Coordinate Regulation of DNA Methylation and H3K27me3 in Mouse Embryonic Stem Cells

Abstract

Chromatin is separated into functional domains distinguished by combinatorial patterns of post-translational histone modifications and DNA methylation. Recent studies examining multiple histone modifications have found numerous chromatin states with distinct profiles of chromatin marks and functional enrichments. There are data showing coordinate regulation between DNAme and H3K27me3, which are both involved in the establishment and maintenance of epigenetic gene silencing, but the data are conflicting. Multiple studies have presented evidence to support the theory that PRC2 and DNAme cooperate to achieve silencing, or alternatively that H3K27me3 and DNAme act antagonistically. Here we examine the effect loss of either PRC2 or DNA methyltransferase activity has on the placement of the reciprocal mark in mouse ES cells. We find that DNAme is acting globally to antagonize the placement of H3K27me3, in accordance with recently published results. At least 471,011 domains in the mouse genome acquire H3K27me3 when DNAme is diminished. Of these 466,563 have been shown to be fully methylated in wildtype ES cells, indicating the effects of DNAme on H3K27me3 are direct. In a reciprocal experiment, we examine the effect loss of PRC2 has on the placement of DNAme. In contrast to the global antagonism DNAme has on the placement of H3K27me3, loss of H3K27me3 has a modest effect on DNAme, with only 4% of genes undergoing changes in DNAme, including 861 showing increases and 552 showing losses of overall DNAme. We anticipate that integrating genomic datasets where the effect of loss of a particular epigenetic mark has on the placement of other marks will help elucidate the rules governing epigenetic regulation and what role coordinate regulation of epigenetic marks plays in development and disease.

Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin

“…While recent observations in both plant and animal systems revealed that removal of DNA methylation can profoundly influence the distribution of H3K27me3 (Mathieu et al 2005;Lindroth et al 2008;Wu et al 2010;Deleris et al 2012;Hagarman et al 2013;Reddington et al 2013), the fact that DNA methylation can indirectly induce H3K9 methylation in plants (Tariq and Paszkowski 2004) and animals (Jin et al 2011) raised the possibility that some, or all, of the observed effects were indirect. We therefore tested for possible effects of knocking out either the single N. crassa H3K9me3 methyltransferase dim-5 (Tamaru and Selker 2001;Tamaru et al 2003) or the single N. crassa DNA methyltransferase gene dim-2 (Kouzminova and Selker 2001).…”

“…This is interesting given the mixed reports from animal cells about whether loss of facultative heterochromatin impacts constitutive heterochromatin. In a study using both undifferentiated and differentiated mouse ES cells, knockdown of Suz12 resulted in loss of H3K9me3, but only in the differentiated cells (de la Cruz et al 2007), while a separate study reported that Eed −/− -null, undifferentiated mouse ES cells showed both increases and decreases in 5mC at developmental genes (Hagarman et al 2013). Values represent the average of at least two technical replicates; dash indicates none detected.…”

“…Studies with animal cells and plants revealed changes in the distribution of H3K27me3 in response to altered H3K9me3 and/ or DNA methylation (Peters et al 2003;Martens et al 2005;Mathieu et al 2005;Lindroth et al 2008;Wu et al 2010;Deleris et al 2012;Hagarman et al 2013;Reddington et al 2013). We considered the possibility that complex interactions among chromatin marks found in higher eukaryotes might be responsible for the apparently conflicting findings on the hierarchy of epigenetic marks in plants and animal cells.…”

“…In early studies with mouse embryonic stem cells, reduced DNA methylation resulting from mutation of either the maintenance methyltransferase gene dnmt1 or the de novo DNA methyltransferase genes dmnt3a and dnmt3b did not result in an obvious change in the distribution of H3K27me (Martens et al 2005). However, subsequent studies with Arabidopsis (Mathieu et al 2005;Deleris et al 2012), mouse embryonic fibroblasts (Lindroth et al 2008;Reddington et al 2013), embryonic stem cells (Hagarman et al 2013), and neural stem cells (Wu et al 2010) revealed that loss of DNA methylation, caused by disruption of DNA methyltransferase genes or treatment with the demethylating agent 5-azacytidine, provided the most potent trigger of H3K27me3 redistribution.…”

Large hypomethylated domains serve as strong repressive machinery for key developmental genes in vertebrates

“…Previously, Polycomb group (PcG) proteins that mediate H3K27me3 accumulation were reported to preferentially bind to CpG islands (Deaton and Bird, 2011;Ku et al, 2008;Woo et al, 2010), but DNA methylation reduces this binding (Hagarman et al, 2013;Wu et al, 2010). We therefore counted the number of low methylated CpG sites inside the K27HMDs and examined their relationship with H3K27me3 levels.…”