In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse (ChIP-Seq mouse)

Methylation of cytosines (5meC) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here we use Saccharomyces cerevisiae as a system lacking DNA methylation to define the chromatin features influencing the activity of the murine DNMT3B. Our data demonstrate that DNMT3B and H3K4 methylation are mutually exclusive and that DNMT3B is co-localized with H3K36 methylated regions. In support of this observation, DNA methylation analysis in yeast strains without Set1 and Set2 show an increase of relative 5meC levels at the TSS and a decrease in the gene-body, respectively. We extend our observation to the murine male germline, where H3K4me3 is strongly anti-correlated while H3K36me3 correlates with accelerated DNA methylation. These results show the importance of H3K36 methylation for gene-body DNA methylation in vivo. Mouse germ-cells ChIPseq

胞嘧啶（cytosine）的甲基化修饰（5meC）是一类广泛分布的可遗传DNA修饰。在哺乳动物发育过程中，先后经历两次全局DNA去甲基化事件，随后伴随多轮从头DNA甲基化浪潮。目前，DNA甲基化建立的体内调控机制在很大程度上仍未被阐明。本研究以缺乏内源DNA甲基化的酿酒酵母（Saccharomyces cerevisiae）为模型系统，解析调控小鼠DNA甲基转移酶3B（DNMT3B）活性的染色质特征。我们的实验数据显示，DNMT3B与组蛋白H3赖氨酸4甲基化相互排斥，且DNMT3B与组蛋白H3赖氨酸36甲基化区域存在共定位现象。为验证上述结论，我们对缺失Set1和Set2的酵母菌株开展DNA甲基化分析，结果分别显示转录起始位点（TSS，Transcription Start Site）处的相对5meC水平升高，而基因体区域的相对5meC水平显著降低。我们将这一发现拓展至小鼠雄性生殖系中，其中组蛋白H3赖氨酸4三甲基化（H3K4me3）与DNA甲基化水平呈显著负相关，而组蛋白H3赖氨酸36三甲基化（H3K36me3）则与DNA甲基化加速进程呈正相关。上述实验结果证实了H3K36甲基化在体内对基因体DNA甲基化的关键调控作用。小鼠生殖细胞染色质免疫共沉淀测序（ChIPseq）