Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome

Gene

Volumn 205, Issue 1-2, 1997, Pages 203-217

  Robertson, Hugh M ^a   Zumpano, Karen L ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

D,D35E motif; Gibbon; Monkey; Prosimian; SET domain; Tarsier

Indexed keywords

COMPLEMENTARY DNA; TRANSPOSASE;

CONFERENCE PAPER; CONSENSUS SEQUENCE; CPG ISLAND; DNA SEQUENCE; EVOLUTION; GENE MUTATION; GENE NUMBER; GENOME; HUMAN; HUMAN GENETICS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; TRANSPOSON;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; DNA TRANSPOSABLE ELEMENTS; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; GENOME, HUMAN; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

CECROPIA; HYLOBATES SP.; LORIS; NYCTICEBUS COUCANG; PRIMATES; STREPSIRHINI; TARSIUS SYRICHTA;

EID: 0031593204     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(97)00472-1     Document Type: Conference Paper

References (58)

1. Adams, M.D., Dubnick, M., Kerlavage, A.R., Moreno, R., Kelley, J.M., Utterback, T.R., Nagle, J.W., Fields, C., Venter, J.C., 1992. Sequence identification of 2375 human brain genes. Nature 355, 632-634.
2. Archibald, J.D., 1996. Fossil evidence for a late Cretaceous origin of hoofed- mammals. Science 272, 1150-1153.
3. Auge-Gouillou, C., Bigot, Y., Pollet, N., Hamelin, M.-H., Meunier-Rotival, M., Periquet, G., 1995. Human and other mammalian genomes contain transposons of the mariner family. FEBS Lett. 368, 541-546.
4. Berry, R., Stevens, T.J., Walter, N.A., Wilcox, A.S., Rubano, T., Hopkins, J.A., Weber, J., Goold, R., Soares, M.B., Sikela, J.M., 1995. Gene-based sequence-tagged-sites (STSs) as the basis for a human gene map. Nature Genet. 10, 415-423.
5. Britten, R.J., 1994. Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago. Proc. Natl. Acad. Sci. USA 91, 6148-6150.
6. Britten, R.J., Baron, W.F., Stout, D.B., Davidson, E.H., 1988. Sources and evolution of human Alu repeated sequences. Proc. Natl. Acad. Sci. USA 85, 4770-4774.
7. Bulmer, M., Wolfe, K.H., Sharp, P.M., 1991. Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders. Proc. Natl. Acad. Sci. USA 88, 5974-5978.
8. Burn, T.C., Petrovick, M.S., Hohaus, S., Rollins, B.J., Tenen, D.G., 1994. Monocyte chemoattractant protein-1 gene is expressed in activated neutrophils and retinoic acid-induced human myeloid cell lines. Blood 84, 2776-2783.
9. Cavener, D.R., Ray, S.C., 1991. Eukaryotic start and stop translation sites. Nucleic Acids Res. 19, 3185-3192.
10. Chissoe, S.L., Bodenteich, A., Wang, Y.-F., Wang, Y.-P., Burian, D., Clifton, S.W. et al., 1995. Sequence and analysis of the human ABL gene, the BCR gene, and regions involved in the Philadelphia chromosomal translocation. Genomics 27, 67-82.
11. Doak, T.G., Doerder, F.P., Jahn, C.L., Herrick, G., 1994. A proposed superfamily of transposase-related genes: new members in transposon-like elements of ciliated protozoa and a common 'D35E' motif. Proc. Natl. Acad. Sci. USA 91, 942-946.
12. Garcia-Fernàndez, J., Bayascas-Ramírez, J.R., Marfany, G., Muñoz-Mármol, A.M., Casali, A., Baguñà, J., Saló, E., 1995. High copy number of highly similar mariner-like transposons in planarian (Platyhelminthe): evidence for a trans-phyla horizontal transfer. Mol. Biol. Evol. 12, 421-431.
13. Gloor, G.B., Nassif, N.A., Johnson-Schlitz, D.M., Preston, C.R., Engels, W.R., 1991. Targeted gene replacement in Drosophila via P element-induced gap repair. Science 253, 1110-1117.
14. Goold, R.D., diSibio, G., Xu, H., Lang, D.B., Dadgar, J., Magrane, G., Dugaiczyk, A., Smith, K.A., Cox, D.R., Masters, S.B., Myers, R.M., 1993. The development of sequence-tagged sites for human chromosome 4. Hum. Mol. Genet. 2, 1271-1288.
