Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts

Kevin S. Lang, Houra Merrikh

Research output: Contribution to journalArticlepeer-review

Abstract

Conflicts between the replication and transcription machineries have profound effects on chromosome duplication, genome organization, and evolution across species. Head-on conflicts (lagging-strand genes) are significantly more detrimental than codirectional conflicts (leading-strand genes). The fundamental reason for this difference is unknown. Here, we report that topological stress significantly contributes to this difference. We find that head-on, but not codirectional, conflict resolution requires the relaxation of positive supercoils by the type II topoisomerases DNA gyrase and Topo IV, at least in the Gram-positive model bacterium Bacillus subtilis. Interestingly, our data suggest that after positive supercoil resolution, gyrase introduces excessive negative supercoils at head-on conflict regions, driving pervasive R-loop formation. Altogether, our results reveal a fundamental mechanistic difference between the two types of encounters, addressing a long-standing question in the field of replication-transcription conflicts. Lang and Merrikh show that resolution of head-on, but not codirectional, conflicts between replication and transcription machineries requires type II topoisomerases, suggesting that a fundamental difference between the two types of conflicts is supercoil buildup in DNA. Furthermore, they show that supercoil resolution at head-on conflict regions drives R-loop formation.

Original languageEnglish (US)
Article number108797
JournalCell reports
Volume34
Issue number9
DOIs
StatePublished - Mar 2 2021
Externally publishedYes

Bibliographical note

Funding Information:
We would like to thank Christopher Merrikh and the other members (past and present) of the Merrikh lab, as well as Neil Osheroff and Felipe Cortés Ledesma for helpful discussions. The authors would also like to thank Sara Mangiameli for revising the manuscript and Peter Graumann for sharing strains. This work was supported by National Institutes of Health awards DP2GM110773 and R01GM128191-02 to H.M., Research Royalty Funds from the University of Washington to H.M., the 5T32-AI055396-13 Bacterial Pathogenesis Training Grant ( University of Washington ) award to K.S.L., and the 1F32 AI140557-01 Ruth L. Kirschstein National Research Postdoctoral award to K.S.L. We would like to dedicate this paper to the late James Champoux, who discovered Top1 and discussed this project with us on various occasions during our time at the University of Washington.

Funding Information:
We would like to thank Christopher Merrikh and the other members (past and present) of the Merrikh lab, as well as Neil Osheroff and Felipe Cort?s Ledesma for helpful discussions. The authors would also like to thank Sara Mangiameli for revising the manuscript and Peter Graumann for sharing strains. This work was supported by National Institutes of Health awards DP2GM110773 and R01GM128191-02 to H.M. Research Royalty Funds from the University of Washington to H.M. the 5T32-AI055396-13 Bacterial Pathogenesis Training Grant (University of Washington) award to K.S.L. and the 1F32 AI140557-01 Ruth L. Kirschstein National Research Postdoctoral award to K.S.L. We would like to dedicate this paper to the late James Champoux, who discovered Top1 and discussed this project with us on various occasions during our time at the University of Washington. K.S.L. and H.M. designed and performed the experiments, analyzed the data, and wrote the paper. The authors declare no competing interests.

Publisher Copyright:
© 2021 The Author(s)

Keywords

  • DNA supercoiling
  • R-loops
  • Replication-transcription conflicts
  • Type II topoisomerases

PubMed: MeSH publication types

  • Journal Article

Fingerprint

Dive into the research topics of 'Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts'. Together they form a unique fingerprint.

Cite this