Functional Interplay between the 53BP1-Ortholog Rad9 and the Mre11 Complex Regulates Resection, End-Tethering and Repair of a Double-Strand Break

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DNA double strand breaks (DSBs) are among the most deleterious types of damage occurring in the genome, as failure to repair these lesions through either non-homologous-end-joining (NHEJ) or homologous recombination (HR) leads to genetic instability. The 5′ strand of a DSB can be nucleolytically degraded by several nucleases and associated factors, including Mre11, CtIP/Sae2, Exo1 and Dna2 together with Bloom helicase/Sgs1, through a finely regulated process called DSB resection. Once resection is initiated, error-prone NHEJ is prevented. Several findings suggest that DSB resection is a double-edged sword, if not finely regulated, since on one hand it is needed for faithful HR, but on the other it may lead to extensive DNA deletions associated with genome instability. Both in mammals and yeast, 53BP1/Rad9 protein binds near the lesion and counteracts the resection process, limiting the formation of ssDNA. By using S. cerevisiae as a model organism, here we show that Rad9 oligomers block the removal of hypo-active Mre11 protein from a persistent DSB, thus limiting initiation of resection and the recruitment of the recombination factor Rad52, in the absence of Sae2. Altogether, these findings pinpoint a critical role of 53BP1/Rad9 in balancing HR and NHEJ repair events throughout the cell cycle.

Vyšlo v časopise: Functional Interplay between the 53BP1-Ortholog Rad9 and the Mre11 Complex Regulates Resection, End-Tethering and Repair of a Double-Strand Break. PLoS Genet 11(1): e32767. doi:10.1371/journal.pgen.1004928
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004928

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Zdroje

1. MimitouEP, SymingtonLS (2010) Ku prevents Exo1 and Sgs1-dependent resection of DNA ends in the absence of a functional MRX complex or Sae2. The EMBO journal 29 : 3358–3369.

2. LangerakP, Mejia-RamirezE, LimboO, RussellP (2011) Release of Ku and MRN from DNA ends by Mre11 nuclease activity and Ctp1 is required for homologous recombination repair of double-strand breaks. PLoS genetics 7: e1002271.

3. FosterSS, BalestriniA, PetriniJH (2011) Functional interplay of the Mre11 nuclease and Ku in the response to replication-associated DNA damage. Molecular and cellular biology 31 : 4379–4389.

4. HuertasP, Cortes-LedesmaF, SartoriAA, AguileraA, JacksonSP (2008) CDK targets Sae2 to control DNA-end resection and homologous recombination. Nature 455 : 689–692.

5. GravelS, ChapmanJR, MagillC, JacksonSP (2008) DNA helicases Sgs1 and BLM promote DNA double-strand break resection. Genes & development 22 : 2767–2772.

6. MimitouEP, SymingtonLS (2008) Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing. Nature 455 : 770–774.

7. ZhuZ, ChungWH, ShimEY, LeeSE, IraG (2008) Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell 134 : 981–994.

8. CejkaP, CannavoE, PolaczekP, Masuda-SasaT, PokharelS, et al. (2010) DNA end resection by Dna2-Sgs1-RPA and its stimulation by Top3-Rmi1 and Mre11-Rad50-Xrs2. Nature 467 : 112–116.

9. NiuH, ChungWH, ZhuZ, KwonY, ZhaoW, et al. (2010) Mechanism of the ATP-dependent DNA end-resection machinery from Saccharomyces cerevisiae. Nature 467 : 108–111.

10. GranataM, PanigadaD, GalatiE, LazzaroF, PellicioliA, et al. (2013) To trim or not to trim: progression and control of DSB end resection. Cell cycle 12 : 1848–1860.

11. ChapmanJR, TaylorMR, BoultonSJ (2012) Playing the end game: DNA double-strand break repair pathway choice. Molecular cell 47 : 497–510.

12. ChungWH, ZhuZ, PapushaA, MalkovaA, IraG (2010) Defective resection at DNA double-strand breaks leads to de novo telomere formation and enhances gene targeting. PLoS genetics 6: e1000948.

13. LydeardJR, Lipkin-MooreZ, JainS, EapenVV, HaberJE (2010) Sgs1 and exo1 redundantly inhibit break-induced replication and de novo telomere addition at broken chromosome ends. PLoS genetics 6: e1000973.

14. McVeyM, LeeSE (2008) MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings. Trends in genetics: TIG 24 : 529–538.

15. ElliottB, JasinM (2002) Double-strand breaks and translocations in cancer. Cellular and molecular life sciences: CMLS 59 : 373–385.

