Physiology of the read-write genome

Journal of Physiology

Volumn 592, Issue 11, 2014, Pages 2319-2341

  Shapiro, James A ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE;

APOPTOSIS; CELL FUNCTION; CELL PROTECTION; CYTOGENETICS; DNA DAMAGE; DNA END JOINING REPAIR; DNA REPAIR; DNA SEQUENCE; GENE FUNCTION; GENE MUTATION; GENE REARRANGEMENT; GENETIC ENGINEERING; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; GENOME; GENOMICS; HOMEOSTASIS; HUMAN; LIFE HISTORY; MISMATCH REPAIR; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; NEOPLASM; NONHUMAN; PHYSIOLOGY; POINT MUTATION; PRIORITY JOURNAL; PROTEIN BINDING; REGULATORY MECHANISM; REVIEW; ANIMAL; GENE EXPRESSION REGULATION; GENETICS;

ANIMALS; GENE EXPRESSION REGULATION; GENOME; HOMEOSTASIS;

EID: 84901038787     PISSN: 00223751     EISSN: 14697793     Source Type: Journal    
DOI: 10.1113/jphysiol.2014.271130     Document Type: Review

References (379)

1. Acuna R, Padilla BE, Florez-Ramos CP, Rubio JD, Herrera JC, Benavides P, Lee SJ, Yeats TH, Egan AN, Doyle JJ & Rose JK (2012). Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee. Proc Natl Acad Sci U S A 109, 4197-4202.
2. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Borresen-Dale AL, Boyault S, Burkhardt B, Butler AP, Caldas C, Davies HR, Desmedt C, Eils R, Eyfjord JE, Foekens JA, Greaves M, Hosoda F, Hutter B, Ilicic T, Imbeaud S, Imielinsk M, Jager N, Jones DT, Jones D, Knappskog S, Kool M, Lakhani SR, Lopez-Otin C, Martin S, Munshi NC, Nakamura H, Northcott PA, Pajic M, Papaemmanuil E, Paradiso A, Pearson JV, Puente XS, Raine K, Ramakrishna M, Richardson AL, Richter J, Rosenstiel P, Schlesner M, Schumacher TN, Span PN, Teague JW, Totoki Y, Tutt AN, Valdes-Mas R, van Buuren MM, van 't Veer L, Vincent-Salomon A, Waddell N, Yates LR, Zucman-Rossi J, Andrew Futreal P, McDermott U, Lichter P, Meyerson M, Grimmond SM, Siebert R, Campo E, Shibata T, Pfister SM, Campbell PJ & Stratton MR (2013). Signatures of mutational processes in human cancer. Nature 500, 415-421.
3. Alperovitch-Lavy A, Sharon I, Rohwer F, Aro EM, Glaser F, Milo R, Nelson N & Beja O (2011). Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets. Environ Microbiol 13, 24-32.
4. Alt FW, Zhang Y, Meng FL, Guo C & Schwer B (2013). Mechanisms of programmed DNA lesions and genomic instability in the immune system. Cell 152, 417-429.
5. Amundsen SK & Smith GR (2007). Chi hotspot activity in Escherichia coli without RecBCD exonuclease activity: implications for the mechanism of recombination. Genetics 175, 41-54.
6. Armengol L, Pujana MA, Cheung J, Scherer SW & Estivill X (2003). Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Hum Mol Genet 12, 2201-2208.
7. Auchtung JM, Lee CA, Monson RE, Lehman AP & Grossman AD (2005). Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc Natl Acad Sci U S A 102, 12554-12559.
8. Bachmann-Waldmann C, Jentsch S, Tobler H & Muller F (2004). Chromatin diminution leads to rapid evolutionary changes in the organization of the germ line genomes of the parasitic nematodes A. suum and P. univalens. Mol Biochem Parasitol 134, 53-64.
9. Baertsch R, Diekhans M, Kent WJ, Haussler D & Brosius J (2008). Retrocopy contributions to the evolution of the human genome. BMC Genomics 9, 466.
10. Barbieri CE, Baca SC, Lawrence MS, Demichelis F, Blattner M, Theurillat JP, White TA, Stojanov P, Van Allen E, Stransky N, Nickerson E, Chae SS, Boysen G, Auclair D, Onofrio RC, Park K, Kitabayashi N, MacDonald TY, Sheikh K, Vuong T, Guiducci C, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Hussain WM, Ramos AH, Winckler W, Redman MC, Ardlie K, Tewari AK, Mosquera JM, Rupp N, Wild PJ, Moch H, Morrissey C, Nelson PS, Kantoff PW, Gabriel SB, Golub TR, Meyerson M, Lander ES, Getz G, Rubin MA & Garraway LA (2012). Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet 44, 685-689.
11. Barbour AG, Dai Q, Restrepo BI, Stoenner HG & Frank SA (2006). Pathogen escape from host immunity by a genome program for antigenic variation. Proc Natl Acad Sci U S A 103, 18290-18295.
12. Barrangou R (2013). CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip Rev RNA 4, 267-278.
13. Barry JD & McCulloch R (2001). Antigenic variation in trypanosomes: enhanced phenotypic variation in a eukaryotic parasite. Adv Parasitol 49, 1-70.
14. Bassing CH, Swat W & Alt FW (2002). The mechanism and regulation of chromosomal V(D)J recombination. Cell 109, S45-55.
15. Baudat F, Imai Y & de Massy B (2013). Meiotic recombination in mammals: localization and regulation. Nat Rev Genet 14, 794-806.
16. Behrens R, Hayles J & Nurse P (2000). Fission yeast retrotransposon Tf1 integration is targeted to 5' ends of open reading frames. Nucleic Acids Res 28, 4709-4716.
17. Bennardo N, Cheng A, Huang N & Stark JM (2008). Alternative-NHEJ is a mechanistically distinct pathway of mammalian chromosome break repair. PLoS Genet 4, e1000110.
18. Bennett G, Papamichos-Chronakis M & Peterson CL (2013). DNA repair choice defines a common pathway for recruitment of chromatin regulators. Nat Commun 4, 2084.
19. Betrán E, Thornton K & Long M (2002). Retroposed new genes out of the X in Drosophila. Genome Res 12, 1854-1859.
20. Beyer U, Moll-Rocek J, Moll UM & Dobbelstein M (2011). Endogenous retrovirus drives hitherto unknown proapoptotic p63 isoforms in the male germ line of humans and great apes. Proc Natl Acad Sci U S A 108, 3624-3629.
21. Bothmer A, Robbiani DF, Di Virgilio M, Bunting SF, Klein IA, Feldhahn N, Barlow J, Chen HT, Bosque D, Callen E, Nussenzweig A & Nussenzweig MC (2011). Regulation of DNA end joining, resection, and immunoglobulin class switch recombination by 53BP1. Mol Cell 42, 319-329.
22. Boehm T, McCurley N, Sutoh Y, Schorpp M, Kasahara M & Cooper MD (2012). VLR-based adaptive immunity. Annu Rev Immunol 30, 203-220.
23. Bothmer A, Rommel PC, Gazumyan A, Polato F, Reczek CR, Muellenbeck MF, Schaetzlein S, Edelmann W, Chen PL, Brosh RM, Jr, Casellas R, Ludwig T, Baer R, Nussenzweig A, Nussenzweig MC & Robbiani DF (2013). Mechanism of DNA resection during intrachromosomal recombination and immunoglobulin class switching. J Exp Med 210, 115-123.
24. Bowater R & Doherty AJ (2006). Making ends meet: repairing breaks in bacterial DNA by non-homologous end-joining. PLoS Genet 2, e8.
25. Boyer M, Yutin N, Pagnier I, Barrassi L, Fournous G, Espinosa L, Robert C, Azza S, Sun S, Rossmann MG, Suzan-Monti M, La Scola B, Koonin EV & Raoult D (2009). Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci U S A 106, 21848-21853.
26. Bozzaro S & Eichinger L (2011). The professional phagocyte Dictyostelium discoideum as a model host for bacterial pathogens. Curr Drug Targets 12, 942-954.
27. Brady TL, Schmidt CL & Voytas DF (2008). Targeting integration of the Saccharomyces Ty5 retrotransposon. Methods Mol Biol 435, 153-163.
28. Breitbart M (2012). Marine viruses: truth or dare. Ann Rev Mar Sci 4, 425-448.
29. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R & Hannon GJ (2007). Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089-1103.
30. Brick K, Smagulova F, Khil P, Camerini-Otero RD & Petukhova GV (2012). Genetic recombination is directed away from functional genomic elements in mice. Nature 485, 642-645.
