Transcriptomics

Dataset Information

65

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells


ABSTRACT: Recent studies have demonstrated that the Ten-eleven translocation (Tet) family proteins can enzymatically convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While 5mC has been studied extensively, little is known about the distribution and function of 5hmC. Here we present a genome-wide profile of 5hmC in mouse embryonic stem (ES) cells. A combined analysis of global 5hmC distribution and gene expression profile in wild-type and Tet1-depleted ES cells revealed suggests that 5hmC is enriched at both gene bodies of actively transcribed genes and extended promoter regions of Polycomb-repressed developmental regulators. Thus, our study reveals the first genome-wide 5hmC distribution in pluripotent stem cells and supports its dual function in regulating gene expression. Genomic DNA extracted from control (Con) or Tet1 knockdown (KD) mouse ES cells was immunoprecipitated with 5-hydroxymethylcytosine (5hmC) antibodies and analyzed by NimbleGen 2.1M mouse whole genome tiling microarrays (a 4-array set covering the entired non-repetitive portion of mouse genome). Whole cell extract (WCE) was used as input controls in IP/input experiments.

ORGANISM(S): Mus musculus  

SUBMITTER: Ana D'Alessio   Keji Zhao  Shinsuke Ito  Zhibin Wang  Yi Zhang  Yi Sun  Hao Wu  Kairong Cui 

PROVIDER: E-GEOD-27613 | ArrayExpress | 2011-03-30

SECONDARY ACCESSION(S): GSE27613PRJNA138263

REPOSITORIES: GEO, ArrayExpress

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Publications

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells.

Wu Hao H   D'Alessio Ana C AC   Ito Shinsuke S   Wang Zhibin Z   Cui Kairong K   Zhao Keji K   Sun Yi Eve YE   Zhang Yi Y  

Genes & development 20110401 7


Recent studies have demonstrated that the Ten-eleven translocation (Tet) family proteins can enzymatically convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While 5mC has been studied extensively, little is known about the distribution and function of 5hmC. Here we present a genome-wide profile of 5hmC in mouse embryonic stem (ES) cells. A combined analysis of global 5hmC distribution and gene expression profile in wild-type and Tet1-depleted ES cells suggests that 5hmC is enrich  ...[more]

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