The influence of LINE-1 and SINE retrotransposons on mammalian genomes

Microbiology Spectrum

Volumn 3, Issue 2, 2015, Pages

  Richardson, Sandra R ^a   Doucet, Aurélien J ^a   Kopera, Huira C ^a   Moldovan, John B ^a   Garcia Perez, José Luis ^b   Moran, John V ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF GRANADA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; GENETIC DISORDER; GENETIC RECOMBINATION; GENETIC VARIATION; GENOME; HUMAN; LONG INTERSPERSED REPEAT; MAMMAL; SHORT INTERSPERSED REPEAT;

ANIMALS; GENETIC DISEASES, INBORN; GENETIC VARIATION; GENOME; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MAMMALS; RECOMBINATION, GENETIC; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

EID: 84952876465     PISSN: None     EISSN: 21650497     Source Type: Journal    
DOI: 10.1128/microbiolspec.MDNA3-0061-2014     Document Type: Article

References (410)

1. Orgel LE, Crick FH, Sapienza C. 1980. Selfish DNA. Nature 288:645-646.
2. Doolittle WF, Sapienza C. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601-603.
3. Craig NL, Craigie R, Gellert M, Lambowitz AM. 2002. p 1-1204. Mobile DNA II. ASM Press, Washington, D.C.
4. McClintock B. 1950. The origin and behavior of mutable loci in maize. Proc Natl Acad Sci U S A 36:344-355.
5. FedoroffN, Wessler S, Shure M. 1983. Isolation of the transposable maize controlling elements Ac and Ds. Cell 35:235-242.
6. Boeke JD, Garfinkel DJ, Styles CA, Fink GR. 1985. Ty elements transpose through an RNA intermediate. Cell 40:491-500.
7. 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, AthanasiouM, 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.
8. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, SimpsonM, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. 2001. The sequence of the human genome. Science 291:1304-1351.
9. Waring M, Britten RJ. 1966. Nucleotide sequence repetition: a rapidly reassociating fraction of mouse DNA. Science 154:791-794.
10. Britten RJ, Kohne DE. 1968. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science 161:529-540.
11. Beck CR, Garcia-Perez JL, Badge RM, Moran JV. 2011. LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet 12:187-215.
12. Belancio VP, Roy-Engel AM, Deininger PL. 2010. All y'all need to know 'bout retroelements in cancer. Semin Cancer Biol 20:200-210.
13. Levin HL, Moran JV. 2011. Dynamic interactions between transposable elements and their hosts. Nat Rev Genet 12:615-627.
14. Hancks DC, Kazazian HH, Jr. 2012. Active human retrotransposons: variation and disease. Curr Opin Genet Dev 22:191-203.
15. Richardson SR, Morell S, Faulkner GJ. 2014. L1 Retrotransposons and somatic mosaicism in the brain. Annu Rev Genet. 48:1-27.
16. Goodier JL, Kazazian HH, Jr. 2008. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 135:23-35.
17. Feschotte C. 2008. Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9:397-405.
18. Babushok DV, Kazazian HH, Jr. 2007. Progress in understanding the biology of the human mutagen LINE-1. Hum Mutat 28:527-539.
19. Burns KH, Boeke JD. 2012. Human transposon tectonics. Cell 149:740-752.
20. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, 3rd, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, CuffJ, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SM, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGeraldM, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES. 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803-819.
21. 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, CuffJ, 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.
22. de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD. 2011. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet 7:e1002384.
23. Ivics Z, Hackett PB, Plasterk RH, Izsvak Z. 1997. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91:501-510.
24. Shapiro JA. 1979. Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc Natl Acad Sci U S A 76:1933-1937.
25. Kleckner N. 1990. Regulation of transposition in bacteria. Annu Rev Cell Biol 6:297-327.
26. Rio DC. 2002. P transposable elements in Drosophila melanogaster, p 484-518. In Craig NL, Craigie R, Gellert M, Lambowitz AM (ed), Mobile DNA II. ASM Press, Washington, D.C.
27. Lazarow K, Doll ML, Kunze R. 2013. Molecular biology of maize Ac/Ds elements: an overview. Methods Mol Biol 1057:59-82.
28. Cary LC, Goebel M, Corsaro BG, Wang HG, Rosen E, Fraser MJ. 1989. Transposon mutagenesis of baculoviruses: analysis of Trichoplusia ni transposon IFP2 insertions within the FP-locus of nuclear polyhedrosis viruses. Virology 172:156-169.
29. Fraser MJ, Cary L, Boonvisudhi K, Wang HG. 1995. Assay for movement of Lepidopteran transposon IFP2 in insect cells using a baculovirus genome as a target DNA. Virology 211:397-407.
30. Ding S, Wu X, Li G, Han M, Zhuang Y, Xu T. 2005. Efficient transposition of the piggyBac (PB) transposon in mammalian cells and mice. Cell 122:473-483.
31. Rad R, Rad L, Wang W, Cadinanos J, Vassiliou G, Rice S, Campos LS, Yusa K, Banerjee R, Li MA, de la Rosa J, Strong A, Lu D, Ellis P, Conte N, Yang FT, Liu P, Bradley A. 2010. PiggyBac transposon mutagenesis: a tool for cancer gene discovery in mice. Science 330:1104-1107.
32. Ivics Z, Li MA, Mates L, Boeke JD, Nagy A, Bradley A, Izsvak Z. 2009. Transposon-mediated genome manipulation in vertebrates. Nat Methods 6:415-422.
33. Largaespada DA. 2009. Transposon mutagenesis in mice. Methods Mol Biol 530:379-390.
34. Ray DA, Feschotte C, Pagan HJ, Smith JD, Pritham EJ, Arensburger P, Atkinson PW, Craig NL. 2008. Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Res 18:717-728.
35. Ray DA, Pagan HJ, Thompson ML, Stevens RD. 2007. Bats with hATs: evidence for recent DNA transposon activity in genus Myotis. Mol Biol Evol 24:632-639.
36. Mitra R, Li X, Kapusta A, Mayhew D, Mitra RD, Feschotte C, Craig NL. 2013. Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon. Proc Natl Acad Sci U S A 110:234-239.
37. Pace JK, 2nd, Feschotte C. 2007. The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage. Genome Res 17:422-432.
38. VolffJN. 2006. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 28:913-922.
39. Kapitonov VV, Jurka J. 2005. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3: e181.
40. Majumdar S, Singh A, Rio DC. 2013. The human THAP9 gene encodes an active P-element DNA transposase. Science 339:446-448.
41. Bannert N, Kurth R. 2006. The evolutionary dynamics of human endogenous retroviral families. Annu Rev Genomics Hum Genet 7:149-173.
42. Belshaw R, Dawson AL, Woolven-Allen J, Redding J, Burt A, Tristem M. 2005. Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K(HML2): implications for present-day activity. J Virol 79:12507-12514.
43. Macfarlane C, Simmonds P. 2004. Allelic variation of HERV-K (HML-2) endogenous retroviral elements in human populations. J Mol Evol 59:642-656.
44. Moyes D, Griffiths DJ, Venables PJ. 2007. Insertional polymorphisms: a new lease of life for endogenous retroviruses in human disease. Trends Genet 23:326-333.
45. Shin W, Lee J, Son SY, Ahn K, Kim HS, Han K. 2013. Human-specific HERV-K insertion causes genomic variations in the human genome. PLoS One 8:e60605.
46. Hughes JF, Coffin JM. 2004. Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: implications for human and viral evolution. Proc Natl Acad Sci U S A 101:1668-1672.
47. Yohn CT, Jiang Z, McGrath SD, Hayden KE, Khaitovich P, Johnson ME, Eichler MY, McPherson JD, Zhao S, Paabo S, Eichler EE. 2005. Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol 3:e110.
48. Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, Heidmann T. 2006. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res 16:1548-1556.
49. Lee YN, Bieniasz PD. 2007. Reconstitution of an infectious human endogenous retrovirus. PLoS Pathog 3:e10.
50. Stocking C, Kozak CA. 2008. Murine endogenous retroviruses. Cell Mol Life Sci 65:3383-3398.
51. 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.
52. Burton FH, Loeb DD, Voliva CF, Martin SL, Edgell MH, Hutchison CA, 3rd. 1986. Conservation throughout mammalia and extensive protein-encoding capacity of the highly repeated DNA long interspersed sequence one. J Mol Biol 187:291-304.
53. Smit AF, Toth G, Riggs AD, Jurka J. 1995. Ancestral, mammalianwide subfamilies of LINE-1 repetitive sequences. J Mol Biol 246:401-417.
54. Yang L, Brunsfeld J, Scott L, Wichman H. 2014. Reviving the dead: history and reactivation of an extinct l1. PLoS Genet 10:e1004395.
55. Khan H, Smit A, Boissinot S. 2006. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res 16:78-87.
56. Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D. 2014. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature [Epub ahead of print].
57. Castro-Diaz N, Ecco G, Coluccio A, Kapopoulou A, Yazdanpanah B, Friedli M, Duc J, Jang SM, Turelli P, Trono D. 2014. Evolutionally dynamic L1 regulation in embryonic stem cells. Genes Dev 28:1397-1409.
58. Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, Badge RM, Moran JV. 2010. LINE-1 retrotransposition activity in human genomes. Cell 141:1159-1170.
59. Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, Kazazian HH, Jr. 2003. Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A 100:5280-5285.
60. Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH, Jr. 1996. High frequency retrotransposition in cultured mammalian cells. Cell 87:917-927.
61. Sassaman DM, Dombroski BA, Moran JV, Kimberland ML, Naas TP, DeBerardinis RJ, Gabriel A, Swergold GD, Kazazian HH, Jr. 1997. Many human L1 elements are capable of retrotransposition. Nat Genet 16:37-43.
62. Skowronski J, Fanning TG, Singer MF. 1988. Unit-length line-1 transcripts in human teratocarcinoma cells. Mol Cell Biol 8:1385-1397.
63. Boissinot S, Chevret P, Furano AV. 2000. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol 17:915-928.
64. Dombroski BA, Mathias SL, Nanthakumar E, Scott AF, Kazazian HH, Jr. 1991. Isolation of an active human transposable element. Science 254:1805-1808.