31. Brissett NC & Doherty AJ (2009). Repairing DNA double-strand breaks by the prokaryotic non-homologous end-joining pathway. Biochem Soc Trans 37, 539-545.
32. Brosius J (2003). The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118, 99-116.
33. Brotcorne-Lannoye A & Maenhaut-Michel G (1986). Role of RecA protein in untargeted UV mutagenesis of bacteriophage lambda: evidence for the requirement for the dinB gene. Proc Natl Acad Sci U S A 83, 3904-3908.
34. Brunmeir R, Lagger S, Simboeck E, Sawicka A, Egger G, Hagelkruys A, Zhang Y, Matthias P, Miller WJ & Seiser C (2010). Epigenetic regulation of a murine retrotransposon by a dual histone modification mark. PLoS Genet 6, e1000927.
35. Brunschwig H, Levi L, Ben-David E, Williams RW, Yakir B & Shifman S (2012). Fine-scale maps of recombination rates and hotspots in the mouse genome. Genetics 191, 757-764.
36. Bundo M, Toyoshima M, Okada Y, Akamatsu W, Ueda J, Nemoto-Miyauchi T, Sunaga F, Toritsuka M, Ikawa D, Kakita A, Kato M, Kasai K, Kishimoto T, Nawa H, Okano H, Yoshikawa T, Kato T & Iwamoto K (2014). Increased L1 retrotransposition in the neuronal genome in schizophrenia. Neuron 81, 396-313.
37. Burgess RC, Sebesta M, Sisakova A, Marini VP, Lisby M, Damborsky J, Klein H, Rothstein R & Krejci L (2013). The PCNA interaction protein box sequence in Rad54 is an integral part of its ATPase domain and is required for efficient DNA repair and recombination. PLoS One 8, e82630.
38. Burns KH & Boeke JD (2008). Great exaptations. J Biol 7, 5.
39. Cahoon LA & Seifert HS (2011). Focusing homologous recombination: pilin antigenic variation in the pathogenic Neisseria. Mol Microbiol 81, 1136-1143.
40. Caillet-Fauquet P & Maenhaut-Michel G (1988). Nature of the SOS mutator activity: genetic characterization of untargeted mutagenesis in Escherichia coli. Mol Gen Genet 213, 491-498.
41. Cambray G, Guerout AM & Mazel D (2010). Integrons. Annu Rev Genet 44, 141-166.
42. Carrasco CD & Golden JW (1995). Two heterocyst-specific DNA rearrangements of nif operons in Anabaena cylindrica and Nostoc sp. strain Mac. Microbiology 141, 2479-2487.
43. Ceballos SJ & Heyer WD (2011). Functions of the Snf2/Swi2 family Rad54 motor protein in homologous recombination. Biochim Biophys Acta 1809, 509-523.
44. Cehovin A, Simpson PJ, McDowell MA, Brown DR, Noschese R, Pallett M, Brady J, Baldwin GS, Lea SM, Matthews SJ & Pelicic V (2013). Specific DNA recognition mediated by a type IV pilin. Proc Natl Acad Sci U S A 110, 3065-3070.
45. Chen I & Dubnau D (2004). DNA uptake during bacterial transformation. Nat Rev Microbiol 2, 241-249.
46. Chen JM, Ferec C & Cooper DN (2012). Transient hypermutability, chromothripsis and replication-based mechanisms in the generation of concurrent clustered mutations. Mutat Res 750, 52-59.
47. Chen S, Zhang YE & Long M (2010). New genes in Drosophila quickly become essential. Science 330, 1682-1685.
48. Chiba S, Kondo H, Tani A, Saisho D, Sakamoto W, Kanematsu S & Suzuki N (2011). Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes. PLoS Pathog 7, e1002146.
49. Christie-Oleza JA, Lanfranconi MP, Nogales B, Lalucat J & Bosch R (2009). Conjugative interaction induces transposition of ISPst9 in Pseudomonas stutzeri AN10. J Bacteriol 191, 1239-1247.
50. Cohen CJ, Lock WM & Mager DL (2009). Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Gene 448, 105-114.
51. Colson P & Raoult D (2010). Gene repertoire of amoeba-associated giant viruses. Intervirology 53, 330-343.
52. Comeau AM, Hatfull GF, Krisch HM, Lindell D, Mann NH & Prangishvili D (2008). Exploring the prokaryotic virosphere. Res Microbiol 159, 306-313.
53. Conley AB & Jordan IK (2012). Endogenous retroviruses and the epigenome. In Viruses: Essential Agents of Life, ed. Witzany G, pp. 309-323. Springer, Dordrecht.
54. Conley AB, Piriyapongsa J & Jordan IK (2008). Retroviral promoters in the human genome. Bioinformatics 24, 1563-1567.
55. Cook LC & Federle MJ (2013). Peptide pheromone signaling in Streptococcus and Enterococcus. FEMS Microbiol Rev doi:10.1111/1574-6976.12046.
56. Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu Y, Lovci MT, Morell M, O'Shea KS, Moran JV & Gage FH (2009). L1 retrotransposition in human neural progenitor cells. Nature 460, 1127-1131.
57. Cowley M, de Burca A, McCole RB, Chahal M, Saadat G, Oakey RJ & Schulz R (2011). Short interspersed element (SINE) depletion and long interspersed element (LINE) abundance are not features universally required for imprinting. PLoS One 6, e18953.
58. Cox MM (2001). Recombinational DNA repair of damaged replication forks in Escherichia coli: questions. Annu Rev Genet 35, 53-82.
59. Craig NL (1991). Tn7: a target site-specific transposon. Mol Microbiol 5, 2569-2573.
60. Cromie GA, Hyppa RW, Cam HP, Farah JA, Grewal SI & Smith GR (2007). A discrete class of intergenic DNA dictates meiotic DNA break hotspots in fission yeast. PLoS Genet 3, e141.
61. Curcio MJ & Derbyshire KM (2003). The outs and ins of transposition: from mu to kangaroo. Nat Rev Mol Cell Biol 4, 865-877.
62. Dai J, Xie W, Brady TL, Gao J & Voytas DF (2007). Phosphorylation regulates integration of the yeast Ty5 retrotransposon into heterochromatin. Mol Cell 27, 289-299.
63. Damert A, Raiz J, Horn AV, Lower J, Wang H, Xing J, Batzer MA, Lower R & Schumann GG (2009). 5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome. Genome Res 19, 1992-2008.
64. Danchin EG & Rosso MN (2012). Lateral gene transfers have polished animal genomes: lessons from nematodes. Front Cell Infect Microbiol 2, 27.
65. Danchin EG, Rosso MN, Vieira P, de Almeida-Engler J, Coutinho PM, Henrissat B & Abad P (2010). Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc Natl Acad Sci U S A 107, 17651-17656.
66. Danielsen AJ & Maihle NJ (2002). The EGF/ErbB receptor family and apoptosis. Growth Factors 20, 1-15.
67. Davies PCW (2013). Implications of read-write genomics for cancer biology. Phys Life Rev 10, 338-340.
68. Deitsch KW, Lukehart SA & Stringer JR (2009). Common strategies for antigenic variation by bacterial, fungal and protozoan pathogens. Nat Rev Microbiol 7, 493-503.
69. Doolittle RF (1995). The multiplicity of domains in proteins. Annu Rev Biochem 64, 287-314.
70. Doolittle RF & Bork P (1993). Evolutionarily mobile modules in proteins. Sci Am 269, 50-56.
71. Doulatov S, Hodes A, Dai L, Mandhana N, Liu M, Deora R, Simons RW, Zimmerly S & Miller JF (2004). Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements. Nature 431, 476-481.
72. Dunn CA, van de Lagemaat LN, Baillie GJ & Mager DL (2005). Endogenous retrovirus long terminal repeats as ready-to-use mobile promoters: the case of primate β3GAL-T5. Gene 364, 2-12.
73. Dunnick WA, Shi J, Holden V, Fontaine C & Collins JT (2011). The role of germline promoters and I exons in cytokine-induced gene-specific class switch recombination. J Immunol 186, 350-358.
74. Dunny GM (2007). The peptide pheromone-inducible conjugation system of Enterococcus faecalis plasmid pCF10: cell-cell signalling, gene transfer, complexity and evolution. Philos Trans R Soc Lond B Biol Sci 362, 1185-1193.
75. Dupressoir A & Heidmann T (1996). Germ line-specific expression of intracisternal A-particle retrotransposons in transgenic mice. Mol Cell Biol 16, 4495-4503.
