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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. 2 experiments, 2 controls

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