Phylogenetic analysis of retroposon family as exemplified on human chromosome 13: Further evidence for recent proliferation

Molecules and Cells

Volumn 10, Issue 3, 2000, Pages 356-360

  Kim, Heui Soo ^a   Hyun, Byung Hwa ^b   Crow, Timothy J ^c  

^a Pusan National University   (South Korea)

^b Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

HERV K LTR; Human Chromosome 13; Phylogeny; SINE R Retroposon

Indexed keywords

COMPLEMENT COMPONENT C2;

ARTICLE; CHROMOSOME 13; DNA SEQUENCE; GENETICS; HUMAN; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; PHYLOGENY; POLYMERASE CHAIN REACTION; RETROPOSON; SEQUENCE ALIGNMENT; SHORT INTERSPERSED REPEAT;

CHROMOSOMES, HUMAN, PAIR 13; COMPLEMENT C2; EVOLUTION, MOLECULAR; HUMANS; PHYLOGENY; POLYMERASE CHAIN REACTION; RETROELEMENTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; TERMINAL REPEAT SEQUENCES;

EID: 0034733194     PISSN: 10168478     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (29)

1. Akopov, S. B., Nikolaev, L. G., Khil, P. P., Lebedev, Y. B., and Sverdlov, E. D. (1998) Long terminal repeats of human endogenous retrovirus K family (HERV-K) specifically bind host cell nuclear proteins. FEBS Lett. 421, 229-233.
2. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Baltimore, D. (1985) Retroviruses and retrotransposons: the role of reverse transcription in shaping the eukaryotic genome. Cell 40, 481-482.
4. Carroll, M. C., Campbell, R. D., Bentley, D. R., and Porter, R. R. (1984) A molecular map of the human major histocompatibility complex class III region linking complement genes C4, C2 and factor B. Nature 307, 237-241.
5. Conrad, B., Weissmahr, R. N., Boni, J., Arcari, R., Schupbach, J., and Mach, B. (1997) A human endogenous retroviral superantigen as candidate autoimmune gene in type I diabetes. Cell 90, 303-313.
6. Haltimeier, M., Seifarth, W., Blusch, J., Erfle, V., Hehlmann, R., and Leib-Mosch, C. (1995) Identification of S71-related human endogenous retroviral sequences with full-length pol genes. Virology 209, 550-560.
7. Kambhu, S., Falldorf, P., and Lee, J. S. (1990) Endogenous retroviral long terminal repeats within the HLA-DQ locus. Proc. Natl. Acad. Sci. USA 87, 4927-4931.
8. Kazazian, H. H. and Moran, J. V. (1998) The impact of the L1 retrotransposons on the human genome. Nature Genet. 19, 19-24.
9. Kim, H. S. and Crow, T. J. (1999) Presence and phylogenetic relationships of a hominoid-specific retroposon family on the human Y chromosome. Zool. Sci. 16, 963-970.
10. Kim, H. S. and Crow, T. J. (2000) Phylogenetic relationships of a class of hominoid-specific retroelements (SINE-R) on human chromosomes 7 and 17. Ann. Hum. Biol. 27, 83-93.
11. Kim, H. S., Hirai, H., and Takenaka, O. (1996) Molecular features of the TSPY gene of gibbons and Old World monkeys. Chrom. Res. 4, 500-506.
12. Kim, H. S., Chen, Y, and Lonai, P. (1998) Complex regulation of multiple cytohesin like genes in murine tissues and cells. FEBS Lett. 433, 312-316.
13. Kim, H. S., Takenaka, O., and Crow, T. J. (1999a) Cloning and nucleotide sequence of retroposons specific to hominoid primates derived from an endogenous retrovirus (HERV-K). AIDS Res. Hum. Retroviruses 15, 595-601.
14. Kim, H. S., Wadekar, R. V., Takenaka, O., Winstanley, C., Mitsunaga, F., Kageyama, T., Hyun, B.-H., and Crow, T. J. (1999b) SINE-R.C2 (a Homo sapiens specific retroposon) is homologous to cDNA from post-mortem brain in schizophrenia and to two loci in the Xq21.3/Yp block linked to handedness and psychosis. Am. J. Med. Genet. (Neuropsychiat. Genet.) 88, 560-566.
15. Kobayashi, K., Nakahori, Y., Miyake, M., Matsumura, K., Kondo-lida, E., Nomura, Y., Segawa, M., Yoshioka, M., Saito, K., Osawa, M., Hamano, K., Sakakihara, Y., Nonaka, I., Nakagome, Y., Kanazawa, I., Nakamura, Y., Tokunaga, K., and Toda, T. (1998) An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy. Nature 394, 388-392.
16. Laval, S. H., Dann, J. C., Butler, R. J., Loftus, J., Rue, J., Leask, S. J., Bass, N., Comazzi, M., Vita, A., Nanko, S., Shaw, S., Peterson, P., Shields, G., Smith, A. B., Stewart, J., DeLisi, L. E., and Crow, T. J. (1998) Evidence for linkage to psychosis and cerebral asymmetry (relative hand skill) on the X chromosome. Am. J. Med. Genet. (Neuropsychiat. Genet.) 81, 420-427.
17. Leib-Mosch, C., Haltmeier, M., Werner, T., Geigl, E.-M., Brack-Werner, R., Francke, U., Erfle, V., and Hehlmann, R. (1993) Genomic distribution and transcription of solitary HERV-K LTRs. Genomics 18, 261-269.
18. Mager, D. L. and Freeman, J. D. (1995) HERV-H endogenous retroviruses: presence in the New World branch but amplification in the Old World primate lineage. Virology 213, 395-404.
19. Medstand, P. and Mager, D. L. (1998) Human-specific integrations of the HERV-K endogenous retrovirus family. J. Virol. 72, 9782-9787.
20. O'Connell, C. D. and Cohen, M. (1984) The long terminal repeat sequence of a novel human endogenous retrovirus. Science 226, 1204-1206.
21. Ono, M., Kawakami, M., and Takezawa, T. (1987) A novel human nonviral retroposon derived from an endogenous retrovirus. Nucleic Acids Res. 21, 8725-8737.
22. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
23. Seidl, C., Donner, H., Petershofen, E., Usadel, K. H., Seifried, E., Kaltwasser, J. P., and Badenhoop, K. (1999) Ar endogenous retroviral long terminal repeat at the HLA-DQB1 gene locus confers susceptibility to rheumatoid arthritis. Hum. Immunol. 60, 63-68.
24. Simon, M., Haltmeier, M., Papakonstantinou, G., Werner, G., Hehlmann, R., and Leib-Mösch, C, (1994) Transcription of HERV-K-related LTRs in human placenta and leukemic cells. Leukemia 8, S12-17.
25. Steinhuber, S., Brack, M., Hunsmann, G., Schwelberger, H., Dierich, M. P., and Vogetseder, W. (1995) Distribution of human endogenous retrovirus HERV-K genomes in humans and different primates. Hum. Genet. 96, 188-192.
26. Sverdlov, E. D. (1998) Perpetually mobile footprints of ancient infections in human genome. FEBS Lett. 428, 1-6.
27. Thompson, J. D, Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
28. Zhu, Z. B., Hsieh, S. L., Bentley, D. R., Campbell, R. D., and Volanakis, J. E. (1992) A variable number of tandem repeats locus within the human complement C2 gene is associated with a retroposon derived from a human endogenous retrovirus. J. Exp. Med. 175, 1783-1787.
29. Zhu, Z. B., Jian, B., and Volanakis, J. E. (1994) Ancestry of SINE-R.C2 a human-specific retroposon. Hum. Genet. 93, 545-551.