Mechanisms of DNA transposition

Microbiology Spectrum

Volumn 3, Issue 2, 2015, Pages

  Hickman, Alison B ^a   Dyda, Fred ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSPOSASE; TRANSPOSON;

GENETIC RECOMBINATION; GENETICS; METABOLISM; TRANSPOSON;

DNA; DNA TRANSPOSABLE ELEMENTS; RECOMBINATION, GENETIC; TRANSPOSASES;

EID: 84959059091     PISSN: None     EISSN: 21650497     Source Type: Journal    
DOI: 10.1128/microbiolspec.MDNA3-0034-2014     Document Type: Article

References (182)

1. Curcio MJ, Derbyshire KM. 2003. The outs and ins of transposition: From Mu to kangaroo. Nature Rev Mol Cell Biol 4:865-877.
2. Montaño SP, Rice PA. 2011. Moving DNA around: DNA transposition and retroviral integration. Curr Opin Struct Biol 21:370-378.
3. Chandler M, de la Cruz F, Dyda F, Hickman AB, Moncalian G, Ton-Hoang B. 2013. Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nature Rev Microbiol 11:525-538.
4. Yang W. 2011. Nucleases: diversity of structure, function and mechanism. Quart Rev Biophys 44:1-93.
5. Dyda F, Hickman AB, Jenkins TM, Engelman A, Craigie R, Davies DR. 1994. Crystal structure of the catalytic domain of HIV-1 integrase: Similarity to other polynucleotidyl transferases. Science 266: 1981-1986.
6. Rice P, Mizuuchi K. 1995. Structure of the bacteriophage Mu transposase core: A common structural motif for DNA transposition and retroviral integration. Cell 82:209-220.
7. Yuan YW, Wessler SR. 2011. The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci USA 108: 7884-7889.
8. Koonin EV, Ilyina TV. 1993. Computer-assisted dissection of rolling circle DNA replication. BioSystems 30:241-268.
9. Smith MCM, Thorpe HM. 2002. Diversity in the serine recombinases. Mol Microbiol 44:299-307.
10. Smith MCM, Brown WRA, McEwan AR, Rowley PA. 2010. Sitespecific recombination by FC31 integrase and other large serine recombinases. Biochem Soc Trans 38:388-394.
11. Rajeev L, Malanowska K, Gardner JF. 2009. Challenging a paradigm: the role of DNA homology in tyrosine recombinase reactions. Microbiol Mol Biol Rev 73:300-309.
12. Beese LS, Steitz TA. 1991. Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J 10:25-33.
13. Nowotny M, Gaidamakov SA, Crouch RJ, Yang W. 2005. Crystal structures of RNase H bound to an RNA/DNA hybrid: Substrate specificity and metal-dependent catalysis. Cell 121:1005-1016.
14. Nowotny M, Yang W. 2006. Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. EMBO J 25:1924-1933.
15. Rosta E, Woodcock HL, Brooks BR, Hummer G. 2009. Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H. J Comput Chem 30:1634-1641.
16. Rosta E, Nowotny M, Yang W, Hummer G. 2011. Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. J Am Chem Soc 133:8934-8941.
17. Mizuuchi K, Adzuma K. 1991. Inversion of the phosphate chirality at the target site of Mu DNA strand transfer: evidence for a one-step transesterification mechanism. Cell 66:129-140.
18. Engelman A, Mizuuchi K, Craigie R. 1991. HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell 67: 1211-1221.
19. Kennedy AK, Haniford DB, Mizuuchi K. 2000. Single active site catalysis of the successive phosphoryl transfer steps by DNA transposases: Insights from phosphorothioate stereoselectivity. Cell 101:295-305.
20. Levchenko I, Luo L, Baker TA. 1995. Disassembly of the Mu transposase tetramer by the ClpX chaperone. Genes Dev 9:2399-2408.
21. Bolland S, Kleckner N. 1996. The three chemical steps of Tn10/IS10 transposition involve repeated utilization of a single active site. Cell 84:223-233.
22. Rosta E, Yang W, Hummer G. 2014. Calcium inhibition of Ribonuclease H1 two-metal ion catalysis. J Am Chem Soc 136:3137-3144.