16. WeinstockDM, RichardsonCA, ElliottB, JasinM (2006) Modeling oncogenic translocations: distinct roles for double-strand break repair pathways in translocation formation in mammalian cells. DNA repair 5 : 1065–1074.

17. MorinI, NgoHP, GreenallA, ZubkoMK, MorriceN, et al. (2008) Checkpoint-dependent phosphorylation of Exo1 modulates the DNA damage response. The EMBO journal 27 : 2400–2410.

18. El-ShemerlyM, HessD, PyakurelAK, MoselhyS, FerrariS (2008) ATR-dependent pathways control hEXO1 stability in response to stalled forks. Nucleic acids research 36 : 511–519.

19. BoldersonE, TomimatsuN, RichardDJ, BoucherD, KumarR, et al. (2010) Phosphorylation of Exo1 modulates homologous recombination repair of DNA double-strand breaks. Nucleic acids research 38 : 1821–1831.

20. HuyenY, ZgheibO, DitullioRAJr, GorgoulisVG, ZacharatosP, et al. (2004) Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 432 : 406–411.

21. GiannattasioM, LazzaroF, PlevaniP, Muzi-FalconiM (2005) The DNA damage checkpoint response requires histone H2B ubiquitination by Rad6-Bre1 and H3 methylation by Dot1. The Journal of biological chemistry 280 : 9879–9886.

22. WysockiR, JavaheriA, AllardS, ShaF, CoteJ, et al. (2005) Role of Dot1-dependent histone H3 methylation in G1 and S phase DNA damage checkpoint functions of Rad9. Molecular and cellular biology 25 : 8430–8443.

23. HammetA, MagillC, HeierhorstJ, JacksonSP (2007) Rad9 BRCT domain interaction with phosphorylated H2AX regulates the G1 checkpoint in budding yeast. EMBO reports 8 : 851–857.

24. Granata M, Lazzaro F, Novarina D, Panigada D, Puddu F, et al. (2010) Dynamics of Rad9 chromatin binding and checkpoint function are mediated by its dimerization and are cell cycle-regulated by CDK1 activity. PLoS genetics 6.

25. PfanderB, DiffleyJF (2011) Dpb11 coordinates Mec1 kinase activation with cell cycle-regulated Rad9 recruitment. The EMBO journal 30 : 4897–4907.

26. ShroffR, Arbel-EdenA, PilchD, IraG, BonnerWM, et al. (2004) Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break. Current biology: CB 14 : 1703–1711.

27. Navadgi-PatilVM, BurgersPM (2008) Yeast DNA replication protein Dpb11 activates the Mec1/ATR checkpoint kinase. The Journal of biological chemistry 283 : 35853–35859.

28. PudduF, GranataM, Di NolaL, BalestriniA, PiergiovanniG, et al. (2008) Phosphorylation of the budding yeast 9-1-1 complex is required for Dpb11 function in the full activation of the UV-induced DNA damage checkpoint. Molecular and cellular biology 28 : 4782–4793.

29. UsuiT, FosterSS, PetriniJH (2009) Maintenance of the DNA-damage checkpoint requires DNA-damage-induced mediator protein oligomerization. Molecular cell 33 : 147–159.

30. SoulierJ, LowndesNF (1999) The BRCT domain of the S. cerevisiae checkpoint protein Rad9 mediates a Rad9-Rad9 interaction after DNA damage. Current biology: CB 9 : 551–554.

31. ZimmermannM, LottersbergerF, BuonomoSB, SfeirA, de LangeT (2013) 53BP1 regulates DSB repair using Rif1 to control 5' end resection. Science 339 : 700–704.

32. ChapmanJR, BarralP, VannierJB, BorelV, StegerM, et al. (2013) RIF1 is essential for 53BP1-dependent nonhomologous end joining and suppression of DNA double-strand break resection. Molecular cell 49 : 858–871.

33. Escribano-DiazC, OrthweinA, Fradet-TurcotteA, XingM, YoungJT, et al. (2013) A cell cycle-dependent regulatory circuit composed of 53BP1-RIF1 and BRCA1-CtIP controls DNA repair pathway choice. Molecular cell 49 : 872–883.

34. FengL, FongKW, WangJ, WangW, ChenJ (2013) RIF1 counteracts BRCA1-mediated end resection during DNA repair. The Journal of biological chemistry 288 : 11135–11143.

35. Di VirgilioM, CallenE, YamaneA, ZhangW, JankovicM, et al. (2013) Rif1 prevents resection of DNA breaks and promotes immunoglobulin class switching. Science 339 : 711–715.

