Retrotransposon replication in plants

Current Opinion in Virology

Volumn 3, Issue 6, 2013, Pages 604-614

  Schulman, Alan H ^a,b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC PROTEINASE; CAPSID PROTEIN; COMPLEMENTARY DNA; GAG PROTEIN; GENOMIC DNA; GENOMIC RNA; PRIMER RNA; RIBONUCLEASE H; RIBONUCLEOPROTEIN; RNA BINDING PROTEIN; RNA DIRECTED DNA POLYMERASE; TRANSFER RNA;

ARABIDOPSIS; BINDING SITE; CELL NUCLEUS MEMBRANE; DNA END JOINING REPAIR; DNA METHYLATION; ENDOGENOUS RETROVIRUS; ENVELOPE GENE; MONOPHYLY; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; OPEN READING FRAME; PLANT GENOME; PRIORITY JOURNAL; PROMOTER REGION; RETROPOSON; REVERSE TRANSCRIPTION; REVIEW; RNA REPLICATION; STOP CODON; TRANSPOSON; VIRUS LIKE AGENT; VIRUS REPLICATION;

DNA REPLICATION; PLANTS; RETROELEMENTS; REVERSE TRANSCRIPTION; TRANSCRIPTION, GENETIC;

EID: 84890126000     PISSN: 18796257     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.coviro.2013.08.009     Document Type: Review

References (116)

1. International Barley Genome Sequencing Consortium K.F. Mayer, R. Waugh, J.W. Brown, A. Schulman, P. Langridge, M. Platzer, G.B. Fincher, G.J. Muehlbauer, and K. Sato A physical, genetic and functional sequence assembly of the barley genome Nature 491 2012 711 716
2. P.S. Schnable, D. Ware, R.S. Fulton, J.C. Stein, F. Wei, S. Pasternak, C. Liang, J. Zhang, L. Fulton, and T.A. Graves The B73 maize genome: complexity, diversity, and dynamics Science 326 2009 1112 1115
3. M.I. Tenaillon, M.B. Hufford, B.S. Gaut, and J. Ross-Ibarra Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians Genome Biol Evol 3 2011 219 229
4. International Brachypodium Initiative Genome sequencing and analysis of the model grass Brachypodium distachyon Nature 463 2010 763 768
5. P. Veselý, P. Bures, P. Smarda, and T. Pavlícek Genome size and DNA base composition of geophytes: the mirror of phenology and ecology? Ann Bot 109 2012 65 75
6. M.C. Estep, J.D. DeBarry, and J.L. Bennetzen The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution Heredity 110 2013 194 204
7. M.J.P. Park, S. Kim, J.K. Kwon, H.M. Park, I.H. Bae, T.J. Yang, Y.H. Lee, B.C. Kang, and D. Choi Evolution of the large genome in Capsicum annuum occurred through accumulation of single-type long terminal repeat retrotransposons and their derivatives Plant J 69 2012 1018 1029
8. H. Xiao, N. Jiang, E. Schaffner, E.J. Stockinger, and E. van der Knaap A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit Science 319 2008 1527 1530 (Pubitemid 351398181)
9. S. Duangpan, W. Zhang, Y. Wu, S.H. Jansky, and J. Jiang Insertional mutagenesis using Tnt1 retrotransposon in potato Plant Physiol 163 2013 21 29 10.1104/pp.1113.221903
10. K. Kashkush, and V. Khasdan Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes Genetics 177 2007 1975 1985 (Pubitemid 350276981)
11. D. Lisch, and J.L. Bennetzen Transposable element origins of epigenetic gene regulation Curr Opin Plant Biol 14 2011 156 161
12. N. Jiang, A.A. Ferguson, R.K. Slotkin, and D. Lisch Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition Proc Natl Acad Sci U S A 108 2011 1537 1542
13. A.M. Barbaglia, K.M. Klusman, J. Higgins, J.R. Shaw, L.C. Hannah, and S. Lal Gene capture by Helitron transposons reshuffles the transcriptome of maize Genetics 190 2012 965 975
14. T. Wicker, J.P. Buchmann, and B. Keller Patching gaps in plant genomes results in gene movement and erosion of colinearity Genome Res 20 2010 1229 1237
15. A. Studer, Q. Zhao, J. Ross-Ibarra, and J. Doebley Identification of a functional transposon insertion in the maize domestication gene tb1 Nat Genet 43 2011 1160 1163
16. Z. Xu, S. Rafi, and W. Ramakrishna Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters Genome 54 2011 629 638
