Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

Abstract

Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here, we present sequential ChIPbisulfite-sequencing (ChIP-BS-seq) as an approach to quantitatively assess DNA methylation patterns associated with chromatin modifications or chromatin-associated factors directly. A chromatin-immunoprecipitation (ChIP)-capturing step is used to obtain a restricted representation of the genome occupied by the epigenetic feature of interest, for which a single-base resolution DNA methylation map is then generated. When applied to H3 lysine 27 trimethylation (H3K27me3), we found that H3K27me3 and DNA methylation are compatible throughout most of the genome, except for CpG islands, where these two marks are mutually exclusive. Further ChIP-BS-seq-based analysis in Dnmt triple-knockout (TKO) embryonic stem cells revealed that total loss of CpG methylation is associated with alteration of H3K27me3 levels throughout the genome: H3K27me3 in localized peaks is decreased while broad local enrichments (BLOCs) of H3K27me3 are formed. At an even broader scale, these BLOCs correspond to regions of high DNA methylation in wild-type ES cells, suggesting that DNA methylation prevents H3K27me3 deposition locally and at a megabase scale. Our strategy provides a unique way of investigating global interdependencies between DNA methylation and other chromatin features.

Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation

“…Additionally, we demonstrate that DNA methylation inhibits H3K27me3 deposition at CpG-rich sequences and that this inhibition can be reversed upon chemical removal of DNA methylation. These observations readily explain the occupancy of H3K27me3 and DNA methylation observed throughout the genome (23,24,33,34). They extend previous studies that already suggested a role for CpG dinucleotides in PRC2 recruitment (22,23) but are also more comprehensive and provide novel mechanistic details.…”

“…Thus, loss of Polycomb recruitment coincides with increased susceptibility to DNA methylation. This finding is compatible with the observation of increased H3K27 methylation upon global loss of DNA methylation (23,24,33,34), which we also observe in our genome-wide datasets (Fig. S7A).…”

“…We have previously suggested that TF binding within CGIs contributes to their low DNA methylation (28), which could be relevant for the recruitment of the H3K27me3 mark because occupancy of DNA methylation and H3K27me3 in ES cells has been observed to be mutually exclusive at CGIs (33), leading to the hypothesis that DNA methylation could inhibit H3K27me3 acquisition. To explore whether increased DNA methylation could account for the absence of H3K27me3 at the two elements with modified sequence backbone, we first determined their DNA methylation state.…”

Factors affecting the persistence of drug-induced reprogramming of the cancer methylome

“…While there is a great deal of literature suggesting that Polycomb occupancy predisposes to DNA methylation in a developmental context 43 and to aberrant hypermethylation in cancer cells, 20 the 2 marks are largely mutually exclusive genome-wide in differentiated cells, especially in CGI. 45,46 Indeed, recent work has demonstrated that genomic regions that lose DNA methylation after azacytidine treatment or deletion of Dnmt1, tend to gain H3K27me3. 47 This implies a model in which loss of DNA methylation enables restoration of PRC2 occupancy and deposition of H3K27me3, which protects from DNA remethylation.…”

Differentiation and adaptation epigenetic networks: Translational research in gastric carcinogenesis

“…Using these databases, scientists can get preliminary information on DiEN networks in individual chromatin regions throughout the whole genome of these cell types. Multiple epigenomes and RNA transcriptomes in more normal cell types need to be sequenced to explore cross-talk between different types of epigenetic modifications in various intragenic and intergenic non-coding regions in the genome [15,16]. Differences in the epigenomes between different cell types are important clues for investigating the functions of the 98% non-coding regions in the genome.…”