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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: 13.85). 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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Available from: Filomena Matarese, Aug 27, 2015
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    • "At face value this might suggest that H3K27me3 and DNA methylation are mutually exclusive. However, in somatic cell types and cancer cell lines H3K27me3 is much less restricted to CpG islands and there is extensive overlap between DNA methylation and H3K27me3 methylation, suggesting that the two are not incompatible [74] [75]. Interestingly, promoters that are marked with H3K27me3 in embryonic stem cells are more likely to gain DNA methylation during differentiation and carcinogenesis than those lacking H3K27me3 [76] [77] [78]. "
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    • "lyzed by quantitative PCR to interrogate a single locus ( ChIP‐ PCR ) or array hybridization ( ChIP‐chip ) or next‐generation sequencing ( ChIP‐seq ) for genome‐wide data ( reviewed in Furey , 2012 ) . New approaches combine bisulfite sequencing of ChIP DNA to simultaneously detect DNA methylation associated with particular histone modifications ( Brinkman et al . , 2012 ; Statham et al . , 2012 ) . Techniques for detecting higher‐order chromatin structure within the nucleus focus on a technique known as chromatin conformation capture ( 3C ) and its derivatives including 4C , 5C , 6C ,"
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