Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (RNA-Seq)

The genomes of mammalian neurons contain uniquely high levels of non-CG DNA methylation that can be bound by the Rett syndrome protein, MeCP2, to regulate gene expression. How patterns of non-CG methylation at genes are established and the mechanism by which this methylation works with MeCP2 to control gene expression is unclear. Here we find that genes repressed by MeCP2 are found within regions of high non-CG methylation that are defined by domains of chromatin folding. Rather than working directly at transcriptional start sites to regulate these genes, MeCP2 represses enhancer elements that are enriched for methylated cytosines occurring in the CA or CG context. Enhancers repressed by MeCP2 are found within genes that are upregulated upon loss of the protein, providing a regulatory logic for how disruption of MeCP2 can lead to wide-spread changes in gene expression. Hence, we have found that DNA topology can shape non-CG DNA methylation across the genome to dictate MeCP2-mediated enhancer regulation in the brain. Total RNA-seq and ChIP-seq from the brains of MeCP2 KO, OE, and WT mice哺乳动物神经元的基因组中存在独有的高水平非CG DNA甲基化修饰，此类修饰可与雷特综合征蛋白MeCP2结合，进而调控基因表达。目前，基因区域的非CG甲基化模式的建立机制，以及该甲基化与MeCP2协同调控基因表达的具体路径，仍未明晰。本研究发现，受MeCP2抑制的基因位于由染色质折叠结构域所界定的高非CG甲基化区域内。MeCP2并非直接在转录起始位点调控此类基因，而是通过抑制富含CA或CG序列背景下甲基化胞嘧啶的增强子元件发挥调控作用。受MeCP2抑制的增强子所在的基因，在该蛋白缺失时会出现表达上调，这为MeCP2功能紊乱如何引发广泛的基因表达变化提供了调控逻辑依据。综上，本研究证实DNA拓扑结构可塑造全基因组范围内的非CG DNA甲基化模式，进而决定大脑中MeCP2介导的增强子调控过程。本研究的测序数据来源于MeCP2敲除（KO）、过表达（OE）及野生型（WT）小鼠的脑组织，包含总RNA测序（RNA-seq）与染色质免疫共沉淀测序（ChIP-seq）。