Pathways and signatures of mutagenesis at targeted DNA nicks
Autoři:
Yinbo Zhang aff001; Luther Davis aff001; Nancy Maizels aff001
Působiště autorů:
Department of Immunology, University of Washington Medical School, Seattle, Washington, United States of America
aff001; Department of Biochemistry, University of Washington Medical School, Seattle, Washington, United States of America
aff002
Vyšlo v časopise:
Pathways and signatures of mutagenesis at targeted DNA nicks. PLoS Genet 17(4): e1009329. doi:10.1371/journal.pgen.1009329
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1009329
Souhrn
Nicks are the most frequent form of DNA damage and a potential source of mutagenesis in human cells. By deep sequencing, we have identified factors and pathways that promote and limit mutagenic repair at a targeted nick in human cells. Mutations were distributed asymmetrically around the nick site. BRCA2 inhibited all categories of mutational events, including indels, SNVs and HDR. DNA2 and RPA promoted resection. DNA2 inhibited 1 bp deletions but contributed to longer deletions, as did REV7. POLQ stimulated SNVs. Parallel analysis of DSBs targeted to the same site identified similar roles for DNA2 and POLQ (but not REV7) in promoting deletions and for POLQ in stimulating SNVs. Insertions were infrequent at nicks, and most were 1 bp in length, as at DSBs. The translesion polymerase REV1 stimulated +1 insertions at one nick site but not another, illustrating the potential importance of sequence context in determining the outcome of mutagenic repair. These results highlight the potential for nicks to promote mutagenesis, especially in BRCA-deficient cells, and identify mutagenic signatures of DNA2, REV1, REV3, REV7 and POLQ.
Klíčová slova:
Cell cycle and cell division – DNA repair – G1 phase – Guide RNA – Insertion mutation – Mutagenesis – Recombinase polymerase amplification – Transfection
Zdroje
1. Maizels N, Davis L. Initiation of homologous recombination at DNA nicks. Nucleic Acids Res. 2018;46(14):6962–73. doi: 10.1093/nar/gky588 29986051
2. Vilenchik MM, Knudson AG. Endogenous DNA double-strand breaks: production, fidelity of repair, and induction of cancer. Proc Natl Acad Sci U S A. 2003;100(22):12871–6. doi: 10.1073/pnas.2135498100 14566050
3. Davis L, Maizels N. Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair. Proc Natl Acad Sci U S A. 2014;111:E924–32. doi: 10.1073/pnas.1400236111 24556991
4. Davis L, Maizels N. Two distinct pathways support gene correction by single-stranded donors at DNA nicks. Cell Rep. 2016;17(7):1872–81. doi: 10.1016/j.celrep.2016.10.049 27829157
5. Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 2014;24(1):132–41. doi: 10.1101/gr.162339.113 24253446
6. Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 2015;33(2):187–97. doi: 10.1038/nbt.3117 25513782
7. Olson HC, Davis L, Kiianitsa K, Khoo KJ, Liu Y, Knijnenburg TA, et al. Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways. Nucleic Acids Res. 2018;46(18):9496–509. doi: 10.1093/nar/gky727 30107528
8. Cejka P, Cannavo E, Polaczek P, Masuda-Sasa T, Pokharel S, Campbell JL, et al. DNA end resection by Dna2-Sgs1-RPA and its stimulation by Top3-Rmi1 and Mre11-Rad50-Xrs2. Nature. 2010;467(7311):112–6. doi: 10.1038/nature09355 20811461
9. Cejka P. DNA End Resection: Nucleases Team Up with the Right Partners to Initiate Homologous Recombination. J Biol Chem. 2015;290(38):22931–8. doi: 10.1074/jbc.R115.675942 26231213
10. Zhou C, Pourmal S, Pavletich NP. Dna2 nuclease-helicase structure, mechanism and regulation by Rpa. Elife. 2015;4. doi: 10.7554/eLife.09832 26491943
11. Ruff P, Donnianni RA, Glancy E, Oh J, Symington LS. RPA Stabilization of Single-Stranded DNA Is Critical for Break-Induced Replication. Cell Rep. 2016;17(12):3359–68. doi: 10.1016/j.celrep.2016.12.003 28009302
