Temporally Distinct Post-replicative Repair Mechanisms Fill PRIMPOL-dependent SsDNA Gaps in Human Cells

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2021 Oct 8

PMID 34624216

Citations 82

Authors

Stephanie Tirman

Annabel Quinet

Matthew Wood

Alice Meroni

Emily Cybulla

Jessica Jackson

Silvia Pegoraro

Antoine Simoneau

Lee Zou

Alessandro Vindigni

Affiliations

Soon will be listed here.

Abstract

PRIMPOL repriming allows DNA replication to skip DNA lesions, leading to ssDNA gaps. These gaps must be filled to preserve genome stability. Using a DNA fiber approach to directly monitor gap filling, we studied the post-replicative mechanisms that fill the ssDNA gaps generated in cisplatin-treated cells upon increased PRIMPOL expression or when replication fork reversal is defective because of SMARCAL1 inactivation or PARP inhibition. We found that a mechanism dependent on the E3 ubiquitin ligase RAD18, PCNA monoubiquitination, and the REV1 and POLζ translesion synthesis polymerases promotes gap filling in G2. The E2-conjugating enzyme UBC13, the RAD51 recombinase, and REV1-POLζ are instead responsible for gap filling in S, suggesting that temporally distinct pathways of gap filling operate throughout the cell cycle. Furthermore, we found that BRCA1 and BRCA2 promote gap filling by limiting MRE11 activity and that simultaneously targeting fork reversal and gap filling enhances chemosensitivity in BRCA-deficient cells.

Citing Articles

Molecular dependencies and genomic consequences of a global DNA damage tolerance defect.

de Groot D, Spanjaard A, Shah R, Kreft M, Morris B, Lieftink C Genome Biol. 2024; 25(1):323.

PMID: 39741332 PMC: 11687044. DOI: 10.1186/s13059-024-03451-z.

CAF-1 promotes efficient PrimPol recruitment to nascent DNA for single-stranded DNA gap formation.

Straka J, Khatib J, Pale L, Nicolae C, Moldovan G Nucleic Acids Res. 2024; 52(22):13865-13880.

PMID: 39558157 PMC: 11662685. DOI: 10.1093/nar/gkae1068.

PARG inhibitor sensitivity correlates with accumulation of single-stranded DNA gaps in preclinical models of ovarian cancer.

Ravindranathan R, Somuncu O, da Costa A, Mukkavalli S, Lamarre B, Nguyen H Proc Natl Acad Sci U S A. 2024; 121(47):e2413954121.

PMID: 39546575 PMC: 11588084. DOI: 10.1073/pnas.2413954121.

CRISPR knockout genome-wide screens identify the HELQ-RAD52 axis in regulating the repair of cisplatin-induced single-stranded DNA gaps.

Pale L, Khatib J, Nusawardhana A, Straka J, Nicolae C, Moldovan G Nucleic Acids Res. 2024; 52(22):13832-13848.

PMID: 39530221 PMC: 11662931. DOI: 10.1093/nar/gkae998.

BRCA1 and BRCA2: from cancer susceptibility to synthetic lethality.

Khalizieva A, Moser S, Bouwman P, Jonkers J Genes Dev. 2024; 39(1-2):86-108.

PMID: 39510841 PMC: 11789497. DOI: 10.1101/gad.352083.124.

References

Xiao W, Chow B, Broomfield S, Hanna M . The Saccharomyces cerevisiae RAD6 group is composed of an error-prone and two error-free postreplication repair pathways. Genetics. 2000; 155(4):1633-41. PMC: 1461201. DOI: 10.1093/genetics/155.4.1633. View

Ohmori H, Hanafusa T, Ohashi E, Vaziri C . Separate roles of structured and unstructured regions of Y-family DNA polymerases. Adv Protein Chem Struct Biol. 2010; 78:99-146. PMC: 3103052. DOI: 10.1016/S1876-1623(08)78004-0. View

Bianchi J, Rudd S, Jozwiakowski S, Bailey L, Soura V, Taylor E . PrimPol bypasses UV photoproducts during eukaryotic chromosomal DNA replication. Mol Cell. 2013; 52(4):566-73. PMC: 4228047. DOI: 10.1016/j.molcel.2013.10.035. View

Quinet A, Tirman S, Jackson J, Svikovic S, Lemacon D, Carvajal-Maldonado D . PRIMPOL-Mediated Adaptive Response Suppresses Replication Fork Reversal in BRCA-Deficient Cells. Mol Cell. 2019; 77(3):461-474.e9. PMC: 7007862. DOI: 10.1016/j.molcel.2019.10.008. View