23. Savilahti H, Rice PA, Mizuuchi K. 1995. The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J 14:4893-4903.
24. Steitz TA, Steitz JA. 1993. A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90:6498-6502.
25. Stahley MR, Strobel SA. 2005. Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science 309:1587-1590.
26. Nowotny M. 2009. Retroviral integrase superfamily: the structural perspective. EMBO Reports 10:144-151.
27. Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W. 2012. Watching DNA polymerase η make a phosphodiester bond. Nature 487:196-201.
28. Hare S, Maertens GN, Cherepanov P. 3'-processing and strand transfer catalysed by retroviral integrase in crystallo. EMBO J 31:3020-3028.
29. Ton-Hoang B, Guynet C, Ronning DR, Cointin-Marty B, Dyda F, Chandler M. 2005. Transposition of ISHp608, member of an unusual family of bacterial insertion sequences. EMBO J 24:3325-3338.
30. Ronning DR, Guynet C, Ton-Hoang B, Perez ZN, Ghirlando R, Chandler M, Dyda F. 2005. Active site sharing and subterminal hairpin recognition in a new class of DNA transposases. Mol Cell 20:143-154.
31. Guynet C, Hickman AB, Barabas O, Dyda F, Chandler M, Ton-Hoang B. 2008. In vitro reconstitution of a single-stranded transposition mechanism of IS608. Mol Cell 29:302-312.
32. Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, Chandler M, Dyda F. 2008. Mechanism of IS200/IS605 family DNA transposases: Activation and transposon-directed target site selection. Cell 132:208-220.
33. Hickman AB, James JA, Barabas O, Pasternak C, Ton-Hoang B, Chandler M, Sommer S, Dyda F. 2010. DNArecognition and the precleavage state during single-stranded DNA transposition in D. radiodurans. EMBOJ 29:3840-3852.
34. He S, Hickman AB, Dyda F, Johnson NP, Chandler M, Ton-Hoang B. 2011. Reconstitution of a functional IS608 single-strand transpososome: role of non-canonical base pairing. Nucl Acids Res 39:8503-8512.
35. He S, Guynet C, Siguier P, Hickman AB, Dyda F, Chandler M, Ton-Hoang B. 2013. IS200/IS605 family single-strand transposition: mechanism of IS608 strand transfer. Nucl Acids Res 41:3302-3313.
36. Hickman AB, Ronning DR, Kotin RM, Dyda F. 2002. Structural unity among viral origin binding proteins: Crystal structure of the nuclease domain of adeno-associated virus Rep. Mol Cell 10:327-337.
37. Guasch A, Lucas M, Moncalián G, Cabezas M, Pérez-Luque R, Gomis-Rüth FX, de la Cruz F, Coll M. 2003. Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Nature Struct Biol 10:1002-1010.
38. Datta S, Larkin C, Schildbach JF. 2003. Structural insights into singlestranded DNA binding and cleavage by F factor TraI. Struct 11:1369-1379.
39. Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Pérez-Luque R, Coll M, de la Cruz F. 2006. Unveiling the molecular mechanism of a conjugative relaxase: The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site. J Mol Biol 358:857-869.
40. Toleman MA, Bennett PM, Walsh TR. 2006. ISCR elements: Novel gene-capturing systems of the 21st century? Microbiol Mol Biol Rev 70: 296-316.
41. Ton-Hoang B, Siguier P, Quentin Y, Onillon S, Marty B, Fichant G, Chandler M. 2012. Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences. Nucl Acids Res 40:3596-3609.
42. Messing SAJ, Ton-Hoang B, Hickman AB, McCubbin AJ, Peaslee GF, Ghirlando R, Chandler M, Dyda F. 2012. The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease. Nucl Acids Res 40:9964-9979.
43. Nunvar J, Huckova T, Licha I. 2010. Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes. BMC Genomics 11:44.
44. Kapitonov VV, Jurka J. 2001. Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci USA 98:8714-8719.
45. Feschotte C, Wessler SR. 2001. Treasures in the attic: Rolling circle transposons discovered in eukaryotic genomes. Proc Natl Acad Sci USA 98:8923-8924.
46. Pritham EJ, Feschotte C. 2007. Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc Natl Acad Sci USA 104:1895-1900.
47. Kersulyte D, Mukhopadhyay AK, Shirai M, Nakazawa T, Berg DE. 2000. Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori. J Bacteriol 182:5300-5308.