12. Zheng L, Meng Y, Campbell JL, Shen B. Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases. Nucleic Acids Res. 2020;48(1):16–35. doi: 10.1093/nar/gkz1101 31754720
13. Certo MT, Ryu BY, Annis JE, Garibov M, Jarjour J, Rawlings DJ, et al. Tracking genome engineering outcome at individual DNA breakpoints. Nat Methods. 2011;8(8):671–6. doi: 10.1038/nmeth.1648 21743461
14. Chen H, Lisby M, Symington LS. RPA coordinates DNA end resection and prevents formation of DNA hairpins. Mol Cell. 2013;50(4):589–600. doi: 10.1016/j.molcel.2013.04.032 23706822
15. Marechal A, Zou L. RPA-coated single-stranded DNA as a platform for post-translational modifications in the DNA damage response. Cell Res. 2015;25(1):9–23. doi: 10.1038/cr.2014.147 25403473
16. Caldwell CC, Spies M. Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair. Crit Rev Biochem Mol Biol. 2020;55(5):482–507. doi: 10.1080/10409238.2020.1813070 32856505
17. Wold MS. Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu Rev Biochem. 1997;66:61–92. doi: 10.1146/annurev.biochem.66.1.61 9242902
18. Sugiyama T, Zaitseva EM, Kowalczykowski SC. A single-stranded DNA-binding protein is needed for efficient presynaptic complex formation by the Saccharomyces cerevisiae Rad51 protein. J Biol Chem. 1997;272(12):7940–5. doi: 10.1074/jbc.272.12.7940 9065463
19. Niu H, Chung WH, Zhu Z, Kwon Y, Zhao W, Chi P, et al. Mechanism of the ATP-dependent DNA end-resection machinery from Saccharomyces cerevisiae. Nature. 2010;467(7311):108–11. doi: 10.1038/nature09318 20811460
20. Sturzenegger A, Burdova K, Kanagaraj R, Levikova M, Pinto C, Cejka P, et al. DNA2 cooperates with the WRN and BLM RecQ helicases to mediate long-range DNA end resection in human cells. J Biol Chem. 2014;289(39):27314–26. doi: 10.1074/jbc.M114.578823 25122754
21. Mazina OM, Somarowthu S, Kadyrova LY, Baranovskiy AG, Tahirov TH, Kadyrov FA, et al. Replication protein A binds RNA and promotes R-loop formation. J Biol Chem. 2020;295(41):14203–13. doi: 10.1074/jbc.RA120.013812 32796030
22. Umezu K, Sugawara N, Chen C, Haber JE, Kolodner RD. Genetic analysis of yeast RPA1 reveals its multiple functions in DNA metabolism. Genetics. 1998;148(3):989–1005. 9539419
23. Wang X, Haber JE. Role of Saccharomyces single-stranded DNA-binding protein RPA in the strand invasion step of double-strand break repair. PLoS Biol. 2004;2(1):E21. doi: 10.1371/journal.pbio.0020021 14737196
24. Kanoh Y, Tamai K, Shirahige K. Different requirements for the association of ATR-ATRIP and 9-1-1 to the stalled replication forks. Gene. 2006;377:88–95. doi: 10.1016/j.gene.2006.03.019 16753272
25. Haring SJ, Mason AC, Binz SK, Wold MS. Cellular functions of human RPA1. Multiple roles of domains in replication, repair, and checkpoints. J Biol Chem. 2008;283(27):19095–111. doi: 10.1074/jbc.M800881200 18469000
26. Xu X, Vaithiyalingam S, Glick GG, Mordes DA, Chazin WJ, Cortez D. The basic cleft of RPA70N binds multiple checkpoint proteins, including RAD9, to regulate ATR signaling. Mol Cell Biol. 2008;28(24):7345–53. doi: 10.1128/MCB.01079-08 18936170
27. Gutschner T, Haemmerle M, Genovese G, Draetta GF, Chin L. Post-translational Regulation of Cas9 during G1 Enhances Homology-Directed Repair. Cell Rep. 2016. doi: 10.1016/j.celrep.2016.01.019 26854237
28. Howden SE, McColl B, Glaser A, Vadolas J, Petrou S, Little MH, et al. A Cas9 Variant for Efficient Generation of Indel-Free Knockin or Gene-Corrected Human Pluripotent Stem Cells. Stem Cell Reports. 2016;7(3):508–17. doi: 10.1016/j.stemcr.2016.07.001 27499201
29. Sakaue-Sawano A, Kurokawa H, Morimura T, Hanyu A, Hama H, Osawa H, et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell. 2008;132(3):487–98. doi: 10.1016/j.cell.2007.12.033 18267078
30. Lemos BR, Kaplan AC, Bae JE, Ferrazzoli AE, Kuo J, Anand RP, et al. CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles. Proc Natl Acad Sci U S A. 2018;115(9):E2040–E7. doi: 10.1073/pnas.1716855115 29440496
