Abstract
DNA methylation is one of a number of modes of epigenetic gene regulation. Here, we profile the DNA methylome, transcriptome, and global occupancy ofhistone modifications (H3K4me1, H3K4me3, H3K27me3, and H3K27ac) in a series of mouse embryonic stem cells (mESCs) with varying DNA methylation levels to study the effects of DNA methylation on deposition of histone modifications. We find that genome-wide DNA demethylation alters occupancy of histone modifications at both promoters and enhancers. This is reversed upon remethylation by Dnmt expression. DNA methylation promotes H3K27me3 deposition at bivalent promoters, while opposing H3K27me3 at silent promoters. DNA methylation also reversibly regulates H3K27ac and H3K27me3 at previously identified tissue-specific enhancers. These effects require DNMT catalytic activity. Collectively, our data show that DNA methylation is essential and instructive for deposition of specific histone modifications across regulatory regions, which together influences gene expression patterns in mESCs.
Highlights
Recent studies have revealed that global DNA methylation is dramatically altered during pre- and post-implantation development (Guo et al, 2014; Smith et al, 2014), primordial germ cell reprogramming (Gkountela et al, 2015; Guo et al, 2015b; Tang et al, 2015), as well as stem cell differentiation (Xie et al, 2013) and cellular reprogramming (Lister et al, 2011)
We have previously found that mouse embryonic stem cells (mESCs) null of DNA methylation show upregulation of genes primarily associated with bivalent (H3K4me3/H3K27me3 positive) or unmarked (H3K4me3/H3K27me3 double negative) gene promoters in wild-type cells (Fouse et al, 2008)
Dnmt Reconstitution in Demethylated mESCs Restores Global Cytosine Methylation and Causes Various Changes in Histone Modifications To dissect causal relationships between DNA methylation and histone modifications, we simultaneously knocked out all three DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b via Cre-lox recombination to generate triple Dnmt knockout (TKO) mouse embryonic stem (ES) cells that are completely devoid of DNA methylation after several cell passages (Figure 1A)
Summary
Recent studies have revealed that global DNA methylation is dramatically altered during pre- and post-implantation development (Guo et al, 2014; Smith et al, 2014), primordial germ cell reprogramming (Gkountela et al, 2015; Guo et al, 2015b; Tang et al, 2015), as well as stem cell differentiation (Xie et al, 2013) and cellular reprogramming (Lister et al, 2011). The prevailing hypothesis posits that DNA methylation is a crucial silencer of pluripotency and tissue-specific genes via promoter hypermethylation. Pluripotency genes can be silenced during differentiation in the absence of promoter methylation (Sinkkonen et al, 2008). It is becoming increasingly clear that DNA methylation works in conjunction with other factors to properly regulate gene expression (Fouse et al, 2008)
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