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DNA Repair Pathway Selection Caused by Defects in , , and Telomere Addition Generates Specific Chromosomal Rearrangement Signatures


Recent advances in the sequencing of human cancer genomes have revealed that some types of genome rearrangements are more common in specific types of cancers. Thus, these cancers may share defects in DNA repair mechanisms, which may play roles in initiation or progression of the disease and may be useful therapeutically. Linking a common rearrangement signature to a specific genetic or epigenetic alteration is currently challenging, because we do not know which rearrangement signatures are linked to which DNA repair defects. Here we used a genetic assay in the model organism Saccharomyces cerevisiae to specifically link two classes of chromosomal rearrangements, interstitial deletions and inverted duplications, to specific genetic defects. These results begin to map out the links between observed chromosomal rearrangements and specific DNA repair defects and in the present case, may provide insights into the chromosomal rearrangements frequently observed in metastatic pancreatic cancer.


Vyšlo v časopise: DNA Repair Pathway Selection Caused by Defects in , , and Telomere Addition Generates Specific Chromosomal Rearrangement Signatures. PLoS Genet 10(4): e32767. doi:10.1371/journal.pgen.1004277
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004277

Souhrn

Recent advances in the sequencing of human cancer genomes have revealed that some types of genome rearrangements are more common in specific types of cancers. Thus, these cancers may share defects in DNA repair mechanisms, which may play roles in initiation or progression of the disease and may be useful therapeutically. Linking a common rearrangement signature to a specific genetic or epigenetic alteration is currently challenging, because we do not know which rearrangement signatures are linked to which DNA repair defects. Here we used a genetic assay in the model organism Saccharomyces cerevisiae to specifically link two classes of chromosomal rearrangements, interstitial deletions and inverted duplications, to specific genetic defects. These results begin to map out the links between observed chromosomal rearrangements and specific DNA repair defects and in the present case, may provide insights into the chromosomal rearrangements frequently observed in metastatic pancreatic cancer.


Zdroje

1. SaundersWS, ShusterM, HuangX, GharaibehB, EnyenihiAH, et al. (2000) Chromosomal instability and cytoskeletal defects in oral cancer cells. Proc Natl Acad Sci U S A 97: 303–308.

2. GisselssonD, PetterssonL, HoglundM, HeidenbladM, GorunovaL, et al. (2000) Chromosomal breakage-fusion-bridge events cause genetic intratumor heterogeneity. Proc Natl Acad Sci U S A 97: 5357–5362.

3. FouladiB, SabatierL, MillerD, PottierG, MurnaneJP (2000) The relationship between spontaneous telomere loss and chromosome instability in a human tumor cell line. Neoplasia 2: 540–554.

4. GisselssonD, HoglundM (2005) Connecting mitotic instability and chromosome aberrations in cancer–can telomeres bridge the gap? Semin Cancer Biol 15: 13–23.

5. ChanKL, NorthPS, HicksonID (2007) BLM is required for faithful chromosome segregation and its localization defines a class of ultrafine anaphase bridges. EMBO J 26: 3397–3409.

6. LeeE, IskowR, YangL, GokcumenO, HaseleyP, et al. (2012) Landscape of somatic retrotransposition in human cancers. Science 337: 967–971.

7. CampbellPJ, YachidaS, MudieLJ, StephensPJ, PleasanceED, et al. (2010) The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467: 1109–1113.

8. McBrideDJ, EtemadmoghadamD, CookeSL, AlsopK, GeorgeJ, et al. (2012) Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes. J Pathol 227: 446–455.

9. StephensPJ, McBrideDJ, LinML, VarelaI, PleasanceED, et al. (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462: 1005–1010.

10. The Cancer Genome Atlas (2011) Integrated genomic analyses of ovarian carcinoma. Nature 474: 609–615.

11. ChenC, KolodnerRD (1999) Gross chromosomal rearrangements in Saccharomyces cerevisiae replication and recombination defective mutants. Nat Genet 23: 81–85.

12. HackettJA, FeldserDM, GreiderCW (2001) Telomere dysfunction increases mutation rate and genomic instability. Cell 106: 275–286.

13. KanellisP, GagliardiM, BanathJP, SzilardRK, NakadaS, et al. (2007) A screen for suppressors of gross chromosomal rearrangements identifies a conserved role for PLP in preventing DNA lesions. PLoS Genet 3: e134.

14. PutnamCD, HayesTK, KolodnerRD (2009) Specific pathways prevent duplication-mediated genome rearrangements. Nature 460: 984–989.

15. ChanJE, KolodnerRD (2011) A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements. PLoS Genet 7: e1002089.

16. MyungK, ChenC, KolodnerRD (2001) Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae. Nature 411: 1073–1076.

17. PutnamCD, PennaneachV, KolodnerRD (2004) Chromosome healing through terminal deletions generated by de novo telomere additions in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 101: 13262–13267.

