Revisiting the evolution of mouse LINE-1 in the genomic era

Mobile DNA

Volumn 4, Issue 1, 2013, Pages

  Sookdeo, Akash ^a   Hepp, Crystal M ^b,c,d   McClure, Marcella A ^d   Boissinot, Stéphane ^a,e  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

^c ARIZONA STATE UNIVERSITY   (United States)

^d MONTANA STATE UNIVERSITY   (United States)

^e CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

L1; LINE 1; Mus musculus; Recombination; Retroposon; Retrotransposon

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CELL LINEAGE; EVOLUTION; GENOMICS; MOUSE; MOUSE LINE 1; MOUSE STRAIN; NONHUMAN; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; RNA STRUCTURE;

EID: 84875313166     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/1759-8753-4-3     Document Type: Article

References (86)

1. Initial sequencing and analysis of the human genome. 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, Nature 2001 409 860 921 10.1038/35057062 11237011 (Pubitemid 32165345)
2. Initial sequencing and comparative analysis of the mouse genome. Mouse Genome Sequencing C, 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, Nature 2002 420 520 562 10.1038/nature01262 12466850 (Pubitemid 35477048)
3. LINE-1 retrotransposons: Modulators of quantity and quality of mammalian gene expression? Han JS, Boeke JD, Bioessays 2005 27 775 784 10.1002/bies.20257 16015595 (Pubitemid 41297400)
4. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Han JS, Szak ST, Boeke JD, Nature 2004 429 268 274 10.1038/nature02536 15152245 (Pubitemid 38684807)
5. Retrotransposons influence the mouse transcriptome: implication for the divergence of genetic traits. Horie K, Saito ES, Keng VW, Ikeda R, Ishihara H, Takeda J, Genetics 2007 176 815 827 17435252 (Pubitemid 46961087)
6. Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Akagi K, Li J, Stephens RM, Volfovsky N, Symer DE, Genome Res 2008 18 869 880 10.1101/gr.075770.107 18381897 (Pubitemid 351793059)
7. Fitness cost of LINE-1 (L1) activity in humans. Boissinot S, Davis J, Entezam A, Petrov D, Furano AV, Proc Natl Acad Sci U S A 2006 103 9590 9594 10.1073/pnas.0603334103 16766655 (Pubitemid 43955869)
8. Selection against deleterious LINE-1-containing loci in the human lineage. Boissinot S, Entezam A, Furano AV, Mol Biol Evol 2001 18 926 935 10.1093/oxfordjournals.molbev.a003893 11371580 (Pubitemid 32520464)
9. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Kazazian HH, Wong C, Youssoufian H, Scott AFDGP, Antonarakis SE, Nature 1988 332 164 166 10.1038/332164a0 2831458 (Pubitemid 18083562)
10. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Chen JM, Stenson PD, Cooper DN, Ferec C, Hum Genet 2005 117 411 427 10.1007/s00439-005-1321-0 15983781 (Pubitemid 41236363)
11. Unequal homologous recombination between LINE-1 elements as a mutational mechanism in human genetic disease. Burwinkel B, Kilimann MW, J Mol Biol 1998 277 513 517 10.1006/jmbi.1998.1641 9533876 (Pubitemid 28190854)
12. Selection against LINE-1 retrotransposons results principally from their ability to mediate ectopic recombination. Song M, Boissinot S, Gene 2007 390 206 213 10.1016/j.gene.2006.09.033 17134851
13. Human L1 element target-primed reverse transcription in vitro. Cost GJ, Feng Q, Jacquier A, Boeke JD, EMBO J 2002 21 5899 5910 10.1093/emboj/cdf592 12411507 (Pubitemid 35315287)
14. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Luan DD, Eickbush TH, Mol Cell Biol 1995 15 3882 3891 7540721
15. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Luan DD, Korman MH, Jakubczak JL, Eickbush TH, Cell 1993 72 595 605 10.1016/0092-8674(93)90078-5 7679954 (Pubitemid 23077747)
16. Identification and solution structure of a highly conserved C-terminal domain within ORF1p required for retrotransposition of long interspersed nuclear element-1. Januszyk K, Li PW, Villareal V, Branciforte D, Wu H, Xie Y, Feigon J, Loo JA, Martin SL, Clubb RT, J Biol Chem 2007 282 24893 24904 10.1074/jbc.M702023200 17569664 (Pubitemid 47347512)
17. Nucleic acid chaperone properties of ORF1p from the non-LTR retrotransposon, LINE-1. Martin SL, RNA Biol 2010 7 706 711 10.4161/rna.7.6. 13766 21045547
18. Trimeric structure for an essential protein in L1 retrotransposition. Martin SL, Branciforte D, Keller D, Bain DL, Proc Natl Acad Sci U S A 2003 100 13815 13820 10.1073/pnas.2336221100 14615577 (Pubitemid 37499149)
19. Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Martin SL, Bushman FD, Mol Cell Biol 2001 21 467 475 10.1128/MCB.21.2.467-475.2001 11134335 (Pubitemid 32037367)
20. LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein. Martin SL, Cruceanu M, Branciforte D, Wai-Lun Li P, Kwok SC, Hodges RS, Williams MC, J Mol Biol 2005 348 549 561 10.1016/j.jmb.2005.03.003 15826653 (Pubitemid 40520490)
21. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Feng Q, Moran JV, Kazazian HH, Boeke JD, Cell 1996 87 905 916 10.1016/S0092-8674(00)81997-2 8945517 (Pubitemid 26404289)
22. Reverse transcriptase encoded by a human transposable element. Mathias SL, Scott AF, Kazazian HH, Boeke JD, Gabriel A, Science 1991 254 1808 1810 10.1126/science.1722352 1722352 (Pubitemid 21917534)
23. Identification of an internal cis-element essential for the human L1 transcription and a nuclear factor(s) binding to the element. Minakami R, Kurose K, Etoh K, Furuhata Y, Hattori M, Sakaki Y, Nucleic Acids Res 1992 20 3139 3145 10.1093/nar/20.12.3139 1320255
24. Identification, characterization, and cell specificity of a human LINE-1 promoter. Swergold GD, Mol Cell Biol 1990 10 6718 6729 1701022 (Pubitemid 120004617)
25. The ability to form intrastrand tetraplexes is an evolutionarily conserved feature of the 3' end of L1 retrotransposons. Howell R, Usdin K, Mol Biol Evol 1997 14 144 155 10.1093/oxfordjournals.molbev.a025747 9029792 (Pubitemid 27061438)
26. The structures of mouse and human L1 elements reflect their insertion mechanism. Martin SL, Li W-HP, Furano AV, Boissinot S, Cytogenet Genome Res 2005 110 223 228 10.1159/000084956 16093676 (Pubitemid 41159901)
27. Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. Ostertag EM, Kazazian HH Jr, Genome Res 2001 11 2059 2065 10.1101/gr.205701 11731496 (Pubitemid 33138803)
28. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Boissinot S, Chevret P, Furano AV, Mol Biol Evol 2000 17 915 928 10.1093/oxfordjournals.molbev.a026372 10833198 (Pubitemid 30346551)
29. An analysis of replacement and synonymous changes in the rodent L1 repeat family. Hardies SC, Martin SL, Voliva CF, Hutchison CA 3rd, Mol Biol Evol 1986 3 109 125 3444397 (Pubitemid 16118384)
30. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Khan H, Smit A, Boissinot S, Genome Res 2006 16 78 87 16344559 (Pubitemid 43048936)
