Signatures of domain shuffling in the human genome

Genome Research

Volumn 12, Issue 11, 2002, Pages 1642-1650

  Kaessmann, Henrik ^a   Zöllner, Sebastian ^a   Nekrutenko, Anton ^a   Li, Wen Hsiung ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DATA ANALYSIS; EUKARYOTE; EXON; GENE REARRANGEMENT; GENETIC CODE; HUMAN; HUMAN GENOME; INTRON; METAZOON; NONHUMAN; PRIORITY JOURNAL; PROGENOTE; PROKARYOTE; PROTEIN DOMAIN; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ANIMALS; CAENORHABDITIS ELEGANS PROTEINS; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; EXONS; GENOME, HUMAN; HUMANS; INTRONS; PROTEIN STRUCTURE, TERTIARY; PROTEOME;

CAENORHABDITIS; CAENORHABDITIS ELEGANS; EUKARYOTA; METAZOA; PROKARYOTA;

EID: 0036851263     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.520702     Document Type: Article

References (44)

1. Andrade, M.A., Perez-Iratxeta, C., and Ponting, C.P. 2001. Protein repeats: Structures, functions, and evolution. J. Struct. Biol. 134: 117-131.
2. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276-280.
3. Beckmann, G. and Bork, P. 1993. An adhesive domain detected in functionally diverse receptors. Trends Biochem. Sci. 18: 40-41.
4. Betts, M.J., Guigo, R., Agarwal, P., and Russell, R.B. 2001. Exon structure conservation despite low sequence similarity: A relic of dramatic events in evolution? EMBO J. 20: 5354-5360.
5. Cavalier-Smith, T. 1985. Selfish DNA and the origin of introns. Nature 315: 283-284.
6. Copley, R.R., Doerks, T., Letunic, I., and Bork, P. 2002. Protein domain analysis in the era of complete genomes. FEBS Lett. 513: 129-134.
7. de Souza, S.J., Long, M., Schoenbach, L., Roy, S.W., and Gilbert, W. 1996. Intron positions correlate with module boundaries in ancient proteins. Proc. Natl. Acad. Sci. 93: 14632-14636.
8. de Souza, S.J., Long, M., Schoenbach, L., Roy, S.W., and Gilbert, W. 1997. The correlation between introns and the three-dimensional structure of proteins. Gene 205: 141-144.
9. de Souza, S.J., Long, M., Klein, R.J., Roy, S., Lin, S., and Gilbert, W. 1998. Toward a resolution of the introns early/late debate: Only phase zero introns are correlated with the structure of ancient proteins. Proc. Natl. Acad. Sci. 95: 5094-5099.
10. Deutsch, M. and Long, M. 1999. Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 27: 3219-3228.
11. Doolittle, W.F. 1978. Genes in pieces: Were they ever together? Nature 272: 581-582.
12. Elofsson, A. and Sonnhammer, E.L. 1999. A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics 15: 480-500.
13. Fedorov, A., Fedorova, L., Starshenko, V., Filatov, V., and Grigor'ev, E. 1998. Influence of exon duplication on intron and exon phase distribution. J. Mol. Evol. 46: 263-271.
14. Fedorov, A., Cao, X., Saxonov, S., de Souza, S.J., Roy, S.W., and Gilbert, W. 2001. Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns. Proc. Natl. Acad. Sci. 98: 13177-13182.
15. Gilbert, W. 1987. The exon theory of genes. Cold Spring Harb. Symp. Quant. Biol. 52: 901-905.
16. Gluecksmann-Kuis, M.A., Tayber, O., Woolf, E.A., Bougueleret, L., Deng, N., Alperin, G.D., Iris, F., Hawkins, F., Munro, C., Lakey, N., et al. 1995. Polycystic kidney disease: The complete structure of the PKD1 gene and its protein. The International Polycystic Kidney Disease Consortium. Cell 81: 289-298.
17. Go, M. and Nosaka, M. 1987. Protein architecture and the origin of introns. Cold Spring Harb. Symp. Quant. Biol. 52: 915-924.
18. Goodier, J.L., Ostertag, E.M., and Kazazian, H.H. 2000. Transduction of 3′-flanking sequences is common in L1 retrotransposition. Hum. Mol. Genet. 9: 653-657.