31. Shou J, Li J, Liu Y, Wu Q. Precise and Predictable CRISPR Chromosomal Rearrangements Reveal Principles of Cas9-Mediated Nucleotide Insertion. Mol Cell. 2018;71(4):498–509 e4. doi: 10.1016/j.molcel.2018.06.021 30033371
32. Taheri-Ghahfarokhi A, Taylor BJM, Nitsch R, Lundin A, Cavallo AL, Madeyski-Bengtson K, et al. Decoding non-random mutational signatures at Cas9 targeted sites. Nucleic Acids Res. 2018;46(16):8417–34. doi: 10.1093/nar/gky653 30032200
33. Tonzi P, Huang TT. Role of Y-family translesion DNA polymerases in replication stress: Implications for new cancer therapeutic targets. DNA Repair (Amst). 2019;78:20–6. doi: 10.1016/j.dnarep.2019.03.016 30954011
34. Martin SK, Wood RD. DNA polymerase zeta in DNA replication and repair. Nucleic Acids Res. 2019;47(16):8348–61. doi: 10.1093/nar/gkz705 31410467
35. Sale JE. REV7/MAD2L2: the multitasking maestro emerges as a barrier to recombination. EMBO J. 2015;34(12):1609–11. doi: 10.15252/embj.201591697 25896508
36. Xu G, Chapman JR, Brandsma I, Yuan J, Mistrik M, Bouwman P, et al. REV7 counteracts DNA double-strand break resection and affects PARP inhibition. Nature. 2015;521(7553):541–4. doi: 10.1038/nature14328 25799992
37. Leland BA, Chen AC, Zhao AY, Wharton RC, King MC. Rev7 and 53BP1/Crb2 prevent RecQ helicase-dependent hyper-resection of DNA double-strand breaks. Elife. 2018;7. doi: 10.7554/eLife.33402 29697047
38. Findlay S, Heath J, Luo VM, Malina A, Morin T, Coulombe Y, et al. SHLD2/FAM35A co-operates with REV7 to coordinate DNA double-strand break repair pathway choice. EMBO J. 2018;37(18). doi: 10.15252/embj.2018100158 30154076
39. Gupta R, Somyajit K, Narita T, Maskey E, Stanlie A, Kremer M, et al. DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity. Cell. 2018;173(4):972–88 e23. doi: 10.1016/j.cell.2018.03.050 29656893
40. Noordermeer SM, Adam S, Setiaputra D, Barazas M, Pettitt SJ, Ling AK, et al. The shieldin complex mediates 53BP1-dependent DNA repair. Nature. 2018;560(7716):117–21. doi: 10.1038/s41586-018-0340-7 30022168
41. Setiaputra D, Durocher D. Shieldin—the protector of DNA ends. EMBO Rep. 2019;20(5). doi: 10.15252/embr.201847560 30948458
42. Yousefzadeh MJ, Wyatt DW, Takata K, Mu Y, Hensley SC, Tomida J, et al. Mechanism of suppression of chromosomal instability by DNA polymerase POLQ. PLoS Genet. 2014;10(10):e1004654. doi: 10.1371/journal.pgen.1004654 25275444
43. Kent T, Chandramouly G, McDevitt SM, Ozdemir AY, Pomerantz RT. Mechanism of microhomology-mediated end-joining promoted by human DNA polymerase theta. Nat Struct Mol Biol. 2015;22(3):230–7. doi: 10.1038/nsmb.2961 25643323
44. Wyatt DW, Feng W, Conlin MP, Yousefzadeh MJ, Roberts SA, Mieczkowski P, et al. Essential Roles for Polymerase theta-Mediated End Joining in the Repair of Chromosome Breaks. Mol Cell. 2016;63(4):662–73. doi: 10.1016/j.molcel.2016.06.020 27453047
45. Saito S, Maeda R, Adachi N. Dual loss of human POLQ and LIG4 abolishes random integration. Nat Commun. 2017;8:16112. doi: 10.1038/ncomms16112 28695890
46. Zelensky AN, Schimmel J, Kool H, Kanaar R, Tijsterman M. Inactivation of Pol theta and C-NHEJ eliminates off-target integration of exogenous DNA. Nat Commun. 2017;8(1):66. doi: 10.1038/s41467-017-00124-3 28687761
47. Brambati A, Barry RM, Sfeir A. DNA polymerase theta (Poltheta)—an error-prone polymerase necessary for genome stability. Curr Opin Genet Dev. 2020;60:119–26. doi: 10.1016/j.gde.2020.02.017 32302896
48. Davis L, Khoo KJ, Zhang Y, Maizels N. POLQ suppresses interhomolog recombination and loss of heterozygosity at targeted DNA breaks. Proc Natl Acad Sci U S A. 2020;117(37):22900–9. doi: 10.1073/pnas.2008073117 32873648
49. Mackay RP, Xu Q, Weinberger PM. R-Loop Physiology and Pathology: A Brief Review. DNA Cell Biol. 2020;39(11):1914–25. doi: 10.1089/dna.2020.5906 33052725
50. Wood RD, Doublie S. DNA polymerase theta (POLQ), double-strand break repair, and cancer. DNA Repair (Amst). 2016;44:22–32.