31. The evolution of long interspersed repeated DNA (L1, LINE 1) as revealed by the analysis of an ancient rodent L1 DNA family. Pascale E, Liu C, Valle E, Usdin K, Furano AV, J Mol Evol 1993 36 9 20 10.1007/BF02407302 8433380 (Pubitemid 23018093)
32. Dispersal process associated with the L1 family of interspersed repetitive DNA sequences. Voliva CF, Martin SL, Hutchison CA 3rd, Edgell MH, J Mol Biol 1984 178 795 813 10.1016/0022-2836(84)90312-7 6492166 (Pubitemid 16223333)
33. Rodent L1 evolution has been driven by a single dominant lineage that has repeatedly acquired new transcriptional regulatory sequences. Adey NB, Schichman SA, Graham DK, Peterson SN, Edgell MH, Hutchison CA 3rd, Mol Biol Evol 1994 11 778 789 7968491 (Pubitemid 24274886)
34. Rapid evolution of a young L1 (LINE-1) clade in recently speciated Rattus taxa. Cabot EL, Angeletti B, Usdin K, Furano AV, J Mol Evol 1997 45 412 423 10.1007/PL00006246 9321420 (Pubitemid 27425913)
35. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. Smit AF, Toth G, Riggs AD, Jurka J, J Mol Biol 1995 246 401 417 10.1006/jmbi.1994.0095 7877164
36. Ecological and immunological determinants of influenza evolution. Ferguson NM, Galvani AP, Bush RM, Nature 2003 422 428 433 10.1038/nature01509 12660783 (Pubitemid 36411395)
37. Discovering the phylodynamics of RNA viruses. Holmes EC, Grenfell BT, PLoS Comput Biol 2009 5 1000505 10.1371/journal.pcbi.1000505 19855824
38. Positive Darwinian evolution in human influenza A viruses. Fitch WM, Leiter JM, Li XQ, Palese P, Proc Natl Acad Sci U S A 1991 88 4270 4274 10.1073/pnas.88.10.4270 1840695 (Pubitemid 21914521)
39. Adaptive evolution in LINE-1 retrotransposons. Boissinot S, Furano AV, Mol Biol Evol 2001 18 2186 2194 10.1093/oxfordjournals.molbev.a003765 11719568 (Pubitemid 33134348)
40. Nucleotide sequence of a mouse full-length F-type L1 element. Adey NB, Comer MB, Edgell MH, Hutchison CA 3rd, Nucleic Acids Res 1991 19 2497 10.1093/nar/19.9.2497 1645871
41. The dynamics of murine LINE-1 subfamily amplification. Casavant NC, Hardies SC, J Mol Biol 1994 241 390 397 10.1006/jmbi.1994.1515 8064855 (Pubitemid 24266052)
42. Rapid amplification of a retrotransposon subfamily is evolving the mouse genome. DeBerardinis RJ, Goodier JL, Ostertag EM, Kazazian HH Jr, Nat Genet 1998 20 288 290 10.1038/3104 9806550 (Pubitemid 28507676)
43. A novel active L1 retrotransposon subfamily in the mouse. Goodier JL, Ostertag EM, Du K, Kazazian HH Jr, Genome Res 2001 11 1677 1685 10.1101/gr.198301 11591644 (Pubitemid 33040494)
44. LINE-1 (L1) lineages in the mouse. Hardies SC, Wang L, Zhou L, Zhao Y, Casavant NC, Huang S, Mol Biol Evol 2000 17 616 628 10.1093/oxfordjournals. molbev.a026340 10742052 (Pubitemid 30210706)
45. The evolution of modern lineages of mouse L1 elements. Mears ML, Hutchison CA 3rd, J Mol Evol 2001 52 51 62 11139294 (Pubitemid 32127940)
46. Recombination between subtypes creates a mosaic lineage of LINE-1 that is expressed and actively retrotransposing in the mouse genome. Saxton JA, Martin SL, J Mol Biol 1998 280 611 622 10.1006/jmbi.1998.1899 9677292 (Pubitemid 28336369)
47. L1 A-monomer tandem arrays have expanded during the course of mouse L1 evolution. Schichman SA, Adey NB, Edgell MH, Hutchison CA 3rd, Mol Biol Evol 1993 10 552 570 8336543 (Pubitemid 23157239)
48. Unrelated sequences at the 5' end of mouse LINE-1 repeated elements define two distinct subfamilies. Wincker P, Jubier-Maurin V, Roizes G, Nucleic Acids Res 1987 15 8593 8606 10.1093/nar/15.21.8593 3684566
