Published: February, 2016
Abstract: Comprehensive genome-wide DNA methylation studies in neuroblastoma (NB), a childhood tumor that originates from precursor cells of the sympathetic nervous system, are scarce. Recently, we profiled the DNA methylome of 102 well-annotated primary NB...
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Identification and validation of WISP1 as an epigenetic regulator of metastasis in oral squamous cell carcinoma
Published: January, 2016
Abstract: Lymph node (LN) metastasis is the most important prognostic factor in oral squamous cell carcinoma (OSCC) patients. However, in approximately one third of OSCC patients nodal metastases remain undetected, and thus are not adequately treated. There...
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DNA methylation in an engineered heart tissue model of cardiac hypertrophy: common signatures and effects of DNA methylation inhibitors
Published: January, 2016
Abstract: DNA methylation affects transcriptional regulation and constitutes a drug target in cancer biology. In cardiac hypertrophy, DNA methylation may control the fetal gene program. We therefore investigated DNA methylation signatures and their dynamics...
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∆ DNMT3B4-del Contributes to Aberrant DNA Methylation Patterns in Lung Tumorigenesis
Published: October, 2015
Abstract: Aberrant DNA methylation is a hallmark of cancer but mechanisms contributing to the abnormality remain elusive. We have previously shown that ∆DNMT3B is the predominantly expressed form of DNMT3B. In this study, we found that most of the lung canc...
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Prenatal Exposure to DEHP Affects Spermatogenesis and Sperm DNA Methylation in a Strain-Dependent Manner.
Published: August, 2015
Abstract: Di-(2-ethylhexyl)phtalate (DEHP) is a plasticizer with endocrine disrupting properties found ubiquitously in the environment and altering reproduction in rodents. Here we investigated the impact of prenatal exposure to DEHP on spermatogenesis and ...
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DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3'-end GC density.
Published: February, 2015
Abstract: Diminished ovarian function occurs early and is a primary cause for age-related decline in female fertility; however, its underlying mechanism remains unclear. This study investigated the roles that genome and epigenome structure play in age-relat...
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Development of a unique epigenetic signature during in vivo Th17 differentiation.
Published: January, 2015
Abstract: Activated naive CD4(+) T cells are highly plastic cells that can differentiate into various T helper (Th) cell fates characterized by the expression of effector cytokines like IFN-γ (Th1), IL-4 (Th2) or IL-17A (Th17). Although previous studies hav...
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Mining for viral fragments in methylation enriched sequencing data
Published: January, 2015
Abstract: Most next generation sequencing experiments generate more data than is required for the experimental set up. For example, methyl-CpG binding domain (MBD) affinity purification based sequencing is often used for DNA-methylation profiling, but up to...
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Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites.
Published: January, 2015
Abstract: BACKGROUND: Primary cells enter replicative senescence after a limited number of cell divisions. This process needs to be considered in cell culture experiments, and it is particularly important for regenerative medicine. Replicative senescence is...
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Strategies for validation and testing of DNA methylation biomarkers.
Published: December, 2014
Abstract: DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and thera...
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SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data.
Published: November, 2014
Abstract: Monoallelic gene expression is typically initiated early in the development of an organism. Dysregulation of monoallelic gene expression has already been linked to several non-Mendelian inherited genetic disorders. In humans, DNA-methylation is de...
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Alterations of the lung methylome in allergic airway hyper-responsiveness.
Published: April, 2014
Abstract: Asthma is a chronic airway disorder characterized by recurrent attacks of breathlessness and wheezing, affecting 300 million people around the world (available at: www.who.int). To date, genetic factors associated with asthma susceptibility have b...
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BayMeth: Improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach
Published: February, 2014
Abstract: DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for reversing the...
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Genome-wide methylation and gene expression changes in newborn rats following maternal protein restriction and reversal by folic acid.
Published: December, 2013
Abstract: A large body of evidence from human and animal studies demonstrates that the maternal diet during pregnancy can programme physiological and metabolic functions in the developing fetus, effectively determining susceptibility to later disease. The m...
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Ten-Eleven Translocation-2 (TET2) Is a Master Regulator of Smooth Muscle Cell Plasticity.
Published: October, 2013
Abstract: BACKGROUND: Smooth muscle cells (SMCs) are remarkably plastic. Their reversible differentiation is required for growth and wound healing but also contributes to pathologies such as atherosclerosis and restenosis. Although key regulators of the SM...
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Differential programming of B cells in AID deficient mice.
Published: July, 2013
Abstract: The Aicda locus encodes the activation induced cytidine deaminase (AID) and is highly expressed in germinal center (GC) B cells to initiate somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes. Besides thes...
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The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos.
Published: April, 2013
Abstract: Genome-wide profiling of DNA methylation and histone modifications answered many questions as to how the genes are regulated on a global scale and what their epigenetic makeup is. Yet, little is known about the function of these marks during early...
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Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
Published: March, 2013
Abstract: DNA-methylation is an important epigenetic feature in health and disease. Methylated sequence capturing by Methyl Binding Domain (MBD) based enrichment followed by second-generation sequencing provides the best combination of sensitivity and cost-...
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Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes.
Published: November, 2011
Abstract: Transcription factor-induced lineage reprogramming or transdifferentiation experiments are essential for understanding the plasticity of differentiated cells. These experiments helped to define the specific role of transcription factors in conferr...
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TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity.
Published: May, 2011
Abstract: Enzymes catalysing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression and maintaining cellular identity. Recently, TET1 was found to hydroxylate the methyl group of mC, converting it to 5-hydroxym...
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Genome-wide DNA Methylation Profiles of Small Intestine and Liver in Fast-growing and Slow-growing Weaning Piglets
Abstract: Although growth rate is one o f the main economic traits of concern in pig production, there is limited knowledge on its epigenetic regulation, such as DNA methylation. In this study, we conducted met hyl - CpG binding domain protein - enriched ge...
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Combining genomic and proteomic approaches for epigenetics research.
Abstract: Epigenetics is the study of changes in gene expression or cellular phenotype that do not change the DNA sequence. In this review, current methods, both genomic and proteomic, associated with epigenetics research are discussed. Among them, chromati...
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Food-derived opioid peptides inhibit cysteine uptake with redox and epigenetic consequences
Abstract: Dietary interventions like gluten-free and casein-free diets have been reported to improve intestinal, autoimmune and neurological symptoms in patients with a variety of conditions; however, the underlying mechanism of benefit for such diets remai...
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