1932

Abstract

It has been long understood that mutation distribution is not completely random across genomic space and in time. Indeed, recent surprising discoveries identified multiple simultaneous mutations occurring in tiny regions within chromosomes while the rest of the genome remains relatively mutation-free. Mechanistic elucidation of these phenomena, called mutation showers, mutation clusters, or kataegis, in parallel with findings of abundant clustered mutagenesis in cancer genomes, is ongoing. So far, the combination of factors most important for clustered mutagenesis is the induction of DNA lesions within unusually long and persistent single-strand DNA intermediates. In addition to being a fascinating phenomenon, clustered mutagenesis also became an indispensable tool for identifying a previously unrecognized major source of mutation in cancer, APOBEC cytidine deaminases. Future research on clustered mutagenesis may shed light onto important mechanistic details of genome maintenance, with potentially profound implications for human health.

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2015-11-23
2024-04-19
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Literature Cited

  1. Aguilera A, Garcia-Muse T. 1.  2012. R loops: from transcription byproducts to threats to genome stability. Mol. Cell 46:115–24 [Google Scholar]
  2. Albin JS, Hache G, Hultquist JF, Brown WL, Harris RS. 2.  2010. Long-term restriction by APOBEC3F selects human immunodeficiency virus type 1 variants with restored Vif function. J. Virol. 84:10209–19 [Google Scholar]
  3. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S. 3.  et al. 2013. Signatures of mutational processes in human cancer. Nature 500:415–21 [Google Scholar]
  4. Alexandrov LB, Nik-Zainal S, Wedge DC, Campbell PJ, Stratton MR. 4.  2013. Deciphering signatures of mutational processes operative in human cancer. Cell Rep. 3:246–59 [Google Scholar]
  5. Alexandrov LB, Stratton MR. 5.  2014. Mutational signatures: the patterns of somatic mutations hidden in cancer genomes. Curr. Opin. Genet. Dev. 24:52–60 [Google Scholar]
  6. Anwar F, Davenport MP, Ebrahimi D. 6.  2013. Footprint of APOBEC3 on the genome of human retroelements. J. Virol. 87:8195–204 [Google Scholar]
  7. Aramayo R, Selker EU. 6a.  2013. Neurospora crassa, a model system for epigenetics research. Cold Spring Harb. Perspect. Biol. 5:a017921 [Google Scholar]
  8. Arias JF, Koyama T, Kinomoto M, Tokunaga K. 7.  2012. Retroelements versus APOBEC3 family members: no great escape from the magnificent seven. Front. Microbiol. 3:275 [Google Scholar]
  9. Auton A, Fledel-Alon A, Pfeifer S, Venn O, Segurel L. 8.  et al. 2012. A fine-scale chimpanzee genetic map from population sequencing. Science 336:193–98 [Google Scholar]
  10. Ayala FJ, Fitch WM. 9.  1997. Genetics and the origin of species: an introduction. PNAS 94:7691–97 [Google Scholar]
  11. Bacolla A, Cooper DN, Vasquez KM. 10.  2014. Mechanisms of base substitution mutagenesis in cancer genomes. Genes 5:108–46 [Google Scholar]
  12. Bebenek K, Kunkel TA. 11.  1990. Frameshift errors initiated by nucleotide misincorporation. PNAS 87:4946–50 [Google Scholar]
  13. Benzer S, Freese E. 12.  1958. Induction of specific mutations with 5-bromouracil. PNAS 44:112–19 [Google Scholar]
  14. Berglund J, Pollard KS, Webster MT. 13.  2009. Hotspots of biased nucleotide substitutions in human genes. PLOS Biol. 7:e26 [Google Scholar]
  15. Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB. 14.  et al. 2014. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat. Commun. 5:2997 [Google Scholar]
  16. Buettner VL, Hill KA, Scaringe WA, Sommer SS. 15.  2000. Evidence that proximal multiple mutations in Big Blue transgenic mice are dependent events. Mutat. Res. 452:219–29 [Google Scholar]