76. Ejima Y & Yang L (2003). Trans mobilization of genomic DNA as a mechanism for retrotransposon-mediated exon shuffling. Hum Mol Genet 12, 1321-1328.
77. El Karoui M, Schaeffer M, Biaudet V, Bolotin A, Sorokin A & Gruss A (2000). Orientation specificity of the Lactococcus lactis Chi site. Genes Cells 5, 453-461.
78. Elledge SJ (1996). Cell cycle checkpoints: preventing an identity crisis. Science 274, 1664-1672.
79. Elleuche S & Poggeler S (2010). Inteins, valuable genetic elements in molecular biology and biotechnology. Appl Microbiol Biotechnol 87, 479-489.
80. Elrouby N & Bureau TE (2010). Bs1, a new chimeric gene formed by retrotransposon-mediated exon shuffling in maize. Plant Physiol 153, 1413-1424.
81. Engelberg-Kulka H, Amitai S, Kolodkin-Gal I & Hazan R (2006). Bacterial programmed cell death and multicellular behavior in bacteria. PLoS Genet 2, e135.
82. Fang SC, de los Reyes C & Umen JG (2006). Cell size checkpoint control by the retinoblastoma tumor suppressor pathway. PLoS Genet 2, e167.
83. Fattah F, Lee EH, Weisensel N, Wang Y, Lichter N & Hendrickson EA (2010). Ku regulates the non-homologous end joining pathway choice of DNA double-strand break repair in human somatic cells. PLoS Genet 6, e1000855.
84. Fazlieva R, Spittle CS, Morrissey D, Hayashi H, Yan H & Matsumoto Y (2009). Proofreading exonuclease activity of human DNA polymerase delta and its effects on lesion-bypass DNA synthesis. Nucleic Acids Res 37, 2854-2866.
85. Feschotte C (2008). Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9, 397-405.
86. Fischer MG, Allen MJ, Wilson WH & Suttle CA (2010). Giant virus with a remarkable complement of genes infects marine zooplankton. Proc Natl Acad Sci U S A 107, 19508-19513.
87. Forterre P (2006). The origin of viruses and their possible roles in major evolutionary transitions. Virus Res 117, 5-16.
88. Forterre P (2010). Defining life: the virus viewpoint. Orig Life Evol Biosph 40, 151-160.
89. Foster PL (1993). Adaptive mutation: the uses of adversity. Annu Rev Microbiol 47, 467-504.
90. 2 in mammalian cells. Radiat Res 170, 784-793.
91. Freudl R, Braun G, Honore N & Cole ST (1987). Evolution of the enterobacterial sulA gene: a component of the SOS system encoding an inhibitor of cell division. Gene 52, 31-40.
92. Frias-Lasserre D (2012). Non coding RNAs and viruses in the framework of the phylogeny of the genes, epigenesis and heredity. Int J Mol Sci 13, 477-490.
93. Fromme JC & Verdine GL (2004). Base excision repair. Adv Protein Chem 69, 1-41.
94. Fu B, Chen M, Zou M, Long M & He S (2010). The rapid generation of chimerical genes expanding protein diversity in zebrafish. BMC Genomics 11, 657.
95. Fuchs RP, Koffel-Schwartz N, Pelet S, Janel-Bintz R, Napolitano R, Becherel OJ, Broschard TH, Burnouf DY & Wagner J (2001). DNA polymerases II and V mediate respectively mutagenic (-2 frameshift) and error-free bypass of a single N-2-acetylaminofluorene adduct. Biochem Soc Trans 29, 191-195.
96. Fujimoto R, Kinoshita Y, Kawabe A, Kinoshita T, Takashima K, Nordborg M, Nasrallah ME, Shimizu KK, Kudoh H & Kakutani T (2008). Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genet 4, e1000048.
97. Fukui K (2010). DNA mismatch repair in eukaryotes and bacteria. J Nucleic Acids 2010, doi:10.4061/2010/260512.
98. Fuqua WC & Winans SC (1994). A LuxR-LuxI type regulatory system activates Agrobacterium Ti plasmid conjugal transfer in the presence of a plant tumor metabolite. J Bacteriol 176, 2796-2806.
99. Galhardo RS, Do R, Yamada M, Friedberg EC, Hastings PJ, Nohmi T & Rosenberg SM (2009). DinB upregulation is the sole role of the SOS response in stress-induced mutagenesis in Escherichia coli. Genetics 182, 55-68.
100. Garcia-Diaz M, Ruiz JF, Juarez R, Terrados G & Blanco L (2003). Are there mutator polymerases? ScientificWorldJournal 3, 422-431.
101. Gehring M, Bubb KL & Henikoff S (2009). Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324, 1447-1451.
102. Giglia-Mari G, Zotter A & Vermeulen W (2011). DNA damage response. Cold Spring Harb Perspect Biol 3, a000745.
103. Gogvadze E & Buzdin A (2009). Retroelements and their impact on genome evolution and functioning. Cell Mol Life Sci 66, 3727-3742.
104. Golden JW & Yoon HS (1998). Heterocyst formation in Anabaena. Curr Opin Microbiol 1, 623-629.
105. Gomez-Gomez JM, Blazquez J, Baquero F & Martinez JL (1997). H-NS and RpoS regulate emergence of Lac Ara+ mutants of Escherichia coli MCS2. J Bacteriol 179, 4620-4622.
106. EL following growth factor withdrawal is a key event in caspase-dependent apoptosis of 661W photoreceptor cells. Eur J Neurosci 24, 981-990.
107. Goodman M (2002). Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Ann Rev Biochem 71, 17-50.
108. Goodman MF (1998). Purposeful mutations. Nature 395, 221-223.
109. Grabarz A, Barascu A, Guirouilh-Barbat J & Lopez BS (2012). Initiation of DNA double strand break repair: signaling and single-stranded resection dictate the choice between homologous recombination, non-homologous end-joining and alternative end-joining. Am J Cancer Res 2, 249-268.
110. Grassi L, Grilli J & Lagomarsino MC (2012). Large-scale dynamics of horizontal transfers. Mob Genet Elements 2, 163-167.
111. Grey C, Barthes P, Chauveau-Le Friec G, Langa F, Baudat F & de Massy B (2011). Mouse PRDM9 DNA-binding specificity determines sites of histone H3 lysine 4 trimethylation for initiation of meiotic recombination. PLoS Biol 9, e1001176.
112. Grey C, Baudat F & de Massy B (2009). Genome-wide control of the distribution of meiotic recombination. PLoS Biol 7, e35.
113. Grindley ND, Whiteson KL & Rice PA (2006). Mechanisms of site-specific recombination. Annu Rev Biochem 75, 567-605.
114. Guetens G, De Boeck G, Highley M, van Oosterom AT & de Bruijn EA (2002). Oxidative DNA damage: biological significance and methods of analysis. Crit Rev Clin Lab Sci 39, 331-457.
115. Gyohda A, Furuya N, Ishiwa A, Zhu S & Komano T (2004). Structure and function of the shufflon in plasmid R64. Adv Biophys 38, 183-213.
116. Haber JE (2012). Mating-type genes and MAT switching in Saccharomyces cerevisiae. Genetics 191, 33-64.
117. Hall BG (1998). Activation of the bgl operon by adaptive mutation. Mol Biol Evol 15, 1-5.
118. Hall RM & Stokes HW (1993). Integrons: novel DNA elements which capture genes by site-specific recombination. Genetica 90, 115-132.
119. Hallet B & Sherratt DJ (2010). Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements. FEMS Microbiol Rev 21, 157-178.
120. Han JS (2010). Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions. Mob DNA 1, 15.
121. Han JS & Boeke JD (2005). LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression? Bioessays 27, 775-784.
122. Han JS, Szak ST & Boeke JD (2004). Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429, 268-274.
123. Hancks DC, Ewing AD, Chen JE, Tokunaga K & Kazazian HH, Jr (2009). Exon-trapping mediated by the human retrotransposon SVA. Genome Res 19, 1983-1991.
124. Handler D, Meixner K, Pizka M, Lauss K, Schmied C, Gruber FS & Brennecke J (2013). The genetic makeup of the Drosophila piRNA pathway. Mol Cell 50, 762-777.
125. Hartwell L & Weinert, TA (1989). Checkpoints: controls that ensure the order of cell cycle events. Science 246, 629-634.
126. Hayes W (1968). The Genetics of Bacteria and their Viruses (2nd edn). Blackwell, London.
127. Hays JB, Hoffman PD & Wang H (2005). Discrimination and versatility in mismatch repair. DNA Repair (Amst) 4, 1463-1474.