65. Ovchinnikov I, Troxel AB, Swergold GD. 2001. Genomic characterization of recent human LINE-1 insertions: evidence supporting random insertion. Genome Res 11:2050-2058.
66. Sheen FM, Sherry ST, Risch GM, Robichaux M, Nasidze I, Stoneking M, Batzer MA, Swergold GD. 2000. Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition. Genome Res 10:1496-508.
67. Badge RM, Alisch RS, Moran JV. 2003. ATLAS: a system to selectively identify human-specific L1 insertions. Am J Hum Genet 72:823-838.
68. Ewing AD, Kazazian HH, Jr. 2010. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res 20:1262-1270.
69. Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE. 2010. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141:1253-1261.
70. Boissinot S, Entezam A, Young L, Munson PJ, Furano AV. 2004. The insertional history of an active family of L1 retrotransposons in humans. Genome Res 14:1221-1231.
71. Myers JS, Vincent BJ, Udall H, Watkins WS, Morrish TA, Kilroy GE, Swergold GD, Henke J, Henke L, Moran JV, Jorde LB, Batzer MA. 2002. A comprehensive analysis of recently integrated human Ta L1 elements. Am J Hum Genet 71:312-326.
72. Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Gibbs RA, Hurles ME, McVean GA. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-1073.
73. Grimaldi G, Skowronski J, Singer MF. 1984. Defining the beginning and end of KpnI family segments. EMBO J 3:1753-1759.
74. Scott AF, Schmeckpeper BJ, Abdelrazik M, Comey CT, O'Hara B, Rossiter JP, Cooley T, Heath P, Smith KD, Margolet L. 1987. Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence. Genomics 1:113-125.
75. Swergold GD. 1990. Identification, characterization, and cell specificity of a human LINE-1 promoter. Mol Cell Biol 10:6718-6729.
76. Speek M. 2001. Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol Cell Biol 21:1973-1985.
77. Holmes SE, Singer MF, Swergold GD. 1992. Studies on p40, the leucine zipper motif-containing protein encoded by the first open reading frame of an active human LINE-1 transposable element. J Biol Chem 267:19765-19768.
78. Hohjoh H, Singer MF. 1996. Cytoplasmic ribonucleoprotein complexes containing human LINE-1 protein and RNA. Embo J 15:630-639.
79. Khazina E, Truffault V, Buttner R, Schmidt S, Coles M, Weichenrieder O. 2011. Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition. Nat Struct Mol Biol 18:1006-1014.
80. Martin SL, Bushman FD. 2001. Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol Cell Biol 21:467-475.
81. Ergun S, Buschmann C, Heukeshoven J, Dammann K, Schnieders F, Lauke H, Chalajour F, Kilic N, Stratling WH, Schumann GG. 2004. Cell type-specific expression of LINE-1 open reading frames 1 and 2 in fetal and adult human tissues. J Biol Chem 279:27753-27763.
82. Doucet AJ, Hulme AE, Sahinovic E, Kulpa DA, Moldovan JB, Kopera HC, Athanikar JN, Hasnaoui M, Bucheton A, Moran JV, Gilbert N. 2010. Characterization of LINE-1 ribonucleoprotein particles. PLoS Genet 6:e1001150.
83. Feng Q, Moran J, Kazazian H, Boeke JD. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87:905-916.
84. Mathias SL, Scott AF, Kazazian HH, Jr., Boeke JD, Gabriel A. 1991. Reverse transcriptase encoded by a human transposable element. Science 254:1808-1810.
85. Fanning T, Singer M. 1987. The LINE-1 DNA sequences in four mammalian orders predict proteins that conserve homologies to retrovirus proteins. Nucleic Acids Res 15:2251-2260.
86. Goodier JL, Ostertag EM, Du K, Kazazian HH, Jr. 2001. A novel active L1 retrotransposon subfamily in the mouse. Genome Res 11:1677-1685.
87. Furano AV. 2000. The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. Prog Nucleic Acid Res Mol Biol 64:255-294.
88. Sookdeo A, Hepp CM, McClure MA, Boissinot S. 2013. Revisiting the evolution of mouse LINE-1 in the genomic era. Mob DNA 4:3.
89. Adey NB, Tollefsbol TO, Sparks AB, Edgell MH, Hutchison CA, 3rd. 1994. Molecular resurrection of an extinct ancestral promoter for mouse L1. Proc Natl Acad Sci U S A 91:1569-1573.
90. Naas TP, DeBerardinis RJ, Moran JV, Ostertag EM, Kingsmore SF, Seldin MF, Hayashizaki Y, Martin SL, Kazazian HH. 1998. An actively retrotransposing, novel subfamily of mouse L1 elements. EMBO J 17: 590-597.
91. DeBerardinis RJ, Goodier JL, Ostertag EM, Kazazian HH, Jr. 1998. Rapid amplification of a retrotransposon subfamily is evolving the mouse genome. Nat Genet 20:288-290.
92. Dewannieux M, Esnault C, Heidmann T. 2003. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35:41-48.
93. Dewannieux M, Heidmann T. 2005. L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells. J Mol Biol 349:241-247.
94. Raiz J, Damert A, Chira S, Held U, Klawitter S, Hamdorf M, Lower J, Stratling WH, Lower R, Schumann GG. 2012. The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. Nucleic Acids Res 40:1666-1683.
95. Hancks DC, Goodier JL, Mandal PK, Cheung LE, Kazazian HH, Jr. 2011. Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum Mol Genet 20:3386-3400.
96. Hancks DC, Mandal PK, Cheung LE, Kazazian HH, Jr. 2012. The minimal active human SVA retrotransposon requires only the 5'-hexamer and Alu-like domains. Mol Cell Biol 32:4718-4726.
97. Esnault C, Maestre J, Heidmann T. 2000. Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24:363-367.
98. Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, Kazazian HH, Boeke JD, Moran JV. 2001. Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 21:1429-1439.
99. Jurka J. 1997. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci U S A 94: 1872-1877.
100. Rubin CM, Houck CM, Deininger PL, Friedmann T, Schmid CW. 1980. Partial nucleotide sequence of the 300-nucleotide interspersed repeated human DNA sequences. Nature 284:372-374.
101. Ullu E, Tschudi C. 1984. Alu sequences are processed 7SL RNA genes. Nature 312:171-172.
102. Chu WM, Liu WM, Schmid CW. 1995. RNA polymerase III promoter and terminator elements affect Alu RNA expression. Nucleic Acids Res 23:1750-1757.
103. Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nat Rev Genet 3:370-379.
104. Chesnokov I, Schmid CW. 1996. Flanking sequences of an Alu source stimulate transcription in vitro by interacting with sequence-specific transcription factors. J Mol Evol 42:30-36.
105. Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL. 2009. Diverse cis factors controlling Alu retrotransposition: what causes Alu elements to die? Genome Res 19:545-555.
106. Dewannieux M, Heidmann T. 2005. Role of poly(A) tail length in Alu retrotransposition. Genomics 86:378-381.
107. Goodier JL, Maraia RJ. 1998. Terminator-specific recycling of a B1-Alu transcription complex by RNA polymerase III is mediated by the RNA terminus-binding protein La. J Biol Chem 273:26110-26116.
108. Liu WM, Schmid CW. 1993. Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation. Nucleic Acids Res 21:1351-1359.
109. Ullu E, Weiner AM. 1985. Upstream sequences modulate the internal promoter of the human 7SL RNA gene. Nature 318:371-374.
110. Jurka J, Smith T. 1988. A fundamental division in the Alu family of repeated sequences. Proc Natl Acad Sci U S A 85:4775-4778.
111. Slagel V, Flemington E, Traina-Dorge V, Bradshaw H, Deininger P. 1987. Clustering and subfamily relationships of the Alu family in the human genome. Mol Biol Evol 4:19-29.
112. Britten RJ, Baron WF, Stout DB, Davidson EH. 1988. Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci U S A 85:4770-4774.
113. Willard C, Nguyen HT, Schmid CW. 1987. Existence of at least three distinct Alu subfamilies. J Mol Evol 26:180-186.
114. Batzer MA, Deininger PL, Hellmann-Blumberg U, Jurka J, Labuda D, Rubin CM, Schmid CW, Zietkiewicz E, Zuckerkandl E. 1996. Standardized nomenclature for Alu repeats. J Mol Evol 42:3-6.
115. Batzer MA, Schmid CW, Deininger PL. 1993. Evolutionary analyses of repetitive DNA sequences. Methods Enzymol 224:213-232.
116. Carroll ML, Roy-Engel AM, Nguyen SV, Salem AH, Vogel E, Vincent B, Myers J, Ahmad Z, Nguyen L, Sammarco M, Watkins WS, Henke J, Makalowski W, Jorde LB, Deininger PL, Batzer MA. 2001. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J Mol Biol 311:17-40.
117. Witherspoon DJ, Zhang Y, Xing J, Watkins WS, Ha H, Batzer MA, Jorde LB. 2013. Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations. Genome Res 23:1170-1181.
118. Minghetti PP, Dugaiczyk A. 1993. The emergence of newDNArepeats and the divergence of primates. Proc Natl Acad Sci U S A 90:1872-1876.
119. Batzer MA, Stoneking M, Alegria-Hartman M, Bazan H, Kass DH, Shaikh TH, Novick GE, Ioannou PA, Scheer WD, Herrera RJ, et al. 1994. African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci U S A 91:12288-12292.
120. Nikaido M, Rooney AP, Okada N. 1999. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales. Proc Natl Acad Sci U S A 96:10261-10266.
121. Okada N. 1991. SINEs. Curr Opin Genet Dev 1:498-504.
122. Ray DA, Xing J, Salem AH, Batzer MA. 2006. SINEs of a nearly perfect character. Syst Biol 55:928-935.
123. Witherspoon DJ, Marchani EE, Watkins WS, Ostler CT, Wooding SP, Anders BA, Fowlkes JD, Boissinot S, Furano AV, Ray DA, Rogers AR, Batzer MA, Jorde LB. 2006. Human population genetic structure and diversity inferred from polymorphic L1(LINE-1) and Alu insertions. Hum Hered 62:30-46.