17. T. Wicker, F. Sabot, A. Hua-Van, J. Bennetzen, P. Capy, B. Chalhoub, A.J. Flavell, P. Leroy, M. Morgante, and O. Panaud A unified classification system for eukaryotic transposable elements Nat Rev Genet 8 2007 973 982 (Pubitemid 350129169)
18. B.S. Gaut, and J. Ross-Ibarra Selection on major components of angiosperm genomes Science 320 2008 484 486 (Pubitemid 351590630)
19. J.L. Goodier, and H.H.J. Kazazian Retrotransposons revisited: the restraint and rehabilitation of parasites Cell 135 2008 23 35
20. J.S. Han, and J.D. Boeke LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression? BioEssays 27 2005 775 784 (Pubitemid 41297400)
21. A.M.Q. King, M.J. Adams, E.B. Carstens, and E.J. Lefkowitz Virus taxonomy: classification and nomenclature of viruses: Ninth Report of the International Committee on Taxonomy of Viruses 2012 Elsevier Academic Press
22. F. Benachenhou, G.O. Sperber, E. Bongcam-Rudloff, G. Andersson, J.D. Boeke, and J. Blomberg Conserved structure and inferred evolutionary history of long terminal repeats (LTRs) Mob DNA 4 2013 5 10.1186/1759-8753-4-5
23. T.H. Eickbush, and V.K. Jamburuthugoda The diversity of retrotransposons and the properties of their reverse transcriptases Virus Res 34 2008 221 234
24. J. Brosius Echoes from the past - are we still in an RNP world? Cytogenet Genome Res 110 2005 8 24 (Pubitemid 41159879)
25. K. Noma, E. Ohtsubo, and H. Ohtsubo Non-LTR retrotransposons (LINEs) as ubiquitous components of plant genomes Mol Gen Genet 261 1999 71 79 (Pubitemid 29137360)
26. T. Schmidt LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes Plant Mol Biol 40 1999 903 910 (Pubitemid 29464041)
27. D.C. Hancks, and H.H.J. Kazazian Active human retrotransposons: variation and disease Curr Opin Genet Dev 22 2012 191 203
28. T. Wenke, D. Holtgräwe, A.V. Horn, B. Weisshaar, and T. Schmidt An abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris Plant Mol Biol 71 2009 585 597
29. E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, and W. FitzHugh Initial sequencing and analysis of the human genome Nature 409 2001 860 921 (Pubitemid 32165345)
30. C.R. Beck, J.L. Garcia-Perez, R.M. Badge, and J.V. Moran LINE-1 elements in structural variation and disease Annu Rev Genom Hum Genet 12 2011 187 215
31. E.N. Kroutter, V.P. Belancio, B.J. Wagstaff, and A.M. Roy-Engel The RNA polymerase dictates ORF1 requirement and timing of LINE and SINE retrotransposition PLoS Genet 5 2009 e1000458 10.1371/journal.pgen.1000458
32. S.L. Martin Nucleic acid chaperone properties of ORF1p from the non-LTR retrotransposon, LINE-1 RNA Biol 7 2010 706 711
33. E.A. Gladyshev, and I.R. Arkhipova A widespread class of reverse transcriptase-related cellular genes Proc Natl Acad Sci U S A 108 2011 20311 20316
34. H.C. Kopera, J.B. Moldovan, T.A. Morrish, J.L. Garcia-Perez, and J.V. Moran Similarities between long interspersed element-1 (LINE-1) reverse transcriptase and telomerase Proc Natl Acad Sci U S A 108 2011 20345 20350
35. T.A. Morrish, J.L. Garcia-Perez, T.D. Stamato, G.E. Taccioli, J. Sekiguchi, and J.V. Moran Endonuclease-independent LINE-1 retrotransposition at mammalian telomeres Nature 446 2007 208 212 (Pubitemid 46398662)
36. S.Q. Gu, X. Cui, S. Mou, S. Mohr, J. Yao, and A.M. Lambowitz Genetic identification of potential RNA-binding regions in a group II intron-encoded reverse transcriptase RNA 16 2010 732 747
37. A.J. Doucet, A.E. Hulme, E. Sahinovic, D.A. Kulpa, J.B. Moldovan, H.C. Kopera, J.N. Athanikar, M. Hasnaoui, A. Bucheton, and J.V. Moran Characterization of LINE-1 ribonucleoprotein particles PLoS Genet 7 2010 6 10.1371/journal.pgen.1001150