128. Hiller R, Hetzer M, Schweyen RJ & Mueller MW (2000). Transposition and exon shuffling by group II intron RNA molecules in pieces. J Mol Biol 297, 301-308.
129. Hollister JD & Gaut BS (2009). Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res 19, 1419-1428.
130. Holoch PA & Griffith TS (2009). TNF-related apoptosis-inducing ligand (TRAIL): a new path to anti-cancer therapies. Eur J Pharmacol 625, 63-72.
131. Honjo T, Kinoshita K & Muramatsu M (2002). Molecular mechanism of class switch recombination: linkage with somatic hypermutation. Annu Rev Immunol 20, 165-196.
132. Horn D (2004). The molecular control of antigenic variation in Trypanosoma brucei. Curr Mol Med 4, 563-576.
133. Houck MA, Clark JB, Peterson KR & Kidwell MG (1991). Possible horizontal transfer of Drosophila genes by the mite Proctolaelaps regalis. Science 253, 1125-1128.
134. Hoyt MA (2001). A new view of the spindle checkpoint. J Cell Biol 154, 909-911.
135. Huang GS & Keil RL (1995). Requirements for activity of the yeast mitotic recombination hotspot HOT1: RNA polymerase I and multiple cis-acting sequences. Genetics 141, 845-855.
136. Huisman O, D'Ari R & Gottesman S (1984). Cell-division control in Escherichia coli: specific induction of the SOS function SfiA protein is sufficient to block septation. Proc Natl Acad Sci U S A 81, 4490-4494.
137. Hurwitz BL, Hallam SJ & Sullivan MB (2013). Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biol 14, R123.
138. Huws SA, Morley RJ, Jones MV, Brown MR & Smith AW (2008). Interactions of some common pathogenic bacteria with Acanthamoeba polyphaga. FEMS Microbiol Lett 282, 258-265.
139. Ibarra B, Chemla YR, Plyasunov S, Smith SB, Lazaro JM, Salas M & Bustamante C (2009). Proofreading dynamics of a processive DNA polymerase. EMBO J 28, 2794-2802.
140. Ishikawa K, Ishii H & Saito T (2006). DNA damage-dependent cell cycle checkpoints and genomic stability. DNA Cell Biol 25, 406-411.
141. Jacobs AL & Schar P (2012). DNA glycosylases: in DNA repair and beyond. Chromosoma 121, 1-20.
142. Jacob F & Wollman EL (1961). Viruses and genes. Sci Am 204, 92-110.
143. Janes KA, Albeck JG, Gaudet S, Sorger PK, Lauffenburger DA & Yaffe MB (2005). A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310, 1646-1653.
144. Jeffreys AJ, Cotton VE, Neumann R & Lam KW (2013). Recombination regulator PRDM9 influences the instability of its own coding sequence in humans. Proc Natl Acad Sci U S A 110, 600-605.
145. Jeggo PA (2005). Genomic instability in cancer development. Adv Exp Med Biol 570, 175-197.
146. Jern P & Coffin JM (2008). Effects of retroviruses on host genome function. Annu Rev Genet 42, 709-732.
147. Jiricny J (2006). The multifaceted mismatch-repair system. Nat Rev Mol Cell Biol 7, 335-346.
148. Joza N, Pospisilik JA, Hangen E, Hanada T, Modjtahedi N, Penninger JM & Kroemer G (2009). AIF: not just an apoptosis-inducing factor. Ann N Y Acad Sci 1171, 2-11.
149. Juranek SA & Lipps HJ (2007). New insights into the macronuclear development in ciliates. Int Rev Cytol 262, 219-251.
150. Kaer K, Branovets J, Hallikma A, Nigumann P & Speek M (2011). Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation. PLoS One 6, e26099.
151. Kasahara M (2007). The 2R hypothesis: an update. Curr Opin Immunol 19, 547-552.
152. Kass EM & Jasin M (2010). Collaboration and competition between DNA double-strand break repair pathways. FEBS Lett 584, 3703-3708.
153. Ke N, Irwin PA & Voytas DF (1997). The pheromone response pathway activates transcription of Ty5 retrotransposons located within silent chromatin of Saccharomyces cerevisiae. EMBO J 16, 6272-6280.
154. Keeling PJ (2009). Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids. Methods Mol Biol 532, 501-515.
155. Keeling PJ & Palmer JD (2008). Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9, 605-618.
156. Keng VW, Ryan BJ, Wangensteen KJ, Balciunas D, Schmedt C, Ekker SC & Largaespada DA (2009). Efficient transposition of Tol2 in the mouse germline. Genetics 183, 1565-1573.
157. Kinoshita K, Tashiro J, Tomita S, Lee CG & Honjo T (1998). Target specificity of immunoglobulin class switch recombination is not determined by nucleotide sequences of S regions. Immunity 9, 849-858.
158. Kinoshita Y, Saze H, Kinoshita T, Miura A, Soppe WJ, Koornneef M & Kakutani T (2007). Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J 49, 38-45.
159. Kinsey PT & Sandmeyer SB (1995). Ty3 transposes in mating populations of yeast: a novel transposition assay for Ty3. Genetics 139, 81-94.
160. Kirchner J, Connolly CM & Sandmeyer SB (1995). Requirement of RNA polymerase III transcription factors for in vitro position-specific integration of a retroviruslike element. Science 267, 1488-1491.
161. Kloosterman WP, Guryev V, van Roosmalen M, Duran KJ, de Bruijn E, Bakker SC, Letteboer T, van Nesselrooij B, Hochstenbach R, Poot M & Cuppen E (2011). Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. Hum Mol Genet 20, 1916-1924.
162. Koga A, Cheah FS, Hamaguchi S, Yeo GH & Chong SS (2008). Germline transgenesis of zebrafish using the medaka Tol1 transposon system. Dev Dyn 237, 2466-2474.
163. Kokosar J & Kordis D (2013). Genesis and regulatory wiring of retroelement-derived domesticated genes: a phylogenomic perspective. Mol Biol Evol 30, 1015-1031.
164. Kolodkin-Gal I & Engelberg-Kulka H (2008). The extracellular death factor: physiological and genetic factors influencing its production and response in Escherichia coli. J Bacteriol 190, 3169-3175.
165. Kolodkin-Gal I, Hazan R, Gaathon A, Carmeli S & Engelberg-Kulka H (2007). A linear pentapeptide is a quorum-sensing factor required for mazEF-mediated cell death in Escherichia coli. Science 318, 652-655.
166. Komano T (1999). Shufflons: multiple inversion systems and integrons. Annu Rev Genet 33, 171-191.
167. Kondo N, Takahashi A, Ono K & Ohnishi T (2010). DNA damage induced by alkylating agents and repair pathways. J Nucleic Acids 2010, 543531.
168. Kondrashov FA, Koonin EV, Morgunov IG, Finogenova TV & Kondrashova MN (2006). Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. Biol Direct 1, 31.
169. Koonin EV (2010). Taming of the shrewd: novel eukaryotic genes from RNA viruses. BMC Biol 8, 2.
170. Korbel JO & Campbell PJ (2013). Criteria for inference of chromothripsis in cancer genomes. Cell 152, 1226-1236.
171. Kowalczykowski SC (2000). Initiation of genetic recombination and recombination-dependent replication. Trends Biochem Sci 25, 156-165.
172. Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD & Rehrauer WM (1994). Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 58, 401-465.
173. Kozlowicz BK, Dworkin M & Dunny GM (2006a). Pheromone-inducible conjugation in Enterococcus faecalis: a model for the evolution of biological complexity? Int J Med Microbiol 296, 141-147.
174. Kozlowicz BK, Shi K, Gu ZY, Ohlendorf DH, Earhart CA & Dunny GM (2006b). Molecular basis for control of conjugation by bacterial pheromone and inhibitor peptides. Mol Microbiol 62, 958-969.
175. Krejci L, Altmannova V, Spirek M & Zhao X (2012). Homologous recombination and its regulation. Nucleic Acids Res 40, 5795-5818.
176. Krieghoff-Henning E & Hofmann TG (2008). Role of nuclear bodies in apoptosis signalling. Biochim Biophys Acta 1783, 2185-2194.
177. Kristensen DM, Mushegian AR, Dolja VV & Koonin EV (2010). New dimensions of the virus world discovered through metagenomics. Trends Microbiol 18, 11-19.
178. Krupovic M, Prangishvili D, Hendrix RW & Bamford DH (2011). Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 75, 610-635.
179. Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, Chan YS, Ng HH & Bourque G (2010). Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42, 631-634.