48. Boocock MR, Rice PA. 2013. A proposed mechanism for IS607-family serine transposases. Mobile DNA 4:24.
49. Bannam TL, Crellin PK, Rood JI. 1995. Molecular genetics of the chloramphenicol-resistance transposon Tn4451 from Clostridium perfringens: the TnpX site-specific recombinase excises a circular transposon molecule. Mol Microbiol 16:535-551.
50. Lyras D, Rood JI. 2000. Transposition of Tn4451 and Tn4453 involves a circular intermediate that forms a promoter for the large resolvase, TnpX. Mol Microbiol 38:588-601.
51. Grindley NDF, Whiteson KL, Rice PA. 2006. Mechanisms of sitespecific recombination. Annu Rev Biochem 75:567-605.
52. Wang H, Smith MCM, Mullany P. 2006. The conjugative transposon Tn5397 has a strong preference for integration into its Clostridium difficile target site. J Bacteriol 188:4871-4878.
53. Kersulyte D, Kalia A, Zhang MJ, Lee HK, Subramaniam D, Kiuduliene L, Chalkauskas H, Berg DE. 2004. Sequence organization and insertion specificity of the novel chimeric ISHp609 transposable element of Helicobacter pylori. J Bacteriol 186:7521-7528.
54. Sanderson MR, Freemont PS, Rice PA, Goldman A, Hatfull GF, Grindley NDF, Steitz TA. 1990. The crystal structure of the catalytic domain of the site-specific recombination enzyme γδ resolvase at 2.7 Å resolution. Cell 63:1323-1329.
55. Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley NDF, Steitz TA. 2005. Structure of a synaptic γδ resolvase tetramer covalently linked to two cleaved DNAs. Science 309:1210-1215.
56. Keenholtz RA, Rowland SJ, Boocock MR, Stark WM, Rice PA. 2011. Structural basis for catalytic activation of a serine recombinase. Struct 19:799-809.
57. Keenholtz RA, Mouw KW, Boocock MR, Li NS, Piccirilli JA, Rice PA. 2013. Arginine as a general acid catalyst in serine recombinasemediated DNA cleavage. J Biol Chem 288:29206-29214.
58. Hickman AB, Waninger S, Scocca JJ, Dyda F. 1997. Molecular organization in site-specific recombination: The catalytic domain of bacteriophage HP1 integrase at 2.7Å resolution. Cell 89:227-237.
59. Kwon HJ, Tirumalai R, Landy A, Ellenberger T. 1997. Flexibility in DNA recombination: Structure of the lambda integrase catalytic core. Science 276:126-131.
60. Chen Y, Rice PA. 2003. New insight into site-specific recombination from Flp recombinase-DNA structures. Annu Rev Biophys Biomol Struct 32:135-159.
61. Roberts AP, Mullany P. 2009. A modular master on the move: the Tn916 family of mobile genetic elements. Trends Microbiol 17:251-258.
62. Waters JL, Salyers AA. 2013. Regulation of CTnDOT conjugative transfer is a complex and highly coordinated series of events. mBio 4: e00569-13.
63. Brochet M, Da Cunha V, Couvé E, Rusniok C, Trieu-Cuot P, Glaser P. 2009. Atypical association of DDE transposition with conjugation specifies a new family of mobile element. Mol Microbiol 71:948-959.
64. Guérillot R, Siguier P, Gourbeyre E, Chandler M, Glaser P. 2014. The diversity of prokaryotic DDE transposases of the Mutator superfamily, insertion specificity, and association with conjugation machineries. Genome Biol Evol 6:260-272.
65. Harshey RM. 2012. The Mu story: how a maverick phage moved the field forward. Mobile DNA 3:21.
66. Mizuuchi K. 1992. Transpositional recombination: Mechanistic insights from studies of Mu and other elements. Annu Rev Biochem 61: 1011-1051.
67. North SH, Kirtland SE, Nakai H. 2007. Translation factor IF2 at the interface of transposition and replication by the PriA-PriC pathway. Mol Microbiol 66:1566-1578.
68. Jones JM, Nakai H. 1999. Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate. J Mol Biol 289:503-515.
69. Duval-Valentin G, Marty-Cointin B, Chandler M. 2004. Requirement of IS911 replication before integration defines a new bacterial transposition pathway. EMBO J 23:3897-3906.