18. PutnamCD, PennaneachV, KolodnerRD (2005) Saccharomyces cerevisiae as a model system to define the chromosomal instability phenotype. Mol Cell Biol 25: 7226–7238.

19. PennaneachV, KolodnerRD (2004) Recombination and the Tel1 and Mec1 checkpoints differentially effect genome rearrangements driven by telomere dysfunction in yeast. Nat Genet 36: 612–617.

20. PennaneachV, KolodnerRD (2009) Stabilization of dicentric translocations through secondary rearrangements mediated by multiple mechanisms in S. cerevisiae. PLoS One 4: e6389.

21. PutnamCD, HayesTK, KolodnerRD (2010) Post-replication repair suppresses duplication-mediated genome instability. PLoS Genet 6: e1000933.

22. MyungK, DattaA, KolodnerRD (2001) Suppression of spontaneous chromosomal rearrangements by S phase checkpoint functions in Saccharomyces cerevisiae. Cell 104: 397–408.

23. ChanSW, BlackburnEH (2003) Telomerase and ATM/Tel1p protect telomeres from nonhomologous end joining. Mol Cell 11: 1379–1387.

24. DuBoisML, HaimbergerZW, McIntoshMW, GottschlingDE (2002) A quantitative assay for telomere protection in Saccharomyces cerevisiae. Genetics 161: 995–1013.

25. RitchieKB, MalloryJC, PetesTD (1999) Interactions of TLC1 (which encodes the RNA subunit of telomerase), TEL1, and MEC1 in regulating telomere length in the yeast Saccharomyces cerevisiae. Mol Cell Biol 19: 6065–6075.

26. SchmidtKH, PennaneachV, PutnamCD, KolodnerRD (2006) Analysis of gross-chromosomal rearrangements in Saccharomyces cerevisiae. Methods Enzymol 409: 462–476.

27. SchoutenJP, McElgunnCJ, WaaijerR, ZwijnenburgD, DiepvensF, et al. (2002) Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 30: e57.

28. ChanJE, KolodnerRD (2012) Rapid analysis of Saccharomyces cerevisiae genome rearrangements by multiplex ligation-dependent probe amplification. PLoS Genet 8: e1002539.

29. DudasovaZ, DudasA, ChovanecM (2004) Non-homologous end-joining factors of Saccharomyces cerevisiae. FEMS Microbiol Rev 28: 581–601.

30. McEachernMJ, HaberJE (2006) Break-induced replication and recombinational telomere elongation in yeast. Annu Rev Biochem 75: 111–135.

31. Flores-RozasH, KolodnerRD (2000) Links between replication, recombination and genome instability in eukaryotes. Trends Biochem Sci 25: 196–200.

32. LengsfeldBM, RattrayAJ, BhaskaraV, GhirlandoR, PaullTT (2007) Sae2 is an endonuclease that processes hairpin DNA cooperatively with the Mre11/Rad50/Xrs2 complex. Mol Cell 28: 638–651.

33. LobachevKS, GordeninDA, ResnickMA (2002) The Mre11 complex is required for repair of hairpin-capped double-strand breaks and prevention of chromosome rearrangements. Cell 108: 183–193.

34. RattrayAJ, ShaferBK, NeelamB, StrathernJN (2005) A mechanism of palindromic gene amplification in Saccharomyces cerevisiae. Genes Dev 19: 1390–1399.

35. BaroniE, ViscardiV, Cartagena-LirolaH, LucchiniG, LongheseMP (2004) The functions of budding yeast Sae2 in the DNA damage response require Mec1- and Tel1-dependent phosphorylation. Mol Cell Biol 24: 4151–4165.

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

37. Cartagena-LirolaH, GueriniI, ViscardiV, LucchiniG, LongheseMP (2006) Budding Yeast Sae2 is an In Vivo Target of the Mec1 and Tel1 Checkpoint Kinases During Meiosis. Cell Cycle 5: 1549–1559.

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

39. NakadaD, MatsumotoK, SugimotoK (2003) ATM-related Tel1 associates with double-strand breaks through an Xrs2-dependent mechanism. Genes Dev 17: 1957–1962.

40. SymingtonLS, GautierJ (2011) Double-strand break end resection and repair pathway choice. Annu Rev Genet 45: 247–271.

41. SmithS, GuptaA, KolodnerRD, MyungK (2005) Suppression of gross chromosomal rearrangements by the multiple functions of the Mre11-Rad50-Xrs2 complex in Saccharomyces cerevisiae. DNA Repair (Amst) 4: 606–617.

42. Tittel-ElmerM, AlabertC, PaseroP, CobbJA (2009) The MRX complex stabilizes the replisome independently of the S phase checkpoint during replication stress. EMBO J 28: 1142–1156.

