Table of Contents
International Journal of Evolutionary Biology
Volume 2013, Article ID 424726, 16 pages
http://dx.doi.org/10.1155/2013/424726
Review Article

RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity

Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama 526-0829, Japan

Received 14 May 2013; Accepted 1 July 2013

Academic Editor: Frédéric Brunet

Copyright © 2013 Kazuhiko Ohshima. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. Ohno, Evolution by Gene Duplication, Springer, New York, NY, USA, 1970.
  2. M. Long, E. Betrán, K. Thornton, and W. Wang, “The origin of new genes: glimpses from the young and old,” Nature Reviews Genetics, vol. 4, no. 11, pp. 865–875, 2003. View at Publisher · View at Google Scholar · View at Scopus
  3. D. V. Babushok, E. M. Ostertag, and H. H. Kazazian Jr., “Current topics in genome evolution: molecular mechanisms of new gene formation,” Cellular and Molecular Life Sciences, vol. 64, no. 5, pp. 542–554, 2007. View at Publisher · View at Google Scholar · View at Scopus
  4. C. Charon, Q. Bruggeman, V. Thareau, and Y. Henry, “Gene duplication within the green lineage: the case of TEL genes,” Journal of Experimental Botany, vol. 63, no. 14, pp. 5061–5077, 2012. View at Google Scholar
  5. E. F. Vanin, “Processed pseudogenes: characteristics and evolution,” Annual Review of Genetics, vol. 19, pp. 253–272, 1985. View at Google Scholar · View at Scopus
  6. A. M. Weiner, P. L. Deininger, and A. Efstratiadis, “Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information,” Annual Review of Biochemistry, vol. 55, pp. 631–661, 1986. View at Google Scholar · View at Scopus
  7. Z. Yu, D. Morais, M. Ivanga, and P. M. Harrison, “Analysis of the role of retrotransposition in gene evolution in vertebrates,” BMC Bioinformatics, vol. 8, article 308, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. Y.-J. Liu, D. Zheng, S. Balasubramanian et al., “Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity,” BMC Genomics, vol. 10, article 480, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. J. Brosius, “RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements,” Gene, vol. 238, no. 1, pp. 115–134, 1999. View at Publisher · View at Google Scholar · View at Scopus
  10. H. Kaessmann, N. Vinckenbosch, and M. Long, “RNA-based gene duplication: mechanistic and evolutionary insights,” Nature Reviews Genetics, vol. 10, no. 1, pp. 19–31, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. H. Sakai, H. Mizuno, Y. Kawahara et al., “Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes,” Genome Biology and Evolution, vol. 3, no. 1, pp. 1357–1368, 2011. View at Publisher · View at Google Scholar · View at Scopus
  12. J. Ciomborowska, W. Rosikiewicz, D. Szklarczyk, W. Makałowski, and I. Makałowska, ““Orphan” retrogenes in the human genome,” Molecular Biology and Evolution, vol. 30, no. 2, pp. 384–396, 2013. View at Google Scholar
  13. H. H. Kazazian Jr., “Mobile elements: drivers of genome evolution,” Science, vol. 303, no. 5664, pp. 1626–1632, 2004. View at Publisher · View at Google Scholar · View at Scopus
  14. J. Brosius, “Retroposons—seeds of evolution,” Science, vol. 251, no. 4995, p. 753, 1991. View at Google Scholar · View at Scopus
  15. J. Jurka, V. V. Kapitonov, A. Pavlicek, P. Klonowski, O. Kohany, and J. Walichiewicz, “Repbase Update, a database of eukaryotic repetitive elements,” Cytogenetic and Genome Research, vol. 110, no. 1–4, pp. 462–467, 2005. View at Publisher · View at Google Scholar · View at Scopus
  16. D. D. Luan, M. H. Korman, J. L. Jakubczak, and T. H. Eickbush, “Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition,” Cell, vol. 72, no. 4, pp. 595–605, 1993. View at Publisher · View at Google Scholar · View at Scopus
  17. D. D. Luan and T. H. Eickbush, “RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element,” Molecular and Cellular Biology, vol. 15, no. 7, pp. 3882–3891, 1995. View at Google Scholar · View at Scopus
  18. J. L. Goodier and H. H. Kazazian Jr., “Retrotransposons revisited: the restraint and rehabilitation of parasites,” Cell, vol. 135, no. 1, pp. 23–35, 2008. View at Publisher · View at Google Scholar · View at Scopus
  19. G. J. Cost, Q. Feng, A. Jacquier, and J. D. Boeke, “Human L1 element target-primed reverse transcription in vitro,” The EMBO Journal, vol. 21, no. 21, pp. 5899–5910, 2002. View at Publisher · View at Google Scholar · View at Scopus