  17. Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M. 16.  et al. 2012. Analysis of human accelerated DNA regions using archaic hominin genomes. PLOS ONE 7:e32877 [Google Scholar]
  18. Burch LH, Yang Y, Sterling JF, Roberts SA, Chao FG. 17.  et al. 2011. Damage-induced localized hypermutability. Cell Cycle 10:1073–85 [Google Scholar]
  19. Burns MB, Lackey L, Carpenter MA, Rathore A, Land AM. 18.  et al. 2013. APOBEC3B is an enzymatic source of mutation in breast cancer. Nature 494:366–70 [Google Scholar]
  20. Burns MB, Temiz NA, Harris RS. 19.  2013. Evidence for APOBEC3B mutagenesis in multiple human cancers. Nat. Genet. 45:977–83 [Google Scholar]
  21. Campbell CD, Chong JX, Malig M, Ko A, Dumont BL. 20.  et al. 2012. Estimating the human mutation rate using autozygosity in a founder population. Nat. Genet. 44:1277–81 [Google Scholar]
  22. Camps M, Herman A, Loh E, Loeb LA. 21.  2007. Genetic constraints on protein evolution. Crit. Rev. Biochem. Mol. Biol. 42:313–26 [Google Scholar]
  23. Carmi S, Church GM, Levanon EY. 22.  2011. Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution. Nat. Commun. 2:519 [Google Scholar]
  24. Caval V, Suspene R, Shapira M, Vartanian JP, Wain-Hobson S. 23.  2014. A prevalent cancer susceptibility APOBEC3A hybrid allele bearing APOBEC3B 3′ UTR enhances chromosomal DNA damage. Nat. Commun. 5:5129 [Google Scholar]
  25. Chan K, Resnick MA, Gordenin DA. 24.  2013. The choice of nucleotide inserted opposite abasic sites formed within chromosomal DNA reveals the polymerase activities participating in translesion DNA synthesis. DNA Repair (Amst.) 12:878–89 [Google Scholar]
  26. Chan K, Roberts SA, Klimczak LJ, Sterling JF, Saini N. 24.  et al. 2015. An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers. Nat. Genet. 47:91067–72 [Google Scholar]
  27. Chan K, Sterling JF, Roberts SA, Bhagwat AS, Resnick MA, Gordenin DA. 25.  2012. Base damage within single-strand DNA underlies in vivo hypermutability induced by a ubiquitous environmental agent. PLOS Genet. 8:e1003149 [Google Scholar]
  28. Chen J, Miller BF, Furano AV. 26.  2014. Repair of naturally occurring mismatches can induce mutations in flanking DNA. eLife 3:e02001 [Google Scholar]
  29. Chen Z, Feng J, Buzin CH, Sommer SS. 27.  2008. Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events. PLOS ONE 3:e3714 [Google Scholar]
  30. Chen Z, Feng J, Saldivar JS, Gu D, Bockholt A, Sommer SS. 28.  2008. EGFR somatic doublets in lung cancer are frequent and generally arise from a pair of driver mutations uncommonly seen as singlet mutations: one-third of doublets occur at five pairs of amino acids. Oncogene 27:4336–43 [Google Scholar]
  31. Chiu YL, Greene WC. 29.  2008. The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu. Rev. Immunol. 26:317–53 [Google Scholar]
  32. Coffin JM, Hughes SH, Varmus H. 30.  1997. Retroviruses Plainview, NY: Cold Spring Harb. Lab. Press
  33. Colgin LM, Hackmann AF, Emond MJ, Monnat RJ Jr. 31.  2002. The unexpected landscape of in vivo somatic mutation in a human epithelial cell lineage. PNAS 99:1437–42 [Google Scholar]
  34. Conticello SG, Thomas CJ, Petersen-Mahrt SK, Neuberger MS. 32.  2005. Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. Mol. Biol. Evol. 22:367–77 [Google Scholar]
  35. Costantino L, Sotiriou SK, Rantala JK, Magin S, Mladenov E. 33.  et al. 2014. Break-induced replication repair of damaged forks induces genomic duplications in human cells. Science 343:88–91 [Google Scholar]
  36. Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD. 34.  et al. 2014. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell 26:319–30 [Google Scholar]