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

44. NairzK, KleinF (1997) mre11S–a yeast mutation that blocks double-strand-break processing and permits nonhomologous synapsis in meiosis. Genes Dev 11: 2272–2290.

45. BressanDA, OlivaresHA, NelmsBE, PetriniJH (1998) Alteration of N-terminal phosphoesterase signature motifs inactivates Saccharomyces cerevisiae Mre11. Genetics 150: 591–600.

46. MoreauS, FergusonJR, SymingtonLS (1999) The nuclease activity of Mre11 is required for meiosis but not for mating type switching, end joining, or telomere maintenance. Mol Cell Biol 19: 556–566.

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

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

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

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

51. 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 Genet 6: e1000973.

52. MorrowDM, TagleDA, ShilohY, CollinsFS, HieterP (1995) TEL1, an S. cerevisiae homolog of the human gene mutated in ataxia telangiectasia, is functionally related to the yeast checkpoint gene MEC1. Cell 82: 831–840.

53. SanchezY, DesanyBA, JonesWJ, LiuQ, WangB, et al. (1996) Regulation of RAD53 by the ATM-like kinases MEC1 and TEL1 in yeast cell cycle checkpoint pathways. Science 271: 357–360.

54. UsuiT, OgawaH, PetriniJH (2001) A DNA damage response pathway controlled by Tel1 and the Mre11 complex. Mol Cell 7: 1255–1266.

55. LustigAJ, PetesTD (1986) Identification of yeast mutants with altered telomere structure. Proc Natl Acad Sci U S A 83: 1398–1402.

56. PennaneachV, PutnamCD, KolodnerRD (2006) Chromosome healing by de novo telomere addition in Saccharomyces cerevisiae. Mol Microbiol 59: 1357–1368.

57. ZhangW, DurocherD (2010) De novo telomere formation is suppressed by the Mec1-dependent inhibition of Cdc13 accumulation at DNA breaks. Genes Dev 24: 502–515.

58. SchulzVP, ZakianVA (1994) The saccharomyces PIF1 DNA helicase inhibits telomere elongation and de novo telomere formation. Cell 76: 145–155.

59. BouleJB, VegaLR, ZakianVA (2005) The yeast Pif1p helicase removes telomerase from telomeric DNA. Nature 438: 57–61.

60. ZhouJ, MonsonEK, TengSC, SchulzVP, ZakianVA (2000) Pif1p helicase, a catalytic inhibitor of telomerase in yeast. Science 289: 771–774.

61. MizunoK, LambertS, BaldacciG, MurrayJM, CarrAM (2009) Nearby inverted repeats fuse to generate acentric and dicentric palindromic chromosomes by a replication template exchange mechanism. Genes Dev 23: 2876–2886.

62. PaekAL, KaocharS, JonesH, ElezabyA, ShanksL, et al. (2009) Fusion of nearby inverted repeats by a replication-based mechanism leads to formation of dicentric and acentric chromosomes that cause genome instability in budding yeast. Genes Dev 23: 2861–2875.

63. McClintockB (1941) The Stability of Broken Ends of Chromosomes in Zea Mays. Genetics 26: 234–282.

64. SchmidtKH, WuJ, KolodnerRD (2006) Control of translocations between highly diverged genes by Sgs1, the Saccharomyces cerevisiae homolog of the Bloom's syndrome protein. Mol Cell Biol 26: 5406–5420.

65. SmithCE, LlorenteB, SymingtonLS (2007) Template switching during break-induced replication. Nature 447: 102–105.

66. RattrayAJ, McGillCB, ShaferBK, StrathernJN (2001) Fidelity of mitotic double-strand-break repair in Saccharomyces cerevisiae: a role for SAE2/COM1. Genetics 158: 109–122.

67. 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.

68. ChenQ, IjpmaA, GreiderCW (2001) Two survivor pathways that allow growth in the absence of telomerase are generated by distinct telomere recombination events. Mol Cell Biol 21: 1819–1827.

69. WellingerRJ, ZakianVA (2012) Everything you ever wanted to know about Saccharomyces cerevisiae telomeres: beginning to end. Genetics 191: 1073–1105.

70. SikorskiRS, HieterP (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19–27.

71. Putnam CD, Kolodner RD (2010) Determination of gross chromosomal rearrangement rates. Cold Spring Harb Protoc 2010: pdb prot5492.

72. Sokal RR, Rohlf FJ (1994) Biometry: the principles and practice of statistics in biological research. New York: Freeman.

73. GerringSL, ConnellyC, HieterP (1991) Positional mapping of genes by chromosome blotting and chromosome fragmentation. Methods Enzymol 194: 57–77.

74. LangmeadB, TrapnellC, PopM, SalzbergSL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.

75. ChenH, LisbyM, SymingtonLS (2013) RPA coordinates DNA end resection and prevents formation of DNA hairpins. Mol Cell 50: 589–600.

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