  20. N. Okada, “SINEs: short interspersed repeated elements of the eukaryotic genome,” Trends in Ecology and Evolution, vol. 6, no. 11, pp. 358–361, 1991. View at Google Scholar · View at Scopus
  21. V. V. Kapitonov and J. Jurka, “A novel class of SINE elements derived from 5S rRNA,” Molecular Biology and Evolution, vol. 20, no. 5, pp. 694–702, 2003. View at Publisher · View at Google Scholar · View at Scopus
  22. N. S. Vassetzky and D. A. Kramerov, “SINEBase: a database and tool for SINE analysis,” Nucleic Acids Research, vol. 41, pp. D83–D89, 2013. View at Google Scholar
  23. K. Ohshima and N. Okada, “SINEs and LINEs: symbionts of eukaryotic genomes with a common tail,” Cytogenetic and Genome Research, vol. 110, no. 1–4, pp. 475–490, 2005. View at Publisher · View at Google Scholar · View at Scopus
  24. J. Schmitz, A. Zemann, G. Churakov et al., “Retroposed SNOfall—a mammalian-wide comparison of platypus snoRNAs,” Genome Research, vol. 18, no. 6, pp. 1005–1010, 2008. View at Publisher · View at Google Scholar · View at Scopus
  25. H. S. Malik, W. D. Burke, and T. H. Eickbush, “The age and evolution of non-LTR retrotransposable elements,” Molecular Biology and Evolution, vol. 16, no. 6, pp. 793–805, 1999. View at Google Scholar · View at Scopus
  26. V. V. Kapitonov, S. Tempel, and J. Jurka, “Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences,” Gene, vol. 448, no. 2, pp. 207–213, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. A. V. Furano, D. D. Duvernell, and S. Boissinot, “L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish,” Trends in Genetics, vol. 20, no. 1, pp. 9–14, 2004. View at Publisher · View at Google Scholar · View at Scopus
  28. D. Kordiš, N. Lovšin, and F. Gubenšek, “Phylogenomic analysis of the L1 retrotransposons in Deuterostomia,” Systematic Biology, vol. 55, no. 6, pp. 886–901, 2006. View at Google Scholar
  29. K. Ichiyanagi, H. Nishihara, D. D. Duvernell, and N. Okada, “Acquisition of endonuclease specificity during evolution of L1 retrotransposon,” Molecular Biology and Evolution, vol. 24, no. 9, pp. 2009–2015, 2007. View at Publisher · View at Google Scholar · View at Scopus
  30. K. K. Kojima and H. Fujiwara, “Cross-genome screening of novel sequence-specific Non-LTR retrotransposons: various multicopy RNA genes and microsatellites are selected as targets,” Molecular Biology and Evolution, vol. 21, no. 2, pp. 207–217, 2004. View at Publisher · View at Google Scholar · View at Scopus
  31. K. Ohshima, M. Hamada, Y. Terai, and N. Okada, “The 3′ ends of tRNA-derived short interspersed repetitive elements are derived from the 3′ ends of long interspersed repetitive elements,” Molecular and Cellular Biology, vol. 16, no. 7, pp. 3756–3764, 1996. View at Google Scholar · View at Scopus
  32. N. Okada, M. Hamada, I. Ogiwara, and K. Ohshima, “SINEs and LINEs share common 3′ sequences: a review,” Gene, vol. 205, no. 1-2, pp. 229–243, 1997. View at Publisher · View at Google Scholar · View at Scopus
  33. A. M. Weiner, “SINEs and LINEs: the art of biting the hand that feeds you,” Current Opinion in Cell Biology, vol. 14, no. 3, pp. 343–350, 2002. View at Publisher · View at Google Scholar · View at Scopus
  34. K. Ohshima, “Parallel relaxation of stringent RNA recognition in plant and mammalian L1 retrotransposons,” Molecular Biology and Evolution, vol. 29, no. 11, pp. 3255–3259, 2012. View at Google Scholar
  35. Y. Yoshioka, S. Matsumoto, S. Kojima, K. Ohshima, N. Okada, and Y. Machida, “Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs,” Proceedings of the National Academy of Sciences of the United States of America, vol. 90, no. 14, pp. 6562–6566, 1993. View at Google Scholar · View at Scopus
  36. M. Kajikawa and N. Okada, “LINEs mobilize SINEs in the eel through a shared 3′ sequence,” Cell, vol. 111, no. 3, pp. 433–444, 2002. View at Publisher · View at Google Scholar · View at Scopus
  37. H. Takahashi and H. Fujiwara, “Transplantation of target site specificity by swapping the endonuclease domains of two LINEs,” The EMBO Journal, vol. 21, no. 3, pp. 408–417, 2002. View at Publisher · View at Google Scholar · View at Scopus
  38. M. Osanai, H. Takahashi, K. K. Kojima, M. Hamada, and H. Fujiwara, “Essential motifs in the 3′ untranslated region required for retrotransposition and the precise start of reverse transcription in non-long-terminal-repeat retrotransposon SART1,” Molecular and Cellular Biology, vol. 24, no. 18, pp. 7902–7913, 2004. View at Publisher · View at Google Scholar · View at Scopus