124. Konkel MK, Walker JA, Batzer MA. 2010. LINEs and SINEs of primate evolution. Evol Anthropol 19:236-249.
125. Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE. 2008. Active Alu retrotransposons in the human genome. Genome Res 18:1875-1883.
126. Sarrowa J, Chang DY, Maraia RJ. 1997. The decline in human Alu retroposition was accompanied by an asymmetric decrease in SRP9/14 binding to dimeric Alu RNA and increased expression of small cytoplasmic Alu RNA. Mol Cell Biol 17:1144-1151.
127. Ostertag EM, Goodier JL, Zhang Y, Kazazian HH, Jr. 2003. SVA elements are nonautonomous retrotransposons that cause disease in humans. Am J Hum Genet 73:1444-1451.
128. Wang H, Xing J, Grover D, Hedges DJ, Han K, Walker JA, Batzer MA. 2005. SVA elements: a hominid-specific retroposon family. J Mol Biol 354:994-1007.
129. Hancks DC, Kazazian HH, Jr. 2010. SVA retrotransposons: Evolution and genetic instability. Semin Cancer Biol 20:234-245.
130. Savage AL, Bubb VJ, Breen G, Quinn JP. 2013. Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns. BMC Evol Biol 13:101.
131. Hara T, Hirai Y, Baicharoen S, Hayakawa T, Hirai H, Koga A. 2012. A novel composite retrotransposon derived from or generated independently of the SVA (SINE/VNTR/Alu) transposon has undergone proliferation in gibbon genomes. Genes Genet Syst 87:181-190.
132. Ianc B, Ochis C, Persch R, Popescu O, Damert A. 2014. Hominoid CompositeNon-LTRRetrotransposons-Variety, Assembly, Evolution, and Structural Determinants of Mobilization. Mol Biol Evol 31:2847-2864.
133. Carbone L, Harris RA, Mootnick AR, Milosavljevic A, Martin DI, Rocchi M, Capozzi O, Archidiacono N, Konkel MK, Walker JA, Batzer MA, de Jong PJ. 2012. Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons. Genome Biol Evol 4:648-658.
134. Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvak Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA. 2014. Gibbon genome and the fast karyotype evolution of small apes. Nature 513:195-201.
135. Krayev AS, Kramerov DA, Skryabin KG, Ryskov AP, Bayev AA, Georgiev GP. 1980. The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA. Nucleic Acids Res 8:1201-1215.
136. Quentin Y. 1994. A master sequence related to a free left Alu monomer (FLAM) at the origin of the B1 family in rodent genomes. Nucleic Acids Res 22:2222-2227.
137. Daniels GR, Deininger PL. 1985. Repeat sequence families derived from mammalian tRNA genes. Nature 317:819-822.
138. DeChiara TM, Brosius J. 1987. Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proc Natl Acad Sci U S A 84:2624-2628.
139. Lee IY, Westaway D, Smit AF, Wang K, Seto J, Chen L, Acharya C, Ankener M, Baskin D, Cooper C, Yao H, Prusiner SB, Hood LE. 1998. Complete genomic sequence and analysis of the prion protein gene region from three mammalian species. Genome Res 8:1022-1037.
140. Serdobova IM, Kramerov DA. 1998. Short retroposons of the B2 superfamily: evolution and application for the study of rodent phylogeny. J Mol Evol 46:202-214.
141. WeinerAM, Deininger PL, EfstratiadisA. 1986. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem 55:631-661.
142. Vanin EF. 1985. Processed pseudogenes: characteristics and evolution. Annu Rev Genet 19:253-272.
143. Torrents D, Suyama M, Zdobnov E, Bork P. 2003. A genome-wide survey of human pseudogenes. Genome Res 13:2559-2567.
144. Zhang Z, Harrison P, Gerstein M. 2002. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res 12:1466-82.
145. Zhang Z, Harrison PM, Liu Y, Gerstein M. 2003. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res 13:2541-58.
146. Ewing AD, Ballinger TJ, Earl D, Harris CC, Ding L, Wilson RK, Haussler D. 2013. Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol 14:R22.
147. Schrider DR, Navarro FC, Galante PA, Parmigiani RB, Camargo AA, Hahn MW, de Souza SJ. 2013. Gene copy-number polymorphism caused by retrotransposition in humans. PLoS Genet 9:e1003242.
148. Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Lee C, Gerstein M. 2013. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Res 23:2042-2052.
149. Richardson SR, Salvador-Palomeque C, Faulkner GJ. 2014. Diversity through duplication: whole-genome sequencing reveals novel gene retrocopies in the human population. Bioessays 36:475-481.
150. Kazazian HH, Jr. 2014. Processed pseudogene insertions in somatic cells. Mob DNA 5:20.
151. Hulme AE, Kulpa DA, Garcia-Perez JL, Moran JV. 2006. p 35-72. In Lupski JR, Stankiewicz P (ed), The impact of LINE-1 retrotransposition on the human genome. Humana Press, Totowa, New Jersey.
152. Sayah DM, Sokolskaja E, Berthoux L, Luban J. 2004. Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1. Nature 430:569-573.
153. Malfavon-Borja R, Wu LI, Emerman M, Malik HS. 2013. Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. Proc Natl Acad Sci U S A 110:E583-E592.
154. Buzdin A, Gogvadze E, Kovalskaya E, Volchkov P, Ustyugova S, Illarionova A, Fushan A, Vinogradova T, Sverdlov E. 2003. The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination. Nucleic Acids Res 31:4385-4390.
155. Buzdin A, Ustyugova S, Gogvadze E, Vinogradova T, Lebedev Y, Sverdlov E. 2002. A new family of chimeric retrotranscripts formed by a full copy of U6 small nuclear RNA fused to the 3' terminus of l1. Genomics 80:402-406.
156. Gilbert N, Lutz S, Morrish TA, Moran JV. 2005. Multiple fates of L1 retrotransposition intermediates in cultured human cells. Mol Cell Biol 25:7780-7795.
157. Garcia-Perez JL, Doucet AJ, Bucheton A, Moran JV, Gilbert N. 2007. Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase. Genome Res 17:602-611.
158. Weber MJ. 2006. Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genet 2:e205.
159. Hasnaoui M, Doucet AJ, Meziane O, Gilbert N. 2009. Ancient repeat sequence derived from U6 snRNA in primate genomes. Gene 448: 139-144.
160. Kazazian HH, Jr., Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE. 1988. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 332:164-166.
161. Dombroski BA, Scott AF, Kazazian HH, Jr. 1993. Two additional potential retrotransposons isolated from a human L1 subfamily that contains an active retrotransposable element. Proc Natl Acad Sci U S A 90:6513-6517.
162. Lutz SM, Vincent BJ, Kazazian HH, Jr., Batzer MA, Moran JV. 2003. Allelic heterogeneity in LINE-1 retrotransposition activity. Am J Hum Genet 73:1431-1437.
163. Skowronski J, Singer MF. 1985. Expression of a cytoplasmic LINE-1 transcript is regulated in a human teratocarcinoma cell line. Proc Natl Acad Sci U S A 82:6050-6054.
164. Wallace MR, Andersen LB, Saulino AM, Gregory PE, Glover TW, Collins FS. 1991. A de novo Alu insertion results in neurofibromatosis type 1. Nature 353:864-866.
165. Hassoun H, Coetzer TL, Vassiliadis JN, Sahr KE, Maalouf GJ, Saad ST, Catanzariti L, Palek J. 1994. A novel mobile element inserted in the alpha spectrin gene: spectrin dayton. A truncated alpha spectrin associated with hereditary elliptocytosis. J Clin Invest 94:643-648.
166. van der Klift HM, Tops CM, Hes FJ, Devilee P, Wijnen JT. 2012. Insertion of an SVA element, a nonautonomous retrotransposon, in PMS2 intron 7 as a novel cause of Lynch syndrome. Hum Mutat 33:1051-1055.
167. Vogt J, Bengesser K, Claes KB, Wimmer K, Mautner VF, van Minkelen R, Legius E, Brems H, Upadhyaya M, Hogel J, Lazaro C, Rosenbaum T, Bammert S, Messiaen L, Cooper DN, Kehrer-Sawatzki H. 2014. SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints. Genome Biol 15:R80.
168. de Boer M, van Leeuwen K, Geissler J, Weemaes CM, van den Berg TK, Kuijpers TW, Warris A, Roos D. 2014. Primary immunodeficiency caused by an exonized retroposed gene copy inserted in the CYBB gene. Hum Mutat 35:486-496.
169. Cooke SL, Shlien A, Marshall J, Pipinikas CP, Martincorena I, Tubio JM, Li Y, Menzies A, Mudie L, RamakrishnaM, Yates L, Davies H, Bolli N, Bignell GR, Tarpey PS, Behjati S, Nik-Zainal S, Papaemmanuil E, Teixeira VH, Raine K, O'Meara S, Dodoran MS, Teague JW, Butler AP, Iacobuzio-Donahue C, Santarius T, Grundy RG, Malkin D, Greaves M, Munshi N, Flanagan AM, Bowtell D, Martin S, Larsimont D, Reis-Filho JS, Boussioutas A, Taylor JA, Hayes ND, Janes SM, Futreal PA, Stratton MR, McDermott U, Campbell PJ. 2014. Processed pseudogenes acquired somatically during cancer development. Nat Commun 5:3644.
170. Wimmer K, Callens T, Wernstedt A, Messiaen L. 2011. The NF1 gene contains hotspots for L1 endonuclease-dependent de novo insertion. PLoS Genet 7:e1002371.
171. Kingsmore SF, Giros B, Suh D, Bieniarz M, Caron MG, Seldin MF. 1994. Glycine receptor beta-subunit gene mutation in spastic mouse associated with LINE-1 element insertion. Nat Genet 7:136-141.
172. Mulhardt C, Fischer M, Gass P, Simon-Chazottes D, Guenet JL, Kuhse J, Betz H, Becker CM. 1994. The spastic mouse: aberrant splicing of glycine receptor beta subunit mRNA caused by intronic insertion of L1 element. Neuron 13:1003-1015.
