MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons [ATAC-seq]

Mutations in the methyl-DNA-binding protein MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT). How MECP2 contributes to transcriptional regulation in normal and disease states is unresolved; it has been reported to be an activator and a repressor. We describe here the first integrated CUT&Tag, transcriptome, and proteome analyses using human neurons with wild-type and mutant MECP2 molecules. MECP2 occupies CpG-rich promoter-proximal regions in over four thousand genes in human neurons, including a plethora of autism risk genes, together with RNA polymerase II (Pol II). MECP2 directly interacts with Pol II, and genes occupied by both proteins showed reduced expression in neurons with MECP2 patient mutations. We conclude that MECP2 acts as a positive cofactor for Pol II gene expression at many neuronal genes that harbor CpG-islands in promoter-proximal regions, and that RTT is due, in part, to the loss of gene activity at these genes in neurons. Overall design: We used ATAC-Seq (Assay for Transposase-Accessible Chromatin using Sequencing), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid epigenomic analysis to identify open chromatin regions in human neurons.

甲基化DNA结合蛋白MECP2的突变可引发神经发育障碍瑞特综合征（Rett syndrome, RTT）。目前，MECP2在生理与疾病状态下如何参与转录调控仍未明确；既往研究显示其兼具转录激活因子与转录抑制因子双重功能。本研究首次针对携带野生型与突变型MECP2的人类神经元，开展了整合型CUT&Tag、转录组与蛋白质组分析。
MECP2可结合人类神经元中逾四千个基因的CpG富集启动子近端区域，其中涵盖大量自闭症风险基因，且此类区域同时富集RNA聚合酶II（RNA polymerase II, Pol II）。MECP2可与Pol II直接相互作用；携带MECP2患者来源突变的神经元中，同时被两种蛋白结合的基因的表达水平显著下调。
本研究证实，在诸多启动子近端区域含有CpG岛的神经元相关基因中，MECP2可作为Pol II转录的正向辅因子发挥作用；而瑞特综合征的部分发病机制，正是源于此类神经元中相关基因的活性丧失。
整体实验设计：本研究采用基于测序接头在天然染色质中直接体外转座的转座酶可及性染色质测序（Assay for Transposase-Accessible Chromatin using Sequencing, ATAC-Seq），作为快速表观基因组分析手段，以鉴定人类神经元中的开放染色质区域。