  39. T. Anzai, M. Osanai, M. Hamada, and H. Fujiwara, “Functional roles of 3′-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm,” Nucleic Acids Research, vol. 33, no. 6, pp. 1993–2002, 2005. View at Publisher · View at Google Scholar · View at Scopus
  40. Q. Feng, J. V. Moran, H. H. Kazazian Jr., and J. D. Boeke, “Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition,” Cell, vol. 87, no. 5, pp. 905–916, 1996. View at Publisher · View at Google Scholar · View at Scopus
  41. J. Jurka, “Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 5, pp. 1872–1877, 1997. View at Publisher · View at Google Scholar · View at Scopus
  42. A. Pavlíček, J. Pačes, D. Elleder, and J. Hejnar, “Processed pseudogenes of human endogenous retroviruses generated by LINEs: their integration, stability, and distribution,” Genome Research, vol. 12, no. 3, pp. 391–399, 2002. View at Publisher · View at Google Scholar · View at Scopus
  43. C. Esnault, J. Maestre, and T. Heidmann, “Human LINE retrotransposons generate processed pseudogenes,” Nature Genetics, vol. 24, no. 4, pp. 363–367, 2000. View at Publisher · View at Google Scholar · View at Scopus
  44. W. Wei, N. Gilbert, S. L. Ooi et al., “Human L1 retrotransposition: cis preference versus trans complementation,” Molecular and Cellular Biology, vol. 21, no. 4, pp. 1429–1439, 2001. View at Publisher · View at Google Scholar · View at Scopus
  45. A. M. Roy-Engel, A.-H. Salem, O. O. Oyeniran et al., “Active Alu element “A-tails”: size does matter,” Genome Research, vol. 12, no. 9, pp. 1333–1344, 2002. View at Publisher · View at Google Scholar · View at Scopus
  46. M. Dewannieux, C. Esnault, and T. Heidmann, “LINE-mediated retrotransposition of marked Alu sequences,” Nature Genetics, vol. 35, no. 1, pp. 41–48, 2003. View at Publisher · View at Google Scholar · View at Scopus
  47. 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 Genetics, vol. 5, no. 4, Article ID e1000458, 2009. View at Publisher · View at Google Scholar · View at Scopus
  48. J. V. Moran, S. E. Holmes, T. P. Naas, R. J. DeBerardinis, J. D. Boeke, and H. H. Kazazian Jr., “High frequency retrotransposition in cultured mammalian cells,” Cell, vol. 87, no. 5, pp. 917–927, 1996. View at Publisher · View at Google Scholar · View at Scopus
  49. J. V. Moran, R. J. DeBerardinis, and H. H. Kazazian Jr., “Exon shuffling by L1 retrotransposition,” Science, vol. 283, no. 5407, pp. 1530–1534, 1999. View at Publisher · View at Google Scholar · View at Scopus
  50. K. Ohshima, M. Hattori, T. Yada, T. Gojobori, Y. Sakaki, and N. Okada, “Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates,” Genome Biology, vol. 4, no. 11, article R74, 2003. View at Publisher · View at Google Scholar · View at Scopus
  51. J. D. Boeke, “LINEs and Alus—the polyA connection,” Nature genetics, vol. 16, no. 1, pp. 6–7, 1997. View at Google Scholar · View at Scopus
  52. J. Schmitz, G. Churakov, H. Zischler, and J. Brosius, “A novel class of mammalian-specific tailless retropseudogenes,” Genome Research, vol. 14, no. 10a, pp. 1911–1915, 2004. View at Publisher · View at Google Scholar · View at Scopus
  53. Z. Zhang, P. M. Harrison, Y. Liu, and M. Gerstein, “Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome,” Genome Research, vol. 13, no. 12, pp. 2541–2558, 2003. View at Publisher · View at Google Scholar · View at Scopus
  54. A. C. Marques, I. Dupanloup, N. Vinckenbosch, A. Reymond, and H. Kaessmann, “Emergence of young human genes after a burst of retroposition in primates,” PLoS Biology, vol. 3, no. 11, article e357, 2005. View at Google Scholar
  55. H. Sakai, K. O. Koyanagi, T. Imanishi, T. Itoh, and T. Gojobori, “Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes,” Gene, vol. 389, no. 2, pp. 196–203, 2007. View at Publisher · View at Google Scholar · View at Scopus
  56. B. J. Wagstaff, E. N. Kroutter, R. S. Derbes, V. P. Belancio, and A. M. Roy-Engel, “Molecular reconstruction of extinct LINE-1 elements and their interaction with nonautonomous elements,” Molecular Biology and Evolution, vol. 30, no. 1, pp. 88–99, 2013. View at Google Scholar
  57. F. Burki and H. Kaessmann, “Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux,” Nature Genetics, vol. 36, no. 10, pp. 1061–1063, 2004. View at Publisher · View at Google Scholar · View at Scopus
  58. L. Rosso, A. C. Marques, M. Weier et al., “Birth and rapid subcellular adaptation of a hominoid-specific CDC14 protein,” PLoS Biology, vol. 6, no. 6, article e140, 2008. View at Publisher · View at Google Scholar · View at Scopus