38. S.L. Mathias, A.F. Scott, H.H. Kazazian Jr., J.D. Boeke, and A. Gabriel Reverse transcriptase encoded by a human transposable element Science 254 1991 1808 1810 (Pubitemid 21917534)
39. S. Kubo, M.C. Seleme, H.S. Soifer, J.L. Perez, J.V. Moran, H.H. Kazazian Jr., and N. Kasahara L1 retrotransposition in nondividing and primary human somatic cells Proc Natl Acad Sci U S A 103 2006 8036 8041 (Pubitemid 43801048)
40. G.J. Cost, Q. Feng, A. Jacquier, and J.D. Boeke Human L1 element target-primed reverse transcription in vitro EMBO J 21 2002 5899 5910 (Pubitemid 35315287)
41. H. Puchta The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution J Exp Bot 56 2005 1 14 (Pubitemid 40078386)
42. T. Wenke, T. Döbel, T.R. Sörensen, H. Junghans, B. Weisshaar, and T. Schmidt Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes Plant Cell 23 2011 3117 3128
43. N.S. Vassetzky, and D.A. Kramerov SINEBase: a database and tool for SINE analysis Nucleic Acids Res 41 2013 D83 D89
44. D. Kramerov, and N. Vassetzky Short retroposons in eukaryotic genomes Int Rev Cytol 247 2005 165 221 (Pubitemid 41774365)
45. J. Deragon, and X. Zhang Short Interspersed Elements (SINEs) in plants: origin, classification, and use as phylogenetic markers Sys Biol 55 2006 949 956
46. M. Dewannieux, C. Esnault, and T. Heidmann LINE-mediated retrotransposition of marked Alu sequences Nat Genet 35 2003 41 48 (Pubitemid 37048594)
47. N. West, A.M. Roy-Engel, H. Imataka, N. Sonenberg, and P. Deininger Shared protein components of SINE RNPs J Mol Biol 321 2002 423 432
48. T. Pélissier, C. Bousquet-Antonelli, L. Lavie, and J.M. Deragon Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana Nucleic Acids Res 32 2004 3957 3966 (Pubitemid 39199087)
49. E. Ramallo, R. Kalendar, A.H. Schulman, and J.A. Martínez- Izquierdo Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light Plant Mol Biol 66 2008 137 150 (Pubitemid 50005025)
50. M. Salazar, E. Gonzalez, J.A. Casaretto, J.M. Casacuberta, and S. Ruiz-Lara The promoter of the TLC1.1 retrotransposon from Solanum chilense is activated by multiple stress-related signaling molecules Plant Cell Rep 26 2007 1861 1868 (Pubitemid 47397495)
51. K.I. Ansari, S. Walter, J.M. Brennan, M. Lemmens, S. Kessans, A. McGahern, D. Egan, and F.M. Doohan Retrotransposon and gene activation in wheat in response to mycotoxigenic and non-mycotoxigenic-associated Fusarium stress Theor Appl Genet 114 2007 927 937 (Pubitemid 46339697)
52. M.A. Grandbastien, C. Audeon, E. Bonnivard, J.M. Casacuberta, B. Chalhoub, A.P. Costa, Q.H. Le, D. Melayah, M. Petit, and C. Poncet Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae Cytogenet Genome Res 110 2005 229 241 (Pubitemid 41159902)
53. R. Kalendar, J. Tanskanen, S. Immonen, E. Nevo, and A.H. Schulman Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence Proc Natl Acad Sci U S A 97 2000 6603 6607 (Pubitemid 30412760)
54. W. Chang, and A.H. Schulman BARE retrotransposons produce multiple groups of rarely polyadenylated transcripts from two differentially regulated promoters Plant J 56 2008 40 50
55. I. Hernández-Pinzón, E. de Jesús, N. Santiago, and J.M. Casacuberta The frequent transcriptional readthrough of the tobacco Tnt1 retrotransposon and its possible implications for the control of resistance genes J Mol Evol 68 2009 269 278
56. T. Beguiristain, M.A. Grandbastien, P. Puigdomènech, and J.M. Casacuberta Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants Plant Physiol 127 2001 212 221 (Pubitemid 32925547)
57. W. Chang, M. Jääskeläinen, S.-P. Li, and A.H. Schulman BARE retrotransposons are translated and replicated via distinct RNA pools PLoS ONE 8 2013 e72270 10.1371/journal.pone.0072270
