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

Radboud University, Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, 6500 HB Nijmegen, The Netherlands.
Genome Research (Impact Factor: 14.63). 03/2012; 22(6):1128-38. DOI: 10.1101/gr.133728.111
Source: PubMed

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 ChIP-bisulfite-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.

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    • "Indeed, the protein Tet1 (ten-eleven translocation 1), which is able to catalyse the oxidation of 5-methylcytosine as the first step of an active demethylation process (Tahiliani et al. 2009), is needed for efficient recruitment of PRC2 to several target sites in mouse ESCs (Wu et al. 2011). As H3k27me3 and 5-methylcytosine have been found to be mutually exclusive specifically at CpG islands (Brinkman et al. 2012), PcG repression and DNA methylation therefore seem to represent rather competing repression mechanisms at CGIs in ES cells. Another possibility how PcG complexes could be targeted might be by recruitment via interactions with noncoding RNAs (ncRNAs) that in flies have been shown to be transcribed at or through PREs and are involved at least in some regions (especially on the inactive X chromosome and in the Hox clusters) in PcG spreading and repressive interactions also in mammals (Hekimoglu and Ringrose 2009; Tsai et al. 2010; Yap et al. 2010). "
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