Wojtaszek J, Chatterjee N, Najeeb J, Ramos A, Lee M, Bian K . A Small Molecule Targeting Mutagenic Translesion Synthesis Improves Chemotherapy. Cell. 2019; 178(1):152-159.e11. PMC: 6644000. DOI: 10.1016/j.cell.2019.05.028. View

Pilie P, Gay C, Byers L, OConnor M, Yap T . PARP Inhibitors: Extending Benefit Beyond -Mutant Cancers. Clin Cancer Res. 2019; 25(13):3759-3771. DOI: 10.1158/1078-0432.CCR-18-0968. View

Mijic S, Zellweger R, Chappidi N, Berti M, Jacobs K, Mutreja K . Replication fork reversal triggers fork degradation in BRCA2-defective cells. Nat Commun. 2017; 8(1):859. PMC: 5643541. DOI: 10.1038/s41467-017-01164-5. View

Lawrence C, HINKLE D . DNA polymerase zeta and the control of DNA damage induced mutagenesis in eukaryotes. Cancer Surv. 1996; 28:21-31. View

Wang A, Kim T, Wagner J, Conti B, Lach F, Huang A . A Dominant Mutation in Human RAD51 Reveals Its Function in DNA Interstrand Crosslink Repair Independent of Homologous Recombination. Mol Cell. 2015; 59(3):478-90. PMC: 4529964. DOI: 10.1016/j.molcel.2015.07.009. View

10.

Hunter T, Pines J . Cyclins and cancer. II: Cyclin D and CDK inhibitors come of age. Cell. 1994; 79(4):573-82. DOI: 10.1016/0092-8674(94)90543-6. View

11.

Petruk S, Sedkov Y, Johnston D, Hodgson J, Black K, Kovermann S . TrxG and PcG proteins but not methylated histones remain associated with DNA through replication. Cell. 2012; 150(5):922-33. PMC: 3432699. DOI: 10.1016/j.cell.2012.06.046. View

12.

Masuda Y, Masutani C . Spatiotemporal regulation of PCNA ubiquitination in damage tolerance pathways. Crit Rev Biochem Mol Biol. 2019; 54(5):418-442. DOI: 10.1080/10409238.2019.1687420. View

13.

Berti M, Ray Chaudhuri A, Thangavel S, Gomathinayagam S, Kenig S, Vujanovic M . Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Nat Struct Mol Biol. 2013; 20(3):347-54. PMC: 3897332. DOI: 10.1038/nsmb.2501. View

14.

Carvajal-Maldonado D, Byrum A, Jackson J, Wessel S, Lemacon D, Guitton-Sert L . Perturbing cohesin dynamics drives MRE11 nuclease-dependent replication fork slowing. Nucleic Acids Res. 2018; 47(3):1294-1310. PMC: 6379725. DOI: 10.1093/nar/gky519. View

15.

Simoneau A, Xiong R, Zou L . The cell cycle effects of PARP inhibitors underlie their selectivity toward BRCA1/2-deficient cells. Genes Dev. 2021; 35(17-18):1271-1289. PMC: 8415318. DOI: 10.1101/gad.348479.121. View

16.

Tian F, Sharma S, Zou J, Lin S, Wang B, Rezvani K . BRCA1 promotes the ubiquitination of PCNA and recruitment of translesion polymerases in response to replication blockade. Proc Natl Acad Sci U S A. 2013; 110(33):13558-63. PMC: 3746927. DOI: 10.1073/pnas.1306534110. View

17.

Hofmann R, Pickart C . Noncanonical MMS2-encoded ubiquitin-conjugating enzyme functions in assembly of novel polyubiquitin chains for DNA repair. Cell. 1999; 96(5):645-53. DOI: 10.1016/s0092-8674(00)80575-9. View

18.

Adar S, Izhar L, Hendel A, Geacintov N, Livneh Z . Repair of gaps opposite lesions by homologous recombination in mammalian cells. Nucleic Acids Res. 2009; 37(17):5737-48. PMC: 2761288. DOI: 10.1093/nar/gkp632. View

19.

Quinet A, Carvajal-Maldonado D, Lemacon D, Vindigni A . DNA Fiber Analysis: Mind the Gap!. Methods Enzymol. 2017; 591:55-82. DOI: 10.1016/bs.mie.2017.03.019. View

20.

Pines J, Hunter T . Isolation of a human cyclin cDNA: evidence for cyclin mRNA and protein regulation in the cell cycle and for interaction with p34cdc2. Cell. 1989; 58(5):833-46. DOI: 10.1016/0092-8674(89)90936-7. View