15. Hartl, D.L., 1989. Transposable element mariner in Drosophila species. In: Berg, D.E., Howe, M.M., (Eds.), Mobile DNA. American Society for Microbiology, Washington, DC, pp. 5531-5536.
16. Hartl, D.L., 1996. The most unkindest cut of all. Nature Genet. 12, 227-229.
17. Hedges, S.B., Parker, P.H., Sibley, C.G., Kumar, S., 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381, 226-229.
18. Hijiya, N., Setoguchi, M., Matsuura, K., Higuchi, Y., Akizuki, S., Yamamoto, S., 1994. Cloning and characterization of the human osteopontin gene and its promoter. Biochem. J. 303, 255-262.
19. Hillier, L., Lennon, G., Becker, M., Bonaldo, M.F., Chiapelli, B., Chissoe, S. et al., 1996. Generation and analysis of 280 000 human expressed sequence tags. Genome Res. 6, 807-828.
20. Jeyaprakash, A., Hoy, M.A., 1995. Complete sequence of a mariner transposable element from the predatory mite Metaseiulus occidentalis isolated by an inverse PCR approach. Insect Mol. Biol. 4, 31-39.
21. Jones, R.S., Gelbart, W.M., 1993. The Drosophila Polycomb-group gene Enhancer of zeste contains a region with sequence similarity to trithorax. Mol. Cell. Biol. 13, 6357-6366.
22. Kapitonov, V., Jurka, J., 1996. The age of Alu subfamilies. J. Mol. Evol. 42, 59-65.
23. Kay, R.F., Ross, C., Williams, B.A., 1997. Anthropoid origins. Science 275, 797-804.
24. Kiyosawa, H., Chance, P.F., 1996. Primate origin of the CMT1A-REP repeat and analysis of a putative transposon-associated recombinational hotspot. Human Mol. Gen. 5, 745-753.
25. Kozak, M., 1996. Interpreting cDNA sequences: some insights from studies on translation. Mamm. Genome 7, 563-574.
26. Lampe, D.J., Churchill, M.E.A., Robertson, H.M., 1996. A purified mariner transposase is sufficient to mediate transposition in vitro. EMBO J. 15, 5470-5479.
27. Larsen, F., Gundersen, G., Lopez, R., Prydz, H., 1992. CpG islands as gene markers in the human genome. Genomics 13, 1095-1107.
28. Lohe, A.R., de Aguiar, D., Hartl, D.L., 1997. Mutations in the mariner transposase: the D,D(35)E consensus sequence is nonfunctional. Proc. Natl. Acad. Sci USA 94, 1293-1297.
29. Maddison, W.P., Maddison, D.R., 1993. MacClade, Analysis of Phylogeny and Character Evolution, version 3. Sinauer Associates, Sunderland, Massachusetts, USA.
30. Martin, R.D., 1993. Primate origins: plugging the gaps. Nature 363, 223-234.
31. Miller, W.J., Paricio, N., Hagemann, S., Martinez-Sebastian, M.J., Pinsker, W., de Frutos, R., 1995. Structure and expression of clustered P element homologues in Drosophila subobscura and Drosophila guanche. Gene 156, 167-174.
32. Milner, C.M., Campbell, R.D., 1993. The G9a gene in the human major histocompatibility complex encodes a novel protein containing ankyrin-like repeats. Biochem. J. 290, 811-818.
33. Morgan, G.T., 1995. Identification in the human genome of mobile elements spread by DNA-mediated transposition. J. Mol. Biol. 254, 1-5.
34. Mount, S.M., 1982. A catalogue of splice junction sequences. Nucleic Acids Res. 10, 459-472.
35. Nei, M., Gojobori, T., 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418-426.
36. Nomura, N., Nagase, T., Miyajima, N., Sazuka, T., Tanaka, A., Sato, S., Seki, N., Kawarabayasi, Y., Ishikawa, K., Tabata, S., 1994. Prediction of the coding sequences of unidentified human genes. II. The coding sequences of 40 new genes (KIAA0041-KIAA0080) deduced by analysis of cDNA clones from human cell line KG-1. DNA Res. 1, 223-229.
37. Oosumi, T., Belknap, W.R., Garlick, B., 1995. Mariner transposons in humans. Nature 378, 672
