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Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation

ABSTRACT: Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation

PROVIDER: PRJNA541566 | ENA |

REPOSITORIES: ENA

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Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation [Expression]

Project description:How cells reach different fates despite using the same DNA template, is a basic question linked to differential patterns of gene expression. Since 5-hydroxymethylcytosine (5hmC) emerged as an intermediate metabolite in active DNA demethylation, there have been increasing efforts to elucidate its function as a stable modification of the genome. Recently we described TET1-mediated enrichment of 5hmC on the promoter region of the master regulator of hepatocyte identity, HNF4A, which precedes differentiation of liver adult progenitor cells in vitro. Here we asked whether 5hmC is involved in hepatocyte differentiation. We found a genome-wide increase of 5hmC as well as a reduction of 5-methylcytosine at early hepatocyte differentiation, a time when the liver transcript program is already established. Furthermore, we suggest that modifying s-adenosylmethionine (SAM) levels through an adenosine derivative could decrease 5hmC enrichment, triggering an impaired acquisition of hepatic identity markers. These results suggest that 5hmC is a regulator of differentiation as well as an imprint related with cell identity. Furthermore, 5hmC modulation could be a useful biomarker in conditions associated with cell de-differentiation such as liver malignancies.

2020-05-02 | GSE130848 | GEO

Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation [Methylation]

2020-05-02 | GSE130844 | GEO

Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation [Expression]

Project description:Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation [Expression]

| PRJNA541569 | ENA

Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation [Methylation]

Project description:Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation [Methylation]

| PRJNA541562 | ENA

Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro differentiation of a putative hepatocyte progenitor.

Project description: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, there have been increasing efforts to elucidate its function as a stable modification of the genome, including a role in establishing such tissue-specific patterns of expression. Recently we described TET1-mediated enrichment of 5hmC on the promoter region of the master regulator of hepatocyte identity, HNF4A, which precedes differentiation of liver adult progenitor cells in vitro. Here, we studied the genome-wide distribution of 5hmC at early in vitro differentiation of human hepatocyte-like cells. We found a global increase in 5hmC as well as a drop in 5-methylcytosine after one week of in vitro differentiation from bipotent progenitors, at a time when the liver transcript program is already established. 5hmC was overall higher at the bodies of overexpressed genes. Furthermore, by modifying the metabolic environment, an adenosine derivative prevents 5hmC enrichment and impairs the acquisition of hepatic identity markers. These results suggest that 5hmC could be a marker of cell identity, as well as a useful biomarker in conditions associated with cell de-differentiation such as liver malignancies.

| S-EPMC7210258 | biostudies-literature

Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-05-02 | GSE130849 | GEO

5-hydroxymethylcytosine (5hmC) profiling of H1 WT hESCs

Project description:5-hydroxymethylcytosine (5hmC) profiling of H1 WT hESCs

| PRJNA630896 | ENA

5-hydroxymethylcytosine (5hmC) methylation profiling of adult mouse brain and liver tissues (hMeDIP-seq)

Project description:5-hydroxymethylcytosine (5hmC) is the first oxidative product of the TET-mediated 5-methylcytosine (5mC) demethylation pathway. It is a key intermediate in cytosine demethylation, and have potential regulatory functions with emerging importance in mammalian biology. In this work, we used a chemical capture-based technique that coupled with next-generation sequencing to investigate the global 5hmC methylation in five brain subregions (cerebellum, cortex, hippocampus, hypothalamus and thalamus) and liver tissues from female and male adult mice. We also performed total RNA sequencing to study the association between 5hmC and gene expression. The enriched 5-hmC library was sequenced on a HiSeq2500 by paired-end sequencing with 100 bp read length.

2017-01-31 | E-MTAB-5167 | biostudies-arrayexpress

The alteration of 5-hydroxymethylcytosine modification contributes to ischemic brain injury [5hmC-seq]

2015-09-08 | GSE67188 | GEO

The alteration of 5-hydroxymethylcytosine modification contributes to ischemic brain injury [5hmC-seq]

Project description:Epigenetic modifications, such as cytosine methylation and histone modification, have been shown involved in the pathology of ischemic brain injury. Recent works have implicated 5-hydroxymethylcytosine (5hmC), a DNA base derived from 5-methylcytosine (5mC) through the oxidation by Ten-Eleven Translocation (TET) enzymes, in DNA methylation-related plasticity. In this study we show that 5hmC abundance could be induced to increase by ischemia injury. Genome-wide profiling of 5hmC identified differentially hydroxymethylated regions (DhMRs) associated with ischemic injury and DhMRs were found enriched among the genes involved in cell junction, neuronal morphogenesis and neurodevelopment. These data together suggest that 5hmC modification could serve as a potential therapeutic target for the treatment of ischemic stroke. To determine the genome-wide 5hmC distribution in both ischemic injury (I/R) and control mice (C57BL/6), we employed a previously established chemical labeling and affinity purification method, coupled with high-throughput sequencing (Song et al, Nature Biotechnology, 2011). The ischemic or matched control brain tissues from three pairs of ischemic mice and control mice were used for the analyses.

2015-09-08 | E-GEOD-67188 | biostudies-arrayexpress

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