58. J.A. Tanskanen, F. Sabot, C. Vicient, and A.H. Schulman Life without GAG: the BARE-2 retrotransposon as a parasite's parasite Gene 390 2007 166 174
59. C. Moisy, K.E. Garrison, C.P. Meredith, and F. Pelsy Characterization of ten novel Ty1/copia-like retrotransposon families of the grapevine genome BMC Genomics 9 2008 469 10.1186/1471-2164-9-469
60. X. Gao, E.R. Havecker, P.V. Baranov, J.F. Atkins, and D.F. Voytas Translational recoding signals between gag and pol in diverse LTR retrotransposons RNA 9 2003 1422 1430 (Pubitemid 37463468)
61. C.M. Vicient, M. Jääskeläinen, R. Kalendar, and A.H. Schulman Active retrotransposons are a common feature of grass genomes Plant Physiol 125 2001 1283 1292 (Pubitemid 32224618)
62. M. Jääskeläinen, A.-H. Mykkänen, T. Arna, C. Vicient, A. Suoniemi, R. Kalendar, H. Savilahti, and A.H. Schulman Retrotransposon BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells Plant J 20 1999 413 422
63. F. Sabot, and A.H. Schulman Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome Heredity 97 2006 381 388 (Pubitemid 44851245)
64. S.K. Lee, M. Potempa, and R. Swanstrom The choreography of HIV-1 proteolytic processing and virion assembly J Biol Chem 287 2012 40867 40874
65. J.M. Lanchy, J.D. Ivanovitch, and J.S. Lodmell A structural linkage between the dimerization and encapsidation signals in HIV-2 leader RNA RNA 9 2003 1007 1018 (Pubitemid 36899243)
66. G. Böhmdorfer, K. Luxa, A. Frosch, K. Garber, A. Tramontano, S. Jelenic, M. Weber, and A. Bachmair Virus-like particle formation and translational start site choice of the plant retrotransposon Tto1 Virology 372 2008 437 446
67. P. Pochart, B. Agoutin, S. Rousset, R. Chanet, V. Doroszkiewicz, and T. Heyman Biochemical and electron microscope analyses of the DNA reverse transcripts present in the virus-like particles of the yeast transposon Ty1. Identification of a second origin of Ty1 DNA plus strand synthesis Nucleic Acids Res 21 1993 3513 3520 (Pubitemid 23241487)
68. R. Kalendar, K. Antonius, P. Smykal, and A.H. Schulman iPBS: a universal method for DNA fingerprinting and retrotransposon isolation Theor Appl Genet 121 2010 1419 1430
69. F. Feuerbach, J. Drouaud, and H. Lucas Retrovirus-like end processing of the tobacco Tnt1 retrotransposon linear intermediates of replication J Virol 71 1997 4000 4005
70. Y. Suzuki, and R. Craigie The road to chromatin - nuclear entry of retroviruses Nat Rev Microbiol 5 2007 187 196 (Pubitemid 46291278)
71. E. Müllers, K. Stirnnagel, S. Kaulfuss, and D. Lindemann Prototype foamy virus gag nuclear localization: a novel pathway among retroviruses J Virol 85 2011 9276 9285
72. M.K. Kim, K.C. Claiborn, and H.L. Levin The long terminal repeat-containing retrotransposon Tf1 possesses amino acids in gag that regulate nuclear localization and particle formation J Virol 79 2005 9540 9555 (Pubitemid 41022297)
73. M.A. Kenna, C.B. Brachmann, S.E. Devine, and J.D. Boeke Invading the yeast nucleus: a nuclear localization signal at the C terminus of Ty1 integrase is required for transposition in vivo Mol Cell Biol 18 1998 1115 1124 (Pubitemid 28063446)
74. E. Gómez-Orte, C.M. Vicient, and J.A. Martínez-Izquierdo Grande retrotransposons contain an accessory gene in the unusually long 3′-internal region that encodes a nuclear protein transcribed from its own promoter Plant Mol Biol 81 2013 541 551
75. L. Krishnan, and A. Engelman Retroviral integrase proteins and HIV-1 DNA integration J Biol Chem 287 2012 40858 40866
76. A.B. Hickman, M. Chandler, and F. Dyda Integrating prokaryotes and eukaryotes: DNA transposases in light of structure Crit Rev Biochem Mol Biol 45 2010 50 69
77. S.P. Montaño, and P.A. Rice Moving DNA around: DNA transposition and retroviral integration Curr Opin Struct Biol 21 2011 370 378
