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5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [RNA-seq]

ABSTRACT: 5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [RNA-seq]

PROVIDER: PRJNA545283 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11806612_1.fastq.gz	Fastqsanger.gz
	SRR11806612_2.fastq.gz	Fastqsanger.gz
	SRR11806613_1.fastq.gz	Fastqsanger.gz
	SRR11806613_2.fastq.gz	Fastqsanger.gz
	SRR11806614_1.fastq.gz	Fastqsanger.gz

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5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies

Project description:5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies

| PRJNA545278 | ENA

5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [TetRIP-seq]

Project description:5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [TetRIP-seq]

| PRJNA545282 | ENA

5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [hMeRIP-seq]

Project description:5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [hMeRIP-seq]

| PRJNA545284 | ENA

5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [RNA-seq]

Project description:Tet-enzyme-mediated 5-hydroxymethylation of cytosine in DNA plays a crucial role in mouse embryonic stem cells (ESCs). In RNA also, 5-hydroxymethylcytosine (5hmC) has recently been evidenced, but its physiological roles are still largely unknown. Here we show the contribution and function of this mark in mouse ESCs and differentiating embryoid bodies. Transcriptome-wide mapping in ESCs revealed hundreds of messenger RNAs marked by 5hmC at sites characterized by a defined unique consensus sequence and particular features. During differentiation a large number of transcripts, including many encoding key pluripotency-related factors (such as Eed and Jarid2), showed decreased cytosine hydroxymethylation. Using Tet-knockout ESCs, we found Tet enzymes to be partly responsible for deposition of 5hmC in mRNA. A transcriptome-wide search further revealed mRNA targets to which Tet1 and Tet2 bind, at sites showing a topology similar to that of 5hmC sites. Tet-mediated RNA hydroxymethylation was found to reduce the stability of crucial pluripotency-promoting transcripts. We propose that RNA cytosine 5-hydroxymethylation by Tets is a mark of transcriptome flexibility, inextricably linked to the balance between pluripotency and lineage commitment.

2020-07-16 | GSE131898 | GEO

5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [hMeRIP-seq]

2020-07-16 | GSE131900 | GEO

5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [TetRIP-seq]

2020-07-16 | GSE131899 | GEO

5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies

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

2020-07-16 | GSE131902 | GEO

5-hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells.

Project description:Hydroxymethylcytosine (5hmC) was recently found to be abundantly present in certain cell types including embryonic stem cells. The function of 5hmC is poorly understood. Here we have generated a genome-wide map of 5hmC in human embryonic stem cells (hESCs) by hydroxymethyl-DNA immunoprecipitation followed by massively parallel sequencing (hmeDIP-seq). We found that 5hmC is enriched over enhancers as well as gene bodies, suggesting a potential role of 5hmC in gene regulation. Consistent with localization of 5hmC at enhancers, 5hmC was significantly enriched in histone modifications associated with enhancers such as H3K4me1 and H3K27ac. 5hmC was enriched in other protein-DNA interaction sites such as OCT4 and NANOG binding sites. Furthermore we found that 5hmC regions tend to be GC-skewed (excess G over C on one strand of DNA). These findings suggest that 5hmC may be targeted to certain genomic regions based both on gene expression and sequence composition.

2011-06-13 | GSE27627 | GEO

5-hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells.

2011-06-13 | E-GEOD-27627 | biostudies-arrayexpress

Loss of Tet enzymes compromises proper differentiation of embryonic stem cells

Project description:Tet enzymes (Tet1/2/3) convert 5-methylcytosine (5mC) to 5-hydroxy-methylcytosine (5hmC) and are dynamically expressed in various embryonic and adult cell types. While loss of individual Tet enzymes or combined deficiency of Tet1/2 allows for embryogenesis, the effect of complete loss of Tet activity and 5hmC marks in development is not established. We have generated Tet1/2/3 triple knockout (TKO) mouse embryonic stem cells (ESCs) and examined their developmental potential. Combined deficiency of all three Tets depleted 5hmC and impaired ESC differentiation as seen in poorly differentiated TKO embryoid bodies (EBs) and teratomas. Consistent with impaired differentiation, TKO-ESCs contributed poorly to chimeric embryos and could not support embryonic development. Global gene expression and methylome analyses of TKO-EBs revealed promoter hypermethylation and deregulation of genes implicated in embryonic development and differentiation. These findings suggest a requirement for Tet- and 5hmC-mediated DNA demethylation in proper regulation of gene expression during differentiation of ESCs and development. To quantify global gene expression in differentiating embryoid bodies (EBs) derived from wild type (WT) and Tet triple knockout (TKO), TKO and WT mouse embryonic stem cells (ESCs) were differentiated in vitro to EBs and cultured for 10 days. RNA was extracted using Qiagen RNeasy kit and subjected to microarray analysis. Global gene expression profile of two technical replicas of WT embryoid bodies (2 samples in total) was compared to two technical replicas of two independent TKO embryoid bodies (4 TKO samples in total).

2014-04-14 | E-GEOD-55574 | biostudies-arrayexpress

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