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


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
    • "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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    ABSTRACT: Lineage-specific phenotypes are the result of characteristic cellular gene expression patterns. Several epigenetic mechanisms have evolved that control the generation of these different phenotypes from the same genotype. Stem cells, in order to prevent differentiation, need to repress lineage-specific transcription factors and maintain the activity of stemness genes that promote self-renewal and pluripotency. In this context differentiation is basically a process governed by changes in gene activity during development that alter the stemness-specific epigenome towards lineage-specific patterns, often in response to transient factors or environmental stimuli. Sophisticated networks of protein complexes maintain epigenomic states in stem cells and determined cells after lineage decision and ensure their transmission through cell division. In addition, they are also essential for the epigenetic changes happening during differentiation induction that are crucial for lineage specification. The Polycomb group of genes codes for a variety of proteins that maintain repressive chromatin states. They are part of a complex cellular memory system that creates a layer of epigenetic information on top of the DNA sequence that ensures the maintenance and transmission of cell-specific expression patterns.
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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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    ABSTRACT: DNA methylation acts as an epigenetic modification in vertebrate DNA. Recently it has become clear that the DNA and histone lysine methylation systems are highly interrelated and rely mechanistically on each other for normal chromatin function in vivo. Here we examine some of the functional links between these systems, with a particular focus on several recent discoveries suggesting how lysine methylation may help to target DNA methylation during development, and vice versa. In addition, the emerging role of non-methylated DNA found in CpG islands in defining histone lysine methylation profiles at gene regulatory elements will be discussed in the context of gene regulation. This article is part of a Special Issue entitled: Methylation: A Multifaceted Modification looking at transcription and beyond. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license
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    • "However, the nature of these hypomethylated promoters marked by H3K27me3 is beginning to be elucidated in the context of development: e.g. the mechanism that regulates the accumulation of H3K27me3. Recent genome-wide analyses using mammalian cells suggested an antagonistic relationship between the patterns of DNA methylation and H3K27me3 (Brinkman et al., 2012; Lindroth et al., 2008). Importantly, in post-natal mouse brains, DNA methylation at regions flanking proximal promoters was shown to facilitate transcription of neuronal genes by antagonizing H3K27 methylation (Wu et al., 2010). "
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    ABSTRACT: DNA methylation is a fundamental epigenetic modification in vertebrate genomes and a small fraction of genomic regions is hypomethylated. Previous studies have implicated hypomethylated regions in gene regulation, but their functions in vertebrate development remain elusive. To address this issue, we generated epigenomic profiles that include base-resolution DNA methylomes and histone modification maps from both pluripotent cells and mature organs of medaka fish and compared the profiles with those of human ES cells. We found that a subset of hypomethylated domains harbor H3K27me3 (K27HMDs) and their size positively correlates with the accumulation of H3K27me3. Large K27HMDs are conserved between medaka and human pluripotent cells and predominantly contain promoters of developmental transcription factor genes. These key genes were found to be under strong transcriptional repression, when compared with other developmental genes with smaller K27HMDs. Furthermore, human-specific K27HMDs show an enrichment of neuronal activity-related genes, which suggests a distinct regulation of these genes in medaka and human. In mature organs, some of the large HMDs become shortened by elevated DNA methylation and associate with sustained gene expression. This study highlights the significance of domain size in epigenetic gene regulation. We propose that large K27HMDs play a crucial role in pluripotent cells by strictly repressing key developmental genes, whereas their shortening consolidates long-term gene expression in adult differentiated cells.
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