78. S.P. Montaño, Y.Z. Pigli, and P.A. Rice The μ transpososome structure sheds light on DDE recombinase evolution Nature 491 2012 413 417
79. P. Lesage, and T. AL Happy together: the life and times of Ty retrotransposons and their hosts Cytogenet Genome Res 110 2005 70 90 (Pubitemid 41159885)
80. X. Qi, E. Vargas, L. Larsen, W. Knapp, G.W. Hatfield, R. Lathrop, and S. Sandmeyer Directed DNA shuffling of retrovirus and retrotransposon integrase protein domains PLoS ONE 8 2013 e63957 10.1371/journal.pone.0063957
81. A.A. Friedl, M. Kiechle, H.G. Maxeiner, R.H. Schiestl, and F. Eckardt-Schupp Ty1 integrase overexpression leads to integration of non-Ty1 DNA fragments into the genome of Saccharomyces cerevisiae Mol Genet Genomics 284 2010 231 242
82. A. Suoniemi, J. Tanskanen, O. Pentikäinen, M.S. Johnson, and A.H. Schulman The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution Mol Biol Evol 15 1998 1135 1144 (Pubitemid 28394949)
83. E. Gómez, A.H. Schulman, J.A. Martínez-Izquierdo, and C.M. Vicient Integrase diversity and transcription of the maize retrotransposon Grande Genome 49 2006 558 562 (Pubitemid 44284780)
84. B. Gorinsek, F. Gubensek, and D. Kordiš Phylogenomic analysis of chromoviruses Cytogenet Genome Res 110 2005 543 552 (Pubitemid 41159931)
85. B. Weber, T. Heitkam, D. Holtgräwe, B. Weisshaar, A.E. Minoche, J.C. Dohm, H. Himmelbauer, and T. Schmidt Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration Mob DNA 4 2013 8 10.1186/1759-8753-1184-1188
86. H. Nakayashiki, T. Awa, Y. Tosa, and S. Mayama The C-terminal chromodomain-like module in the integrase domain is crucial for high transposition efficiency of the retrotransposon MAGGY FEBS Lett 579 2005 488 492 (Pubitemid 40092432)
87. T.K. Wolfgruber, A. Sharma, K.L. Schneider, P.S. Albert, D.H. Koo, J. Shi, Z. Gao, F. Han, H. Lee, and R. Xu Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic Loci shaped primarily by retrotransposons PLoS Genetics 5 2009 e1000743 10.1371/journal.pgen.1000743
88. A. Sharma, and G.G. Presting Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity Mol Genet Genomics 279 2008 133 147
89. P. Neumann, A. Navrátilová, A. Koblíž ková, E. Kejnovský, E. Hřibová, R. Hobza, A. Widmer, J. Doležel, and J. Macas Plant centromeric retrotransposons: a structural and cytogenetic perspective Mob DNA 2 2011 4 10.1186/1759-8753-2-4
90. E. Fukai, Y. Umehara, S. Sato, M. Endo, H. Kouchi, M. Hayashi, J. Stougaard, and H. Hirochika Derepression of the plant Chromovirus LORE1 induces germline transposition in regenerated plants PLoS Genet 6 2010 e1000868 10.1371/journal.pgen.1000868
91. A.H. Schulman Hitching a ride: nonautonomous retrotransposons and parasitism as a lifestyle M.-A. Grandbastien, J.M. Casacuberta, Plant Transposable Elements, Topics in Current Genetics vol 24 2012 Springer Verlag 71 88
92. R. Kalendar, C.M. Vicient, O. Peleg, K. Anamthawat-Jonsson, A. Bolshoy, and A.H. Schulman LARD retroelements: novel, non-autonomous components of barley and related genomes Genetics 166 2004 1437 1450 (Pubitemid 38507061)
93. C.P. Witte, Q.H. Le, T. Bureau, and A. Kumar Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes Proc Natl Acad Sci U S A 98 2001 13778 13783 (Pubitemid 33115975)
94. S.J. Kwon, D.H. Kim, M.H. Lim, Y. Long, J.L. Meng, K.B. Lim, J.A. Kim, J.S. Kim, M. Jin, and H.I. Kim Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives Mol Genet Genom 278 2007 361 370 (Pubitemid 47437680)
95. Z. Kraitshtein, B. Yaakov, V. Khasdan, and K. Kashkush Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat Genetics 186 2010 801 812
96. K. Antonius-Klemola, R. Kalendar, and A.H. Schulman TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports Theor Appl Genet 112 2006 999 1008