  59. D. V. Babushok, K. Ohshima, E. M. Ostertag et al., “A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids,” Genome Research, vol. 17, no. 8, pp. 1129–1138, 2007. View at Publisher · View at Google Scholar · View at Scopus
  60. Y. Zhang, S. Lu, S. Zhao, X. Zheng, M. Long, and L. Wei, “Positive selection for themale functionality of a co-retroposed gene in the hominoids,” BMC Evolutionary Biology, vol. 9, article 252, 2009. View at Google Scholar
  61. K. Ohshima and K. Igarashi, “Inference for the initial stage of domain shuffling: tracing the evolutionary fate of the PIPSL retrogene in hominoids,” Molecular Biology and Evolution, vol. 27, no. 11, pp. 2522–2533, 2010. View at Publisher · View at Google Scholar · View at Scopus
  62. P. M. Harrison, D. Zheng, Z. Zhang, N. Carriero, and M. Gerstein, “Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability,” Nucleic Acids Research, vol. 33, no. 8, pp. 2374–2383, 2005. View at Publisher · View at Google Scholar · View at Scopus
  63. N. Vinckenbosch, I. Dupanloup, and H. Kaessmann, “Evolutionary fate of retroposed gene copies in the human genome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 9, pp. 3220–3225, 2006. View at Publisher · View at Google Scholar · View at Scopus
  64. R. Baertsch, M. Diekhans, W. J. Kent, D. Haussler, and J. Brosius, “Retrocopy contributions to the evolution of the human genome,” BMC Genomics, vol. 9, article 466, 2008. View at Publisher · View at Google Scholar · View at Scopus
  65. K. K. Kojima and N. Okada, “mRNA retrotransposition coupled with 5′ inversion as a possible source of new genes,” Molecular Biology and Evolution, vol. 26, no. 6, pp. 1405–1420, 2009. View at Publisher · View at Google Scholar · View at Scopus
  66. R. S. Baucom, J. C. Estill, C. Chaparro et al., “Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome,” PLoS Genetics, vol. 5, no. 11, Article ID e1000732, 2009. View at Publisher · View at Google Scholar · View at Scopus
  67. K. Noma, H. Ohtsubo, and E. Ohtsubo, “ATLN elements, LINEs from Arabidopsis thaliana: identification and characterization,” DNA Research, vol. 7, no. 5, pp. 291–303, 2000. View at Google Scholar · View at Scopus
  68. A. Lenoir, L. Lavie, J.-L. Prieto et al., “The evolutionary origin and genomic organization of SINEs in Arabidopsis thaliana,” Molecular Biology and Evolution, vol. 18, no. 12, pp. 2315–2322, 2001. View at Google Scholar · View at Scopus
  69. F. Myouga, S. Tsuchimoto, K. Noma, H. Ohtsubo, and E. Ohtsubo, “Identification and structural analysis of SINE elements in the Arabidopsis thaliana genome,” Genes and Genetic Systems, vol. 76, no. 3, pp. 169–179, 2001. View at Publisher · View at Google Scholar · View at Scopus
  70. J. Faris, A. Sirikhachornkit, R. Haselkorn, B. Gill, and P. Gornicki, “Chromosome mapping and phylogenetic analysis of the cytosolic acetyl-CoA carboxylase loci in wheat,” Molecular Biology and Evolution, vol. 18, no. 9, pp. 1720–1733, 2001. View at Google Scholar · View at Scopus
  71. Y. Zhang, Y. Wu, Y. Liu, and B. Han, “Computational identification of 69 retroposons in Arabidopsis,” Plant Physiology, vol. 138, no. 2, pp. 935–948, 2005. View at Publisher · View at Google Scholar · View at Scopus
  72. D. Benovoy and G. Drouin, “Processed pseudogenes, processed genes, and spontaneous mutations in the Arabidopsis genome,” Journal of Molecular Evolution, vol. 62, no. 5, pp. 511–522, 2006. View at Publisher · View at Google Scholar · View at Scopus
  73. N. Nurhayati, D. Gondé, and D. Ober, “Evolution of pyrrolizidine alkaloids in Phalaenopsis orchids and other monocotyledons: identification of deoxyhypusine synthase, homospermidine synthase and related pseudogenes,” Phytochemistry, vol. 70, no. 4, pp. 508–516, 2009. View at Publisher · View at Google Scholar · View at Scopus
  74. K. Mochizuki, M. Umeda, H. Ohtsubo, and E. Ohtsubo, “Characterization of a plant SINE, p-SINE1, in rice genomes,” Japanese Journal of Genetics, vol. 67, no. 2, pp. 155–166, 1992. View at Publisher · View at Google Scholar · View at Scopus
  75. J.-H. Xu, I. Osawa, S. Tsuchimoto, E. Ohtsubo, and H. Ohtsubo, “Two new SINE elements, p-SINE2 and p-SINE3, from rice,” Genes and Genetic Systems, vol. 80, no. 3, pp. 161–171, 2005. View at Publisher · View at Google Scholar · View at Scopus
