A role of Polycomb in the maintenance of hypomethylation for DNA methylation valley

DNA methylation valleys (DMVs) are large loci that are devoid of DNA methylation in the genome. We show that DMVs are hypomethylated at most stages in development and are highly conserved across vertebrates. Importantly, DMVs are hotspots of regulatory regions for key developmental regulator genes. 4C-seq analyses indicate that DMVs are insulated and self-interacting domains. By analyzing a panel of DNA methylomes for the mouse tissues, we have identified a subset of DMVs that are dynamically methylated. These DMVs are strongly enriched by Polycomb and their histone substrate H3K27me3 when the associated genes are silenced, and surprisingly show elevated DNA methylation upon gene activation. In support of a role of Polycomb in DMV hypomethylation, we observed aberrant methylation in DMVs in mESCs deficient for Eed. Finally, we showed that Polycomb regulates hypomethylation of DMVs likely through TET proteins. Through a global survey DMVs in different species and different developmental stages , we validated DMVs play important role in gene regulation and development. Further studying different types of DMVs in vivo, Polycomb-target DMVs are more enriched TFs. Next, we continue to finding out what roles Polycomb plays in maintenance hypomethylation of DMVs and how it regulates DNA methylation in DMVs.

DNA甲基化谷（DNA methylation valleys, DMVs）是基因组中缺乏DNA甲基化的大型基因座。本研究证实，DMVs在发育的多数阶段均处于低甲基化状态，且在脊椎动物中高度保守。值得注意的是，DMVs是关键发育调控基因的调控区域热点。4C-seq分析表明，DMVs属于绝缘且自互作结构域。通过分析一组小鼠组织的DNA甲基化组，我们鉴定出一类动态甲基化的DMVs亚群。当相关基因处于沉默状态时，这类DMVs会被多梳蛋白（Polycomb）及其组蛋白修饰底物H3K27me3显著富集；而令人意外的是，在基因激活时，这些DMVs的DNA甲基化水平反而升高。为验证多梳蛋白在DMV低甲基化中的功能，我们在缺失Eed的小鼠胚胎干细胞（mouse embryonic stem cells, mESCs）的DMVs中观察到了异常甲基化现象。最终我们证实，多梳蛋白可能通过TET蛋白（TET proteins）调控DMV的低甲基化状态。通过对不同物种、不同发育阶段的DMVs开展全局分析，我们验证了DMVs在基因调控与发育过程中发挥关键作用。进一步的体内DMVs分型研究显示，靶向多梳蛋白的DMVs更易富集转录因子（transcription factors, TFs）。后续我们将继续探究多梳蛋白在维持DMV低甲基化过程中所承担的功能，以及其调控DMV内DNA甲基化的具体机制。