70. Ton-Hoang B, Polard P, Chandler M. 1998. Efficient transposition of IS911 circles in vitro. EMBO J 17:1169-1181.
71. Polard P, Chandler M. 1995. An in vivo transposase-catalyzed singlestranded DNA circularization reaction. Genes Dev 9:2846-2858.
72. Ton-Hoang B, Bétermier M, Polard P, Chandler M. 1997. Assembly of a strong promoter following IS911 circularization and the role of circles in transposition. EMBO J 16:3357-3371.
73. Turlan C, Chandler M. 2000. Playing second fiddle: second-strand processing and liberation of transposable elements from donor DNA. Trends Microbiol 8:268-274.
74. Hickman AB, Chandler M, Dyda F. 2010. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol 45:50-69.
75. Dawson A, Finnegan DJ. 2003. Excision of the Drosophila mariner transposon Mos1: Comparison with bacterial transposition and V(D)J recombination. Mol Cell 11:225-235.
76. Claeys Bouuaert C, Chalmers R. 2010. Transposition of the human Hsmar1 transposon: rate-limiting steps and the importance of the flanking TA dinucleotide in second strand cleavage. Nucl Acids Res 38:190-202.
77. Lampe DJ, Churchill MEA, Robertson HM. 1996. A purified mariner transposase is sufficient to mediate transposition in vitro. EMBO J 15: 5470-5479.
78. Beall EL, Rio DC. 1997. Drosophila P-element transposase is a novel site-specific endonuclease. Genes Dev 11:2137-2151.
79. Steiniger-White M, Rayment I, ReznikoffWS. 2004. Structure/function insights into Tn5 transposition. Curr Opin Struct Biol 14:50-57.
80. Mitra R, Fain-Thornton J, Craig NL. 2008. piggyBac can bypass DNA synthesis during cut and paste transposition. EMBO J 27:1097-1109.
81. Zhou L, Mitra R, Atkinson PW, Hickman AB, Dyda F, Craig NL. 2004. Transposition of hAT elements links transposable elements and V(D)J recombination. Nature 432:995-1001.
82. Schatz DG, Swanson PC. 2011. V(D)J recombination: Mechanisms of initiation. Annu Rev Genet 45:167-202.
83. Kapitonov VV, Jurka J. 2005. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3: e181.
84. Tang M, Cecconi C, Bustamante C, Rio DC. 2007. Analysis of P element transposase protein-DNA interactions during the early stages of transposition. J Biol Chem 282:29002-29012.
85. Biery MC, Lopata M, Craig NL. 2000. A minimal system for Tn7 transposition: The transposon-encoded proteins TnsA and TnsB can execute DNA breakage and joining reactions that generate circularized Tn7 species. J Mol Biol 297:25-37.
86. Choi KY, Li Y, Sarnovsky R, Craig NL. 2013. Direct interaction between the TnsA and TnsB subunits controls the heteromeric Tn7 transposase. Proc Natl Acad Sci USA 110:E2038-E2045.
87. Hickman AB, Li Y, Mathew SV, May EW, Craig NL, Dyda F. 2000. Unexpected structural diversity in DNA recombination: The restriction endonuclease connection. Mol Cell 5:1025-1034.
88. May EW, Craig NL. 1996. Switching from cut-and-paste to replicative Tn7 transposition. Science 272:401-404.
89. Davies DR, Goryshin IY, ReznikoffWS, Rayment I. 2000. Threedimensional structure of the Tn5 synaptic complex transposition intermediate. Science 289:77-85.
90. Richardson JM, Colloms SD, Finnegan DJ, Walkinshaw MD. 2009. Molecular architecture of the Mos1 paired-end complex: The structural basis of DNA transposition in a eukaryote. Cell 138:1096-1108.
91. Hickman AB, et al. 2014. Structural basis of hAT transposon end recognition by Hermes, an octameric DNA transposase from Musca domestica. Cell 158:353-367.
92. Dyda F, Chandler M, Hickman AB. 2012. The emerging diversity of transpososome architectures. Quart Rev Biophys 45:493-521.
93. Montaño SP, Pigli YZ, Rice PA. 2012. The Mu transpososome structure sheds light on DDE recombinase evolution. Nature 491:413-417.
94. Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P. 2010. Retroviral intasome assembly and inhibition of DNA strand transfer. Nature 464:232-236.
95. Maertens GN, Hare S, Cherepanov P. 2010. The mechanism of retroviral integration from X-ray structures of its key intermediates. Nature 468:326-329.
96. Schumacher S, Clubb RT, Cai M, Mizuuchi K, Clore GM, Gronenborn AM. 1997. Solution structure of the Mu end DNA-binding Iβ subdomain of phage Mu transposase: modular DNA recognition by two tethered domains. EMBO J 16:7532-7541.
97. Watkins S, van Pouderoyen G, Sixma TK. 2004. Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to the transposon DNA. Nucl Acids Res 32:4306-4312.
98. Arciszewska LK, Craig NL. 1991. Interaction of the Tn7-encoded transposition protein TnsB with the ends of the transposon. Nucl Acids Res 19:5021-5029.
99. Braam LAM, ReznikoffWS. 1998. Functional characterization of the Tn5 transposase by limited proteolysis. J Biol Chem 273:10908-10913.
100. Kwon D, Chalmers RM, Kleckner N. 1995. Structural domains of IS10 transposase and reconstitution of transposition activity from proteolytic fragments lacking an interdomain linker. Proc Natl Acad Sci USA 92:8234-8238.
101. Wintjens R, Rooman M. 1996. Structural classification of HTH DNA-binding domains and protein-DNA interaction modes. J Mol Biol 262:294-313.
102. Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer LM. 2005. The many faces of the helix-turn-helix domain:Transcription regulation and beyond. FEMS Microbiol Rev 29:231-262.
103. Rousseau P, Gueguen E, Duval-Valentin G, Chandler M. 2004. The helix-turn-helix motif of bacterial insertion sequence IS911 transposase is required for DNA binding. Nucl Acids Res 32:1335-1344.
104. Nagy Z, Szabó M, Chandler M, Olasz F. 2004. Analysis of the N-terminal DNA binding domain of the IS30 transposase. Mol Microbiol 54:478-488.
105. Feschotte C, Pritham EJ. 2007. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331-368.
106. Beall EL, Rio DC. 1998. Transposase makes critical contacts with, and is stimulated by, single-stranded DNA at the P element termini in vitro. EMBO J 17:2122-2136.
107. Aravind L. 2000. The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases. Trends Biochem Sci 25:421-423.
108. Braam LAM, Goryshin IY, ReznikoffWS. 1999. A mechanism for Tn5 inhibition: Carboxyl-terminal dimerization. J Biol Chem 274:86-92.
109. Richardson JM, Dawson A, O'Hagan N, Taylor P, Finnegan DJ, Walkinshaw MD. 2006. Mechanism of Mos1 transposition: insights from structural analysis. EMBO J 25:1324-1334.
110. Cuypers MG, TrubitsynaM, Callow P, Forsyth VT, Richardson JM. 2013. Solution conformations of early intermediates in Mos1 transposition. Nucl Acids Res 41:2020-2033.
111. Augé-Gouillou C, Hamelin MH, Demattei MV, Periquet M, Bigot Y. 2001. The wild-type conformation of the Mos-1 inverted terminal repeats is suboptimal for transposition in bacteria. Mol Genet Genomics 265: 51-57.
112. Zhang L, Dawson A, Finnegan DJ. 2001. DNA-binding activity and subunit interaction of the mariner transposase. Nucl Acids Res 29: 3566-3575.
113. Bainton RJ, Kubo KM, Feng JN, Craig NL. 1993. Tn7 transposition: Target DNA recognition is mediated by multiple Tn7-encoded proteins in a purified in vitro system. Cell 72:931-943.
114. Skelding Z, Sarnovsky R, Craig NL. 2002. Formation of a nucleoprotein complex containing Tn7 and its target DNA regulates transposition initiation. EMBO J 21:3494-3504.
115. Holder JW, Craig NL. 2010. Architecture of the Tn7 posttransposition complex: an elaborate nucleoprotein structure. J Mol Biol 401: 167-181.
116. Kim YJ, Hice RH, O'Brochta DA, Atkinson PW. 2011. DNA sequence requirements for hobo transposable element transposition in Drosophila melanogaster. Genetica 139:985-997.