  76. Y. Yasui, S. Nasuda, Y. Matsuoka, and T. Kawahara, “The Au family, a novel short interspersed element (SINE) from Aegilops umbellulata,” Theoretical and Applied Genetics, vol. 102, no. 4, pp. 463–470, 2001. View at Publisher · View at Google Scholar · View at Scopus
  77. J. A. Fawcett, T. Kawahara, H. Watanabe, and Y. Yasui, “A SINE family widely distributed in the plant kingdom and its evolutionary history,” Plant Molecular Biology, vol. 61, no. 3, pp. 505–514, 2006. View at Publisher · View at Google Scholar · View at Scopus
  78. E. Yagi, T. Akita, and T. Kawahara, “A novel Au SINE sequence found in a gymnosperm,” Genes and Genetic Systems, vol. 86, no. 1, pp. 19–25, 2011. View at Publisher · View at Google Scholar · View at Scopus
  79. Y. Shu, Y. Li, X. Bai et al., “Identification and characterization of a new member of the SINE Au retroposon family (GmAu1) in the soybean, Glycine max (L.) Merr., genome and its potential application,” Plant Cell Reports, vol. 30, no. 12, pp. 2207–2213, 2011. View at Publisher · View at Google Scholar · View at Scopus
  80. M. J. Moore, C. D. Bell, P. S. Soltis, and D. E. Soltis, “Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 49, pp. 19363–19368, 2007. View at Publisher · View at Google Scholar · View at Scopus
  81. D. H. Mathews, A. R. Banerjee, D. D. Luan, T. H. Eickbush, and D. H. Turner, “Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element,” RNA, vol. 3, no. 1, pp. 1–16, 1997. View at Google Scholar · View at Scopus
  82. Y. Nomura, M. Kajikawa, S. Baba et al., “Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2,” Nucleic Acids Research, vol. 34, no. 18, pp. 5184–5193, 2006. View at Publisher · View at Google Scholar · View at Scopus
  83. V. Cognat, J.-M. Deragon, E. Vinogradova, T. Salinas, C. Remacle, and L. Maréchal-Drouard, “On the evolution and expression of Chlamydomonas reinhardtii nucleus-encoded transfer RNA genes,” Genetics, vol. 179, no. 1, pp. 113–123, 2008. View at Publisher · View at Google Scholar · View at Scopus
  84. K. G. Karol, R. M. McCourt, M. T. Cimino, and C. F. Delwiche, “The closest living relatives of land plants,” Science, vol. 294, no. 5550, pp. 2351–2353, 2001. View at Publisher · View at Google Scholar · View at Scopus
  85. M. G. Kidwell and D. Lisch, “Transposable elements as sources of variation in animals and plants,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 15, pp. 7704–7711, 1997. View at Publisher · View at Google Scholar · View at Scopus
  86. D. Kordiš and F. Gubenšek, “Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 18, pp. 10704–10709, 1998. View at Publisher · View at Google Scholar · View at Scopus
  87. A. M. Walsh, R. D. Kortschak, M. G. Gardner, T. Bertozzi, and D. L. Adelson, “Widespread horizontal transfer of retrotransposons,” Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 3, pp. 1012–1016, 2013. View at Google Scholar
  88. S. Chambeyron, A. Bucheton, and I. Busseau, “Tandem UAA repeats at the 3′-end of the transcript are essential for the precise initiation of reverse transcription of the I factor in Drosophila melanogaster,” Journal of Biological Chemistry, vol. 277, no. 20, pp. 17877–17882, 2002. View at Publisher · View at Google Scholar · View at Scopus
  89. M. Komatsu, K. Shimamoto, and J. Kyozuka, “Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma,” Plant Cell, vol. 15, no. 8, pp. 1934–1944, 2003. View at Publisher · View at Google Scholar · View at Scopus
  90. X. Zhang and S. R. Wessler, “Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 15, pp. 5589–5594, 2004. View at Publisher · View at Google Scholar · View at Scopus
  91. H. Yamashita and M. Tahara, “A LINE-type retrotransposon active in meristem stem cells causes heritable transpositions in the sweet potato genome,” Plant Molecular Biology, vol. 61, no. 1-2, pp. 79–94, 2006. View at Publisher · View at Google Scholar · View at Scopus
  92. T. Heitkam and T. Schmidt, “BNR—a LINE family from Beta vulgaris—contains a RRM domain in open reading frame 1 and defines a L1 sub-clade present in diverse plant genomes,” Plant Journal, vol. 59, no. 6, pp. 872–882, 2009. View at Publisher · View at Google Scholar · View at Scopus
  93. J. D. Hollister, L. M. Smith, Y.-L. Guo, F. Ott, D. Weigel, and B. S. Gaut, “Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 6, pp. 2322–2327, 2011. View at Publisher · View at Google Scholar · View at Scopus
