Abstract
Background5-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.ResultsHere, 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.ConclusionsOur findings suggest that 5hmC may be targeted to certain genomic regions based both on gene expression and sequence composition.
Highlights
Cytosine DNA methylation (5-methylcytosine (5mC)) is an epigenetic mark that is widespread in both animals and plants, and appears to play important roles in various biological processes, such as gene silencing and imprinting
Studies have shown that embryonic stem cells (ESCs) and Purkinje neurons contain high levels of 5-hydroxymethylcytosine (5hmC) [1,2]
We generated genome-wide maps of 5hmC in human ESCs by performing hydroxymethyl-DNA immunoprecipitation followed by massively parallel sequencing with an Illumina Genome Analyzer
Summary
Cytosine DNA methylation (5-methylcytosine (5mC)) is an epigenetic mark that is widespread in both animals and plants, and appears to play important roles in various biological processes, such as gene silencing and imprinting. Studies have shown that embryonic stem cells (ESCs) and Purkinje neurons contain high levels of 5-hydroxymethylcytosine (5hmC) [1,2]. Human TET1, a 2-oxoglutarate- and Fe(II)-dependent enzyme, has been shown to catalyze the conversion of 5mC to 5hmC both in vitro and in vivo [1]. Studies have suggested that 5hmC inhibits the methyl-CpG-binding protein MeCP2 from binding DNA [6]. In addition to Recently, commercial antibodies specific to 5hmC have become available. We generated genome-wide maps of 5hmC in human ESCs (hESCs) by performing hydroxymethyl-DNA immunoprecipitation followed by massively parallel sequencing with an Illumina Genome Analyzer (hmeDIP-seq). As did Song et al [8], we found that a large fraction of 5hmC peaks were enriched over genes. We found that 5hmC regions correspond to genomic regions that are GC-skewed
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