173. Takahara T, Ohsumi T, Kuromitsu J, Shibata K, Sasaki N, Okazaki Y, Shibata H, Sato S, Yoshiki A, Kusakabe M, Muramatsu M, Ueki M, Okuda K, Hayashizaki Y. 1996. Dysfunction of the Orleans reeler gene arising from exon skipping due to transposition of a full-length copy of an active L1 sequence into the skipped exon. Hum Mol Genet 5:989-993.
174. Kojima T, Nakajima K, Mikoshiba K. 2000. The disabled 1 gene is disrupted by a replacement with L1 fragment in yotari mice. Brain Res Mol Brain Res 75:121-127.
175. PerouCM, Pryor RJ, Naas TP, Kaplan J. 1997. The bg allele mutation is due to a LINE1 element retrotransposition. Genomics 42:366-368.
176. Yajima I, Sato S, Kimura T, Yasumoto K, Shibahara S, Goding CR, Yamamoto H. 1999. An L1 element intronic insertion in the black-eyed white (Mitf[mi-bw]) gene: the loss of a singleMitf isoformresponsible for the pigmentary defect and inner ear deafness. Hum Mol Genet 8:1431-1441.
177. Kohrman DC, Harris JB, Meisler MH. 1996. Mutation detection in the med and medJ alleles of the sodium channel Scn8a. Unusual splicing due to a minor class AT-AC intron. J Biol Chem 271:17576-17581.
178. Bomar JM, Benke PJ, Slattery EL, Puttagunta R, Taylor LP, Seong E, Nystuen A, Chen W, Albin RL, Patel PD, Kittles RA, Sheffield VC, Burmeister M. 2003. Mutations in a novel gene encoding a CRAL-TRIO domain cause human Cayman ataxia and ataxia/dystonia in the jittery mouse. Nat Genet 35:264-269.
179. Gilbert N, Bomar JM, Burmeister M, Moran JV. 2004. Characterization of a mutagenic B1 retrotransposon insertion in the jittery mouse. Hum Mutat 24:9-13.
180. Katzir N, Rechavi G, Cohen JB, Unger T, Simoni F, Segal S, Cohen D, Givol D. 1985. "Retroposon" insertion into the cellular oncogene c-myc in canine transmissible venereal tumor. Proc Natl Acad Sci U S A 82:1054-1058.
181. Choi Y, Ishiguro N, Shinagawa M, Kim CJ, Okamoto Y, Minami S, Ogihara K. 1999. Molecular structure of canine LINE-1 elements in canine transmissible venereal tumor. Anim Genet 30:51-53.
182. Brooks MB, Gu W, Barnas JL, Ray J, Ray K. 2003. A Line 1 insertion in the Factor IX gene segregates with mild hemophilia B in dogs. Mamm Genome 14:788-795.
183. Smith BF, Yue Y, Woods PR, Kornegay JN, Shin JH, Williams RR, Duan D. 2011. An intronic LINE-1 element insertion in the dystrophin gene aborts dystrophin expression and results in Duchenne-like muscular dystrophy in the corgi breed. Lab Invest 91:216-231.
184. Wolf ZT, Leslie EJ, Arzi B, Jayashankar K, Karmi N, Jia Z, Rowland DJ, Young A, Safra N, Sliskovic S, Murray JC, Wade CM, Bannasch DL. 2014. A LINE-1 insertion in DLX6 is responsible for cleft palate and mandibular abnormalities in a canine model of Pierre Robin sequence. PLoS Genet 10:e1004257.
185. Downs LM, Mellersh CS. 2014. An Intronic SINE insertion in FAM161A that causes exon-skipping is associated with progressive retinal atrophy in Tibetan Spaniels and Tibetan Terriers. PLoS One 9:e93990.
186. Clark LA, Wahl JM, Rees CA, Murphy KE. 2006. Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog. Proc Natl Acad Sci U S A 103:1376-1381.
187. Lin L, Faraco J, Li R, Kadotani H, Rogers W, Lin X, Qiu X, de Jong PJ, Nishino S, Mignot E. 1999. The sleep disorder canine narcolepsy is caused by a mutation in the hypocretin (orexin) receptor 2 gene. Cell 98:365-376.
188. Pele M, Tiret L, Kessler JL, Blot S, Panthier JJ. 2005. SINE exonic insertion in the PTPLA gene leads to multiple splicing defects and segregates with the autosomal recessive centronuclear myopathy in dogs. Hum Mol Genet 14:1417-1427.
189. Parker HG, VonHoldt BM, Quignon P, Margulies EH, Shao S, Mosher DS, Spady TC, Elkahloun A, Cargill M, Jones PG, Maslen CL, Acland GM, Sutter NB, Kuroki K, Bustamante CD, Wayne RK, Ostrander EA. 2009. An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science 325:995-998.
190. Heidmann T, Heidmann O, Nicolas JF. 1988. An indicator gene to demonstrate intracellular transposition of defective retroviruses. Proc Natl Acad Sci U S A 85:2219-2223.
191. Curcio MJ, Garfinkel DJ. 1991. Single-step selection for Ty1 element retrotransposition. Proc Natl Acad Sci USA 88:936-940.
192. Wei W, Morrish TA, Alisch RS, Moran JV. 2000. A transient assay reveals that cultured human cells can accommodate multiple LINE-1 retrotransposition events. Anal Biochem 284:435-438.
193. Freeman JD, Goodchild NL, Mager DL. 1994. A modified indicator gene for selection of retrotransposition events in mammalian cells. Biotechniques 17:46, 8-9, 52.
194. Xie Y, Rosser JM, Thompson TL, Boeke JD, An W. 2011. Characterization of L1 retrotransposition with high-throughput dual-luciferase assays. Nucleic Acids Res 39:e16.
195. Ostertag EM, Prak ET, DeBerardinis RJ, Moran JV, Kazazian HH, Jr. 2000. Determination of L1 retrotransposition kinetics in cultured cells. Nucleic Acids Res 28:1418-1423.
196. Morrish TA, Gilbert N, Myers JS, Vincent BJ, Stamato TD, Taccioli GE, Batzer MA, Moran JV. 2002. DNA repair mediated by endonucleaseindependent LINE-1 retrotransposition. Nat Genet 31:159-165.
197. Goodier JL, Zhang L, Vetter MR, Kazazian HH, Jr. 2007. LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNA interference RNA-induced silencing complex. Mol Cell Biol 27:6469-6483.
198. Kulpa DA, Moran JV. 2005. Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition. Hum Mol Genet 14:3237-3248.
199. Kulpa DA, Moran JV. 2006. Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol 13:655-660.
200. Taylor MS, Lacava J, Mita P, Molloy KR, Huang CR, Li D, Adney EM, Jiang H, Burns KH, Chait BT, Rout MP, Boeke JD, Dai L. 2013. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 155:1034-1048.
201. Goodier JL, Cheung LE, Kazazian HH, Jr. 2013. Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition. Nucleic Acids Res 41:7401-7419.
202. Gilbert N, Lutz-Prigge S, Moran JV. 2002. Genomic deletions created upon LINE-1 retrotransposition. Cell 110:315-325.
203. Symer DE, Connelly C, Szak ST, Caputo EM, Cost GJ, Parmigiani G, Boeke JD. 2002. Human l1 retrotransposition is associated with genetic instability in vivo. Cell 110:327-338.
204. Kajikawa M, Okada N. 2002. LINEs mobilize SINEs in the eel through a shared 3' sequence. Cell 111:433-444.
205. Sugano T, Kajikawa M, Okada N. 2006. Isolation and characterization of retrotransposition-competent LINEs from zebrafish. Gene 365: 74-82.
206. Seleme MC, Vetter MR, Cordaux R, Bastone L, Batzer MA, Kazazian HH, Jr. 2006. Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity. Proc Natl Acad Sci U S A 103:6611-6616.
207. Becker KG, Swergold GD, Ozato K, Thayer RE. 1993. Binding of the ubiquitous nuclear transcription factor YY1 to a cis regulatory sequence in the human LINE-1 transposable element. Hum Mol Genet 2:1697-1702.
208. Athanikar JN, Badge RM, Moran JV. 2004. A YY1-binding site is required for accurate human LINE-1 transcription initiation. Nucleic Acids Res 32:3846-3855.
209. Dmitriev SE, Andreev DE, Terenin IM, Olovnikov IA, Prassolov VS, Merrick WC, Shatsky IN. 2007. Efficient translation initiation directed by the 900-nucleotide-long and GC-rich 5' untranslated region of the human retrotransposon LINE-1 mRNA is strictly cap dependent rather than internal ribosome entry site mediated. Mol Cell Biol 27:4685-4697.
210. Tchenio T, Casella JF, Heidmann T. 2000. Members of the SRY family regulate the human LINE retrotransposons. Nucleic Acids Res 28:411-415.
211. Yang N, Zhang L, Zhang Y, Kazazian HH, Jr. 2003. An important role for RUNX3 in human L1 transcription and retrotransposition. Nucleic Acids Res 31:4929-4940.
212. Nigumann P, Redik K, Matlik K, Speek M. 2002. Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics 79:628-634.
213. Macia A, Munoz-Lopez M, Cortes JL, Hastings RK, Morell S, Lucena-Aguilar G, Marchal JA, Badge RM, Garcia-Perez JL. 2011. Epigenetic control of retrotransposon expression in human embryonic stem cells. Mol Cell Biol 31:300-316.
214. Uesaka M, Nishimura O, Go Y, Nakashima K, Agata K, Imamura T. 2014. Bidirectional promoters are the major source of gene activationassociated non-coding RNAs in mammals. BMC Genomics 15:35.
215. DeBerardinis RJ, Kazazian HH, Jr. 1999. Analysis of the promoter from an expanding mouse retrotransposon subfamily. Genomics 56:317-323.
216. Severynse DM, Hutchison CA, 3rd, Edgell MH. 1992. Identification of transcriptional regulatory activity within the 5' A-type monomer sequence of the mouse LINE-1 retroposon. Mamm Genome 2:41-50.
217. 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.
218. Li J, Kannan M, Trivett AL, Liao H, Wu X, Akagi K, Symer DE. 2014. An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition. Nucleic Acids Res 42:4546-4562.
219. Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A, Bonetti A, Voineagu I, Bertin N, Kratz A, Noro Y, Wong CH, de Hoon M, Andersson R, Sandelin A, Suzuki H, Wei CL, Koseki H, Hasegawa Y, Forrest AR, Carninci P. 2014. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat Genet 46:558-566.
220. Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C. 2013. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet 9:e1003470.
221. Kapusta A, Feschotte C. 2014. Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet 30:439-452.
222. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. 2011. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477:295-300.
223. Macia A, Blanco-Jimenez E, Garcia-Perez JL. 2014. Retrotransposons in pluripotent cells: Impact and new roles in cellular plasticity. Biochim Biophys Acta [Epub ahead of print].
224. Leibold DM, Swergold GD, Singer MF, Thayer RE, Dombroski BA, Fanning TG. 1990. Translation of LINE-1 DNA elements in vitro and in human cells. Proc Natl Acad Sci U S A 87:6990-6994.
225. Kolosha VO, Martin SL. 2003. High-affinity, non-sequence-specific RNA binding by the open reading frame 1 (ORF1) protein from long interspersed nuclear element 1 (LINE-1). J Biol Chem 278:8112-8117.
226. Kolosha VO, Martin SL. 1997. In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retrotransposition. ProcNatl Acad SciUSA94:10155-10160.
227. Martin SL. 1991. Ribonucleoprotein particles with LINE-1 RNA in mouse embryonal carcinoma cells. Mol Cell Biol 11:4804-4807.
228. Hohjoh H, Singer MF. 1997. Ribonuclease and high salt sensitivity of the ribonucleoprotein complex formed by the human LINE-1 retrotransposon. J Mol Biol 271:7-12.
229. Martin SL, Branciforte D, Keller D, Bain DL. 2003. Trimeric structure for an essential protein in L1 retrotransposition. Proc Natl Acad Sci U S A 100:13815-13820.
230. Basame S, Wai-lun Li P, Howard G, Branciforte D, Keller D, Martin SL. 2006. Spatial assembly and RNA binding stoichiometry of a LINE-1 protein essential for retrotransposition. J Mol Biol 357:351-357.
231. Khazina E, Weichenrieder O. 2009. Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame. Proc Natl Acad Sci U S A 106:731-736.
232. Callahan KE, Hickman AB, Jones CE, Ghirlando R, Furano AV. 2012. Polymerization and nucleic acid-binding properties of human L1 ORF1 protein. Nucleic Acids Res 40:813-827.
233. Januszyk K, Li PW, Villareal V, Branciforte D, Wu H, Xie Y, Feigon J, Loo JA, Martin SL, Clubb RT. 2007. Identification and solution structure of a highly conserved C-terminal domain within ORF1p required for retrotransposition of long interspersed nuclear element-1. J Biol Chem 282:24893-24904.
234. Martin SL. 2010. Nucleic acid chaperone properties of ORF1p from the non-LTR retrotransposon, LINE-1. RNA Biol 7:706-711.
235. Martin SL, Bushman D, Wang F, Li PW, Walker A, Cummiskey J, Branciforte D, Williams MC. 2008. A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity. Nucleic Acids Res 36:5845-5854.
236. Evans JD, Peddigari S, Chaurasiya KR, Williams MC, Martin SL. 2011. Paired mutations abolish and restore the balanced annealing and melting activities of ORF1p that are required for LINE-1 retrotransposition. Nucleic Acids Res 39:5611-5621.
237. Heras SR, Lopez MC, Garcia-Perez JL, Martin SL, Thomas MC. 2005. The L1Tc C-terminal domain from Trypanosoma cruzi non-long terminal repeat retrotransposon codes for a protein that bears two C2H2 zinc finger motifs and is endowed with nucleic acid chaperone activity. Mol Cell Biol 25:9209-9220.
238. Dawson A, Hartswood E, Paterson T, Finnegan DJ. 1997. A LINElike transposable element in Drosophila, the I factor, encodes a protein with properties similar to those of retroviral nucleocapsids. EMBO J 16:4448-44455.
239. Nakamura M, Okada N, Kajikawa M. 2012. Self-interaction, nucleic acid binding, and nucleic acid chaperone activities are unexpectedly retained in the unique ORF1p of zebrafish LINE. Mol Cell Biol 32:458-469.
240. Kajikawa M, Sugano T, Sakurai R, Okada N. 2012. Low dependency of retrotransposition on the ORF1 protein of the zebrafish LINE, ZfL2-1. Gene 499:41-47.
241. Goodier JL, Mandal PK, Zhang L, Kazazian HH, Jr. 2010. Discrete subcellular partitioning of human retrotransposon RNAs despite a common mechanism of genome insertion. Hum Mol Genet 19:1712-1725.
242. Martin F, Maranon C, Olivares M, Alonso C, Lopez MC. 1995. Characterization of a non-long terminal repeat retrotransposon cDNA (L1Tc) from Trypanosoma cruzi: homology of the first ORF with the ape family of DNA repair enzymes. J Mol Biol 247:49-59.
243. Mol CD, Kuo CF, Thayer MM, Cunningham RP, Tainer JA. 1995. Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature 374:381-386.
244. Weichenrieder O, Repanas K, Perrakis A. 2004. Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon. Structure (Camb) 12:975-986.
245. Cost GJ, Boeke JD. 1998. Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry 37:18081-18093.
246. Cost GJ, Golding A, Schlissel MS, Boeke JD. 2001. Target DNA chromatinization modulates nicking by L1 endonuclease. Nucleic Acids Res 29:573-577.
247. Xiong Y, Eickbush TH. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9:3353-3362.
248. Malik HS, Burke WD, Eickbush TH. 1999. The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol 16:793-805.
249. Evgen'ev MB, Arkhipova IR. 2005. Penelope-like elements-a new class of retroelements: distribution, function and possible evolutionary significance. Cytogenet Genome Res 110:510-521.
250. Dombroski BA, Feng Q, Mathias SL, Sassaman DM, Scott AF, Kazazian HH, Jr., Boeke JD. 1994. An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae. Mol Cell Biol 14:4485-4492.
251. Piskareva O, Denmukhametova S, SchmatchenkoV. 2003. Functional reverse transcriptase encoded by the human LINE-1 from baculovirusinfected insect cells. Protein Expr Purif 28:125-130.
252. Bibillo A, Eickbush TH. 2002. High processivity of the reverse transcriptase from a non-long terminal repeat retrotransposon. J Biol Chem 277:34836-34845.
253. Piskareva O, Schmatchenko V. 2006. DNA polymerization by the reverse transcriptase of the human L1 retrotransposon on its own template in vitro. FEBS Lett 580:661-668.
254. Monot C, Kuciak M, Viollet S, Mir AA, Gabus C, Darlix JL, Cristofari G. 2013. The specificity and flexibility of l1 reverse transcription priming at imperfect T-tracts. PLoS Genet 9:e1003499.
255. Piskareva O, Ernst C, Higgins N, Schmatchenko V. 2013. The carboxy-terminal segment of the human LINE-1 ORF2 protein is involved in RNA binding. FEBS Open Bio 3:433-437.
256. Alisch RS, Garcia-Perez JL, Muotri AR, Gage FH, Moran JV. 2006. Unconventional translation of mammalian LINE-1 retrotransposons. Genes Dev 20:210-224.
257. Li PW, Li J, Timmerman SL, Krushel LA, Martin SL. 2006. The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition. Nucleic Acids Res 34:853-864.
258. An W, Dai L, Niewiadomska AM, Yetil A, O'Donnell KA, Han JS, Boeke JD. 2011. Characterization of a synthetic human LINE-1 retrotransposon ORFeus-Hs. Mob DNA 2:2.
259. Han JS, Boeke JD. 2004. A highly active synthetic mammalian retrotransposon. Nature 429:314-318.
260. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-223.
261. SlavoffSA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, Karger AD, Budnik BA, Rinn JL, Saghatelian A. 2013. Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol 9:59-64.
262. Usdin K, Furano AV. 1989. The structure of the guanine-rich polypurine:polypyrimidine sequence at the right end of the rat L1 (LINE) element. J Biol Chem 264:15681-15687.
263. Moran JV, DeBerardinis RJ, Kazazian HH, Jr. 1999. Exon shuffling by L1 retrotransposition. Science 283:1530-1534.
264. Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. 2009. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41:563-571.
265. Luan DD, Korman MH, Jakubczak JL, Eickbush TH. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72:595-605.
266. Mandal PK, Ewing AD, Hancks DC, Kazazian HH, Jr. 2013. Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles. Hum Mol Genet 22:3730-3748.
267. Dutko JA, Kenny AE, Gamache ER, Curcio MJ. 2010. 5' to 3' mRNA decay factors colocalize with Ty1 gag and human APOBEC3G and promote Ty1 retrotransposition. J Virol 84:5052-5066.
268. Larsen LS, Beliakova-Bethell N, Bilanchone V, Zhang M, Lamsa A, Dasilva R, Hatfield GW, Nagashima K, Sandmeyer S. 2008. Ty3 nucleocapsid controls localization of particle assembly. J Virol 82:2501-2514.
269. Larsen LS, Zhang M, Beliakova-Bethell N, Bilanchone V, Lamsa A, Nagashima K, Najdi R, Kosaka K, Kovacevic V, Cheng J, Baldi P, Hatfield GW, Sandmeyer S. 2007. Ty3 capsid mutations reveal early and late functions of the amino-terminal domain. J Virol 81:6957-6972.
270. Kubo S, Seleme MC, Soifer HS, Perez JL, Moran JV, Kazazian HH, Jr., Kasahara N. 2006. L1 retrotransposition in nondividing and primary human somatic cells. Proc Natl Acad Sci U S A 103:8036-8041.
271. Goodwin TJ, Ormandy JE, Poulter RT. 2001. L1-like non-LTR retrotransposons in the yeast Candida albicans. Curr Genet 39:83-91.
272. Dong C, Poulter RT, Han JS. 2009. LINE-like retrotransposition in Saccharomyces cerevisiae. Genetics 181:301-311.
273. Kinsey JA. 1993. Transnuclear retrotransposition of the Tad element of Neurospora. Proc Natl Acad Sci U S A 90:9384-9387.
