Endogenous DNA Damage at Sites of Terminated Transcripts

Authors

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

Language

English

Publication Date

4-1-2025

Journal

Nature

DOI

10.1038/s41586-024-08578-4

PMID

39972147

PMCID

PMC12629516

PubMedCentral® Posted Date

2-19-2026

PubMedCentral® Full Text Version

Author MSS

Abstract

DNA damage promotes mutations that fuel cancer, aging, and neurodegenerative diseases1–3, but surprisingly, the causes and types of damage remain largely unknown. There are three identified mechanisms that damage DNA during transcription: RNA polymerase (RNAP) colliding with DNA-replication machinery head-on and co-directionally4–6, and R-loop-induced DNA breakage7–10. Here, we identify DNA-damage reaction intermediates11,12 uncharacterized previously in living cells, and uncover a surprising fourth transcription-related source: endogenous DNA damage at sites of terminated transcripts. We engineered proteins to capture single-stranded (ss)DNA ends with 3'-polarity, in both 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 dependent on DNA replication. A pathway associated with double-strand breaks (DSBs) was suppressed by overproduction of replicative DNA polymerase (pol) III, suggesting competition between pol III and DNA-damage-promoting proteins. We developed ThreeSSeq, genomic profiling and found distinct 3'-ssEnd-hotspots, mostly unrelated to DSBs, next to the 5'CCTTTTTT transcription-terminator-like sequence. These 3'-ssDNA-termini coincide with RNA 3'-termini identified by DirectRNA sequencing13 or SEnd-seq14 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.

Keywords

Escherichia coli, DNA Damage, Humans, DNA Replication, DNA, Single-Stranded, Transcription, Genetic, DNA Polymerase III, DNA Breaks, Double-Stranded, Transcription Termination, Genetic, DNA-Directed RNA Polymerases

Published Open-Access

yes

Recommended Citation

Liu, Jingjing; Perren, Jullian O; Rogers, Cody M; et al., "Endogenous DNA Damage at Sites of Terminated Transcripts" (2025). Faculty, Staff and Students Publications. 6324.
https://digitalcommons.library.tmc.edu/baylor_docs/6324