  37. Deem A, Keszthelyi A, Blackgrove T, Vayl A, Coffey B. 35.  et al. 2011. Break-induced replication is highly inaccurate. PLOS Biol. 9:e1000594 [Google Scholar]
  38. Degtyareva NP, Heyburn L, Sterling J, Resnick MA, Gordenin DA, Doetsch PW. 36.  2013. Oxidative stress-induced mutagenesis in single-strand DNA occurs primarily at cytosines and is DNA polymerase zeta-dependent only for adenines and guanines. Nucleic Acids Res. 41:8995–9005 [Google Scholar]
  39. Dewar JM, Lydall D. 37.  2012. Similarities and differences between “uncapped” telomeres and DNA double-strand breaks. Chromosoma 121:117–30 [Google Scholar]
  40. Dobzhansky TG. 38.  1937. Genetics and the Origin of Species New York: Columbia Univ. Press
  41. Drake JW. 39.  1999. The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes. Ann. N. Y. Acad. Sci. 870:100–7 [Google Scholar]
  42. Drake JW. 40.  2007. Too many mutants with multiple mutations. Crit. Rev. Biochem. Mol. Biol. 42:247–58 [Google Scholar]
  43. Dreszer TR, Wall GD, Haussler D, Pollard KS. 41.  2007. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res. 17:1420–30 [Google Scholar]
  44. Duret L, Arndt PF. 42.  2008. The impact of recombination on nucleotide substitutions in the human genome. PLOS Genet. 4:e1000071 [Google Scholar]
  45. Francioli LC, Polak PP, Koren A, Menelaou A, Chun S. 43.  2015. Genome-wide patterns and properties of de novo mutations in humans. Nat Genet 47822–26
  46. Friedberg E, Walker G, Siede W, Wood R, Schultz R, Ellenberger T. 44.  2005. DNA Repair and Mutagenesis Washington, DC: ASM Press, 2nd ed..
  47. Friedberg EC. 45.  2003. DNA damage and repair. Nature 421:436–40 [Google Scholar]
  48. Fumagalli M, Rossiello F, Clerici M, Barozzi S, Cittaro D. 46.  et al. 2012. Telomeric DNA damage is irreparable and causes persistent DNA-damage-response activation. Nat. Cell Biol. 14:355–65 [Google Scholar]
  49. Gladyshev E, Kleckner N. 46a.  2014. Direct recognition of homology between double helices of DNA in Neurospora crassa. Nat. Comm. 5:3509 [Google Scholar]
  50. Gómez-González B, Aguilera A. 47.  2007. Activation-induced cytidine deaminase action is strongly stimulated by mutations of the THO complex. PNAS 104:8409–14 [Google Scholar]
  51. Guthrie VB, Allen J, Camps M, Karchin R. 48.  2011. Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories. PLOS Comput. Biol. 7:e1002184 [Google Scholar]
  52. Harfe BD, Jinks-Robertson S. 49.  2000. DNA polymerase zeta introduces multiple mutations when bypassing spontaneous DNA damage in Saccharomyces cerevisiae. Mol. Cell 6:1491–99 [Google Scholar]
  53. Harris RS, Bishop KN, Sheehy AM, Craig HM, Petersen-Mahrt SK. 50.  et al. 2003. DNA deamination mediates innate immunity to retroviral infection. Cell 113:803–9 [Google Scholar]
  54. Harris RS, Longerich S, Rosenberg SM. 51.  1994. Recombination in adaptive mutation. Science 264:258–60 [Google Scholar]
  55. Harris RS, Petersen-Mahrt SK, Neuberger MS. 52.  2002. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol. Cell 10:1247–53 [Google Scholar]
  56. Helleday T, Eshtad S, Nik-Zainal S. 53.  2014. Mechanisms underlying mutational signatures in human cancers. Nat. Rev. Genet. 15:585–98 [Google Scholar]
  57. Hicks WM, Kim M, Haber JE. 54.  2010. Increased mutagenesis and unique mutation signature associated with mitotic gene conversion. Science 329:82–85 [Google Scholar]
  58. Hill KA, Wang J, Farwell KD, Scaringe WA, Sommer SS. 55.  2004. Spontaneous multiple mutations show both proximal spacing consistent with chronocoordinate events and alterations with p53-deficiency. Mutat. Res. 554:223–40 [Google Scholar]