180. Kunkel B, Losick R & Stragier P (1990). The Bacillus subtilis gene for the development transcription factor sigma K is generated by excision of a dispensable DNA element containing a sporulation recombinase gene. Genes Dev 4, 525-535.
181. Kunkel TA & Bebenek K (2000). DNA replication fidelity. Annu Rev Biochem 69, 497-529.
182. Kurosawa A, Saito S, So S, Hashimoto M, Iwabuchi K, Watabe H & Adachi N (2013). DNA ligase IV and artemis act cooperatively to suppress homologous recombination in human cells: implications for DNA double-strand break repair. PLoS One 8, e72253.
183. Lambowitz AM & Zimmerly S (2011). Group II introns: mobile ribozymes that invade DNA. Cold Spring Harb Perspect Biol 3, a003616.
184. Lamrani S, Ranquet C, Gama MJ, Nakai H, Shapiro JA, Toussaint A & Maenhaut-Michel G (1999). Starvation-induced Mucts62-mediated coding sequence fusion: a role for ClpXP, Lon, RpoS and Crp. Mol Microbiol 32, 327-343.
185. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S & Chen YJ (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921.
186. Landy A (1989). Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu Rev Biochem 58, 913-949.
187. Lang AS & Beatty JT (2007). Importance of widespread gene transfer agent genes in alpha-proteobacteria. Trends Microbiol 15, 54-62.
188. Laski FA, Rio DC & Rubin GM (1986). Tissue specificity of Drosophila P element transposition is regulated at the level of mRNA splicing. Cell 44, 7-19.
189. Leclercq S, Gilbert C & Cordaux R (2012). Cargo capacity of phages and plasmids and other factors influencing horizontal transfers of prokaryote transposable elements. Mob Genet Elements 2, 115-118.
190. Leem YE, Ripmaster TL, Kelly FD, Ebina H, Heincelman ME, Zhang K, Grewal SI, Hoffman CS & Levin HL (2008). Retrotransposon Tf1 is targeted to Pol II promoters by transcription activators. Mol Cell 30, 98-107.
191. Leung MM, Florizone SM, Taylor TA, Lang AS & Beatty JT (2010). The gene transfer agent of Rhodobacter capsulatus. Adv Exp Med Biol 675, 253-264.
192. Lev-Maor G, Sorek R, Levanon EY, Paz N, Eisenberg E & Ast G (2007). RNA-editing-mediated exon evolution. Genome Biol 8, R29.
193. Levin HL & Moran JV (2011). Dynamic interactions between transposable elements and their hosts. Nat Rev Genet 12, 615-627.
194. -/- mice suggests that UNG and A:T mutagenesis pathway target different U:G lesions. Mol Immunol 53, 214-217.
195. Lieber MR (2010). The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79, 181-211.
196. Lin C, Yang L, Tanasa B, Hutt K, Ju BG, Ohgi K, Zhang J, Rose DW, Fu XD, Glass CK & Rosenfeld MG (2009). Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer. Cell 139, 1069-1083.
197. Linseman DA, McClure ML, Bouchard RJ, Laessig TA, Ahmadi FA & Heidenreich KA (2002). Suppression of death receptor signalling in cerebellar Purkinje neurons protects neighboring granule neurons from apoptosis via an insulin-like growth factor I-dependent mechanism. J Biol Chem 277, 24546-24553.
198. Lisby M, Antunez de Mayolo A, Mortensen UH & Rothstein R (2003a). Cell cycle-regulated centers of DNA double-strand break repair. Cell Cycle 2, 479-483.
199. Lisby M, Mortensen UH & Rothstein R (2003b). Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre. Nat Cell Biol 5, 572-577.
200. Lisby M & Rothstein R (2004). DNA damage checkpoint and repair centers. Curr Opin Cell Biol 16, 328-334.
201. Lisby M & Rothstein R (2005). Localization of checkpoint and repair proteins in eukaryotes. Biochimie 87, 579-589.
202. Lisby M, Rothstein R & Mortensen UH (2001). Rad52 forms DNA repair and recombination centers during S phase. Proc Natl Acad Sci U S A 98, 8276-8282.
203. Little JW & Mount DW (1982). The SOS regulatory system of Escherichia coli. Cell 29, 11-22.
204. Liu H, Fu Y, Jiang D, Li G, Xie J, Cheng J, Peng Y, Ghabrial SA & Yi X (2010). Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. J Virol 84, 11876-11887.
205. Liu H, Fu Y, Li B, Yu X, Xie J, Cheng J, Ghabrial SA, Li G, Yi X & Jiang D (2011a). Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes. BMC Evol Biol 11, 276.
206. Liu H, Fu Y, Xie J, Cheng J, Ghabrial SA, Li G, Peng Y, Yi X & Jiang D (2011b). Widespread endogenization of densoviruses and parvoviruses in animal and human genomes. J Virol 85, 9863-9876.
207. Liu M & Grigoriev A (2004). Protein domains correlate strongly with exons in multiple eukaryotic genomes-evidence of exon shuffling? Trends Genet 20, 399-403.
208. Lloyd AH & Timmis JN (2011). The origin and characterization of new nuclear genes originating from a cytoplasmic organellar genome. Mol Biol Evol 28, 2019-2028.
209. Lo Scrudato M & Blokesch M (2012). The regulatory network of natural competence and transformation of Vibrio cholerae. PLoS Genet 8, e1002778.
210. Loewer A & Lahav G (2006). Cellular conference call: external feedback affects cell-fate decisions. Cell 124, 1128-1130.
211. Long M (2001). Evolution of novel genes. Curr Opin Genet Dev 11, 673-680.
212. Longerich S, Basu U, Alt F & Storb U (2006). AID in somatic hypermutation and class switch recombination. Curr Opin Immunol 18, 164-174.
213. Lu AL, Li X, Gu Y, Wright PM & Chang DY (2001). Repair of oxidative DNA damage: mechanisms and functions. Cell Biochem Biophys 35, 141-170.
214. Lusetti SL & Cox MM (2002). The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Annu Rev Biochem 71, 71-100.
215. Lwoff A (1954). The life cycle of a virus. Sci Am 190, 34-37.
216. Lwoff A (1957). The concept of virus. J Gen Microbiol 17, 239-253.
217. Lwoff A (1966). Interaction among virus, cell, and organism. Science 152, 1216-1220.
218. Lynch VJ, Leclerc RD, May G & Wagner GP (2011). Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet 43, 1154-1159.
219. Macfarlan TS, Gifford WD, Agarwal S, Driscoll S, Lettieri K, Wang J, Andrews SE, Franco L, Rosenfeld MG, Ren B & Pfaff SL (2011). Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev 25, 594-607.
220. Maenhaut-Michel G (1985). Mechanism of SOS-induced targeted and untargeted mutagenesis in E. coli. Biochimie 67, 365-369.
221. Maenhaut-Michel G & Caillet-Fauquet P (1990). Genetic control of the UV-induced SOS mutator effect in single- and double-stranded DNA phages. Mutat Res 230, 241-254.
222. Maenhaut-Michel G, Janel-Bintz R & Fuchs RP (1992). A umuDC-independent SOS pathway for frameshift mutagenesis. Mol Gen Genet 235, 373-380.
223. Maenhaut-Michel G & Shapiro JA (1994). The roles of starvation and selective substrates in the emergence of araB-lacZ fusion clones. EMBO J 13, 5229-5239.
224. Maksakova IA, Romanish MT, Gagnier L, Dunn CA, van de Lagemaat LN & Mager DL (2006). Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line. PLoS Genet 2, e2.
225. Mandal AK, Pandey R, Jha V & Mukerji M (2013). Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. Nucleic Acids Res 41, 2121-2137.
226. Martin TJ, Peer CJ & Figg WD (2013). Uncovering the genetic landscape driving castration-resistant prostate cancer. Cancer Biol Ther 14, 399-400.
227. Martin-Castellanos C, Fowler KR & Smith GR (2013). Making chromosomes hot for breakage. Cell Cycle 12, 1327-1328.
228. Mazin AV, Mazina OM, Bugreev DV & Rossi MJ (2010). Rad54, the motor of homologous recombination. DNA Repair (Amst) 9, 286-302.
229. McClintock B (1932). A correlation of ring-shaped chromosomes with variegation in Zea mays. Proc Natl Acad Sci U S A 18, 677-681.
230. McClintock B (1939). The behavior in successive nuclear divisions of a chromosome broken at meiosis. Proc Nat Acad Sci U S A 25, 405-416.
