Repair of Replication-dependent Double-strand Breaks Differs Between the Leading and Lagging Strands

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2024 Dec 4

PMID 39631395

Authors

Michael T Kimble

Aakanksha Sane

Robert J D Reid

Matthew J Johnson

Rodney Rothstein

Lorraine S Symington

Affiliations

Soon will be listed here.

Abstract

Single-strand breaks (SSBs) are one of the most commonly occurring endogenous lesions with the potential to give rise to cytotoxic double-strand breaks (DSBs) during DNA replication. To investigate how replication-dependent DSBs are repaired, we employed Cas9 nickase (nCas9) to generate site- and strand-specific nicks in the budding yeast genome. We found that nCas9-induced nicks are converted to mostly double-ended DSBs during S phase. Repair of replication-associated DSBs requires homologous recombination (HR) and is independent of classical non-homologous end joining. Consistent with a strong bias to repair these lesions using a sister-chromatid template, we observed minimal induction of inter-chromosomal HR by nCas9. In a genome-wide screen to identify factors necessary for the repair of replication-dependent DSBs, we recovered components of the replication-coupled nucleosome assembly (RCNA) pathway. Our findings suggest that the RCNA pathway is especially important to repair DSBs arising from nicks in the leading-strand template through acetylation of histone H3K56.

Citing Articles

Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes.

Sasaki M, Kobayashi T Nucleic Acids Res. 2025; 53(3).

PMID: 39876709 PMC: 11760980. DOI: 10.1093/nar/gkaf014.

Two-ended recombination at a Flp-nickase-broken replication fork.

Elango R, Nilavar N, Li A, Nguyen D, Rass E, Duffey E Mol Cell. 2024; 85(1):78-90.e3.

PMID: 39631396 PMC: 11733529. DOI: 10.1016/j.molcel.2024.11.006.

One-ended and two-ended breaks at nickase-broken replication forks.

Scully R, Walter J, Nussenzweig A DNA Repair (Amst). 2024; 144:103783.

PMID: 39504607 PMC: 11681922. DOI: 10.1016/j.dnarep.2024.103783.

References

Munoz-Galvan S, Jimeno S, Rothstein R, Aguilera A . Histone H3K56 acetylation, Rad52, and non-DNA repair factors control double-strand break repair choice with the sister chromatid. PLoS Genet. 2013; 9(1):e1003237. PMC: 3554610. DOI: 10.1371/journal.pgen.1003237. View

Kimble M, Johnson M, Nester M, Symington L . Long-range DNA end resection supports homologous recombination by checkpoint activation rather than extensive homology generation. Elife. 2023; 12. PMC: 10400078. DOI: 10.7554/eLife.84322. View

Zhang J, Shi D, Li X, Ding L, Tang J, Liu C . Rtt101-Mms1-Mms22 coordinates replication-coupled sister chromatid cohesion and nucleosome assembly. EMBO Rep. 2017; 18(8):1294-1305. PMC: 5538422. DOI: 10.15252/embr.201643807. View

Krejci L, Van Komen S, Li Y, Villemain J, Reddy M, Klein H . DNA helicase Srs2 disrupts the Rad51 presynaptic filament. Nature. 2003; 423(6937):305-9. DOI: 10.1038/nature01577. View

Cortes-Ledesma F, Aguilera A . Double-strand breaks arising by replication through a nick are repaired by cohesin-dependent sister-chromatid exchange. EMBO Rep. 2006; 7(9):919-26. PMC: 1559660. DOI: 10.1038/sj.embor.7400774. View

Roy S, Juste S, Sneider M, Auradkar A, Klanseck C, Li Z . Cas9/Nickase-induced allelic conversion by homologous chromosome-templated repair in somatic cells. Sci Adv. 2022; 8(26):eabo0721. PMC: 10883370. DOI: 10.1126/sciadv.abo0721. View

Masumoto H, Hawke D, Kobayashi R, Verreault A . A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response. Nature. 2005; 436(7048):294-8. DOI: 10.1038/nature03714. View

Mayer M, Gygi S, Aebersold R, Hieter P . Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative RFC complex required for sister chromatid cohesion in S. cerevisiae. Mol Cell. 2001; 7(5):959-70. DOI: 10.1016/s1097-2765(01)00254-4. View

Reid R, Gonzalez-Barrera S, Sunjevaric I, Alvaro D, Ciccone S, Wagner M . Selective ploidy ablation, a high-throughput plasmid transfer protocol, identifies new genes affecting topoisomerase I-induced DNA damage. Genome Res. 2010; 21(3):477-86. PMC: 3044861. DOI: 10.1101/gr.109033.110. View

10.

Westhorpe R, Roske J, Yeeles J . Mechanisms controlling replication fork stalling and collapse at topoisomerase 1 cleavage complexes. Mol Cell. 2024; 84(18):3469-3481.e7. PMC: 7617106. DOI: 10.1016/j.molcel.2024.08.004. View

11.

Vasianovich Y, Altmannova V, Kotenko O, Newton M, Krejci L, Makovets S . Unloading of homologous recombination factors is required for restoring double-stranded DNA at damage repair loci. EMBO J. 2016; 36(2):213-231. PMC: 5239998. DOI: 10.15252/embj.201694628. View

12.

Zhu M, Zhao H, Limbo O, Russell P . Mre11 complex links sister chromatids to promote repair of a collapsed replication fork. Proc Natl Acad Sci U S A. 2018; 115(35):8793-8798. PMC: 6126713. DOI: 10.1073/pnas.1808189115. View

13.

Clemente-Ruiz M, Gonzalez-Prieto R, Prado F . Histone H3K56 acetylation, CAF1, and Rtt106 coordinate nucleosome assembly and stability of advancing replication forks. PLoS Genet. 2011; 7(11):e1002376. PMC: 3213180. DOI: 10.1371/journal.pgen.1002376. View

14.

Vriend L, Prakash R, Chen C, Vanoli F, Cavallo F, Zhang Y . Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks. Nucleic Acids Res. 2016; 44(11):5204-17. PMC: 4914091. DOI: 10.1093/nar/gkw179. View

15.

Johansson E, Diffley J . Unchecked nick ligation can promote localized genome re-replication. Curr Biol. 2021; 31(11):R710-R711. PMC: 8209288. DOI: 10.1016/j.cub.2021.03.043. View

16.

Scherzer M, Giordano F, Ferran M, Strom L . Recruitment of Scc2/4 to double-strand breaks depends on γH2A and DNA end resection. Life Sci Alliance. 2022; 5(5). PMC: 8807874. DOI: 10.26508/lsa.202101244. View

17.

Pavani R, Tripathi V, Vrtis K, Zong D, Chari R, Callen E . Structure and repair of replication-coupled DNA breaks. Science. 2024; 385(6710):eado3867. PMC: 11620331. DOI: 10.1126/science.ado3867. View

18.

Cejka P, Symington L . DNA End Resection: Mechanism and Control. Annu Rev Genet. 2021; 55:285-307. DOI: 10.1146/annurev-genet-071719-020312. View

19.

Strom L, Lindroos H, Shirahige K, Sjogren C . Postreplicative recruitment of cohesin to double-strand breaks is required for DNA repair. Mol Cell. 2004; 16(6):1003-15. DOI: 10.1016/j.molcel.2004.11.026. View

20.

Mayle R, Campbell I, Beck C, Yu Y, Wilson M, Shaw C . DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage. Science. 2015; 349(6249):742-7. PMC: 4782627. DOI: 10.1126/science.aaa8391. View