49. Smit AFA, Hubley R, Green P, RepeatMasker Open-3.0 2010
50. A new 5' sequence associated with mouse L1 elements is representative of a major class of L1 termini. Jubier-Maurin V, Cuny G, Laurent A-M, Paquereau L, Roizes G, Mol Biol Evol 1992 9 41 55 1552840
51. The relationships between the 5' end repeats and the largest members of the L1 interspersed repeated family in the mouse genome. Jubier-Maurin V, Wincker P, Cuny G, Roizes G, Nucleic Acids Res 1987 15 7395 7410 10.1093/nar/15.18.7395 3658697
52. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Saitou N, Nei M, Mol Biol Evol 1987 4 406 425 3447015
53. The age of Mus-Rattus divergence: paleontological data compared with the molecular clock. Jaeger J-J, Tong H, Buffetaut E, C R Acad Sci III 1986 302 917 922
54. Analyzing the mosaic structure of genes. Maynard Smith J, J Mol Evol 1992 34 126 129 1556748
55. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Posada D, Crandall KA, Proc Natl Acad Sci U S A 2001 98 13757 13762 10.1073/pnas.241370698 11717435 (Pubitemid 33115971)
56. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. Martin DP, Posada D, Crandall KA, Williamson C, AIDS Res Hum Retroviruses 2005 21 98 102 10.1089/aid.2005.21.98 15665649 (Pubitemid 40179806)
57. RDP: detection of recombination amongst aligned sequences. Martin D, Rybicki E, Bioinformatics 2000 16 562 563 10.1093/bioinformatics/16.6.562 10980155
58. High frequency retrotransposition in cultured mammalian cells. Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH Jr, Cell 1996 87 917 927 10.1016/S0092-8674(00)81998-4 8945518 (Pubitemid 26404290)
59. Sequence-specific single-strand RNA binding protein encoded by the human LINE-1 retrotransposon. Hohjoh H, Singer MF, EMBO J 1997 16 6034 6043 10.1093/emboj/16.19.6034 9312060 (Pubitemid 27427298)
60. Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame. Khazina E, Weichenrieder O, Proc Natl Acad Sci U S A 2009 106 731 736 10.1073/pnas.0809964106 19139409
61. Strand-specific LINE-1 transcription in mouse F9 cells originates from the youngest phylogenetic subgroup of LINE-1 elements. Schichman SA, Severynse DM, Edgell MH, Hutchison CA 3rd, J Mol Biol 1992 224 559 574 10.1016/0022-2836(92)90544-T 1314898
62. Predicting coiled coils from protein sequences. Lupas A, Van Dyke M, Stock J, Science 1991 252 1162 1164 10.1126/science.252.5009.1162 2031185 (Pubitemid 21917026)
63. Phylogenomic analysis of the L1 retrotransposons in Deuterostomia. Kordis D, Lovsin N, Gubensek F, Syst Biol 2006 55 886 901 10.1080/10635150601052637 17345671
64. Shared sequence variants of Mus spretus LINE-1 elements tracing dispersal to within the last 1 million years. Casavant NC, Hardies SC, Genetics 1994 137 565 572 8070666 (Pubitemid 24157015)
65. Mus spretus LINE-1 sequences detected in the Mus musculus inbred strain C57BL/6J using LINE-1 DNA probes. Rikke BA, Zhao Y, Daggett LP, Reyes R, Hardies SC, Genetics 1995 139 901 906 7713440
66. Molecular evolution of two lineages of L1 (LINE-1) retrotransposons in the california mouse, Peromyscus californicus. Casavant NC, Lee RN, Sherman AN, Wichman HA, Genetics 1998 150 345 357 9725851 (Pubitemid 28415528)
67. Tempo and mode of concerted evolution in the L1 repeat family of mice. Martin SL, Voliva CF, Hardies SC, Edgell MH, Hutchison CA 3rd, Mol Biol Evol 1985 2 127 140 3870857 (Pubitemid 15239735)