274. Xie Y, Mates L, Ivics Z, Izsvak Z, Martin SL, An W. 2013. Cell division promotes efficient retrotransposition in a stable L1 reporter cell line. Mob DNA 4:10.
275. Shi X, Seluanov A, Gorbunova V. 2007. Cell divisions are required for L1 retrotransposition. Mol Cell Biol 27:1264-1270.
276. Cost GJ, Feng Q, Jacquier A, Boeke JD. 2002. Human L1 element target-primed reverse transcription in vitro. EMBO J 21:5899-5910.
277. Christensen SM, Eickbush TH. 2005. R2 target-primed reverse transcription: ordered cleavage and polymerization steps by protein subunits asymmetrically bound to the target DNA. Mol Cell Biol 25:6617-6628.
278. Ostertag EM, Kazazian HH, Jr. 2001. Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res 11:2059-2065.
279. Zingler N, Willhoeft U, Brose HP, Schoder V, Jahns T, Hanschmann KM, Morrish TA, Lower J, Schumann GG. 2005. Analysis of 5' junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5'-end attachment requiring microhomology-mediated end-joining. Genome Res 15:780-789.
280. Gasior SL, Wakeman TP, Xu B, Deininger PL. 2006. The human LINE-1 retrotransposon creates DNA double-strand breaks. J Mol Biol 357:1383-1393.
281. Gasior SL, Roy-Engel AM, Deininger PL. 2008. ERCC1/XPF limits L1 retrotransposition. DNA Repair (Amst) 7:983-989.
282. Coufal NG, Garcia-Perez JL, Peng GE, Marchetto MC, Muotri AR, Mu Y, Carson CT, Macia A, Moran JV, Gage FH. 2011. Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells. Proc Natl Acad Sci U S A 108:20382-20387.
283. Boboila C, Alt FW, Schwer B. 2012. Classical and alternative endjoining pathways for repair of lymphocyte-specific and general DNA double-strand breaks. Adv Immunol 116:1-49.
284. Lavie L, Maldener E, Brouha B, Meese EU, Mayer J. 2004. The human L1 promoter: variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity. Genome Res 14:2253-2260.
285. Babushok DV, Ostertag EM, Courtney CE, Choi JM, Kazazian HH, Jr. 2006. L1 integration in a transgenic mouse model. Genome Res 16:240-250.
286. Ichiyanagi K, Nakajima R, Kajikawa M, Okada N. 2007. Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts. Genome Res 17:33-41.
287. Chen J, Rattner A, Nathans J. 2006. Effects of L1 retrotransposon insertion on transcript processing, localization and accumulation: lessons from the retinal degeneration 7 mouse and implications for the genomic ecology of L1 elements. Hum Mol Genet 15:2146-2156.
288. Goodier JL, Ostertag EM, Kazazian HH, Jr. 2000. Transduction of 3'-flanking sequences is common in L1 retrotransposition. Hum Mol Genet 9:653-657.
289. Pickeral OK, Makalowski W, Boguski MS, Boeke JD. 2000. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res 10:411-415.
290. Holmes SE, Dombroski BA, Krebs CM, Boehm CD, Kazazian HH, Jr. 1994. A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion. Nat Genet 7:143-148.
291. Moran JV. 1999. Human L1 retrotransposition: insights and peculiarities learned from a cultured cell retrotransposition assay. Genetica 107:39-51.
292. Moran JV, Gilbert N. 2002. Mammalian LINE-1 retrotransposons and related elements, p 836-869. In Craig NL, Craigie R, Gellert M, Lambowitz AM (ed), Mobile DNA II. ASM Press, Washington, D.C.
293. Eickbush T. 1999. Exon shuffling in retrospect. Science 283:1465-1467.
294. Macfarlane CM, Collier P, Rahbari R, Beck CR, WagstaffJF, Igoe S, Moran JV, Badge RM. 2013. Transduction-Specific ATLAS Reveals a Cohort of Highly Active L1 Retrotransposons in Human Populations. Hum Mutat 34:974-985.
295. Solyom S, Ewing AD, Hancks DC, Takeshima Y, Awano H, Matsuo M, Kazazian HH, Jr. 2012. Pathogenic orphan transduction created by a nonreference LINE-1 retrotransposon. Hum Mutat 33:369-371.
296. Tubio JM, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K, Menzies A, Roman-Garcia P, Fullam A, Gerstung M, Shlien A, Tarpey PS, Papaemmanuil E, Knappskog S, Van Loo P, Ramakrishna M, Davies HR, Marshall J, Wedge DC, Teague JW, Butler AP, Nik-Zainal S, Alexandrov L, Behjati S, Yates LR, Bolli N, Mudie L, Hardy C, Martin S, McLaren S, O'Meara S, Anderson E, Maddison M, Gamble S, Foster C, Warren AY, Whitaker H, Brewer D, Eeles R, Cooper C, Neal D, Lynch AG, Visakorpi T, Isaacs WB, van't Veer L, Caldas C, Desmedt C, Sotiriou C, Aparicio S, Foekens JA, Eyfjord JE, Lakhani SR, Thomas G, Myklebost O, Span PN, Borresen-Dale AL, Richardson AL, Van de Vijver M, Vincent-Salomon A, Van den Eynden GG, Flanagan AM, Futreal PA, Janes SM, Bova GS, Stratton MR, McDermott U, Campbell PJ. 2014. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science 345:1251343.
297. 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.
298. Xing J, Wang H, Belancio VP, Cordaux R, Deininger PL, Batzer MA. 2006. Emergence of primate genes by retrotransposon-mediated sequence transduction. Proc Natl Acad Sci U S A 103:17608-17613.
299. 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.
300. Mine M, Chen JM, Brivet M, Desguerre I, Marchant D, de Lonlay P, Bernard A, Ferec C, Abitbol M, Ricquier D, Marsac C. 2007. A large genomic deletion in the PDHX gene caused by the retrotranspositional insertion of a full-length LINE-1 element. Hum Mutat 28:137-142.
301. Chou HH, Hayakawa T, Diaz S, Krings M, Indriati E, Leakey M, Paabo S, Satta Y, Takahata N, Varki A. 2002. Inactivation of CMP-Nacetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution. Proc Natl Acad Sci U S A 99:11736-11741.
302. Takasu M, Hayashi R, Maruya E, Ota M, Imura K, Kougo K, Kobayashi C, Saji H, Ishikawa Y, Asai T, Tokunaga K. 2007. Deletion of entire HLA-A gene accompanied by an insertion of a retrotransposon. Tissue Antigens 70:144-150.
303. Han K, Sen SK, Wang J, Callinan PA, Lee J, Cordaux R, Liang P, Batzer MA. 2005. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res 33: 4040-4052.
304. Callinan PA, Wang J, Herke SW, Garber RK, Liang P, Batzer MA. 2005. Alu retrotransposition-mediated deletion. J Mol Biol 348:791-800.
305. Chen JM, Cooper DN, Ferec C, Kehrer-Sawatzki H, Patrinos GP. 2010. Genomic rearrangements in inherited disease and cancer. Semin Cancer Biol 20:222-233.
306. Ade C, Roy-Engel AM, Deininger PL. 2013. Alu elements: an intrinsic source of human genome instability. Curr Opin Virol 3:639-645.
307. Deininger PL, Moran JV, Batzer MA, Kazazian HH, Jr. 2003. Mobile elements and mammalian genome evolution. Curr Opin Genet Dev 13:651-658.
308. Eickbush TH. 2002. Repair by retrotransposition. Nat Genet 31: 126-127.
309. Morrish TA, Garcia-Perez JL, Stamato TD, Taccioli GE, Sekiguchi J, Moran JV. 2007. Endonuclease-independent LINE-1 retrotransposition at mammalian telomeres. Nature 446:208-212.
310. Kopera HC, Moldovan JB, Morrish TA, Garcia-Perez JL, Moran JV. 2011. Similarities between long interspersed element-1 (LINE-1) reverse transcriptase and telomerase. Proc Natl Acad Sci U S A 108:20345-20350.
311. Belfort M, Curcio MJ, Lue NF. 2011. Telomerase and retrotransposons: reverse transcriptases that shaped genomes. Proc Natl Acad Sci U S A 108:20304-20310.
312. Eickbush TH. 1997. Telomerase and retrotransposons: which came first? Science 277:911-912.
313. Levis RW, Ganesan R, Houtchens K, Tolar LA, Sheen FM. 1993. Transposons in place of telomeric repeats at a Drosophila telomere. Cell 75:1083-1093.
314. Biessmann H, Valgeirsdottir K, Lofsky A, Chin C, Ginther B, Levis RW, Pardue ML. 1992. HeT-A, a transposable element specifically involved in "healing" broken chromosome ends in Drosophila melanogaster. Mol Cell Biol 12:3910-3918.
315. Gladyshev EA, Arkhipova IR. 2007. Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes. Proc Natl Acad Sci U S A 104:9352-9357.
316. Sen SK, Huang CT, Han K, Batzer MA. 2007. Endonucleaseindependent insertion provides an alternative pathway for L1 retrotransposition in the human genome. Nucleic Acids Res 35:3741-3751.
317. Morisada N, RendtorffND, Nozu K, Morishita T, Miyakawa T, Matsumoto T, Hisano S, Iijima K, Tranebjaerg L, Shirahata A, Matsuo M, Kusuhara K. 2010. Branchio-oto-renal syndrome caused by partial EYA1 deletion due to LINE-1 insertion. Pediatr Nephrol 25:1343-1348.
318. Zhong J, Lambowitz AM. 2003. Group II intron mobility using nascent strands at DNA replication forks to prime reverse transcription. EMBO J 22:4555-4565.
319. Yoder JA, Walsh CP, Bestor TH. 1997. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13:335-340.
320. Bestor TH, Bourc'his D. 2004. Transposon silencing and imprint establishment in mammalian germ cells. Cold Spring Harb Symp Quant Biol 69:381-387.
321. Ooi SK, O'Donnell AH, Bestor TH. 2009. Mammalian cytosine methylation at a glance. J Cell Sci 122:2787-2791.
322. Bourc'his D, Bestor TH. 2004. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431:96-99.
323. Soper SF, van der Heijden GW, Hardiman TC, Goodheart M, Martin SL, de Boer P, Bortvin A. 2008. Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. Dev Cell 15:285-297.