  59. Kaiser SM, Emerman M. 56.  2006. Uracil DNA glycosylase is dispensable for human immunodeficiency virus type 1 replication and does not contribute to the antiviral effects of the cytidine deaminase APOBEC3G. J. Virol. 80:875–82 [Google Scholar]
  60. Kashuba VI, Pavlova TV, Grigorieva EV, Kutsenko A, Yenamandra SP. 57.  et al. 2009. High mutability of the tumor suppressor genes RASSF1 and RBSP3 (CTDSPL) in cancer. PLOS ONE 4:e5231 [Google Scholar]
  61. Kasiviswanathan R, Collins TR, Copeland WC. 58.  2012. The interface of transcription and DNA replication in the mitochondria. Biochim. Biophys. Acta 1819:970–78 [Google Scholar]
  62. Kaufmann WK. 59.  2007. Initiating the uninitiated: replication of damaged DNA and carcinogenesis. Cell Cycle 6:1460–67 [Google Scholar]
  63. Kimura M. 60.  1984. The Neutral Theory of Molecular Evolution Cambridge, UK: Cambridge Univ. Press
  64. Kogenaru M, de Vos MG, Tans SJ. 61.  2009. Revealing evolutionary pathways by fitness landscape reconstruction. Crit. Rev. Biochem. Mol. Biol. 44:169–74 [Google Scholar]
  65. Kohler SW, Provost GS, Fieck A, Kretz PL, Bullock WO. 62.  et al. 1991. Spectra of spontaneous and mutagen-induced mutations in the lacI gene in transgenic mice. PNAS 88:7958–62 [Google Scholar]
  66. Lada AG, Dhar A, Boissy RJ, Hirano M, Rubel AA. 63.  et al. 2012. AID/APOBEC cytosine deaminase induces genome-wide kataegis. Biol. Direct 7:47 [Google Scholar]
  67. Lada AG, Stepchenkova EI, Waisertreiger ISR, Noskov VN, Dhar A. 64.  et al. 2013. Genome-wide mutation avalanches induced in diploid yeast cells by a base analog or an APOBEC deaminase. PLOS Genet. 9:e1003736 [Google Scholar]
  68. Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K. 65.  et al. 2013. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499:214–18 [Google Scholar]
  69. Leman AR, Noguchi E. 66.  2012. Local and global functions of Timeless and Tipin in replication fork protection. Cell Cycle 11:3945–55 [Google Scholar]
  70. Lercher MJ, Hurst LD. 67.  2002. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18:337–40 [Google Scholar]
  71. Levine JG, Schaaper RM, DeMarini DM. 68.  1994. Complex frameshift mutations mediated by plasmid pKM101: mutational mechanisms deduced from 4-aminobiphenyl-induced mutation spectra in Salmonella. Genetics 136:731–46 [Google Scholar]
  72. Lindahl T, Barnes DE. 69.  2000. Repair of endogenous DNA damage. Cold Spring Harb. Symp. Quant. Biol. 65:127–33 [Google Scholar]
  73. Liu M, Schatz DG. 70.  2009. Balancing AID and DNA repair during somatic hypermutation. Trends Immunol. 30:173–81 [Google Scholar]
  74. Long J, Delahanty RJ, Li G, Gao YT, Lu W. 71.  et al. 2013. A common deletion in the APOBEC3 genes and breast cancer risk. J. Natl. Cancer Inst. 105:573–79 [Google Scholar]
  75. Ma W, Resnick MA, Gordenin DA. 72.  2008. Apn1 and Apn2 endonucleases prevent accumulation of repair-associated DNA breaks in budding yeast as revealed by direct chromosomal analysis. Nucleic Acids Res. 36:1836–46 [Google Scholar]
  76. Magni GE, Von Borstel RC. 73.  1962. Different rates of spontaneous mutation during mitosis and meiosis in yeast. Genetics 47:1097–108 [Google Scholar]
  77. Malkova A, Haber JE. 74.  2012. Mutations arising during repair of chromosome breaks. Annu. Rev. Genet. 46:455–73 [Google Scholar]
  78. Malkova A, Ira G. 75.  2013. Break-induced replication: functions and molecular mechanism. Curr. Opin. Genet. Dev. 23:271–79 [Google Scholar]
  79. Mannervik B, Runarsdottir A. 76.  2010. The quest for molecular quasi-species in ligand-activity space and its application to directed enzyme evolution. FEBS Lett. 584:2565–71 [Google Scholar]
  80. Matsuda T, Bebenek K, Masutani C, Hanaoka F, Kunkel TA. 77.  2000. Low fidelity DNA synthesis by human DNA polymerase-eta. Nature 404:1011–13 [Google Scholar]