19. Graur, D. and Li, W.H. 1999. Fundamentals of molecular evolution. Sinauer Associates, Sunderland, MA.
20. Gu, Z., Cavalcanti, A., Chen, F.C., Bouman, P., and Li, W.H. 2002. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol. 19: 256-262.
21. Hickey, D.A. and Benkel, B. 1986. Introns as relict retrotransposons: Implications for the evolutionary origin of eukaryotic mRNA splicing mechanisms. J. Theor. Biol. 121: 283-291.
22. Hide, W.A., Babenko, V.N., van Heusden, P.A., Seoighe, C., and Kelso, J.F. 2001. The contribution of exon-skipping events on chromosome 22 to protein coding diversity. Genome Res. 11: 1848-1853.
23. Hubbard, T., Barker, D., Birney, E., Cameron, G., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen, V., Down, T., et al. 2002. The Ensembl genome database project. Nucleic Acids Res. 30: 38-41.
24. Kazazian Jr., H.H., 2000. Genetics. L1 retrotransposons shape the mammalian genome. Science 289: 1152-1153.
25. Koonin, E.V., Aravind, L., and Kondrashov, A.S. 2000. The impact of comparative genomics on our understanding of evolution. Cell 101: 573-576.
26. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C. Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
27. Li, W.H., Gu, Z., Wang, H., and Nekrutenko, A. 2001. Evolutionary analyses of the human genome. Nature 409: 847-849.
28. Long, M., de Souza, S.J., and Gilbert, W. 1995a. Evolution of the intron-exon structure of eukaryotic genes. Curr. Opin. Genet. Dev. 5: 774-778.
29. Long, M., Rosenberg, C., and Gilbert, W. 1995b. Intron phase correlations and the evolution of the intron/exon structure of genes. Proc. Natl. Acad. Sci. 92: 12495-12499.
30. Lynch, M. 2002. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. 99: 6118-6123.
31. Moran, J.V., DeBerardinis, R.J., and Kazazian Jr., H.H., 1999. Exon shuffling by L1 retrotransposition. Science 283: 1530-1534.
32. Orgel, L.E. and Crick, F.H. 1980. Selfish DNA: The ultimate parasite. Nature 284: 604-607.
33. Patthy, L. 1999a. Genome evolution and the evolution of exon-shuffling-a review. Gene 238: 103-114.
34. Patthy, L. 1999b. Protein evolution, p. 228. Blackwell Science, Oxford, UK.
35. Pawson, T. and Nash, P. 2000. Protein-protein interactions define specificity in signal transduction. Genes & Dev. 14: 1027-1047.
36. Pickeral, O.K., Makalowski, W., Boguski, M.S., and Boeke, J.D. 2000. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res. 10: 411-415.
37. Roy, S.W., Nosaka, M., de Souza, S.J., and Gilbert, W. 1999. Centripetal modules and ancient introns. Gene 238: 85-91.
38. Rubin, G.M., Yandell, M.D., Wortman, J.R., Gabor Miklos, G.L., Nelson, C.R., Hariharan, I.K., Fortini, M.E., Li, P.W., Apweiler, R., Fleischmann, W., et al. 2000. Comparative genomics of the eukaryotes. Science 287: 2204-2215.
39. Sakharkar, M., Passetti, F., de Souza, J.E., Long, M., and de Souza, S.J. 2002. ExInt: An exon intron database. Nucleic Acids Res. 30: 191-194.
40. Sharp, P.A. 1985. On the origin of RNA splicing and introns. Cell 42: 397-400.
41. Tomita, M., Shimizu, N., and Brutlag, D.L. 1996. Introns and reading frames: Correlation between splicing sites and their codon positions. Mol. Biol. Evol. 13: 1219-1223.
42. Tordai, H., Banyai, L., and Patthy, L. 1999. The PAN module: The N-terminal domains of plasminogen and hepatocyte growth factor are homologous with the apple domains of the prekallikrein family and with a novel domain found in numerous nematode proteins. FEBS Lett. 461: 63-67.
43. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., and Yandell, M. 2001. The sequence of the human genome. Science 291: 1304-1351.
44. Zdobnov, E.M. and Apweiler, R. 2001. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.