  94. E. Khazina, V. Truffault, R. Büttner, S. Schmidt, M. Coles, and O. Weichenrieder, “Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition,” Nature Structural and Molecular Biology, vol. 18, no. 9, pp. 1006–1014, 2011. View at Publisher · View at Google Scholar · View at Scopus
  95. S. J. Smerdon, J. Jäger, J. Wang et al., “Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 9, pp. 3911–3915, 1994. View at Google Scholar · View at Scopus
  96. M. Zuker, “Mfold web server for nucleic acid folding and hybridization prediction,” Nucleic Acids Research, vol. 31, no. 13, pp. 3406–3415, 2003. View at Publisher · View at Google Scholar · View at Scopus
  97. A. F. A. Smit and A. D. Riggs, “MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation,” Nucleic Acids Research, vol. 23, no. 1, pp. 98–102, 1995. View at Google Scholar · View at Scopus
  98. J. Jurka, E. Zietkiewicz, and D. Labuda, “Ubiquitous mammalian-wide interspersed repeats (MIRs) are molecular fossils from the mesozoic era,” Nucleic Acids Research, vol. 23, no. 1, pp. 170–175, 1995. View at Google Scholar · View at Scopus
  99. N. Gilbert and D. Labuda, “Evolutionary inventions and continuity of CORE-SINEs in mammals,” Journal of Molecular Biology, vol. 298, no. 3, pp. 365–377, 2000. View at Publisher · View at Google Scholar · View at Scopus
  100. A. F. A. Smit, “The origin of interspersed repeats in the human genome,” Current Opinion in Genetics and Development, vol. 6, no. 6, pp. 743–748, 1996. View at Publisher · View at Google Scholar · View at Scopus
  101. V. V. Kapitonov and J. Jurka, “The esterase and PHD domains in CR1-like non-LTR retrotransposons,” Molecular Biology and Evolution, vol. 20, no. 1, pp. 38–46, 2003. View at Publisher · View at Google Scholar · View at Scopus
  102. N. Gilbert and D. Labuda, “CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 6, pp. 2869–2874, 1999. View at Publisher · View at Google Scholar · View at Scopus
  103. K. P. Gogolevsky, N. S. Vassetzky, and D. A. Kramerov, “Bov-B-mobilized SINEs in vertebrate genomes,” Gene, vol. 407, no. 1-2, pp. 75–85, 2008. View at Publisher · View at Google Scholar · View at Scopus
  104. N. Okada and M. Hamada, “The 3′ ends of tRNA-derived SINEs originated from the 3′ ends of LINEs: a new example from the bovine genome,” Journal of Molecular Evolution, vol. 44, supplement 1, pp. S52–S56, 1997. View at Google Scholar · View at Scopus
  105. J. A. Lenstra, J. A. van Boxtel, K. A. Zwaagstra, and M. Schwerin, “Short interspersed nuclear element (SINE) sequences of the Bovidae,” Animal Genetics, vol. 24, no. 1, pp. 33–39, 1993. View at Google Scholar · View at Scopus
  106. J. Szemraj, G. Płucienniczak, J. Jaworski, and A. Płucienniczak, “Bovine Alu-like sequences mediate transposition of a new site-specific retroelement,” Gene, vol. 152, no. 2, pp. 261–264, 1995. View at Publisher · View at Google Scholar · View at Scopus
  107. M. Nikaido, H. Nishihara, Y. Hukumoto, and N. Okada, “Ancient SINEs from African endemic mammals,” Molecular Biology and Evolution, vol. 20, no. 4, pp. 522–527, 2003. View at Publisher · View at Google Scholar · View at Scopus
  108. C. Gilbert, J. K. Pace II, and P. D. Waters, “Target site analysis of RTE1_LA and its AfroSINE partner in the elephant genome,” Gene, vol. 425, no. 1-2, pp. 1–8, 2008. View at Publisher · View at Google Scholar · View at Scopus
  109. H. Endoh and N. Okada, “Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures,” Proceedings of the National Academy of Sciences of the United States of America, vol. 83, no. 2, pp. 251–255, 1986. View at Google Scholar · View at Scopus
  110. H. Endoh, S. Nagahashi, and N. Okada, “A highly repetitive and transcribable sequence in the tortoise genome is probably a retroposon,” European Journal of Biochemistry, vol. 189, no. 1, pp. 25–31, 1990. View at Google Scholar · View at Scopus
  111. T. Sasaki, K. Takahashi, M. Nikaido, S. Miura, Y. Yasukawa, and N. Okada, “First application of the SINE (Short Interspersed Repetitive Element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily testudinoidea,” Molecular Biology and Evolution, vol. 21, no. 4, pp. 705–715, 2004. View at Publisher · View at Google Scholar · View at Scopus
  112. M. Kajikawa, K. Ohshima, and N. Okada, “Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif,” Molecular Biology and Evolution, vol. 14, no. 12, pp. 1206–1217, 1997. View at Google Scholar · View at Scopus