117. Ivics Z, Hackett PB, Plasterk RH, Izsvák Z. 1997. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91:501-510.
118. Izsvák Z, Khare D, Behlke J, Heinemann U, Plasterk RH, Ivics Z. 2002. Involvement of a bifunctional, paired-like DNA-binding domain and a transpositional enhancer in Sleepy Beauty transposition. J Biol Chem 277:34581-34588.
119. Lohe AR, Hartl DL. 1996. Autoregulation of mariner transposase activity by overproduction and dominant-negative complementation. Mol Biol Evol 13:549-555.
120. Waddell CS, Craig NL. 1989. Tn7 transposition: Recognition of the attTn7 target sequence. Proc Natl Acad Sci USA 86:3958-3962.
121. Chakrabarti A, Desai P, Wickstrom E. 2004. Transposon Tn7 protein TnsD binding to Escherichia coli attTn7 DNA and its eukaryotic orthologs. Biochem 43:2941-2946.
122. Peters JE, Craig NL. 2001. Tn7: Smarter than we thought. Nature Rev Mol Cell Biol 2:806-814.
123. Peters JE, Craig NL. 2000. Tn7 transposes proximal to DNA doublestrand breaks and into regions where chromosomal DNA replication terminates. Mol Cell 6:573-582.
124. 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.
125. Plasterk RHA, Izsvák Z, Ivics Z. 1999. Resident aliens: the Tc1/mariner superfamily of transposable elements. Trends Genet 15:326-332.
126. Fraser MJ, Cary L, Boonvisudhi K, Wang HH. 1995. Assay for movement of Lepidopteran transposon IFP2 in insect cells using a baculovirus genome as a target DNA. Virol 211:397-407.
127. Linheiro RS, Bergman CM. 2008. Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element. Nucl Acids Res 36:6199-6208.
128. Halling SM, Kleckner N. 1982. A symmetrical six-base-pair target site sequence determines Tn10 insertion specificity. Cell 28:155-163.
129. Davies CJ, Hutchison III CA. 1995. Insertion site specificity of the transposon Tn3. Nucl Acids Res 23:507-514.
130. Liao GC, Rehm EJ, Rubin GM. 2000. Insertion site preferences of the P transposable element in Drosophila melanogaster. Proc Natl Acad Sci USA 97:3347-3351.
131. Shevchenko Y, Bouffard GG, Butterfield YSN, Blakesley RW, Hartley JL, Young AC, Marra MA, Jones SJM, Touchman JW, Green ED. 2002. Systematic sequencing of cDNA clones using the transposon Tn5. Nucl Acids Res 30:2469-2477.
132. Vigdal TJ, Kaufman CD, Izsvák Z, Voytas DF, Ivics Z. 2002. Common physical properties of DNA affecting target site selection of Sleeping Beauty and other Tc1/mariner transposable elements. J Mol Biol 323:441-452.
133. Manna D, Deng S, Breier AM, Higgins NP. 2005. Bacteriophage Mu targets the trinucleotide sequence CGG. J Bacteriol 187:3586-3588.
134. Liu S, Yeh CT, Ji T, Ying K, Wu H, Tang HM, Fu Y, Nettleton D, Schnable PS. 2009. Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet 5:e1000733.
135. Woodard LE, Li X, Malani N, Kaja A, Hice RH, Atkinson PW, Bushman FD, Craig NL, Wilson MH. 2012. Comparative analysis of the recently discovered hAT transposon TcBuster in human cells. PLoS ONE 7:e42666.
136. Linheiro RS, Bergman CM. 2012. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS ONE 7:e30008.
137. Guo Y, Park JM, Cui B, Humes E, Gangadharan S, Hung S, FitzGerald PC, Hoe KL, Grewal SIS, Craig NL, Levin HL. 2013. Integration profiling of gene function with dense maps of transposon integration. Genetics 195:599-609.
138. Kuduvalli PN, Rao JE, Craig NL. 2001. Target DNA structure plays a critical role in Tn7 transposition. EMBO J 20:924-932.
139. Pribil PA, Haniford DB. 2003. Target DNA bending is an important specificity determinant in target site selection in Tn10 transposition. J Mol Biol 330:247-259.
