A novel composite retrotransposon derived from or generated independently of the SVA (SINE/VNTR/Alu) transposon has undergone proliferationin gibbon genomes

Genes and Genetic Systems

Volumn 87, Issue 3, 2012, Pages 181-190

  Hara, Toru ^a   Hirai, Yuriko ^a   Baicharoen, Sudarath ^b   Hayakawa, Takashi ^a,c   Hirai, Hirohisa ^a   Koga, Akihiko ^a  

^a KYOTO UNIVERSITY   (Japan)

^b Zoological Park Organization Bangkok   (Thailand)

^c JAPAN SOCIETY FOR THE PROMOTION OF SCIENCE   (Japan)

Author keywords

Alu; Gibbon; Hominoids; LINE1; Retrotransposon; SVA

Indexed keywords

DNA; OXIDOREDUCTASE; PROSTAGLANDIN REDUCTASE 2; UNCLASSIFIED DRUG; RETROPOSON;

ADULT; ALU SEQUENCE; ANIMAL CELL; ARTICLE; FEMALE; GENE SEQUENCE; GENETIC MANIPULATION; GENOME; HUMAN; HUMAN CELL; HYLOBATIDAE; MALE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; RETROPOSON; SEQUENCE ANALYSIS; TRANSPOSON; VARIABLE NUMBER OF TANDEM REPEAT; ANIMAL; EVOLUTION; HYLOBATES;

ANIMALS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; EVOLUTION, MOLECULAR; GENOME; HUMANS; HYLOBATES; MINISATELLITE REPEATS; RETROELEMENTS;

EID: 84867905608     PISSN: 13417568     EISSN: 18805779     Source Type: Journal    
DOI: 10.1266/ggs.87.181     Document Type: Article

References (27)

1. Bantysh, O. B., and Buzdin, A. A. (2009) Novel family of human transposable elements formed due to fusion of the first exon of gene MAST2 with retrotransposon SVA. Biochemistry (Moscow) 74, 1393-1399.
2. Buzdin, A. A. (2004) Retroelements and formation of chimeric retrogenes. Cell. Mol. Life Sci. 61, 2046-2059.
3. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T. L. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10, 421.
4. Carbone, L., Harris, R. A., Mootnick, A. R., Milosavljevic, A., Martin, D. I. K., Rocchi, M., Capozzi, O., Archidiacono, N., Konkel, M. K., Walker, J. A., et al. (2012) Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons. Genome Biol. Evol. doi:10.1093/gbe/evs048.
5. Damert, A., Raiz, J., Horn, A. V., Lower, J., Wang, H., Xing, J., Batzer, M. A., Lower, R., and Schumann, G. G. (2009) 5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome. Genome Res. 19, 1992-2008.
6. Dewannieux, M., Esnault, C., and Heidmann, T. (2003) LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35, 41-48.
7. Hancks, D. C., and Kazazian, H. H., Jr. (2010) SVA retrotransposons: evolution and genetic instability. Semin. Cancer Biol. 20, 234-245.
8. Hancks, D. C., Ewing, A. D., Chen, J. E., Tokunaga, K., and Kazazian, H. H., Jr. (2009) Exon-trapping mediated by the human retrotransposon SVA. Genome Res. 19, 1983-1991.
9. Hancks, D. C., Goodier, J. L., Mandal, P. K., Cheung, L. E., and Kazazian, H. H., Jr. (2011) Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum. Mol. Genet. 20, 3386-3400.
10. Hirai, H., Matsubayashi, K., Kumazaki, K., Kato, A., Maeda, N., and Kim, H. S. (2005) Chimpanzee chromosomes: retrotransposable compound repeat DNA organization (RCRO) and its influence on meiotic prophase and crossing-over. Cytogenet. Genome Res. 108, 248-254.
11. Jurka, J. (2004) Evolutionary impact of human Alu repetitive elements. Curr. Opin. Genet. Dev. 14, 603-608.
12. Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., and Walichiewicz, J. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogent. Genome Res. 110, 462-467.
13. Kato, K., and Toh, H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform. 9, 286-298.
14. Koga, A., Shimada, A., Kuroki, T., Hori, H., Kusumi, J., Kyono-Hamaguchi, Y., and Hamaguchi, S. (2007) The Tol1 transposable element of the medaka fish moves in human and mouse cells. J. Hum. Genet. 52, 628-635.
15. Koga, A., Notohara, M., and Hirai, H. (2011) Evolution of subterminal satellite (StSat) repeats in hominids. Genetica 139, 167-175.
16. Lee, J., Ha, J., Son, S. Y., and Han, K. (2012) Human genomic deletions generated by SVA-associated events. Comp. Funct. Genomics 2012, 807270. Epub, doi: 10.1155/2012/807270.
17. Makino, S., Kaji, R., Ando, S., Tomizawa, M., Yasuno, K., Goto, S., Matsumoto, S., Tabuena, D., Maranon, E., Dantes, M., et al. (2007) Reduced neuron-specific expression of the TAF1 gene is associated with X-linked dystonia-parkinsonism. Am. J. Hum. Genet. 80, 393-406.
18. Mills, R. E., Bennett, E. A., Iskow, R. C., and Devine, S. E. (2007) Which transposable elements are active in the human genome? Trends Genet. 23, 183-191.
19. Molaro, A., Hodges, E., Fang, F., Song, Q., McCombie, W. R., Hannon, G. J., and Smith, A. D. (2011) Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 146, 1029-1041.
20. Ostertag, E. M., and Kazazian, H. H., Jr. (2001) Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res. 11, 2059-2065.
21. Ostertag, E. M., Goodier, J. L., Zhang, Y., and Kazazian, H. H., Jr. (2003) SVA elements are nonautonomous retrotransposons that cause disease in humans. Am. J. Hum. Genet. 73, 1444-1451.
22. Raiz, J., Damert, A., Chira, S., Held, U., Klawitter, S., Hamdorf, M., Löwer, J., Strätling, W. H., Löwer, R., and Schumann, G. G. (2012) The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. Nucleic Acids Res. 40, 1666-1683.
23. Wang, H., Xing, J., Grover, D., Hedges, D. J., Han, K., Walker, J. A., and Batzer, M. A. (2005) SVA elements: a hominid-specific retroposon family. J. Mol. Biol. 354, 994-1007.
24. Watanabe, M., Kobayashi, K., Jin, F., Park, K. S., Yamada, T., Tokunaga, K., and Toda, T. (2005) Founder SVA retrotransposal insertion in Fukuyama-type congenital muscular dystrophy and its origin in Japanese and northeast Asian populations. Am. J. Med. Genet. Part A 138, 344-348.
25. Wu, Y. H., Ko, T. P., Guo, R. T., Hu, S. M., Chuang, L. M., and Wang, A. H. (2008) Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2. Structure (London) 16, 1714-1723.
26. Zabolotneva, A. A., Bantysh, O., Suntsova, M. V., Efimova, N., Malakhova, G. V., Schumann, G. G., Gayfullin, N. M., and Buzdin, A. A. (2012) Transcriptional regulation of human-specific SVAF1 retrotransposons by cis-regulatory MAST2sequences. Gene doi: 10.1016/j.gene.2012.05.016
27. Zhang, L., Zhang, F., and Huo, K. (2003) Cloning and characterization of a novel splicing variant of the ZADH1 gene. Cytogenet. Genome Res. 103, 79-83.