Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells

Abstract

SUMMARY DNA methylation at the 5-position of cytosine (5mC) in the mammalian genome is a key epigenetic event critical for various cellular processes. The Ten-eleven translocation (Tet) family of 5mC-hydroxylases, which convert 5mC to 5-hydroxymethylcytosine (5hmC), offers a way for dynamic regulation of DNA methylation. Here we report that Tet1 binds unmodified C, 5mC- or 5hmC-modified CpG-rich DNA through its CXXC domain. Genome-wide mapping of Tet1 and 5hmC reveals mechanisms by which Tet1 controls 5hmC and 5mC levels in mouse embryonic stem cells (mESCs). We also uncover a comprehensive gene network influenced by Tet1. Collectively, our data suggest that Tet1 controls DNA methylation both by binding to CpG-rich regions to prevent unwanted DNA methyltransferase activity, and by converting 5mC to 5hmC through hydroxylase activity. This Tet1-mediated antagonism of CpG methylation imparts differential maintenance of DNA methylation status at Tet1 targets, ultimately contributing to mESC differentiation and the onset of embryonic development.

Active DNA demethylation by oxidation and repair

“…One prediction is that TET proteins may activate the expression of their targeted genes via their role in active DNA demethylation. However, genome-wide analysis of 5hmC distribution reveals that TET1 has dual functions in transcriptional regulation because it both enhances and inhibits the expression of some genes in mESCs [16][17][18][19]. TET1 is highly expressed in mESCs that accumulate relatively high levels of 5hmC, while 5hmC levels are significantly decreased after mESC differentiation [7].…”

“…Downregulation of TET proteins by RNAi decreases the accumulation of 5hmC but increases 5mC. These results suggest a dynamic regulation of 5hmC by TET proteins [16][17][18][19]. Using various chromatin immunoprecipitation methods combined with high-throughput DNA sequencing, several laboratories analyzed the genome-wide distribution of 5hmC and TET1 binding sites [16][17][18][19].…”

“…These results suggest a dynamic regulation of 5hmC by TET proteins [16][17][18][19]. Using various chromatin immunoprecipitation methods combined with high-throughput DNA sequencing, several laboratories analyzed the genome-wide distribution of 5hmC and TET1 binding sites [16][17][18][19]. Interestingly, TET1 is preferentially bound to CpG-rich regions at transcriptional start sites in promoters of both transcriptionally active and Polycomb-targeted repressive genes and also within exons [16][17][18].…”

Analysis of DNA modifications in aging research

“…Although mC and hmC are recognized by common DNA binding proteins, they also have modification-specific binders (Spruijt et al 2013), thereby providing a potential mechanism for the differential effects on gene expression between mC and hmC (Xu et al 2011). Additionally, TET enzymes may prefer CG sites (Hu et al 2013) which raises the intriguing possibility that mCH may be resistant to oxidation and elimination.…”

Differentiation and adaptation epigenetic networks: Translational research in gastric carcinogenesis

“…Recent studies have shown that the status of DNA methylation at some regions in the gene body may be the consequence of a dynamic balance between methylation and hydroxymethylation or demethylation [17][18][19]. Moreover, rather than being actively transcribed or completely silenced, many genes are transcribed at different levels in tissues.…”