231. McClintock B (1942). The fusion of broken ends of chromosomes following nuclear fusion. Proc Nat Acad Sci U S A 28, 458-463.
232. McClintock B (1984). The significance of responses of the genome to challenge. Science 226, 792-801.
233. McClintock B (1987). Discovery and Characterization of Transposable Elements: The Collected Papers of Barbara McClintock. Garland, New York.
234. McDonald JF, Matyunina LV, Wilson S, Jordan IK, Bowen NJ & Miller WJ (1997). LTR retrotransposons and the evolution of eukaryotic enhancers. Genetica 100, 3-13.
235. McKenzie GJ, Magner DB, Lee PL & Rosenberg SM (2003). The dinB operon and spontaneous mutation in Escherichia coli. J Bacteriol 185, 3972-3977.
236. McKenzie GJ & Rosenberg SM (2001). Adaptive mutations, mutator DNA polymerases and genetic change strategies of pathogens. Curr Opin Microbiol 4, 586-594.
237. Medhekar B & Miller JF (2007). Diversity-generating retroelements. Curr Opin Microbiol 10, 388-395.
238. Meibom KL, Blokesch M, Dolganov NA, Wu CY & Schoolnik GK (2005). Chitin induces natural competence in Vibrio cholerae. Science 310, 1824-1827.
239. Modrich P (2006). Mechanisms in eukaryotic mismatch repair. J Biol Chem 281, 30305-30309.
240. Modrich P & Lahue R (1996). Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu Rev Biochem 65, 101-133.
241. Moerman DG, Kiff JE & Waterston RH (1991). Germline excision of the transposable element Tc1 in C. elegans. Nucleic Acids Res 19, 5669-5672.
242. Moliner C, Fournier PE & Raoult D (2010). Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution. FEMS Microbiol Rev 34, 281-294.
243. Moran JV, DeBerardinis RJ & Kazazian HH, Jr (1999). Exon shuffling by L1 retrotransposition. Science 283, 1530-1534.
244. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A & Rafalski A (2005). Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37, 997-1002.
245. Mou Z, Kenny AE & Curcio MJ (2006). Hos2 and Set3 promote integration of Ty1 retrotransposons at tRNA genes in Saccharomyces cerevisiae. Genetics 172, 2157-2167.
246. Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan SJ & Boeke JD (2012). Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots. Genome Res 22, 693-703.
247. Muller F & Tobler H (2000). Chromatin diminution in the parasitic nematodes Ascaris suum and Parascaris univalens. Int J Parasitol 30, 391-399.
248. Muotri AR, Chu VT, Marchetto MC, Deng W, Moran JV & Gage FH (2005). Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435, 903-910.
249. Muotri AR & Gage FH (2006). Generation of neuronal variability and complexity. Nature 441, 1087-1093.
250. Muotri AR, Marchetto MC, Coufal NG & Gage FH (2007). The necessary junk: new functions for transposable elements. Hum Mol Genet 16 (R2), R159-167.
251. Muotri AR, Marchetto MCN, Coufal NG, Oefner R, Yeo GW, Nakashima K & Gage FH (2010). L1 retrotransposition in neurons is modulated by MeCP2. Nature 468, 443-446.
252. Nakayashiki H (2011). The Trickster in the genome: contribution and control of transposable elements. Genes Cells 16, 827-841.
253. Nambiar M & Raghavan SC (2011). How does DNA break during chromosomal translocations? Nucleic Acids Res 39, 5813-5825.
254. Napolitano R, Janel-Bintz R, Wagner J & Fuchs RP (2000). All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis. EMBO J 19, 6259-6265.
255. Navas TA, Zhou Z & Elledge SJ (1995). DNA polymerase epsilon links the DNA replication machinery to the S phase checkpoint. Cell 80, 29-39.
256. Nezi L & Musacchio A (2009). Sister chromatid tension and the spindle assembly checkpoint. Curr Opin Cell Biol 21, 785-795.
257. North JA, Amunugama R, Klajner M, Bruns AN, Poirier MG & Fishel R (2013). ATP-dependent nucleosome unwrapping catalyzed by human RAD51. Nucleic Acids Res 41, 7302-7312.
258. Novikova O (2009). Chromodomains and LTR retrotransposons in plants. Commun Integr Biol 2, 158-162.
259. Nowacki M, Shetty K & Landweber LF (2011). RNA-mediated epigenetic programming of genome rearrangements. Annu Rev Genomics Hum Genet 12, 367-389.
260. Nuthikattu S, McCue AD, Panda K, Fultz D, Defraia C, Thomas EN & Slotkin RK (2013). The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs. Plant Physiol 162, 116-131.
261. Oliver KM, Degnan PH, Burke GR & Moran NA (2010). Facultative symbionts in aphids and the horizontal transfer of ecologically important traits. Annu Rev Entomol 55, 247-266.
262. Parks AR, Li Z, Shi Q, Owens RM, Jin MM & Peters JE (2009). Transposition into replicating DNA occurs through interaction with the processivity factor. Cell 138, 685-695.
263. Parks AR & Peters JE (2009). Tn7 elements: engendering diversity from chromosomes to episomes. Plasmid 61, 1-14.
264. Pask AJ, Papenfuss AT, Ager EI, McColl KA, Speed TP & Renfree MB (2009). Analysis of the platypus genome suggests a transposon origin for mammalian imprinting. Genome Biol 10, R1.
265. Pastwa E & Blasiak J (2003). Non-homologous DNA end joining. Acta Biochim Pol 50, 891-908.
266. Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D & Knowles BB (2004). Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell 7, 597-606.
267. Peled JU, Kuang FL, Iglesias-Ussel MD, Roa S, Kalis SL, Goodman MF & Scharff MD (2008). The biochemistry of somatic hypermutation. Annu Rev Immunol 26, 481-511.
268. Perez-Duran P, Belver L, de Yebenes VG, Delgado P, Pisano DG & Ramiro AR (2012). UNG shapes the specificity of AID-induced somatic hypermutation. J Exp Med 209, 1379-1389.
269. Perrino FW & Loeb LA (1989). Proofreading by the epsilon subunit of Escherichia coli DNA polymerase III increases the fidelity of calf thymus DNA polymerase alpha. Proc Natl Acad Sci U S A 86, 3085-3088.
270. Peters JE & Craig NL (2001). Tn7 recognizes transposition target structures associated with DNA replication using the DNA-binding protein TnsE. Genes Dev 15, 737-747.
271. Petit C & Sancar A (1999). Nucleotide excision repair: from E. coli to man. Biochimie 81, 15-25.
272. Piriyapongsa J, Polavarapu N, Borodovsky M & McDonald J (2007). Exonization of the LTR transposable elements in human genome. BMC Genomics 8, 291.
273. Pitcher RS, Wilson TE & Doherty AJ (2005). New insights into NHEJ repair processes in prokaryotes. Cell Cycle 4, 675-678.
274. Plasterk RH, Simon MI & Barbour AG (1985). Transposition of structural genes to an expression sequence on a linear plasmid causes antigenic variation in the bacterium Borrelia hermsii. Nature 318, 257-263.
275. Prescott DM (2000). Genome gymnastics: unique modes of DNA evolution and processing in ciliates. Nat Rev Genet 1, 191-198.
276. Rechkunova NI & Lavrik OI (2010). Nucleotide excision repair in higher eukaryotes: mechanism of primary damage recognition in global genome repair. Subcell Biochem 50, 251-277.
277. Remacle-Bonnet MM, Garrouste FL, Heller S, Andre F, Marvaldi JL & Pommier GJ (2000). Insulin-like growth factor-I protects colon cancer cells from death factor- induced apoptosis by potentiating tumor necrosis factor α-induced mitogen-activated protein kinase and nuclear factor κB signaling pathways. Cancer Res 60, 2007-2017.
278. Reuven NB, Arad G, Maor-Shoshani A & Livneh Z (1999). The mutagenesis protein UmuC is a DNA polymerase activated by UmuD', RecA, and SSB and is specialized for translesion replication. J Biol Chem 274, 31763-31766.
279. Rho M, Choi JH, Kim S, Lynch M & Tang H (2007). De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics 8, 90.
280. Richards RI (2001). Fragile and unstable chromosomes in cancer: causes and consequences. Trends Genet 17, 339-345.
281. Robertson AB, Klungland A, Rognes T & Leiros I (2009). DNA repair in mammalian cells: Base excision repair: the long and short of it. Cell Mol Life Sci 66, 981-993.