97. R. Kalendar, J.A. Tanskanen, W. Chang, K. Antonius, H. Sela, P. Peleg, and A.H. Schulman Cassandra retrotransposons carry independently transcribed 5S RNA Proc Natl Acad Sci U S A 105 2008 5833 5838 (Pubitemid 351758458)
98. O. Baruch, and K. Kashkush Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains Plant Cell Rep 31 2012 885 893
99. X. Cui, P. Jin, X. Cui, L. Gu, Z. Lu, Y. Xue, L. Wei, J. Qi, X. Song, and M. Luo Control of transposon activity by a histone H3K4 demethylase in rice Proc Natl Acad Sci U S A 110 2013 1953 1958
100. T.F. Lee, S.G. Gurazada, J. Zhai, S. Li, S.A. Simon, M.A. Matzke, X. Chen, and B.C. Meyers RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats Epigenetics 7 2012 781 795
101. S.R. Eichten, N.A. Ellis, I. Makarevitch, C.T. Yeh, J.I. Gent, L. Guo, K.M. McGinnis, X. Zhang, P.S. Schnable, and M.W. Vaughn Spreading of heterochromatin is limited to specific families of maize retrotransposons PLoS Genet 8 2012 e1003127 10.1371/journal.pgen.1003127
102. A.D. McCue, S. Nuthikattu, S.H. Reeder, and R.K. Slotkin Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA PLoS Genet 8 2012 e1002474 10.1371/journal.pgen.1002474
103. A. Marí-Ordóñez, A. Marchais, M. Etcheverry, A. Martin, V. Colot, and O. Voinnet Reconstructing de novo silencing of an active plant retrotransposon Nat Genet 45 2013 1029 1039 10.1038/ng.2703
104. I. Hernández-Pinzón, M. Cifuentes, E. Hénaff, N. Santiago, M.L. Espinás, and J.M. Casacuberta The Tnt1 retrotransposon escapes silencing in tobacco, its natural host PLoS ONE 7 2012 e33816 10.1371/journal.pone.0033816
105. M. Jääskeläinen, W. Chang, C. Moisy, and A.H. Schulman Retrotransposon BARE displays strong tissue-specific differences in expression New Phytol 2013 in press
106. A.D. McCue, S. Nuthikattu, and R.K. Slotkin Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs RNA Biol 10 2013 76 92
107. C.M. Vicient, R. Kalendar, and A.H. Schulman Envelope-containing retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants Genome Res 11 2001 2041 2049 (Pubitemid 33138801)
108. E.R. Havecker, X. Gao, and D.F. Voytas The Sireviruses, a plant-specific lineage of the Ty1/copia retrotransposons, interact with a family of proteins related to dynein light chain 8 Plant Physiol 139 2005 857 868 (Pubitemid 43907112)
109. A. Bousios, N. Darzentas, A. Tsaftaris, and S.R. Pearce Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants? BMC Genomics 11 2010 89
110. C. Llorens, M.A. Fares, and A. Moya Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis BMC Evol Biol 8 2008 276 10.1186/1471-2148-8-276
111. N. Bannert, and R. Kurth The evolutionary dynamics of human endogenous retroviral families Annu Rev Genom Hum Genet 7 2006 149 173 (Pubitemid 44627926)
112. Y. Zhou, and S.H. Cahan A novel family of terminal-repeat retrotransposon in miniature (TRIM) in the genome of the red harvester ant, Pogonomyrmex barbatus PLoS ONE 7 2012 e53401 10.1371/journal.pone.0053401
113. A. Roulin, B. Piegu, R.A. Wing, and O. Panaud Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza Plant J 53 2008 950 959 (Pubitemid 351357817)
114. A. Ludwig, V.L. Valente, and E.L. Loreto Multiple invasions of Errantivirus in the genus Drosophila Insect Mol Biol 17 2008 113 124 (Pubitemid 351392995)
115. A.H. Schulman, and T. Wicker A field guide to transposable elements N.V. Fedoroff, Plant transposons and genome dynamics in evolution 2013 John Wiley and Sons 15 40
116. A. Telesnitsky, and S.P. Goff Reverse transcriptase and the generation of retroviral DNA J.M. Coffin, S.H. Hughes, H.E. Varmus, Retroviruses 1997 Cold Spring Harbor Laboratory Press 121 160