Li Fangle, Zhang Feifan, Li Jie, Zhang Yu, Gong Wenxuan, Zhang Yawei, Liu Mengxia, Ren Jie, Han Dali
China National Center for Bioinformation, Beijing, 100101, China.
State Key Laboratory of RNA Innovation, Science and Engineering, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
Sci China Life Sci. 2025 Jul 9. doi: 10.1007/s11427-024-2947-6.
N-methyladenosine (mA) in RNA within R-loops plays pivotal roles in transcription regulation and genome stability. However, the precise impacts and distinct mechanisms of mA on both regulatory and aberrant R-loops remain poorly understood. Here, we reveal that METTL3, the nuclear mA writer, ensures genome integrity by differentially modulating R-loops in a position- and length-dependent manner. In mouse embryonic stem cells (mESCs), Mettl3 depletion results in impaired cell proliferation and increased cell death due to excessive DNA damage. Notably, Mettl3 knockout reduces the overall abundance of R-loops, with a decrease in broad R-loops and an increase in sharp R-loops. R-loops are diminished near transcription end sites (TESs), leading to transcriptional readthrough of genes with mA-modified transcripts and potentially contributing to genome instability. Conversely, increased sharp R-loops located in the antisense orientation relative to gene transcription are associated with DNA damage hotspots. These findings unveil a dual regulatory mechanism in which METTL3-mA orchestrates transcription fidelity and genome stability through distinct R-loop-dependent manners.
R环内RNA中的N-甲基腺苷（mA）在转录调控和基因组稳定性中起关键作用。然而，mA对调控性和异常R环的确切影响及不同机制仍知之甚少。在此，我们揭示了核mA写入酶METTL3通过以位置和长度依赖的方式差异调节R环来确保基因组完整性。在小鼠胚胎干细胞（mESCs）中，Mettl3缺失导致细胞增殖受损以及由于过度DNA损伤而增加细胞死亡。值得注意的是，Mettl3基因敲除降低了R环的总体丰度，宽R环减少而尖锐R环增加。R环在转录终止位点（TESs）附近减少，导致具有mA修饰转录本的基因发生转录通读，并可能导致基因组不稳定。相反，相对于基因转录以反义方向定位的尖锐R环增加与DNA损伤热点相关。这些发现揭示了一种双重调控机制，其中METTL3-mA通过不同的R环依赖方式协调转录保真度和基因组稳定性。
