Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.
Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.
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DOI：
10.1101/gr.133728.111
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发表时间：
2012-06
期刊：
影响因子：
7
通讯作者：
Stunnenberg HG
中科院分区：
文献类型：
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作者：
Brinkman AB;Gu H;Bartels SJ;Zhang Y;Matarese F;Simmer F;Marks H;Bock C;Gnirke A;Meissner A;Stunnenberg HG
DNA甲基化和组蛋白修饰之间的相互作用推动了复合表观遗传特征的建立，传统上使用相关而非直接方法进行研究。在这里，我们提出了连续的ChIP-亚硫酸氢盐测序（ChIP-BS-seq）作为一种方法来定量评估DNA甲基化模式与染色质修饰或染色质相关的因素直接。染色质免疫沉淀（ChIP）捕获步骤用于获得由感兴趣的表观遗传特征占据的基因组的限制性表示，然后生成单碱基分辨率DNA甲基化图谱。当应用于H3赖氨酸27三甲基化（H3 K27 me 3）时，我们发现H3 K27 me 3和DNA甲基化在大多数基因组中是相容的，除了CpG岛，其中这两个标记是相互排斥的。在Dnmt三重敲除（TKO）胚胎干细胞中进行的进一步基于ChIP-BS-seq的分析显示，CpG甲基化的完全丧失与整个基因组中H3 K27 me 3水平的改变相关：局部峰中的H3 K27 me 3减少，而形成H3 K27 me 3的广泛局部富集（BLOC）。在更广泛的范围内，这些BLOC对应于野生型ES细胞中的高DNA甲基化区域，表明DNA甲基化阻止了H3 K27 me 3在局部和兆碱基范围内的沉积。我们的策略提供了一种独特的方式来研究DNA甲基化和其他染色质特征之间的全局相互依赖性。
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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影响因子：
64.5
作者：
Lee JS;Smith E;Shilatifard A
通讯作者：
Shilatifard A
影响因子：
10.5
作者：
Fischle, Wolfgang
通讯作者：
Fischle, Wolfgang
影响因子：
64.8
作者：
Hark, AT;Schoenherr, CJ;Tilghman, SM
通讯作者：
Tilghman, SM
影响因子：
64.8
作者：
Guelen, Lars;Pagie, Ludo;van Steensel, Bas
通讯作者：
van Steensel, Bas
影响因子：
46.9
作者：
通讯作者：
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