  81. Maul RW, Gearhart PJ. 78.  2010. AID and somatic hypermutation. Adv. Immunol. 105:159–91 [Google Scholar]
  82. Michaelson JJ, Shi Y, Gujral M, Zheng H, Malhotra D. 79.  et al. 2012. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell 151:1431–42 [Google Scholar]
  83. Miller AS, Balakrishnan L, Buncher NA, Opresko PL, Bambara RA. 80.  2012. Telomere proteins POT1, TRF1 and TRF2 augment long-patch base excision repair in vitro. Cell Cycle 11:998–1007 [Google Scholar]
  84. Mimitou EP, Symington LS. 81.  2011. DNA end resection: unraveling the tail. DNA Repair (Amst.) 10:344–48 [Google Scholar]
  85. Nachman MW. 82.  2001. Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17:481–85 [Google Scholar]
  86. Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD. 83.  et al. 2012. Mutational processes molding the genomes of 21 breast cancers. Cell 149:979–93 [Google Scholar]
  87. Nik-Zainal S, Wedge DC, Alexandrov LB, Petljak M, Butler AP. 84.  et al. 2014. Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer. Nat. Genet. 46:487–91 [Google Scholar]
  88. Northam MR, Moore EA, Mertz TM, Binz SK, Stith CM. 85.  et al. 2014. DNA polymerases ζ and Rev1 mediate error-prone bypass of non-B DNA structures. Nucleic Acids Res. 42:290–306 [Google Scholar]
  89. Northam MR, Robinson HA, Kochenova OV, Shcherbakova PV. 86.  2010. Participation of DNA polymerase zeta in replication of undamaged DNA in Saccharomyces cerevisiae. Genetics 184:27–42 [Google Scholar]
  90. Ohta T. 87.  1987. Simulating evolution by gene duplication. Genetics 115:207–13 [Google Scholar]
  91. Parkhomchuk D, Amstislavskiy V, Soldatov A, Ogryzko V. 88.  2009. Use of high throughput sequencing to observe genome dynamics at a single cell level. PNAS 106:20830–35 [Google Scholar]
  92. Pavri R, Nussenzweig MC. 89.  2011. AID targeting in antibody diversity. Adv. Immunol. 110:1–26 [Google Scholar]
  93. Peled JU, Kuang FL, Iglesias-Ussel MD, Roa S, Kalis SL. 90.  et al. 2008. The biochemistry of somatic hypermutation. Annu. Rev. Immunol. 26:481–511 [Google Scholar]
  94. Pettersen HS, Galashevskaya A, Doseth B, Sousa MM, Sarno A. 91.  et al. 2015. AID expression in B-cell lymphomas causes accumulation of genomic uracil and a distinct AID mutational signature. DNA Repair (Amst.) 25:60–71 [Google Scholar]
  95. Plosky BS, Woodgate R. 92.  2004. Switching from high-fidelity replicases to low-fidelity lesion-bypass polymerases. Curr. Opin. Genet. Dev. 14:113–19 [Google Scholar]
  96. Pollard KS, Salama SR, King B, Kern AD, Dreszer T. 93.  et al. 2006. Forces shaping the fastest evolving regions in the human genome. PLOS Genet. 2:e168 [Google Scholar]
  97. Poon S, McPherson J, Tan P, Teh B, Rozen S. 94.  2014. Mutation signatures of carcinogen exposure: genome-wide detection and new opportunities for cancer prevention. Genome Med. 6:24 [Google Scholar]
  98. Pope-Varsalona H, Liu F-J, Guzik L, Opresko PL. 95.  2014. Polymerase η suppresses telomere defects induced by DNA damaging agents. Nucleic Acids Res. 42:13096–109 [Google Scholar]
  99. Povolotskaya IS, Kondrashov FA. 96.  2010. Sequence space and the ongoing expansion of the protein universe. Nature 465:922–26 [Google Scholar]
  100. Pratto F, Brick K, Khil P, Smagulova F, Petukhova GV, Camerini-Otero RD. 97.  2014. Recombination initiation maps of individual human genomes. Science 346:6211 [Google Scholar]
  101. Qian J, Wang Q, Dose M, Pruett N, Kieffer-Kwon KR. 98.  et al. 2014. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell 159:1524–37 [Google Scholar]
  102. Rebhandl S, Huemer M, Gassner FJ, Zaborsky N, Hebenstreit D. 99.  et al. 2014. APOBEC3 signature mutations in chronic lymphocytic leukemia. Leukemia 28:1929–32 [Google Scholar]