36. LazzaroF, SapountziV, GranataM, PellicioliA, VazeM, et al. (2008) Histone methyltransferase Dot1 and Rad9 inhibit single-stranded DNA accumulation at DSBs and uncapped telomeres. The EMBO journal 27 : 1502–1512.

37. ChenX, CuiD, PapushaA, ZhangX, ChuCD, et al. (2012) The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends. Nature 489 : 576–580.

38. MimitouEP, SymingtonLS (2009) DNA end resection: many nucleases make light work. DNA repair 8 : 983–995.

39. VazeMB, PellicioliA, LeeSE, IraG, LiberiG, et al. (2002) Recovery from checkpoint-mediated arrest after repair of a double-strand break requires Srs2 helicase. Molecular cell 10 : 373–385.

40. OoiSL, ShoemakerDD, BoekeJD (2003) DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nature genetics 35 : 277–286.

41. TongAH, EvangelistaM, ParsonsAB, XuH, BaderGD, et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294 : 2364–2368.

42. ClericiM, MantieroD, LucchiniG, LongheseMP (2005) The Saccharomyces cerevisiae Sae2 protein promotes resection and bridging of double strand break ends. The Journal of biological chemistry 280 : 38631–38638.

43. MullenJR, KaliramanV, BrillSJ (2000) Bipartite structure of the SGS1 DNA helicase in Saccharomyces cerevisiae. Genetics 154 : 1101–1114.

44. Cannavo E, Cejka P (2014) Sae2 promotes dsDNA endonuclease activity within Mre11-Rad50-Xrs2 to resect DNA breaks. Nature.

45. MoreauS, FergusonJR, SymingtonLS (1999) The nuclease activity of Mre11 is required for meiosis but not for mating type switching, end joining, or telomere maintenance. Molecular and cellular biology 19 : 556–566.

46. PommierY (2004) Camptothecins and topoisomerase I: a foot in the door. Targeting the genome beyond topoisomerase I with camptothecins and novel anticancer drugs: importance of DNA replication, repair and cell cycle checkpoints. Current medicinal chemistry Anti-cancer agents 4 : 429–434.

47. NishimuraK, FukagawaT, TakisawaH, KakimotoT, KanemakiM (2009) An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nature methods 6 : 917–922.

48. JainS, SugawaraN, LydeardJ, VazeM, Tanguy Le GacN, et al. (2009) A recombination execution checkpoint regulates the choice of homologous recombination pathway during DNA double-strand break repair. Genes & development 23 : 291–303.

49. LeeSE, MooreJK, HolmesA, UmezuK, KolodnerRD, et al. (1998) Saccharomyces Ku70, mre11/rad50 and RPA proteins regulate adaptation to G2/M arrest after DNA damage. Cell 94 : 399–409.

50. WhiteCI, HaberJE (1990) Intermediates of recombination during mating type switching in Saccharomyces cerevisiae. The EMBO journal 9 : 663–673.

51. ClericiM, MantieroD, LucchiniG, LongheseMP (2006) The Saccharomyces cerevisiae Sae2 protein negatively regulates DNA damage checkpoint signalling. EMBO reports 7 : 212–218.

52. ZierhutC, DiffleyJF (2008) Break dosage, cell cycle stage and DNA replication influence DNA double strand break response. The EMBO journal 27 : 1875–1885.

53. LeeK, LeeSE (2007) Saccharomyces cerevisiae Sae2 -⁠ and Tel1-dependent single-strand DNA formation at DNA break promotes microhomology-mediated end joining. Genetics 176 : 2003–2014.

54. MooreJK, HaberJE (1996) Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Molecular and cellular biology 16 : 2164–2173.

55. KimHS, VijayakumarS, RegerM, HarrisonJC, HaberJE, et al. (2008) Functional interactions between Sae2 and the Mre11 complex. Genetics 178 : 711–723.

56. BernsteinKA, MimitouEP, MihalevicMJ, ChenH, SunjavericI, et al. (2013) Resection activity of the Sgs1 helicase alters the affinity of DNA ends for homologous recombination proteins in Saccharomyces cerevisiae. Genetics 195 : 1241–1251.

57. LisbyM, BarlowJH, BurgessRC, RothsteinR (2004) Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell 118 : 699–713.

58. KayeJA, MeloJA, CheungSK, VazeMB, HaberJE, et al. (2004) DNA breaks promote genomic instability by impeding proper chromosome segregation. Current biology: CB 14 : 2096–2106.

59. LisbyM, RothsteinR (2004) DNA repair: keeping it together. Current biology: CB 14: R994–996.

60. LobachevK, VitriolE, StempleJ, ResnickMA, BloomK (2004) Chromosome fragmentation after induction of a double-strand break is an active process prevented by the RMX repair complex. Current biology: CB 14 : 2107–2112.