38. Reiter, L.T., Murakami, T., Koeuth, T., Pentao, L., Muzny, D.M., Gibbs, R.A., Lupski, J.R., 1996. A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. Nature. Genet. 12, 288-297.
39. Robertson, H.M., 1993. The mariner transposable element is widespread in insects. Nature 362, 241-245.
40. Robertson, H.M., 1995. The Tc1-mariner superfamily of transposons in animals. J. Insect Physiol. 41, 99-105.
41. Robertson, H.M., 1996. Members of the pogo superfamily of DNA-mediated transposons in the human genome. Mol. Gen. Genet. 252, 761-766.
42. Robertson, H.M., 1997. Multiple mariner transposons in flatworms and hydras are related to those of insects. J. Hered. 88, 195-201.
43. Robertson, H.M., Asplund, M.L., 1996. Bmmar1: a basal lineage of the mariner family of transposable elements in the silkworm moth Bombyx mori. Insect Biochem. Mol. Biol. 26, 945-954.
44. Robertson, H.M., MacLeod, E.G., 1993. Five major subfamilies of mariner transposable elements in insects, including the Mediterranean fruit fly, and related arthropods. Insect Mol. Biol. 2, 125-139.
45. Robertson, H.M., Martos, R., 1997. Molecular evolution of the second ancient human mariner transposon, Hsmar2, illustrates patterns of neutral evolution in the human genome lineage. Gene 205, 219-228.
46. Robertson, H.M., Soto-Adames, F.N., Walden, K.K.O., Avancini, R.M.P., Lampe, D.J., 1997. The mariner transposons of animals: horizontally jumping genes. In: Syvanen, M., Kado, C. (Eds.), Horizontal Gene Transfer. Chapman and Hall, London, in press.
47. Robertson, H.M., Zumpano, K.L., Lohe, A.R., Hartl, D.L., 1996. Reconstructing the ancient mariners of humans. Nature Genet. 12, 360-361.
48. Rowen, L., Koop, B.F., Hood, L., 1996. The complete 685-kilobase DNA sequence of the human β T cell receptor locus. Science 272, 1755-1762.
49. Saitou, N., Ueda, S., 1994. Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates. Mol. Biol. Evol. 11, 504-512.
50. Schlötterer, C., Tautz, D., 1992. Slippage synthesis of simple sequence DNA. Nucleic Acids Res. 20, 211-215.
51. Schneider, H., Schneider, M.P.C., Sampaio, I., Harada, M.L., Stanhope, M., Czelusniak, J., Goodman, M., 1993. Molecular phylogeny of the New World Monkeys (Platyrrhini, Primates). Mol. Phylo. Evol. 2, 225-242.
52. Sedensky, M.M., Hudson, S.J., Everson, B., Morgan, P.G., 1994. Identification of a mariner-like repetitive sequence in C. elegans. Nucleic Acids Res. 22, 1719-1723.
53. Smit, A.F.A., 1996. The origin of interspersed repeats in the human genome. Cur. Opin. Genet. Dev. 6, 743-748.
54. Smit, A.F.A., Riggs, A.D., 1996. Tiggers and other DNA transposon fossils in the human genome. Proc. Natl. Acad. Sci. USA 93, 1443-1448.
55. Stassen, M.J., Bailey, D., Nelson, S., Chinwalla, V., Harte, P.J., 1995. The Drosophila trithorax proteins contain a novel variant of the nuclear receptor type DNA binding domain and an ancient conserved motif found in other chromosomal proteins. Mech. Dev. 52, 209-223.
56. Swofford, D.L., 1993. PAUP: Phylogenetic Analysis Using Parsimony, Version 3.1.1. Smithsonian Institution, Washington, DC.
57. Tschiersch, B., Hofmann, A., Krauss, V., Dorn, R., Korge, G., Reuter, G., 1994. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var) 3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J. 13, 3822-3831.
58. Zhang, Q., Wrana, J.L., Sodek, J., Characterization of the promoter region of the porcine opn (osteopontin secreted phosphoprotein 1) gene: identification of positive and negative regulatory elements and a 'silent' second promoter. 1992. Eur. J. Biochem. 207, 649-659.