324. Branco MR, Ficz G, Reik W. 2012. Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet 13:7-13.
325. Siomi MC, Sato K, Pezic D, Aravin AA. 2011. PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12:246-258.
326. Aravin AA, Hannon GJ, Brennecke J. 2007. The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318:761-764.
327. Malone CD, Brennecke J, Dus M, Stark A, McCombie WR, Sachidanandam R, Hannon GJ. 2009. Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell 137:522-535.
328. Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ. 2008. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322:1387-1392.
329. 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 128:1089-103.
330. Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, Siomi H, Siomi MC. 2007. A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila. Science 315: 1587-1590.
331. Ghildiyal M, Zamore PD. 2009. Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94-108.
332. Malone CD, Hannon GJ. 2009. Small RNAs as guardians of the genome. Cell 136:656-668.
333. Aravin AA, Sachidanandam R, Bourc'his D, Schaefer C, Pezic D, Toth KF, Bestor T, Hannon GJ. 2008. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 31:785-799.
334. Aravin AA, Bourc'his D. 2008. Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev 22:970-975.
335. Carmell MA, Girard A, van de Kant HJ, Bourc'his D, Bestor TH, de Rooij DG, Hannon GJ. 2007. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev Cell 12:503-514.
336. Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Totoki Y, Toyoda A, Ikawa M, Asada N, Kojima K, Yamaguchi Y, Ijiri TW, Hata K, Li E, Matsuda Y, Kimura T, Okabe M, Sakaki Y, Sasaki H, Nakano T. 2008. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev 22: 908-917.
337. Reuter M, Chuma S, Tanaka T, Franz T, Stark A, Pillai RS. 2009. Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nat Struct Mol Biol 16:639-646.
338. Yang N, Kazazian HH, Jr. 2006. L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat Struct Mol Biol 13:763-771.
339. Heras SR, Macias S, Plass M, Fernandez N, Cano D, Eyras E, Garcia-Perez JL, Caceres JF. 2013. The Microprocessor controls the activity of mammalian retrotransposons. Nat Struct Mol Biol 20:1173-1181.
340. Ciaudo C, Jay F, Okamoto I, Chen CJ, Sarazin A, Servant N, Barillot E, Heard E, Voinnet O. 2013. RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PLoS Genet 9:e1003791.
341. Faulkner GJ. 2013. Retrotransposon silencing during embryogenesis: dicer cuts in LINE. PLoS Genet 9:e1003944.
342. Belancio VP, Hedges DJ, Deininger P. 2006. LINE-1 RNA splicing and influences on mammalian gene expression. Nucleic Acids Res 34: 1512-1521.
343. Belancio VP, Roy-Engel AM, Deininger P. 2008. The impact of multiple splice sites in human L1 elements. Gene 411:38-45.
344. Perepelitsa-Belancio V, Deininger P. 2003. RNA truncation by premature polyadenylation attenuates human mobile element activity. Nat Genet 35:363-366.
345. Han JS, Szak ST, Boeke JD. 2004. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429:268-274.
346. Peddigari S, Li PW, Rabe JL, Martin SL. 2013. hnRNPL and nucleolin bind LINE-1 RNA and function as host factors to modulate retrotransposition. Nucleic Acids Res 41:575-585.
347. Dai L, Taylor MS, O'Donnell KA, Boeke JD. 2012. Poly(A) binding protein C1 is essential for efficient L1 retrotransposition and affects L1 RNP formation. Mol Cell Biol 32:4323-4336.
348. Zhang A, Dong B, Doucet AJ, Moldovan JB, Moran JV, Silverman RH. 2014. RNase L restricts the mobility of engineered retrotransposons in cultured human cells. Nucleic Acids Res 42:3803-3820.
349. Chiu YL, Greene WC. 2008. The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu Rev Immunol 26:317-353.
350. Sheehy AM, Gaddis NC, Choi JD, Malim MH. 2002. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature 418:646-650.
351. Bogerd HP, Wiegand HL, Hulme AE, Garcia-Perez JL, O'Shea KS, Moran JV, Cullen BR. 2006. Cellular inhibitors of long interspersed element 1 and Alu retrotransposition. Proc Natl Acad Sci U S A 103:8780-8785.
352. Chen H, Lilley CE, Yu Q, Lee DV, Chou J, Narvaiza I, Landau NR, Weitzman MD. 2006. APOBEC3A is a potent inhibitor of adenoassociated virus and retrotransposons. Curr Biol 16:480-485.
353. Hulme AE, Bogerd HP, Cullen BR, Moran JV. 2007. Selective inhibition of Alu retrotransposition by APOBEC3G. Gene 390:199-205.
354. Muckenfuss H, Hamdorf M, Held U, Perkovic M, Lower J, Cichutek K, Flory E, Schumann GG, Munk C. 2006. APOBEC3 proteins inhibit human LINE-1 retrotransposition. J Biol Chem 281:22161-22172.
355. Schumann GG. 2007. APOBEC3 proteins: major players in intracellular defence against LINE-1-mediated retrotransposition. Biochem Soc Trans 35:637-642.
356. Wissing S, Montano M, Garcia-Perez JL, Moran JV, Greene WC. 2011. Endogenous APOBEC3B restricts LINE-1 retrotransposition in transformed cells and human embryonic stem cells. J Biol Chem 286: 36427-36437.
357. Horn AV, Klawitter S, Held U, Berger A, Vasudevan AA, Bock A, Hofmann H, Hanschmann KM, Trosemeier JH, Flory E, Jabulowsky RA, Han JS, Lower J, Lower R, Munk C, Schumann GG. 2014. Human LINE-1 restriction by APOBEC3C is deaminase independent and mediated by an ORF1p interaction that affects LINE reverse transcriptase activity. Nucleic Acids Res 42:396-416.
358. Richardson SR, Narvaiza I, Planegger RA, Weitzman MD, Moran JV. 2014. APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition. Elife 3:e02008.
359. Nik-Zainal S, Wedge DC, Alexandrov LB, Petljak M, Butler AP, Bolli N, Davies HR, Knappskog S, Martin S, Papaemmanuil E, Ramakrishna M, Shlien A, Simonic I, Xue Y, Tyler-Smith C, Campbell PJ, Stratton MR. 2014. Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer. Nat Genet 46:487-491.
360. Helleday T, Eshtad S, Nik-Zainal S. 2014. Mechanisms underlying mutational signatures in human cancers. Nat Rev Genet 15:585-598.
361. Crow YJ. 2013. Aicardi-Goutières syndrome. Handb Clin Neurol 113:1629-1635.
362. Crow YJ, Rehwinkel J. 2009. Aicardi-Goutières syndrome and related phenotypes: linking nucleic acid metabolism with autoimmunity. Hum Mol Genet 18:R130-R136.
363. Crow YJ, Leitch A, Hayward BE, Garner A, Parmar R, Griffith E, Ali M, Semple C, Aicardi J, Babul-Hirji R, Baumann C, Baxter P, Bertini E, Chandler KE, Chitayat D, Cau D, Dery C, Fazzi E, Goizet C, King MD, Klepper J, Lacombe D, Lanzi G, Lyall H, Martinez-Frias ML, Mathieu M, McKeown C, Monier A, Oade Y, Quarrell OW, Rittey CD, Rogers RC, Sanchis A, Stephenson JB, Tacke U, Till M, Tolmie JL, Tomlin P, Voit T, Weschke B, Woods CG, Lebon P, Bonthron DT, Ponting CP, Jackson AP. 2006. Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutières syndrome and mimic congenital viral brain infection. Nat Genet 38:910-916.
364. Crow YJ, Hayward BE, Parmar R, Robins P, Leitch A, Ali M, Black DN, van Bokhoven H, Brunner HG, Hamel BC, Corry PC, Cowan FM, Frints SG, Klepper J, Livingston JH, Lynch SA, Massey RF, Meritet JF, Michaud JL, Ponsot G, Voit T, Lebon P, Bonthron DT, Jackson AP, Barnes DE, Lindahl T. 2006. Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 cause Aicardi-Goutières syndrome at the AGS1 locus. Nat Genet 38:917-920.
365. Rice GI, Bond J, Asipu A, Brunette RL, Manfield IW, Carr IM, Fuller JC, Jackson RM, Lamb T, Briggs TA, Ali M, Gornall H, Couthard LR, Aeby A, Attard-Montalto SP, Bertini E, Bodemer C, Brockmann K, Brueton LA, Corry PC, Desguerre I, Fazzi E, Cazorla AG, Gener B, Hamel BC, Heiberg A, Hunter M, van der Knaap MS, Kumar R, Lagae L, Landrieu PG, Lourenco CM, Marom D, McDermott MF, van der Merwe W, Orcesi S, Prendiville JS, Rasmussen M, Shalev SA, Soler DM, Shinawi M, Spiegel R, Tan TY, Vanderver A, Wakeling EL, Wassmer E, Whittaker E, Lebon P, Stetson DB, Bonthron DT, Crow YJ. 2009. Mutations involved in Aicardi-Goutières syndrome implicate SAMHD1 as regulator of the innate immune response. Nat Genet 41:829-832.
366. Stetson DB, Ko JS, Heidmann T, Medzhitov R. 2008. Trex1 prevents cell-intrinsic initiation of autoimmunity. Cell 134:587-598.
367. Zhao K, Du J, Han X, Goodier JL, Li P, Zhou X, Wei W, Evans SL, Li L, Zhang W, Cheung LE, Wang G, Kazazian HH, Jr., Yu XF. 2013. Modulation of LINE-1 and Alu/SVA retrotransposition by Aicardi-Goutières syndrome-related SAMHD1. Cell Rep 4:1108-1115.
