美国贝勒医学院Susan M. Rosenberg研究小组揭示了终止转录物位点的内源性DNA损伤。相关论文于2025年2月19日发表在《自然》杂志上。

在这里，小组发现了新的DNA损伤反应中间体，并揭示了与转录相关的第五种DNA损伤机制：终止转录物位点的内源性DNA损伤。该课题组人员设计了蛋白质来捕获细菌和人类细胞中具有3'极性的单链DNA （ssDNA）末端。在大肠杆菌中，自发的3'- ssdna端灶出乎意料地频繁，每次细胞分裂一个或多个，并且通过两种可识别的途径产生，这两种途径都依赖于DNA复制。

复制性DNA聚合酶（pol） III的过度表达抑制了与双链断裂相关的途径，这表明pol III与DNA损伤促进蛋白之间存在竞争。对反复出现的3' - ssdna末端的定位发现了不同的3'- ssdna末端热点，这些热点大多与双链断裂无关，位于5'-CCTTTTTT转录终止子样序列旁边。这些3'- ssdna末端与通过DirectRNA测序或同时进行的5'和3'端RNA测序（SEnd-seq）鉴定的RNA 3' -末端一致，并被一个通过终止子读取的突变RNAP阻止。他们的发现揭示了转录终止或路径化可以促进DNA损伤和随后的基因组不稳定。

据了解，DNA损伤促进突变，从而引发癌症、衰老和神经退行性疾病，但令人惊讶的是，损伤的主题和类型在很大程度上仍然未知。在转录过程中，有三种已确定的损伤DNA的机制：RNA聚合酶（RNAP）与DNA复制机制正面和共方向的碰撞，以及R环诱导的DNA断裂。

附：英文原文

Title: Endogenous DNA damage at sites of terminated transcripts

Author: Liu, Jingjing, Perren, Jullian O., Rogers, Cody M., Nimer, Sadeieh, Wen, Alice X., Halliday, Jennifer A., Fitzgerald, Devon M., Mei, Qian, Nehring, Ralf B., Crum, Mary, Kozmin, Stanislav G., Xia, Jun, Cooke, Matthew B., Zhai, Yin, Bates, David, Li, Lei, Hastings, P. J., Artsimovitch, Irina, Herman, Christophe, Sung, Patrick M., Miller, Kyle M., Rosenberg, Susan M.

Issue&Volume: 2025-02-19

Abstract: DNA damage promotes mutations that fuel cancer, ageing and neurodegenerative diseases1,2,3, but surprisingly, the causes and types of damage remain largely unknown. There are three identified mechanisms that damage DNA during transcription: collision of RNA polymerase (RNAP) with the DNA-replication machinery head-on and co-directionally4,5,6, and R-loop-induced DNA breakage7,8,9,10. Here we identify novel DNA damage reaction intermediates11,12 and uncover a fourth transcription-related source of DNA damage: endogenous DNA damage at sites of terminated transcripts. We engineered proteins to capture single-stranded DNA (ssDNA) ends with 3′ polarity in bacterial and human cells. In Escherichia coli, spontaneous 3′-ssDNA-end foci were unexpectedly frequent, at one or more per cell division, and arose via two identifiable pathways, both of which were dependent on DNA replication. A pathway associated with double-strand breaks was suppressed by overexpression of replicative DNA polymerase (pol) III, suggesting competition between pol III and DNA damage-promoting proteins. Mapping of recurrent 3′-ssDNA-ends identified distinct 3′-ssDNA-end-hotspots, mostly unrelated to double-strand breaks, next to the 5′-CCTTTTTT transcription-terminator-like sequence. These 3′-ssDNA-termini coincide with RNA 3′-termini identified by DirectRNA sequencing13 or simultaneous 5′ and 3′ end RNA sequencing (SEnd-seq)14 and were prevented by a mutant RNAP that reads through terminators. Our findings reveal that transcription termination or pausing can promote DNA damage and subsequent genomic instability.

DOI: 10.1038/s41586-024-08578-4

Source: https://www.nature.com/articles/s41586-024-08578-4