51. Arana ME, Seki M, Wood RD, Rogozin IB, Kunkel TA. Low-fidelity DNA synthesis by human DNA polymerase theta. Nucleic Acids Res. 2008;36(11):3847–56. doi: 10.1093/nar/gkn310 18503084
52. Masuda K, Ouchida R, Takeuchi A, Saito T, Koseki H, Kawamura K, et al. DNA polymerase theta contributes to the generation of C/G mutations during somatic hypermutation of Ig genes. Proc Natl Acad Sci U S A. 2005;102(39):13986–91. doi: 10.1073/pnas.0505636102 16172387
53. Zan H, Shima N, Xu Z, Al-Qahtani A, Evinger Iii AJ, Zhong Y, et al. The translesion DNA polymerase theta plays a dominant role in immunoglobulin gene somatic hypermutation. EMBO J. 2005;24(21):3757–69. doi: 10.1038/sj.emboj.7600833 16222339
54. Shinmura K, Kato H, Kawanishi Y, Yoshimura K, Tsuchiya K, Takahara Y, et al. POLQ Overexpression Is Associated with an Increased Somatic Mutation Load and PLK4 Overexpression in Lung Adenocarcinoma. Cancers (Basel). 2019;11(5). doi: 10.3390/cancers11050722 31137743
55. Lord CJ, Ashworth A. BRCAness revisited. Nat Rev Cancer. 2016;16(2):110–20. doi: 10.1038/nrc.2015.21 26775620
56. Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci U S A. 2011;108(23):9530–5. doi: 10.1073/pnas.1105422108 21586637
57. Kennedy SR, Schmitt MW, Fox EJ, Kohrn BF, Salk JJ, Ahn EH, et al. Detecting ultralow-frequency mutations by Duplex Sequencing. Nat Protoc. 2014;9(11):2586–606. doi: 10.1038/nprot.2014.170 25299156
58. Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol. 2019;37(3):224–6. doi: 10.1038/s41587-019-0032-3 30809026
59. Davis L, Zhang Y, Maizels N. Assaying Repair at DNA Nicks. Methods Enzymol. 2018;601:71–89. doi: 10.1016/bs.mie.2017.12.001 29523243
60. Liu H, Naismith JH. An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol. BMC Biotechnol. 2008;8:91. doi: 10.1186/1472-6750-8-91 19055817
61. Bryksin A, Matsumura I. Overlap extension PCR cloning. Methods Mol Biol. 2013;1073:31–42. doi: 10.1007/978-1-62703-625-2_4 23996437
62. Le Q, Maizels N. Cell Cycle Regulates Nuclear Stability of AID and Determines the Cellular Response to AID. PLoS Genet. 2015;11(9):e1005411. doi: 10.1371/journal.pgen.1005411 26355458
Článek vyšel v časopise
PLOS Genetics
2021 Číslo 4
- Případ Bulovka: Jak postupují jiné nemocnice, aby podobným tragédiím zabránily?
- Jak často se u masových střelců vyskytují duševní choroby?
- FDA varuje před selfmonitoringem cukru pomocí chytrých hodinek. Jak je to v Česku?
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
- Není statin jako statin aneb praktický přehled rozdílů jednotlivých molekul
Nejčtenější v tomto čísle
- Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription–replication conflict regions
- Pathways and signatures of mutagenesis at targeted DNA nicks
- Using genetic variants to evaluate the causal effect of cholesterol lowering on head and neck cancer risk: A Mendelian randomization study
- Functional assessment of the “two-hit” model for neurodevelopmental defects in Drosophila and X. laevis