368. Rice GI, Kasher PR, Forte GM, Mannion NM, Greenwood SM, Szynkiewicz M, Dickerson JE, Bhaskar SS, Zampini M, Briggs TA, Jenkinson EM, Bacino CA, Battini R, Bertini E, Brogan PA, Brueton LA, Carpanelli M, De Laet C, de Lonlay P, del Toro M, Desguerre I, Fazzi E, Garcia-Cazorla A, Heiberg A, Kawaguchi M, Kumar R, Lin JP, Lourenco CM, Male AM, Marques W, Jr., Mignot C, Olivieri I, Orcesi S, Prabhakar P, Rasmussen M, Robinson RA, Rozenberg F, Schmidt JL, Steindl K, Tan TY, van der Merwe WG, Vanderver A, Vassallo G, Wakeling EL, Wassmer E, Whittaker E, Livingston JH, Lebon P, Suzuki T, McLaughlin PJ, Keegan LP, O'Connell MA, Lovell SC, Crow YJ. 2012. Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature. Nat Genet 44:1243-1248.
369. Oda H, Nakagawa K, Abe J, Awaya T, Funabiki M, Hijikata A, Nishikomori R, Funatsuka M, Ohshima Y, Sugawara Y, Yasumi T, Kato H, Shirai T, Ohara O, Fujita T, Heike T. 2014. Aicardi-Goutières syndrome is caused by IFIH1 mutations. Am J Hum Genet 95:121-125.
370. Rice GI, del Toro Duany Y, Jenkinson EM, Forte GM, Anderson BH, Ariaudo G, Bader-Meunier B, Baildam EM, Battini R, Beresford MW, Casarano M, Chouchane M, Cimaz R, Collins AE, Cordeiro NJ, Dale RC, Davidson JE, De Waele L, Desguerre I, Faivre L, Fazzi E, Isidor B, Lagae L, Latchman AR, Lebon P, Li C, Livingston JH, Lourenco CM, Mancardi MM, Masurel-Paulet A, McInnes IB, Menezes MP, Mignot C, O'Sullivan J, Orcesi S, Picco PP, Riva E, Robinson RA, Rodriguez D, Salvatici E, Scott C, Szybowska M, Tolmie JL, Vanderver A, Vanhulle C, Vieira JP, Webb K, Whitney RN, Williams SG, Wolfe LA, Zuberi SM, Hur S, Crow YJ. 2014. Gain-of-function mutations in IFIH1 cause a spectrum of human disease phenotypes associated with upregulated type I interferon signaling. Nat Genet 46:503-509.
371. Zheng YH, Jeang KT, Tokunaga K. 2012. Host restriction factors in retroviral infection: promises in virus-host interaction. Retrovirology 9:112.
372. Arjan-Odedra S, Swanson CM, Sherer NM, Wolinsky SM, Malim MH. 2012. Endogenous MOV10 inhibits the retrotransposition of endogenous retroelements but not the replication of exogenous retroviruses. Retrovirology 9:53.
373. Goodier JL, Cheung LE, Kazazian HH, Jr. 2012. MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells. PLoS Genet 8: e1002941.
374. Li X, Zhang J, Jia R, Cheng V, Xu X, Qiao W, Guo F, Liang C, Cen S. 2013. The MOV10 helicase inhibits LINE-1 mobility. J Biol Chem 288:21148-21160.
375. Gregersen LH, Schueler M, Munschauer M, Mastrobuoni G, Chen W, Kempa S, Dieterich C, Landthaler M. 2014. MOV10 Is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3' UTRs. Mol Cell 54:573-585.
376. Frost RJ, Hamra FK, Richardson JA, Qi X, Bassel-Duby R, Olson EN. 2010. MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs. Proc Natl Acad Sci U S A 107:11847-11852.
377. Zheng K, Xiol J, Reuter M, Eckardt S, Leu NA, McLaughlin KJ, Stark A, Sachidanandam R, Pillai RS, Wang PJ. 2010. Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwiinteracting RNA (piRNA) pathway. Proc Natl Acad Sci U S A 107:11841-11846.
378. Cordaux R, Batzer MA. 2009. The impact of retrotransposons on human genome evolution. Nat Rev Genet 10:691-703.
379. Branciforte D, Martin SL. 1994. Developmental and cell type specificity of LINE-1 expression in mouse testis: implications for transposition. Mol Cell Biol 14:2584-2592.
380. Trelogan SA, Martin SL. 1995. Tightly regulated, developmentally specific expression of the first open reading frame from LINE-1 during mouse embryogenesis. Proc Natl Acad Sci U S A 92:1520-1524.
381. Georgiou I, Noutsopoulos D, Dimitriadou E, Markopoulos G, Apergi A, Lazaros L, Vaxevanoglou T, Pantos K, Syrrou M, Tzavaras T. 2009. Retrotransposon RNA expression and evidence for retrotransposition events in human oocytes. Hum Mol Genet 18:1221-1228.
382. Ostertag EM, DeBerardinis RJ, Goodier JL, Zhang Y, Yang N, Gerton GL, Kazazian HH, Jr. 2002. A mouse model of human L1 retrotransposition. Nat Genet 32:655-660.
383. Athanikar JN, Morrish TA, Moran JV. 2002. Of man in mice. Nat Genet 32:562-563.
384. Kano H, Godoy I, Courtney C, Vetter MR, Gerton GL, Ostertag EM, Kazazian HH, Jr. 2009. L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev 23:1303-1312.
385. Malki S, van der Heijden GW, O'Donnell KA, Martin SL, Bortvin A. 2014. A role for retrotransposon LINE-1 in fetal oocyte attrition in mice. Dev Cell 29:521-533.
386. Freeman P, Macfarlane C, Collier P, Jeffreys AJ, Badge RM. 2011. L1 hybridization enrichment: a method for directly accessing de novo L1 insertions in the human germline. Hum Mutat 32:978-988.
387. van den Hurk JA, Meij IC, Seleme MC, Kano H, Nikopoulos K, Hoefsloot LH, Sistermans EA, de Wijs IJ, Mukhopadhyay A, Plomp AS, de Jong PT, Kazazian HH, Cremers FP. 2007. L1 retrotransposition can occur early in human embryonic development. Hum Mol Genet 16:1587-1592.
388. Garcia-Perez JL, Marchetto MC, Muotri AR, Coufal NG, Gage FH, O'Shea KS, Moran JV. 2007. LINE-1 retrotransposition in human embryonic stem cells. Hum Mol Genet 16:1569-1577.
389. Garcia-Perez JL, Morell M, Scheys JO, Kulpa DA, Morell S, Carter CC, Hammer GD, Collins KL, O'Shea KS, Menendez P, Moran JV. 2010. Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. Nature 466:769-773.
390. Wissing S, Munoz-Lopez M, Macia A, Yang Z, Montano M, Collins W, Garcia-Perez JL, Moran JV, Greene WC. 2012. Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility. Hum Mol Genet 21:208-218.
391. 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.
392. 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. 393.MuotriAR, MarchettoMC, CoufalNG, Oefner R, YeoG, Nakashima K, Gage FH. 2010. L1 retrotransposition in neurons is modulated by MeCP2. Nature 468:443-446.
393. MuotriAR, MarchettoMC, CoufalNG, Oefner R, YeoG, Nakashima K, Gage FH. 2010. L1 retrotransposition in neurons is modulated by MeCP2. Nature 468:443-446
394. Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ. 2011. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479:534-537.
395. Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A, Park PJ, Walsh CA. 2012. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151:483-496.
396. Li W, Prazak L, Chatterjee N, Gruninger S, Krug L, Theodorou D, Dubnau J. 2013. Activation of transposable elements during aging and neuronal decline in Drosophila. Nat Neurosci 16:529-531.
397. Perrat PN, DasGupta S, Wang J, Theurkauf W, Weng Z, Rosbash M, Waddell S. 2013. Transposition-driven genomic heterogeneity in the Drosophila brain. Science 340:91-95.
398. Miki Y, Nishisho I, Horii A, Miyoshi Y, Utsunomiya J, Kinzler KW, Vogelstein B, Nakamura Y. 1992. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res 52:643-645.
399. Solyom S, Ewing AD, Rahrmann EP, Doucet T, Nelson HH, Burns MB, Harris RS, Sigmon DF, Casella A, Erlanger B, Wheelan S, Upton KR, Shukla R, Faulkner GJ, Largaespada DA, Kazazian HH, Jr. 2012. Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res 22:2328-2338.
400. Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, 3rd, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ. 2012. Landscape of somatic retrotransposition in human cancers. Science 337:967-971.
401. Helman E, Lawrence MS, Stewart C, Sougnez C, Getz G, Meyerson M. 2014. Somatic retrotransposition in human cancer revealed by wholegenome and exome sequencing. Genome Res 24:1053-1063.
402. Shukla R, Upton KR, Munoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S, Sinha S, Iannelli F, Radaelli E, Dos Santos A, Rapoud D, Guettier C, Samuel D, Natoli G, Carninci P, Ciccarelli FD, Garcia-Perez JL, Faivre J, Faulkner GJ. 2013. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153:101-111.
403. Rodic N, Burns KH. 2013. Long interspersed element-1 (LINE-1): passenger or driver in human neoplasms? PLoS Genet 9:e1003402.
404. Bulut-Karslioglu A, De La Rosa-Velazquez IA, Ramirez F, Barenboim M, Onishi-Seebacher M, Arand J, Galan C, Winter GE, Engist B, Gerle B, O'Sullivan RJ, Martens JH, Walter J, Manke T, Lachner M, Jenuwein T. 2014. Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells. Mol Cell 55:277-290.
405. Chow JC, Ciaudo C, Fazzari MJ, Mise N, Servant N, Glass JL, Attreed M, Avner P, Wutz A, Barillot E, Greally JM, Voinnet O, Heard E. 2010. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 141:956-969.
406. Bailey JA, Carrel L, Chakravarti A, Eichler EE. 2000. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. Proc Natl Acad Sci U S A 97: 6634-6639.
407. Lyon MF. 1998. X-chromosome inactivation: a repeat hypothesis. Cytogenet Cell Genet 80:133-137.
408. Richardson SR. 2013. A mechanistic examination of APOBEC3-mediated LINE-1 inhibition, Doctoral Dissertation Thesis, University of Michigan, Ann Arbor.
409. Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singer RH, Long RM. 1998. Localization of ASH1 mRNA particles in living yeast. Mol Cell 2:437-445.
410. Wallace N, WagstaffBJ, Deininger PL, Roy-Engel AM. 2008. LINE-1 ORF1 protein enhances Alu SINE retrotransposition. Gene 419:1-6.