140. Pflieger A, Jaillet J, Petit A, Augé-Gouillou C, Renault S. 2014. Target capture during Mos1 transposition. J Biol Chem 289:100-111.
141. Cherepanov P, Maertens GN, Hare S. 2011. Structural insights into the retroviral DNA integration apparatus. Curr Opin Struct Biol 21:249-256.
142. Sakai J, Kleckner N. 1997. The Tn10 synaptic complex can capture a target DNA only after transposon excision. Cell 89:205-214.
143. Gradman RJ, Ptacin JL, Bhasin A, ReznikoffWS, Goryshin IY. 2008. A bifunctional DNA binding region in Tn5 transposase. Mol Microbiol 67:528-540.
144. Yusa K, Zhou L, Li MA, Bradley A, Craig NL. 2011. A hyperactive piggyBac transposase for mammalian applications. Proc Natl Acad Sci USA 108:1531-1536.
145. Claeys Bouuaert C, Chalmers RM. 2010. Gene therapy vectors: the prospects and potentials of the cut-and-paste transposons. Genetica 138:473-484.
146. VandenDriessche T, Ivics Z, Izsvák Z, Chuah MKL. 2009. Emerging potential of transposons for gene therapy and generation of induced pluripotent stem cells. Blood 114:1461-1468.
147. Copeland NG, Jenkins NA. 2010. Harnessing transposons for cancer gene discovery. Nature Rev Cancer 10:696-706.
148. Adzuma K, Mizuuchi K. 1988. Target immunity of Mu transposition reflects a differential distribution of Mu B protein. Cell 53:257-266.
149. Greene EC, Mizuuchi K. 2002. Target immunity during Mu DNA transposition: Transpososome assembly and DNA looping enhance MuAmediated disassembly of the MuB target complex. Mol Cell 10:1367-1378.
150. Stellwagen AE, Craig NL. 1997. Avoiding self: two Tn7-encoded proteins mediate target immunity in Tn7 transposition. EMBOJ 16:6823-6834.
151. Lambin M, Nicolas E, Oger CA, Nguyen N, Prozzi D, Hallet B. 2012. Separate structural and functional domains of Tn4430 transposase contribute to target immunity. Mol Microbiol 83:805-820.
152. Lavoie BD, Chaconas G. 1993. Site-specific HU binding in the Mu transpososome: conversion of sequence-independent DNA-binding protein into a chemical nuclease. Genes Dev 7:2510-2519.
153. Chalmers R, Guhathakurta A, Benjamin H, Kleckner N. 1998. IHF modulation of Tn10 transposition: Sensory transduction of supercoiling status via a proposed protein/DNA molecular spring. Cell 93:897-908.
154. Haniford DB. 2006. Transpososome dynamics and regulation in Tn10 transposition. Crit Rev Biochem Mol Biol 41:407-424.
155. Whitfield CR, Wardle SJ, Haniford DB. 2009. The global bacterial regulator H-NS promotes transpososome formation and transposition in the Tn5 system. Nucl Acids Res 37:309-321.
156. Liu D, Haniford DB, Chalmers RM. 2011. H-NS mediates the dissociation of a refractory protein-DNA complex during Tn10/IS10 transposition. Nucl Acids Res 39:6660-6668.
157. Zayed H, Izsvák Z, Khare D, Heinemann U, Ivics Z. 2003. The DNA-bending protein HMGB1 is a cellular cofactor of Sleeping Beauty transposition. Nucl Acids Res 31:2313-2322.
158. van Gent DC, Hiom K, Paull TT, Gellert M. 1997. Stimulation of V(D)J cleavage by high mobility group proteins. EMBO J 16:2665-2670.
159. Little AJ, Corbett E, Ortega F, Schatz DG. 2013. Cooperative recruitment of HMGB1 during V(D)J recombination through interactions with RAG1 and DNA. Nucl Acids Res 41:3289-3301.
160. Ton-Hoang B, Pasternak C, Siguier P, Guynet C, Hickman AB, Dyda F, Sommer S, Chandler M. 2010. Single-stranded DNA transposition is coupled to host replication. Cell 142:398-408.
161. Mennecier S, Servant P, Coste G, Bailone A, Sommer S. 2006. Mutagenesis via IS transposition in Deinococcus radiodurans. Mol Microbiol 59:317-325.
