The RNA N6-methyladenosine regulates chromatin remodeling and transcription [HEC-1-A_seq_RNA_MeRIP]

The N6-methyladenosine (m6A) has been shown to regulate stability and translation of messenger RNA (mRNA) in various biological processes. Here, we show that the knockout of the m6A writer Mettl3 or a nuclear reader Ythdc1 in mouse embryonic stem cells (mESCs) induces chromatin openness and transcription activation in an m6A-dependent manner. We identified extensive m6A modifications on caRNAs (chromosome-associated RNAs, including promoter-associated RNAs, enhancer RNAs and repeats) that are installed by METTL3. YTHDC1 can bind to a portion of these m6A-modified RNAs and facilitate their decay through the NEXT-mediated nuclear degradation. Therefore, the m6A methylation of these caRNAs reduces their abundances. The knockout of Mettl3 elevates levels of caRNAs and promote open chromatin state and downstream transcription. Collectively, our results reveal that m6A on caRNAs can globally tune chromatin state and transcription. chromatin-associated RNA m6A profiles of METTL3 knockdown HEC-1-A and its control were generated by deep sequencing, in diplicate, using Illumina NovaSeq.

N6-甲基腺苷（N6-methyladenosine，m6A）已被证实可在多种生物学过程中调控信使RNA（messenger RNA，mRNA）的稳定性与翻译过程。本研究证实，在小鼠胚胎干细胞（mouse embryonic stem cells，mESCs）中敲除m6A写入酶METTL3或核阅读器蛋白YTHDC1，可通过m6A依赖的方式诱导染色质开放与转录激活。研究团队鉴定出由METTL3催化修饰的大量染色体相关RNA（chromosome-associated RNAs，caRNAs）上的m6A修饰位点，这类caRNAs涵盖启动子相关RNA、增强子RNA及重复序列RNA。YTHDC1可结合其中部分带有m6A修饰的RNA，并通过NEXT复合物介导的核降解途径促进其降解，因此这类caRNAs的m6A甲基化会降低其分子丰度。敲除METTL3会提升caRNAs的表达水平，并促进染色质开放状态与下游转录过程。综上，本研究结果揭示，caRNAs上的m6A修饰可全局性调控染色质状态与转录水平。本数据集通过Illumina NovaSeq平台开展双重复深度测序，获取了METTL3敲低的HEC-1-A细胞及其对照细胞的染色体相关RNA m6A图谱。