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

Hume Stroud1, Suhua Feng12, Shannon Morey Kinney3, Sriharsa Pradhan3 and Steven E Jacobsen12*

Author affiliations

1 Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA

2 Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA

3 New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA

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Citation and License

Genome Biology 2011, 12:R54  doi:10.1186/gb-2011-12-6-r54

Published: 20 June 2011

Abstract

Background

5-Hydroxymethylcytosine (5hmC) was recently found to be abundantly present in certain cell types, including embryonic stem cells. There is growing evidence that TET proteins, which convert 5-methylcytosine (5mC) to 5hmC, play important biological roles. To further understand the function of 5hmC, an analysis of the genome-wide localization of this mark is required.

Results

Here, we have generated a genome-wide map of 5hmC in human embryonic stem cells by hmeDIP-seq, in which hydroxymethyl-DNA immunoprecipitation is followed by massively parallel sequencing. We found that 5hmC is enriched in enhancers as well as in gene bodies, suggesting a potential role for 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 also enriched in other protein-DNA interaction sites, such as OCT4 and NANOG binding sites. Furthermore, we found that 5hmC regions tend to have an excess of G over C on one strand of DNA.

Conclusions

Our findings suggest that 5hmC may be targeted to certain genomic regions based both on gene expression and sequence composition.