162. Mendiola MV, Bernales I, de la Cruz F. 1994. Differential roles of the transposon termini in IS91 transposition. Proc Natl Acad Sci USA 91:1922-1926.
163. Garcillán-Barcia MP, Bernales I, Mendiola MV, de la Cruz F. 2001. Single-stranded DNA intermediates in IS91 rolling-circle transposition. Mol Microbiol 39:494-501.
164. Kersulyte D, Akopyants NS, Clifton SW, Roe BA, Berg DE. 1998. Novel sequence organization and insertion specficity of IS605 and IS606: chimaeric transposable elements of Helicobacter pylori. Gene 223:175-186.
165. Kersulyte D, Velapatiño B, Dailide G, Mukhopadhyay AK, Ito Y, Cahuayme L, Parkinson AJ, Gilman RH, Berg DE. 2002. Transposable element ISHp608 of Helicobacter pylori: Nonrandom geographic distribution, functional organization, and insertion specificity. J Bacteriol 184: 992-1002.
166. Pennisi E. 2013. The CRISPR craze. Science 341:833-836.
167. Garcillán-Barcia MP, de la Cruz F. 2002. Distribution of IS91 family insertion sequences in bacterial genomes: evolutionary implications. FEMS Microbiol Ecol 42:303-313.
168. Guynet C, Achard A, Ton-Hoang B, Barabas O, Hickman AB, Dyda F, Chandler M. 2009. Resetting the site: Redirecting integration of an insertion sequence in a predictable way. Mol Cell 34:612-619.
169. Du C, Fefelova N, Caronna J, He L, Dooner HK. 2009. The polychromatic Helitron landscape of the maize genome. Proc Natl Acad Sci USA 106:19916-19921.
170. Yang L, Bennetzen JL. 2009. Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc Natl Acad Sci USA 106:19922-19927.
171. Hagemann AT, Craig NL. 1993. Tn7 transposition creates a hotspot for homologous recombination at the transposon donor site. Genetics 133:9-16.
172. Jang S, Sandler SJ, Harshey RM. 2012. Mu insertions are repaired by the double-strand break repair pathway of Escherichia coli. PLoS Genet 8: e1002642.
173. McBlane JF, van Gent DC, Ramsden DA, Romeo C, Cuomo CA, Gellert M, Oettinger MA. 1995. Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell 83:387-395.
174. Ma Y, Pannicke U, Schwarz K, Lieber MR. 2002. Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell 108:781-794.
175. Malu S, Malshetty V, Francis D, Cortes P. 2012. Role of nonhomologous end joining in V(D)J recombination. Immunol Res 54:233-246.
176. Beall EL, Rio DC. 1996. Drosophila IRBP/Ku p70 corresponds to the mutagen-sensitive mus309 gene and is involved in P-element excision in vivo. Genes Dev 10:921-933.
177. Mhammedi-Alaoui A, Pato M, Gama MJ, Toussaint A. 1994. A new component of bacteriophage Mu replicative transposition machinery: the Escherichia coli ClpX protein. Mol Microbiol 11:1109-1116.
178. Abdelhakim AH, Sauer RT, Baker TA. 2010. The AAA+ ClpX machine unfolds a keystone subunit to remodel the Mu transpososome. Proc Natl Acad Sci USA 107:2437-2442.
179. Kruklitis R, Welty DJ, Nakai H. 1996. ClpX protein of Escherichia coli activates bacteriophage Mu transposase in the strand transfer complex for initiation of Mu DNA synthesis. EMBO J 15:935-944.
180. Burton BM, Baker TA. 2003. Mu transpososome architecture ensures that unfolding by ClpX or proteolysis by ClpXP remodels but does not destroy the complex. Chem Biol 10:463-472.
181. Gibb B, Gupta K, Ghosh K, Sharp R, Chen J, Van Duyne GD. 2010. Requirements for catalysis in the Cre recombinase active site. Nucl Acids Res 38:5817-5832.
182. Marmignon A, Bischerour J, Silve A, Fojcik C, Dubois E, Arnaiz O, Kapusta A, Malinsky S, Betermier M. 2014. Ku-mediated coupling of DNA cleavage and repair during programmed genome rearrangements in the ciliate Paramecium tetraurelia. PLoS Genet 10:e1004552.