  103. Refsland EW, Harris RS. 100.  2013. The APOBEC3 family of retroelement restriction factors. Curr. Top. Microbiol. Immunol. 371:1–27 [Google Scholar]
  104. Rhind N, Gilbert DM. 101.  2013. DNA replication timing. Cold Spring Harb. Perspect. Biol. 5:a010132 [Google Scholar]
  105. Richardson SR, Narvaiza I, Planegger RA, Weitzman MD, Moran JV. 102.  2014. APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition. eLife 3:e02008 [Google Scholar]
  106. Ripley LS. 103.  1990. Frameshift mutation: determinants of specificity. Annu. Rev. Genet. 24:189–213 [Google Scholar]
  107. Roberts SA, Gordenin DA. 104.  2014. Clustered and genome-wide transient mutagenesis in human cancers: hypermutation without permanent mutators or loss of fitness. BioEssays 36:382–93 [Google Scholar]
  108. Roberts SA, Gordenin DA. 105.  2014. Clustered mutations in human cancer. eLS doi: 10.1002/9780470015902.a0024941
  109. Roberts SA, Gordenin DA. 106.  2014. Hypermutation in human cancer genomes: footprints and mechanisms. Nat. Rev. Cancer 14:786–800 [Google Scholar]
  110. Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D. 107.  et al. 2013. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat. Genet. 45:970–76 [Google Scholar]
  111. Roberts SA, Sterling J, Thompson C, Harris S, Mav D. 108.  et al. 2012. Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. Mol. Cell 46:424–35 [Google Scholar]
  112. Rochette PJ, Brash DE. 109.  2010. Human telomeres are hypersensitive to UV-induced DNA damage and refractory to repair. PLOS Genet. 6:e1000926 [Google Scholar]
  113. Rogozin IB, Pavlov YI. 110.  2003. Theoretical analysis of mutation hotspots and their DNA sequence context specificity. Mutat. Res. Rev. Mutat. 544:65–85 [Google Scholar]
  114. Rogozin IB, Pavlov YI, Bebenek K, Matsuda T, Kunkel TA. 111.  2001. Somatic mutation hotspots correlate with DNA polymerase η error spectrum. Nat. Immunol. 2:530–36 [Google Scholar]
  115. Saini N, Ramakrishnan S, Elango R, Ayyar S, Zhang Y. 112.  et al. 2013. Migrating bubble during break-induced replication drives conservative DNA synthesis. Nature 502:389–92 [Google Scholar]
  116. Sakofsky CJ, Roberts SA, Malc E, Mieczkowski PA, Resnick MA. 113.  et al. 2014. Break-induced replication is a source of mutation clusters underlying kataegis. Cell Rep. 7:1640–48 [Google Scholar]
  117. Sale JE. 114.  2013. Translesion DNA synthesis and mutagenesis in eukaryotes. Cold Spring Harb. Perspect. Biol. 5:a012708 [Google Scholar]
  118. Schumacher AJ, Hache G, Macduff DA, Brown WL, Harris RS. 115.  2008. The DNA deaminase activity of human APOBEC3G is required for Ty1, MusD, and human immunodeficiency virus type 1 restriction. J. Virol. 82:2652–60 [Google Scholar]
  119. Schumacher AJ, Nissley DV, Harris RS. 116.  2005. APOBEC3G hypermutates genomic DNA and inhibits Ty1 retrotransposition in yeast. PNAS 102:9854–59 [Google Scholar]
  120. Shcherbakova PV, Fijalkowska IJ. 117.  2006. Translesion synthesis DNA polymerases and control of genome stability. Front. Biosci. 11:2496–517 [Google Scholar]
  121. Sima J, Gilbert DM. 118.  2014. Complex correlations: replication timing and mutational landscapes during cancer and genome evolution. Curr. Opin. Genet. Dev. 25:93–100 [Google Scholar]
  122. Smith JM. 119.  1970. Natural selection and the concept of a protein space. Nature 225:563–64 [Google Scholar]
  123. Spencer CC, Deloukas P, Hunt S, Mullikin J, Myers S. 120.  et al. 2006. The influence of recombination on human genetic diversity. PLOS Genet. 2:e148 [Google Scholar]
  124. Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. 121.  2009. Human mutation rate associated with DNA replication timing. Nat. Genet. 41:393–95 [Google Scholar]
