N6-methyladenosine (m⁶A) is a crucial RNA modification that regulates diverse biological processes in human cells, but its co-transcriptional deposition and functions remain poorly understood. Here, we identified the RNA helicase DDX21 with a previously unrecognized role in directing m⁶A modification on nascent RNA for co-transcriptional regulation. DDX21 interacts with METTL3 for co-recruitment to chromatin through its recognition of R-loops, which can be formed co-transcriptionally as nascent transcripts hybridize onto the template DNA strand. Moreover, DDX21’s helicase activity is needed for METTL3-mediated m⁶A deposition onto nascent RNA following recruitment. At transcription termination regions, this nexus of actions promotes XRN2-mediated termination of RNAPII transcription. Disruption of any of these steps, including the loss of DDX21, METTL3, or their enzymatic activities, leads to defective termination that can induce DNA damage. Therefore, we propose that the R-loop-DDX21-METTL3 nexus forges the missing link for co-transcriptional modification of m⁶A, coordinating transcription termination and genome stability.

N6-甲基腺苷 (m ⁶ A) 是一种重要的 RNA 修饰，可调节人类细胞中的多种生物过程，但其共转录沉积和功能仍知之甚少。在这里，我们鉴定了 RNA 解旋酶 DDX21 在指导新生 RNA 上的 m ⁶ A 修饰以实现共转录调节方面具有先前未被认识的作用。 DDX21 与 METTL3 相互作用，通过识别 R 环来共同招募染色质，当新生转录物杂交到模板 DNA 链上时，可以通过共转录方式形成 R 环。此外，DDX21 的解旋酶活性是 METTL3 介导的 m ⁶ A 在招募后沉积到新生 RNA 上所必需的。在转录终止区，这种作用关系促进 XRN2 介导的 RNAPII 转录终止。任何这些步骤的中断，包括 DDX21、METTL3 或其酶活性的丧失，都会导致终止缺陷，从而诱发 DNA 损伤。因此，我们认为 R-loop-DDX21-METTL3 连接形成了 m ⁶ A共转录修饰缺失的环节，协调转录终止和基因组稳定性。