  113. T. L. Vandergon and M. Reitman, “Evolution of chicken repeat 1 (CR1) elements: evidence for ancient subfamilies and multiple progenitors,” Molecular Biology and Evolution, vol. 11, no. 6, pp. 886–898, 1994. View at Google Scholar · View at Scopus
  114. O. Piskurek, C. C. Austin, and N. Okada, “Sauria SINEs: novel short interspersed retroposable elements that are widespread in reptile genomes,” Journal of Molecular Evolution, vol. 62, no. 5, pp. 630–644, 2006. View at Publisher · View at Google Scholar · View at Scopus
  115. O. Piskurek, H. Nishihara, and N. Okada, “The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis,” Gene, vol. 441, no. 1-2, pp. 111–118, 2009. View at Publisher · View at Google Scholar · View at Scopus
  116. K. K. Kojima, V. V. Kapitonov, and J. Jurka, “Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs,” Molecular Biology and Evolution, vol. 28, no. 1, pp. 17–20, 2011. View at Publisher · View at Google Scholar · View at Scopus
  117. K.-I. Matsumoto, K. Murakami, and N. Okada, “Gene for lysine tRNA1 may be a progenitor of the highly repetitive and transcribable sequences present in the salmon genome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 83, no. 10, pp. 3156–3160, 1986. View at Google Scholar · View at Scopus
  118. Y. Kido, M. Aono, T. Yamaki et al., “Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 88, no. 6, pp. 2326–2330, 1991. View at Google Scholar · View at Scopus
  119. V. Matveev, H. Nishihara, and N. Okada, “Novel SINE families from salmons validate Parahucho (Salmonidae) as a distinct genus and give evidence that SINEs can incorporate LINE-related 3′-tails of other SINEs,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1656–1666, 2007. View at Publisher · View at Google Scholar · View at Scopus
  120. R. J. Winkfein, R. D. Moir, S. A. Krawetz, J. Blanco, J. C. States, and G. H. Dixon, “A new family of repetitive, retroposon-like sequences in the genome of the rainbow trout,” European Journal of Biochemistry, vol. 176, no. 2, pp. 255–264, 1988. View at Google Scholar · View at Scopus
  121. Y. Terai, K. Takahashi, and N. Okada, “SINE cousins: the 3′-end tails of the two oldest and distantly related families of SINEs are descended from the 3′ ends of LINEs with the same genealogical origin,” Molecular Biology and Evolution, vol. 15, no. 11, pp. 1460–1471, 1998. View at Google Scholar · View at Scopus
  122. K. Takahashi, Y. Terai, M. Nishida, and N. Okada, “A novel family of short interspersed repetitive elements (SINEs) from cichlids: the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika,” Molecular Biology and Evolution, vol. 15, no. 4, pp. 391–407, 1998. View at Google Scholar · View at Scopus
  123. M. Kajikawa, K. Ichiyanagi, N. Tanaka, and N. Okada, “Isolation and characterization of active LINE and SINEs from the eel,” Molecular Biology and Evolution, vol. 22, no. 3, pp. 673–682, 2005. View at Publisher · View at Google Scholar · View at Scopus
  124. C. Tong, B. Guo, and S. He, “Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation,” BMC Genomics, vol. 10, article 83, 2009. View at Publisher · View at Google Scholar · View at Scopus
  125. H. Nishihara, A. F. A. Smit, and N. Okada, “Functional noncoding sequences derived from SINEs in the mammalian genome,” Genome Research, vol. 16, no. 7, pp. 864–874, 2006. View at Publisher · View at Google Scholar · View at Scopus
  126. I. Ogiwara, M. Miya, K. Ohshima, and N. Okada, “Retropositional parasitism of SINEs on LINEs: identification of SINEs and LINEs in elasmobranchs,” Molecular Biology and Evolution, vol. 16, no. 9, pp. 1238–1250, 1999. View at Google Scholar · View at Scopus
  127. I. Ogiwara, M. Miya, K. Ohshima, and N. Okada, “V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit,” Genome Research, vol. 12, no. 2, pp. 316–324, 2002. View at Publisher · View at Google Scholar · View at Scopus
  128. Z. Izsvák, Z. Ivics, D. Garcia-Estefania, S. C. Fahrenkrug, and P. B. Hackett, “DANA elements: a family of composite, tRNA-derived short interspersed DNA elements associated with mutational activities in zebrafish (Danio rerio),” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 3, pp. 1077–1081, 1996. View at Publisher · View at Google Scholar · View at Scopus
  129. N. Shimoda, M. Chevrette, M. Ekker, Y. Kikuchi, Y. Hotta, and H. Okamoto, “Mermaid, a family of short interspersed repetitive elements, is useful for zebrafish genome mapping,” Biochemical and Biophysical Research Communications, vol. 220, no. 1, pp. 233–237, 1996. View at Publisher · View at Google Scholar · View at Scopus