68. The F-type 5' motif of mouse L1 elements: a major class of L1 termini similar to the A-type in organization but unrelated in sequence. Padgett RW, Hutchison CA 3rd, Edgell MH, Nucleic Acids Res 1988 16 739 749 10.1093/nar/16.2.739 3340553
69. The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. Furano AV, Prog Nucleic Acid Res Mol Biol 2000 64 255 294 10697412
70. Recombination creates novel L1 (LINE-1) elements in Rattus norvegicus. Hayward BE, Zavanelli M, Furano AV, Genetics 1997 146 641 654 9178013 (Pubitemid 27251401)
71. Human L1 retrotransposition is associated with genetic instability in vivo. Symer DE, Connelly C, Szak ST, Caputo EM, Cost GJ, Parmigiani G, Boeke JD, Cell 2002 110 327 338 10.1016/S0092-8674(02)00839-5 12176320
72. Structure, replication, and recombination of retrovirus genomes: some unifying hypotheses. Coffin JM, J Gen Virol 1979 42 1 26 10.1099/0022-1317-42-1- 1 215703 (Pubitemid 9077528)
73. A detailed model of reverse transcription and tests of crucial aspects. Gilboa E, Mitra SW, Goff S, Baltimore D, Cell 1979 18 93 100 10.1016/0092-8674(79)90357-X 509527 (Pubitemid 10228240)
74. In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retrotransposition. Kolosha VO, Martin SL, Proc Natl Acad Sci U S A 1997 94 10155 10160 10.1073/pnas.94.19.10155 9294179 (Pubitemid 27407010)
75. High-affinity, non-sequence-specific RNA binding by the open reading frame 1 (ORF1) protein from long interspersed nuclear element 1 (LINE-1). Kolosha VO, Martin SL, J Biol Chem 2003 278 8112 8117 10.1074/jbc.M210487200 12506113 (Pubitemid 36800552)
76. Ribonucleoprotein particles with LINE-1 RNA in mouse embryonal carcinoma cells. Martin SL, Mol Cell Biol 1991 11 4804 4807 1715025 (Pubitemid 21895879)
77. The ORF1 protein encoded by LINE-1: structure and function during L1 retrotransposition. Martin SL, J Biomed Biotechnol 2006 2006 45621 16877816
78. Polymerization and nucleic acid-binding properties of human L1 ORF1 protein. Callahan KE, Hickman AB, Jones CE, Ghirlando R, Furano AV, Nucleic Acids Res 2012 40 813 827 10.1093/nar/gkr728 21937507
79. Automated characterization of potentially active retroid agents in the human genome. McClure MA, Richardson HS, Clinton RA, Hepp CM, Crowther BA, Donaldson EF, Genomics 2005 85 512 523 10.1016/j.ygeno.2004.12.006 15780754 (Pubitemid 40386480)
80. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 2731 2739 10.1093/molbev/msr121 21546353
81. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Delport W, Poon AF, Frost SD, Kosakovsky Pond SL, Bioinformatics 2010 26 2455 2457 10.1093/bioinformatics/btq429 20671151
82. HyPhy: hypothesis testing using phylogenies. Pond SL, Frost SD, Muse SV, Bioinformatics 2005 21 676 679 10.1093/bioinformatics/bti079 15509596 (Pubitemid 40424796)
83. Robust inference of positive selection from recombining coding sequences. Scheffler K, Martin DP, Seoighe C, Bioinformatics 2006 22 2493 2499 10.1093/bioinformatics/btl427 16895925 (Pubitemid 44560756)
84. A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Pond SL, Frost SD, Mol Biol Evol 2005 22 478 485 15509724 (Pubitemid 40299496)
85. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Kosakovsky Pond SL, Frost SD, Mol Biol Evol 2005 22 1208 1222 10.1093/molbev/msi105 15703242 (Pubitemid 40577758)
86. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Nature 2004 428 493 521 15057822