282. Rocha PP, Micsinai M, Kim JR, Hewitt SL, Souza PP, Trimarchi T, Strino F, Parisi F, Kluger Y & Skok JA (2012). Close proximity to Igh is a contributing factor to AID-mediated translocations. Mol Cell 47, 873-885.
283. Rocha PP & Skok JA (2013). The origin of recurrent translocations in recombining lymphocytes: a balance between break frequency and nuclear proximity. Curr Opin Cell Biol 25, 365-371.
284. Rogozin IB, Iyer LM, Liang L, Glazko GV, Liston VG, Pavlov YI, Aravind L & Pancer Z (2007). Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. Nat Immunol 8, 647-656.
285. Rosenberg SM (2001). Evolving responsively: adaptive mutation. Nat Rev Genet 2, 504-515.
286. Roth JR, Kugelberg E, Reams AB, Kofoid E & Andersson DI (2006). Origin of mutations under selection: the adaptive mutation controversy. Annu Rev Microbiol 60, 477-501.
287. Rousseau-Gueutin M, Ayliffe MA & Timmis JN (2012). Plastid DNA in the nucleus: new genes for old. Plant Signal Behav 7, 269-272.
288. Roux S, Krupovic M, Debroas D, Forterre P & Enault F (2013). Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences. Open Biol 3, 130160.
289. Rowley JD (1973). Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 243, 290-293.
290. Rowley JD (2008). Chromosomal translocations: revisited yet again. Blood 112, 2183-2189.
291. Rupes I, Webb BA, Mak A & Young PG (2001). G2/M arrest caused by actin disruption is a manifestation of the cell size checkpoint in fission yeast. Mol Biol Cell 12, 3892-3903.
292. Sabelli PA, Liu Y, Dante RA, Lizarraga LE, Nguyen HN, Brown SW, Klingler JP, Yu J, LaBrant E, Layton TM, Feldman M & Larkins BA (2013). Control of cell proliferation, endoreduplication, cell size, and cell death by the retinoblastoma-related pathway in maize endosperm. Proc Natl Acad Sci U S A 110, E1827-1836.
293. Saisongkorh W, Robert C, La Scola B, Raoult D & Rolain JM (2010). Evidence of transfer by conjugation of type IV secretion system genes between Bartonella species and Rhizobium radiobacter in amoeba. PLoS One 5, e12666.
294. San Filippo J, Sung P & Klein H (2008). Mechanism of eukaryotic homologous recombination. Annu Rev Biochem 77, 229-257.
295. Schlereth K, Beinoraviciute-Kellner R, Zeitlinger MK, Bretz AC, Sauer M, Charles JP, Vogiatzi F, Leich E, Samans B, Eilers M, Kisker C, Rosenwald A & Stiewe T (2010). DNA binding cooperativity of p53 modulates the decision between cell-cycle arrest and apoptosis. Mol Cell 38, 356-368.
296. Schmidt T (1999). LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes. Plant Mol Biol 40, 903-910.
297. Schmitz J & Brosius J (2011). Exonization of transposed elements: a challenge and opportunity for evolution. Biochimie 93, 1928-1934.
298. Schoemaker JM, Gayda RC & Markovitz A (1984). Regulation of cell division in Escherichia coli: SOS induction and cellular location of the sulA protein, a key to lon-associated filamentation and death. J Bacteriol 158, 551-561.
299. Schoenfeld TW, Murugapiran SK, Dodsworth JA, Floyd S, Lodes M, Mead DA & Hedlund BP (2013). Lateral gene transfer of family A DNA polymerases between thermophilic viruses, aquificae, and apicomplexa. Mol Biol Evol 30, 1653-1664.
300. Seeber A, Hauer M & Gasser SM (2013). Nucleosome remodelers in double-strand break repair. Curr Opin Genet Dev 23, 174-184.
301. Segurado M & Tercero JA (2009). The S-phase checkpoint: targeting the replication fork. Biol Cell 101, 617-627.
302. Segurel L, Leffler EM & Przeworski M (2011). The case of the fickle fingers: how the PRDM9 zinc finger protein specifies meiotic recombination hotspots in humans. PLoS Biol 9, e1001211.
303. Shapiro JA (1984). Observations on the formation of clones containing araB-lacZ cistron fusions. Mol Gen Genet 194, 79-90.
304. Shapiro JA (1993). A role for the Clp protease in activating Mu-mediated DNA rearrangements. J Bacteriol 175, 2625-2631.
305. Shapiro JA (1997). Genome organization, natural genetic engineering and adaptive mutation. Trends Genet 13, 98-104.
306. Shapiro JA (2011). Evolution: A View from the 21st Century. FT Press Science, Upper Saddle River, NJ.
307. Shapiro JA (2013). How life changes itself: the read-write (RW) genome. Phys Life Rev 10, 287-323.
308. Shapiro JA & Leach D (1990). Action of a transposable element in coding sequence fusions. Genetics 126, 293-299.
309. Sharon I, Battchikova N, Aro EM, Giglione C, Meinnel T, Glaser F, Pinter RY, Breitbart M, Rohwer F & Beja O (2011). Comparative metagenomics of microbial traits within oceanic viral communities. ISME J 5, 1178-1190.
310. Siebel CW & Rio DC (1990). Regulated splicing of the Drosophila P transposable element third intron in vitro: somatic repression. Science 248, 1200-1208.
311. Smillie C, Garcillan-Barcia MP, Francia MV, Rocha EP & de la Cruz F (2010). Mobility of plasmids. Microbiol Mol Biol Rev 74, 434-452.
312. Smith GR (1994). Hotspots of homologous recombination. Experientia 50, 234-241.
313. Sonea S (1987). Bacterial viruses, prophages, and plasmids, reconsidered. Ann N Y Acad Sci 503, 251-260.
314. Sonea S (1971). A tentative unifying view of bacteria. Rev Can Biol 30, 239-244.
315. Sonea S & Mathieu LG (2001). Evolution of the genomic systems of prokaryotes and its momentous consequences. Int Microbiol 4, 67-71.
316. Sonea S & Panisset M (1983). A New Bacteriology. Jones and Batlett, Boston.
317. Song J (2007). EMT or apoptosis: a decision for TGF-β. Cell Res 17, 289-290.
318. Sorek R, Lawrence CM & Wiedenheft B (2013). CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem 82, 237-266.
319. Sorek R (2007). The birth of new exons: mechanisms and evolutionary consequences. RNA 13, 1603-1608.
320. Spies M, Bianco PR, Dillingham MS, Handa N, Baskin RJ & Kowalczykowski SC (2003). A molecular throttle: the recombination hotspot chi controls DNA translocation by the RecBCD helicase. Cell 114, 647-654.
321. Stanton TB (2007). Prophage-like gene transfer agents - novel mechanisms of gene exchange for Methanococcus, Desulfovibrio, Brachyspira, and Rhodobacter species. Anaerobe 13, 43-49.
322. Steiner WW & Steiner EM (2012). Fission yeast hotspot sequence motifs are also active in budding yeast. PLoS One 7, e53090.
323. Steinert M (2011). Pathogen-host interactions in Dictyostelium, Legionella, Mycobacterium and other pathogens. Semin Cell Dev Biol 22, 70-76.
324. Stragier P, Kunkel B, Kroos L & Losick R (1989). Chromosomal rearrangement generating a composite gene for a developmental transcription factor. Science 243, 507-512.
325. Suckow G, Seitz P & Blokesch M (2011). Quorum sensing contributes to natural transformation of Vibrio cholerae in a species-specific manner. J Bacteriol 193, 4914-4924.
326. Sutton MD, Smith BT, Godoy VG & Walker GC (2000). The SOS response: recent insights into umuDC-dependent mutagenesis and DNA damage tolerance. Annu Rev Genet 34, 479-497.
327. Suzuki S, Ono R, Narita T, Pask AJ, Shaw G, Wang C, Kohda T, Alsop AE, Marshall Graves JA, Kohara Y, Ishino F, Renfree MB & Kaneko-Ishino T (2007). Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genet 3, e55.
328. Symington LS & Gautier J (2011). Double-strand break end resection and repair pathway choice. Annu Rev Genet 45, 247-271.
329. Takeda J, Keng VW & Horie K (2007). Germline mutagenesis mediated by Sleeping Beauty transposon system in mice. Genome Biol 8 (Suppl 1), S14.
330. 2C is an error-prone DNA polymerase, Escherichia coli pol V. Proc Natl Acad Sci U S A 96, 8919-8924.
331. Taylor DJ & Bruenn J (2009). The evolution of novel fungal genes from non-retroviral RNA viruses. BMC Biol 7, 88.
332. Taylor SS, Scott MI & Holland AJ (2004). The spindle checkpoint: a quality control mechanism which ensures accurate chromosome segregation. Chromosome Res 12, 599-616.
