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Genome-wide profiling of DNA methylation patterns in iAs-transformed cells

ABSTRACT: To examine the global impact of iAs on DNA methylation patterns. Genomic DNA was Bisulfite converted and analyzed using Mini methly-seq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE85012 | GEO | 2017/03/08

SECONDARY ACCESSION(S): PRJNA335883

REPOSITORIES: GEO

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Transient and permanent changes in DNA methylation patterns in inorganic arsenic-mediated epithelial-to-mesenchymal transition

Project description:To examine the global impact of iAs on DNA methylation patterns. Genomic DNA was bisulfite converted and analyzed using Infinium MethylationEPIC BeadChip.

2017-06-23 | GSE95232 | GEO

Genome-wide profiling of DNA hydroxymethylation patterns in iAs-transformed cells

Project description:To examine the global impact of iAs on DNA hdroxymethylation patterns. Genomic DNA was glucosylated, digested and analyzed using Reduced Representation Hydroxymethylation Profiling.

2018-02-13 | GSE103626 | GEO

Genome-wide profiling of gene expression/splicing patterns in iAs-transformed cells

Project description:Chronic low dose inorganic arsenic (iAs) exposure leads to changes in gene expression and epithelial-to-mesenchymal transformation. During this transformation, cells adopt a fibroblast-like phenotype accompanied by profound gene expression changes. While many mechanisms have been implicated in this transformation, studies that focus on the role of epigenetic alterations in this process are just emerging. DNA methylation controls gene expression in physiologic and pathologic states. Several studies show alterations in DNA methylation patterns in iAs-mediated pathogenesis, but these studies focused on single genes. We present a comprehensive genome-wide DNA methylation analysis using methyl-sequencing to measure changes between normal and iAs-transformed cells. Additionally, these differential methylation changes correlated positively with changes in gene expression and alternative splicing. Interestingly, most of these differentially methylated genes function in cell adhesion and communication pathways. To gain insight into how genomic DNA methylation patterns are regulated iAs-mediated carcinogenesis, we show that iAs probably targets CTCF binding at the promoter of DNA methyltransferases, regulating their expression. These findings reveal how transcription factor binding regulates DNA methyltransferase to reprogram the methylome in response to an environmental toxin.

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Selective inhibition of CTCF binding by iAs directs TET-mediated reprogramming of 5-hydroxymethylation patterns in iAs-transformed cells.

Project description: Not available

| S-EPMC5738917 | biostudies-literature

Gene expression analysis of 120 hpf zebrafish livers following 24 hour iAs exposure

Project description:This study was carried out to compare the changes in the gene expression in the liver of 5 day post fertilization zebrafish larvae in response to 24 hour exposure to 1.0 and 1.5mM iAs and to compare this to changes in gene expression as a result of overexpress as3mt in hepatocytes. CL1 CAAX 1.5 = WT larvae exposed to 1.5 mM iAs; CL2 CAAX 1 = WT larvae exposed to 1.5 mM iAs

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and 2.5ppm iAs Treated Mouse Gastrocnemius Muscle Transcriptomes

Project description:Inorganic arsenic (iAs) is a widespread environmental toxin. In addition to being a human carcinogen, its effect on systemic glucose metabolism has started to gain recognition recently. However, its in vivo effect on insulin sensitivity is not clear. Here we use mouse models to dissect the dose-dependent effects of iAs in glucose metabolism. We found that a low-dose exposure (0.25 ppm iAs in drinking water) caused glucose intolerance in adult male C57BL/6 mice, likely by disrupting glucose-induced insulin secretion without affecting peripheral insulin sensitivity. However, a higher-dose exposure (2.5 ppm iAs) has diminished effects on glucose tolerance despite disrupted pancreatic insulin secretion. We performed hyperinsulinemic euglycemic clamp, the gold standard analysis of systemic insulin sensitivity, and found that the 2.5 ppm iAs enhanced systemic insulin sensitivity by simultaneously enhancing insulin-stimulated glucose uptake in skeletal muscles and insulin-mediated suppression of endogenous glucose production. RNA-seq analysis of muscles revealed that 2.5 ppm iAs regulated expression of many genes involved in the metabolism of fatty acids, pyruvate, and amino acids. These findings suggest that iAs has distinct effects on distinct metabolic tissues at different dose thresholds, which could help reconcile some of the conflicting epidemiological results. The study shed light on the complex interactions between an environmental factor and the systemic glucose metabolism.

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Genome-wide methylation profiles of saliva

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Methylation profiling of choroid plexus carcinoma cell lines

Project description:Genomic DNA was extracted from two choroid plexus carcinoma cell lines using the GeneJET genomic DNA (Thermo Fisher). DNA was quantified using the DENOVIX Fluorometer. The quality of the extracted DNA samples was assessed by the Illumina FFPE QC kit (Illumina). Bisulfite conversion of the DNA was performed using the EZ DNA methylation kit (Zymo). Bisulfite-converted DNA was hybridized to the Illumina Infinium Human Methylation EPIC array bead chip and scanned using the Illumina iScan microarray scanner (Illumina) according to the manufacturer protocol.

2024-01-01 | GSE236509 | GEO

CGGBP1 inhibits cytosine methylation at repetitive DNA sequences

Project description:By depleting CGGBP1 in normal human fibroblasts and by performing genome-wide sequencing (with and without bisulfite conversion) we show that upon CGGBP1 depletion cytosine methylation increases significantly at repeat regions. Using Pacbio sequencing of Alu and LINE-1 repeats amplified genome-wide from bisulfite converted DNA, we further establish the cytosine methylation-inhibitory functions of CGGBP1.

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