61. NakaiW, WestmorelandJ, YehE, BloomK, ResnickMA (2011) Chromosome integrity at a double-strand break requires exonuclease 1 and MRX. DNA repair 10 : 102–110.

62. LeeK, ZhangY, LeeSE (2008) Saccharomyces cerevisiae ATM orthologue suppresses break-induced chromosome translocations. Nature 454 : 543–546.

63. EapenVV, SugawaraN, TsabarM, WuWH, HaberJE (2012) The Saccharomyces cerevisiae chromatin remodeler Fun30 regulates DNA end resection and checkpoint deactivation. Molecular and cellular biology 32 : 4727–4740.

64. SchwartzMF, DuongJK, SunZ, MorrowJS, PradhanD, et al. (2002) Rad9 phosphorylation sites couple Rad53 to the Saccharomyces cerevisiae DNA damage checkpoint. Molecular cell 9 : 1055–1065.

65. GarciaV, PhelpsSE, GrayS, NealeMJ (2011) Bidirectional resection of DNA double-strand breaks by Mre11 and Exo1. Nature 479 : 241–244.

66. ShibataA, MoianiD, ArvaiAS, PerryJ, HardingSM, et al. (2014) DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities. Molecular cell 53 : 7–18.

67. ClericiM, MantieroD, GueriniI, LucchiniG, LongheseMP (2008) The Yku70-Yku80 complex contributes to regulate double-strand break processing and checkpoint activation during the cell cycle. EMBO reports 9 : 810–818.

68. TrovesiC, FalcettoniM, LucchiniG, ClericiM, LongheseMP (2011) Distinct Cdk1 requirements during single-strand annealing, noncrossover, and crossover recombination. PLoS genetics 7: e1002263.

69. DonnianniRA, FerrariM, LazzaroF, ClericiM, Tamilselvan NachimuthuB, et al. (2010) Elevated levels of the polo kinase Cdc5 override the Mec1/ATR checkpoint in budding yeast by acting at different steps of the signaling pathway. PLoS genetics 6: e1000763.

70. MajkaJ, BurgersPM (2003) Yeast Rad17/Mec3/Ddc1: a sliding clamp for the DNA damage checkpoint. Proceedings of the National Academy of Sciences of the United States of America 100 : 2249–2254.

71. LeeCS, LeeK, LegubeG, HaberJE (2014) Dynamics of yeast histone H2A and H2B phosphorylation in response to a double-strand break. Nature structural & molecular biology 21 : 103–109.

72. ShimEY, HongSJ, OumJH, YanezY, ZhangY, et al. (2007) RSC mobilizes nucleosomes to improve accessibility of repair machinery to the damaged chromatin. Molecular and cellular biology 27 : 1602–1613.

73. TsukudaT, FlemingAB, NickoloffJA, OsleyMA (2005) Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae. Nature 438 : 379–383.

74. WestmorelandJW, ResnickMA (2013) Coincident resection at both ends of random, gamma-induced double-strand breaks requires MRX (MRN), Sae2 (Ctp1), and Mre11-nuclease. PLoS genetics 9: e1003420.

75. GrabarzA, Guirouilh-BarbatJ, BarascuA, PennarunG, GenetD, et al. (2013) A role for BLM in double-strand break repair pathway choice: prevention of CtIP/Mre11-mediated alternative nonhomologous end-joining. Cell reports 5 : 21–28.

76. BouwmanP, AlyA, EscandellJM, PieterseM, BartkovaJ, et al. (2010) 53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers. Nature structural & molecular biology 17 : 688–695.

77. BuntingSF, CallenE, WongN, ChenHT, PolatoF, et al. (2010) 53BP1 inhibits homologous recombination in Brca1-deficient cells by blocking resection of DNA breaks. Cell 141 : 243–254.

78. PolatoF, CallenE, WongN, FaryabiR, BuntingS, et al. (2014) CtIP-mediated resection is essential for viability and can operate independently of BRCA1. The Journal of experimental medicine 211 : 1027–1036.

79. LongtineMS, McKenzieA3rd, DemariniDJ, ShahNG, WachA, et al. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14 : 953–961.

80. Muzi FalconiM, PiseriA, FerrariM, LucchiniG, PlevaniP, et al. (1993) De novo synthesis of budding yeast DNA polymerase alpha and POL1 transcription at the G1/S boundary are not required for entrance into S phase. Proceedings of the National Academy of Sciences of the United States of America 90 : 10519–10523.