  125. Steele EJ. 122.  2009. Mechanism of somatic hypermutation: critical analysis of strand biased mutation signatures at A:T and G:C base pairs. Mol. Immunol. 46:305–20 [Google Scholar]
  126. Stone JE, Lujan SA, Kunkel TA. 123.  2012. DNA polymerase zeta generates clustered mutations during bypass of endogenous DNA lesions in Saccharomyces cerevisiae. Environ. Mol. Mutagen. 53:777–86 [Google Scholar]
  127. Strathern JN, Shafer BK, McGill CB. 124.  1995. DNA synthesis errors associated with double-strand-break repair. Genetics 140:965–72 [Google Scholar]
  128. Stumpf JD, Copeland WC. 125.  2014. MMS exposure promotes increased MtDNA mutagenesis in the presence of replication-defective disease-associated DNA polymerase γ variants. PLOS Genet. 10:e1004748 [Google Scholar]
  129. Sunagar K, Fry BG, Jackson TN, Casewell NR, Undheim EA. 126.  et al. 2013. Molecular evolution of vertebrate neurotrophins: co-option of the highly conserved nerve growth factor gene into the advanced snake venom arsenal. PLOS ONE 8:e81827 [Google Scholar]
  130. Tang H, Kuhen KL, Wong-Staal F. 127.  1999. Lentivirus replication and regulation. Annu. Rev. Genet. 33:133–70 [Google Scholar]
  131. Taylor BJ, Nik-Zainal S, Wu YL, Stebbings LA, Raine K. 128.  et al. 2013. DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis. eLife 2:e00534 [Google Scholar]
  132. Taylor BJ, Wu YL, Rada C. 129.  2014. Active RNAP pre-initiation sites are highly mutated by cytidine deaminases in yeast, with AID targeting small RNA genes. eLife 3:e03553 [Google Scholar]
  133. Teng G, Papavasiliou FN. 130.  2007. Immunoglobulin somatic hypermutation. Annu. Rev. Genet. 41:107–20 [Google Scholar]
  134. Timoféeff-Ressovsky N, Zimmer K, Delbrück M. 131.  1935. The nature of genetic mutations and structure of the gene. Nachr. Biol. Ges. Wiss. Gött. 1:189–245 [Google Scholar]
  135. Wang J, Gonzalez KD, Scaringe WA, Tsai K, Liu N. 132.  et al. 2007. Evidence for mutation showers. PNAS 104:8403–8 [Google Scholar]
  136. Weinreich DM, Watson RA, Chao L. 133.  2005. Perspective: sign epistasis and genetic constraint on evolutionary trajectories. Evolution 59:1165–74 [Google Scholar]
  137. Wilburn DB, Bowen KE, Doty KA, Arumugam S, Lane AN. 134.  et al. 2014. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani. PLOS ONE 9:e96975 [Google Scholar]
  138. Willis NA, Chandramouly G, Huang B, Kwok A, Follonier C. 135.  et al. 2014. BRCA1 controls homologous recombination at Tus/Ter-stalled mammalian replication forks. Nature 510:556–59 [Google Scholar]
  139. Wright S. 136.  1932. The roles of mutation, inbreeding, crossbreading and selection in evolution. Proc. Sixth Int. Congr. Genet. 1:356–66 [Google Scholar]
  140. Xuan D, Li G, Cai Q, Deming-Halverson S, Shrubsole MJ. 137.  et al. 2013. APOBEC3 deletion polymorphism is associated with breast cancer risk among women of European ancestry. Carcinogenesis 34:2240–43 [Google Scholar]
  141. Yang B, Chen K, Zhang C, Huang S, Zhang H. 138.  2007. Virion-associated uracil DNA glycosylase-2 and apurinic/apyrimidinic endonuclease are involved in the degradation of APOBEC3G-edited nascent HIV-1 DNA. J. Biol. Chem. 282:11667–75 [Google Scholar]
  142. Yang Y, Gordenin DA, Resnick MA. 139.  2010. A single-strand specific lesion drives MMS-induced hyper-mutability at a double-strand break in yeast. DNA Repair Amst. 9:914–21 [Google Scholar]
  143. Yang Y, Sterling J, Storici F, Resnick MA, Gordenin DA. 140.  2008. Hypermutability of damaged single-strand DNA formed at double-strand breaks and uncapped telomeres in yeast Saccharomyces cerevisiae. PLOS Genet. 4:e1000264 [Google Scholar]
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