333. Teichmann SA & Babu MM (2004). Gene regulatory network growth by duplication. Nat Genet 36, 492-496.
334. Tentner AR, Lee MJ, Ostheimer GJ, Samson LD, Lauffenburger DA & Yaffe MB (2012). Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress. Mol Syst Biol 8, 568.
335. Thomas CA, Paquola AC & Muotri AR (2012). LINE-1 retrotransposition in the nervous system. Annu Rev Cell Dev Biol 28, 555-573.
336. Toll-Riera M & Alba MM (2013). Emergence of novel domains in proteins. BMC Evol Biol 13, 47.
337. Toll-Riera M, Castelo R, Bellora N & Alba MM (2009). Evolution of primate orphan proteins. Biochem Soc Trans 37, 778-782.
338. Truss M, Chalepakis G & Beato M (1992). Interplay of steroid hormone receptors and transcription factors on the mouse mammary tumor virus promoter. J Steroid Biochem Mol Biol 43, 365-378.
339. van Gent DC, Hoeijmakers JH & Kanaar R (2001). Chromosomal stability and the DNA double-stranded break connection. Nat Rev Genet 2, 196-206.
340. van Gent DC & van der Burg M (2007). Non-homologous end-joining, a sticky affair. Oncogene 26, 7731-7740.
341. Varetti G & Musacchio A (2008). The spindle assembly checkpoint. Curr Biol 18, R591-595.
342. Wagner J, Gruz P, Kim SR, Yamada M, Matsui K, Fuchs RP & Nohmi T (1999). The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV, involved in mutagenesis. Mol Cell 4, 281-286.
343. Walker GC (2000). Understanding the complexity of an organism's responses to DNA damage. Cold Spring Harb Symp Quant Biol 65, 1-10.
344. Walsh CM & Edinger AL (2010). The complex interplay between autophagy, apoptosis, and necrotic signals promotes T-cell homeostasis. Immunol Rev 236, 95-109.
345. Ward MC, Wilson MD, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe BJ & Odom DT (2013). Latent regulatory potential of human-specific repetitive elements. Mol Cell 49, 262-272.
346. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC & Lander ES (2002). Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562.
347. Weigle JJ (1953). Induction of mutations in a bacterial virus. Proc Natl Acad Sci U S A 39, 628-636.
348. Weigle JJ & Bertani G (1953). Variations des bacteriophages conditionnees par les bacteries hotes [Variations of bacteriophage conditioned by host bacteria.]. Ann Inst Pasteur (Paris) 84, 175-179.
349. Weinert T & Hartwell L (1989). Control of G2 delay by the rad9 gene of Saccharomyces cerevisiae. J Cell Sci Suppl 12, 145-148.
350. Weinert TA (1992). Dual cell cycle checkpoints sensitive to chromosome replication and DNA damage in the budding yeast Saccharomyces cerevisiae. Radiat Res 132, 141-143.
351. Weinert TA & Hartwell LH (1988). The RAD9 gene controls the cell cycle response to DNA damage in Saccharomyces cerevisiae. Science 241, 317-322.
352. Wheelan SJ, Aizawa Y, Han JS & Boeke JD (2005). Gene- breaking: a new paradigm for human retrotransposon- mediated gene evolution. Genome Res 15, 1073-1078.
353. Whitaker JW, McConkey GA & Westhead DR (2009). The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes. Genome Biol 10, R36.
354. Williamson SJ, Rusch DB, Yooseph S, Halpern AL, Heidelberg KB, Glass JI, Andrews-Pfannkoch C, Fadrosh D, Miller CS, Sutton G, Frazier M & Venter JC (2008). The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS One 3, e1456.
355. Wilson WH, Van Etten JL & Allen MJ (2009). The Phycodnaviridae: the story of how tiny giants rule the world. Curr Top Microbiol Immunol 328, 1-42.
356. 6-methylguanine-DNA methyltransferase protect against methylation-induced colon carcinogenesis. Carcinogenesis 31, 2111-2117.
357. Wisniewski-Dye F & Vial L (2008). Phase and antigenic variation mediated by genome modifications. Antonie Van Leeuwenhoek 94, 493-515.
358. Wissler L, Gadau J, Simola DF, Helmkampf M & Bornberg-Bauer E (2013). Mechanisms and dynamics of orphan gene emergence in insect genomes. Genome Biol Evol 5, 439-455.
359. Witkin EM (1973). Ultraviolet mutagenesis in bacteria: the inducible nature of error-prone repair. An Acad Bras Cienc 45 (Suppl), 185-191.
360. Witkin EM (1975). Relationships among repair, mutagenesis, and survival: overview. Basic Life Sci 5A, 347-353.
361. Witkin EM (1991). RecA protein in the SOS response: milestones and mysteries. Biochimie 73, 133-141.
362. Woehle C, Dagan T, Martin WF & Gould SB (2011). Red and problematic green phylogenetic signals among thousands of nuclear genes from the photosynthetic and apicomplexa-related Chromera velia. Genome Biol Evol 3, 1220-1230.
363. Wolkow CA, DeBoy RT & Craig NL (1996). Conjugating plasmids are preferred targets for Tn7. Genes Dev 10, 2145-2157.
364. Wollman EL & Jacob F (1961). Sexuality and the Genetics of Bacteria. Academic Press, New York.
365. Wu D, Zhang C, Shen Y, Nephew KP & Wang Q (2011). Androgen receptor-driven chromatin looping in prostate cancer. Trends Endocrinol Metab 22, 474-480.
366. Xi Z, Bradley RK, Wurdack KJ, Wong KM, Sugumaran M, Bomblies K, Rest JS & Davis CC (2012). Horizontal transfer of expressed genes in a parasitic flowering plant. BMC Genomics 13, 227.
367. Xie C, Zhang YE, Chen JY, Liu CJ, Zhou WZ, Li Y, Zhang M, Zhang R, Wei L & Li CY (2012). Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genet 8, e1002942.
368. Xie W, Gai X, Zhu Y, Zappulla DC, Sternglanz R & Voytas DF (2001). Targeting of the yeast Ty5 retrotransposon to silent chromatin is mediated by interactions between integrase and Sir4p. Mol Cell Biol 21, 6606-6614.
369. Xu Y, Ayrapetov MK, Xu C, Gursoy-Yuzugullu O, Hu Y & Price BD (2012). Histone H2A.Z controls a critical chromatin remodeling step required for DNA double-strand break repair. Mol Cell 48, 723-733.
370. Yamada M, Nunoshiba T, Shimizu M, Gruz P, Kamiya H, Harashima H & Nohmi T (2006). Involvement of Y-family DNA polymerases in mutagenesis caused by oxidized nucleotides in Escherichia coli. J Bacteriol 188, 4992-4995.
371. Yamada S, Ohta K & Yamada T (2013). Acetylated Histone H3K9 is associated with meiotic recombination hotspots, and plays a role in recombination redundantly with other factors including the H3K4 methylase Set1 in fission yeast. Nucleic Acids Res 41, 3504-3517.
372. Yin XM (2000). Signal transduction mediated by Bid, a pro-death Bcl-2 family proteins, connects the death receptor and mitochondria apoptosis pathways. Cell Res 10, 161-167.
373. Youngson NA, Kocialkowski S, Peel N & Ferguson-Smith AC (2005). A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting. J Mol Evol 61, 481-490.
374. Yousuf FA, Siddiqui R & Khan NA (2013). Acanthamoeba castellanii of the T4 genotype is a potential environmental host for Enterobacter aerogenes and Aeromonas hydrophila. Parasit Vectors 6, 169.
375. Yutin N, Colson P, Raoult D & Koonin EV (2013). Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family. Virol J 10, 106.
376. Zemojtel T, Penzkofer T, Schultz J, Dandekar T, Badge R & Vingron M (2007). Exonization of active mouse L1s: a driver of transcriptome evolution? BMC Genomics 8, 392.
377. Zhao Y, Wang K, Budinoff C, Buchan A, Lang A, Jiao N & Chen F (2009). Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay. ISME J 3, 364-373.
378. Zmasek CM, Zhang Q, Ye Y & Godzik A (2007). Surprising complexity of the ancestral apoptosis network. Genome Biol 8, R226.
379. Zupan J, Muth TR, Draper O & Zambryski P (2000). The transfer of DNA from Agrobacterium tumefaciens into plants: a feast of fundamental insights. Plant J 23, 11-28.