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5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation (hmeDIP-seq).

ABSTRACT: Background: Cytosine hydroxymethylation (5hmC) was recently identified in mammalian DNA as the product of oxidation of methylated cytosines (5mC) by Ten-Eleven-Translocation (TET) enzymes. The TETs have been shown to influence 5mC metabolism, pluripotency and differentiation during early embryonic development. However, a functional relationship between gene expression and 5hmC in adult (somatic) stem cell differentiation is however mainly unknown. To explore the role of this novel DNA modification in adult stem cell differentiation we profiled 5hmC and gene activity in purified mouse intestinal progenitors and differentiated progeny. Results: We show that the hydroxymethylome is highly dynamic with tens of thousands of differentially hydroxymethylated regions between progenitors and differentiated progeny. In progenitors 5hmC does not correlate with gene expression levels, however, upon differentiation a global increase in 5hmC is observed with an overall positive correlation between 5hmC and gene expression together with prominent associations with histone modifications that typify active genes and enhancer elements. Conclusions: In the context of recent evidence of near identical methylomes between mouse intestinal stem and differentiated cells, our data imply that a gene regulatory role for 5hmC is predominant over its role in controlling DNA methylation states. Our study provides an insight into the dynamics of 5hmC and of epigenetic machineries in differentiation of the mouse intestine.

ORGANISM(S): Mus musculus

PROVIDER: GSE132631 | GEO | 2019/06/13

REPOSITORIES: GEO

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5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation (RNA-Seq).

Project description:Background: Cytosine hydroxymethylation (5hmC) was recently identified in mammalian DNA as the product of oxidation of methylated cytosines (5mC) by Ten-Eleven-Translocation (TET) enzymes. The TETs have been shown to influence 5mC metabolism, pluripotency and differentiation during early embryonic development. However, a functional relationship between gene expression and 5hmC in adult (somatic) stem cell differentiation is however mainly unknown. To explore the role of this novel DNA modification in adult stem cell differentiation we profiled 5hmC and gene activity in purified mouse intestinal progenitors and differentiated progeny. Results: We show that the hydroxymethylome is highly dynamic with tens of thousands of differentially hydroxymethylated regions between progenitors and differentiated progeny. In progenitors 5hmC does not correlate with gene expression levels, however, upon differentiation a global increase in 5hmC is observed with an overall positive correlation between 5hmC and gene expression together with prominent associations with histone modifications that typify active genes and enhancer elements. Conclusions: In the context of recent evidence of near identical methylomes between mouse intestinal stem and differentiated cells, our data imply that a gene regulatory role for 5hmC is predominant over its role in controlling DNA methylation states. Our study provides an insight into the dynamics of 5hmC and of epigenetic machineries in differentiation of the mouse intestine.

2019-06-13 | GSE132632 | GEO

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2014-12-12 | E-GEOD-60225 | biostudies-arrayexpress

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2014-12-12 | GSE60225 | GEO

Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency

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2020-07-24 | PXD019514 | Pride

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