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Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells

Authors
 Keith E. Szulwach  ;  Xuekun Li  ;  Yujing Li  ;  Chun-Xiao Song  ;  Ji Woong Han  ;  SangSung Kim  ;  Sandeep Namburi  ;  Karen Hermetz  ;  Julie J. Kim  ;  M. Katharine Rudd  ;  Young-Sup Yoon  ;  Bing Ren  ;  Chuan He  ;  Peng Jin 
Citation
 PLoS Genetics, Vol.7(6) : e1002154, 2011 
Journal Title
 PLoS Genetics 
ISSN
 1553-7390 
Issue Date
2011
MeSH
5-Methylcytosine/metabolism ; Binding Sites ; Cell Line ; Chromosome Mapping ; Cytosine/analogs & derivatives* ; Cytosine/metabolism ; DNA Methylation ; Embryonic Stem Cells/cytology* ; Embryonic Stem Cells/metabolism ; Epigenomics* ; Gene Expression Regulation ; Gene Library ; Genome, Human* ; Heterochromatin/chemistry ; Histones/metabolism ; Humans ; Immunoblotting ; Metaphase ; Promoter Regions, Genetic ; Sequence Alignment ; Transcription Factors/metabolism
Abstract
Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a novel regulatory paradigm to modulate the epigenetic landscape of pluripotency. To understand the role of 5-hmC in the epigenomic landscape of pluripotent cells, here we profile the genome-wide 5-hmC distribution and correlate it with the genomic profiles of 11 diverse histone modifications and six transcription factors in human ES cells. By integrating genomic 5-hmC signals with maps of histone enrichment, we link particular pluripotency-associated chromatin contexts with 5-hmC. Intriguingly, through additional correlations with defined chromatin signatures at promoter and enhancer subtypes, we show distinct enrichment of 5-hmC at enhancers marked with H3K4me1 and H3K27ac. These results suggest potential role(s) for 5-hmC in the regulation of specific promoters and enhancers. In addition, our results provide a detailed epigenomic map of 5-hmC from which to pursue future functional studies on the diverse regulatory roles associated with 5-hmC.
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DOI
10.1371/journal.pgen.1002154
Appears in Collections:
1. College of Medicine (의과대학) > BioMedical Science Institute (의생명과학부) > 1. Journal Papers
Yonsei Authors
Yoon, Young Sup(윤영섭)
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URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/158207
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