  130. B. Venkatesh, E. F. Kirkness, Y.-H. Loh et al., “Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome,” PLoS Biology, vol. 5, no. 4, article e101, 2007. View at Publisher · View at Google Scholar · View at Scopus
  131. P. E. Nisson, R. J. Hickey, M. F. Boshar, and W. R. Crain Jr., “Identification of a repeated sequence in the genome of the sea urchin which is traescribed by RNA polymerase III and contains the features of a retroposon,” Nucleic Acids Research, vol. 16, no. 4, pp. 1431–1452, 1988. View at Publisher · View at Google Scholar · View at Scopus
  132. Z. Tu, S. Li, and C. Mao, “The changing tails of a novel short interspersed element in Aedes aegypti: genomic evidence for slippage retrotransposition and the relationship between 3′ tandem repeats and the poly(dA) tail,” Genetics, vol. 168, no. 4, pp. 2037–2047, 2004. View at Publisher · View at Google Scholar · View at Scopus
  133. Z. Tu and J. J. Hill, “MosquI, a novel family of mosquito retrotransposons distantly related to the Drosophila I factors, may consist of elements of more than one origin,” Molecular Biology and Evolution, vol. 16, no. 12, pp. 1675–1686, 1999. View at Google Scholar · View at Scopus
  134. O. Piskurek and D. J. Jackson, “Tracking the ancestry of a deeply conserved eumetazoan SINE domain,” Molecular Biology and Evolution, vol. 28, no. 10, pp. 2727–2730, 2011. View at Publisher · View at Google Scholar · View at Scopus
  135. P. Kachroo, S. A. Leong, and B. B. Chattoo, “Mg-SINE: a short interspersed nuclear element from the rice blast fungus, Magnaporthe grisea,” Proceedings of the National Academy of Sciences of the United States of America, vol. 92, no. 24, pp. 11125–11129, 1995. View at Publisher · View at Google Scholar · View at Scopus
  136. A. M. Shire and J. P. Ackers, “SINE elements of Entamoeba dispar,” Molecular and Biochemical Parasitology, vol. 152, no. 1, pp. 47–52, 2007. View at Publisher · View at Google Scholar · View at Scopus
  137. K. Van Dellen, J. Field, Z. Wang, B. Loftus, and J. Samuelson, “LINEs and SINE-like elements of the protist Entamoeba histolytica,” Gene, vol. 297, no. 1-2, pp. 229–239, 2002. View at Publisher · View at Google Scholar · View at Scopus
  138. U. Willhoeft, H. Buß, and E. Tannich, “The abundant polyadenylated transcript 2 DNA sequence of the pathogenic protozoan parasite Entamoeba histolytica represents a nonautonomous non-long-terminal-repeat retrotransposon-like element which is absent in the closely related nonpathogenic species Entamoeba dispar,” Infection and Immunity, vol. 70, no. 12, pp. 6798–6804, 2002. View at Publisher · View at Google Scholar · View at Scopus
  139. K. K. Kojima and H. Fujiwara, “An extraordinary retrotransposon family encoding dual endonucleases,” Genome Research, vol. 15, no. 8, pp. 1106–1117, 2005. View at Publisher · View at Google Scholar · View at Scopus
  140. S. Tsuchimoto, Y. Hirao, E. Ohtsubo, and H. Ohtsubo, “New SINE families from rice, OsSN, with poly(A) at the 3′ ends,” Genes and Genetic Systems, vol. 83, no. 3, pp. 227–236, 2008. View at Publisher · View at Google Scholar · View at Scopus
  141. J.-M. Deragon, B. S. Landry, T. Pélissier, S. Tutois, S. Tourmente, and G. Picard, “An analysis of retroposition in plants based on a family of SINEs from Brassica napus,” Journal of Molecular Evolution, vol. 39, no. 4, pp. 378–386, 1994. View at Publisher · View at Google Scholar · View at Scopus
  142. A. Lenoir, T. Pélissier, C. Bousquet-Antonelli, and J. M. Deragon, “Comparative evolution history of SINEs in Arabidopsis thaliana and Brassica oleracea: evidence for a high rate of SINE loss,” Cytogenetic and Genome Research, vol. 110, no. 1–4, pp. 441–447, 2005. View at Publisher · View at Google Scholar · View at Scopus
  143. X. Zhang and S. R. Wessler, “BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea,” Journal of Molecular Evolution, vol. 60, no. 5, pp. 677–687, 2005. View at Publisher · View at Google Scholar · View at Scopus
  144. J.-M. Deragon and X. Zhang, “Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers,” Systematic Biology, vol. 55, no. 6, pp. 949–956, 2006. View at Publisher · View at Google Scholar · View at Scopus
  145. M. Gadzalski and T. Sakowicz, “Novel SINEs families in Medicago truncatula and Lotus japonicus: bioinformatic analysis,” Gene, vol. 480, no. 1-2, pp. 21–27, 2011. View at Publisher · View at Google Scholar · View at Scopus