Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes

RNA

Volumn 10, Issue 7, 2004, Pages 1005-1018

  Itoh, Hitomi ^a   Washio, Takanori ^a,b   Tomita, Masaru ^a  

^a KEIO UNIVERSITY   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

Alternative splicing; ESEs; Exonic splicing enhancers; Splice site strength

Indexed keywords

COMPLEMENTARY DNA;

ARABIDOPSIS; ARTICLE; COMBINATORIAL LIBRARY; COMPARATIVE ANATOMY; DNA MICROARRAY; DROSOPHILA MELANOGASTER; EUKARYOTE; EXON; GENETIC VARIABILITY; HUMAN; MAMMAL; MOLECULAR CLONING; MUS MUSCULUS; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; REGULATORY SEQUENCE; RICE; RNA SPLICING;

ALTERNATIVE SPLICING; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; DNA, COMPLEMENTARY; DROSOPHILA MELANOGASTER; EVOLUTION; EXONS; HUMANS; INTRONS; MICE; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; REGULATORY SEQUENCES, NUCLEIC ACID; SPECIES SPECIFICITY;

ARABIDOPSIS; ARABIDOPSIS THALIANA; DROSOPHILA MELANOGASTER; EUKARYOTA; HOMO; HOMO SAPIENS; MAMMALIA; MELANOGASTER; MUS; MUS MUSCULUS; MUSCULUS; ORYZA SATIVA;

EID: 3042675114     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5221604     Document Type: Article

References (35)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Blanchette, M. and Tompa, M. 2002. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12: 739-748.
3. Cartegni, L. and Krainer, A.R. 2002. Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat. Genet. 30: 377-384.
4. Claverie, J.M. 2001. Gene number. What if there are only 30,000 human genes? Science 291: 1255-1257.
5. Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A., and Johnston, M. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
6. Fairbrother, W.G., Yeh, R.F., Sharp, P.A., and Burge, C.B. 2002. Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007-1013.
7. Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., and Miller, W. 1998. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8: 967-974.
8. Graveley, B.R. 2000. Sorting out the complexity of SR protein functions. RNA 6: 1197-1211.
9. Khan, S.G., Muniz-Medina, V., Shahlavi, T., Baker, C.C., Inui, H., Ueda, T., Emmert, S., Schneider, T.D., and Kraemer, K.H. 2002. The human XPC DNA repair gene: Arrangement, splice site information content and influence of a single nucleotide polymorphism in a splice acceptor site on alternative splicing and function. Nucleic Acids Res. 30: 3624-3631.
10. Kochiwa, H., Suzuki, R., Washio, T., Saito, R., Bono, H., Carninci, P., Okazaki, Y., Miki, R., Hayashizaki, Y., and Tomita, M. 2002. Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome Res. 12: 1286-1293.
11. Lim, L.P. and Burge, CB. 2001. A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. 98: 11193-11198.
12. McCue, L.A., Thompson, W., Carmack, C.S., and Lawrence, C.E. 2002. Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res. 12: 1523-1532.
13. McCullough, A.J., Lou, H., and Schuler, M.A. 1993. Factors affecting authentic 5′ splice site selection in plant nuclei. Mol. Cell. Biol. 13: 1323-1331.
14. McKeown, M. 1992. Alternative mRNA splicing. Annu. Rev. Cell Biol. 8: 133-155.
15. Michelet, B. and Boutry, M. 1995. The plasma membrane H+-ATPase (a highly regulated enzyme with multiple physiological functions). Plant Physiol. 108: 1-6.
16. Mironov, A.A., Fickett, J.W., and Gelfand, M.S. 1999. Frequent alternative splicing of human genes. Genome Res. 9: 1288-1293.
17. Modrek, B. and Lee, C. 2002. A genomic view of alternative splicing. Nat. Genet. 30: 13-19.
18. -. 2003. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat. Genet. 34: 177-180.
19. Moller, L.B., Turner, Z., Lund, C., Petersen, C., Cole, T., Hanusch, R., Seidel, J., Jensen, L.R., and Horn, N. 2000. Similar splice-site mutations of the ATP7A gene lead to different phenotypes: Classical Menkes disease or occipital horn syndrome. Am. J. Hum. Genet. 66: 1211-1220.
20. Pagani, F., Stuani, C., Tzetis, M., Kanavakis, E., Efthymiadou, A., Doudounakis, S., Casals, T., and Baralle, F.E. 2003. New type of disease causing mutations: The example of the composite exonic regulatory elements of splicing in CFTR exon 12. Hum. Mol. Genet. 12: 1111-1120.
21. Rogan, P.K. and Schneider, T.D. 1995. Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites. Hum. Mutat. 6: 74-76.
22. Schneider, T.D. 1997. Information content of individual genetic sequences. J. Theor. Biol. 189: 427-441.
23. Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama, K., Oono, Y., et al. 2002. Functional annotation of a full-length Arabidopsis cDNA collection. Science 296: 141-145.
24. Shapiro, M.B. and Senapathy, P. 1987. RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression. Nucleic Acids Res. 15: 7155-7174.
25. Sorek, R. and Safer, H.M. 2003. A novel algorithm for computational identification of contaminated EST libraries. Nucleic Acids Res. 31: 1067-1074.
26. Sorek, R., Shamir, R., and Ast, G. 2004. How prevalent is functional alternative splicing in the human genome? Trends Genet. 20: 68-71.
27. Stamm, S., Zhang, M.Q., Marr, T.G., and Helfman, D.M. 1994. A sequence compilation and comparison of exons that are alternatively spliced in neurons. Nucleic Acids Res. 22: 1515-1526.
28. Stapleton, M., Carlson, J., Brokstein, P., Yu, C., Champe, M., George, R., Guarin, H., Kronmiller, B., Pacleb, J., Park, S., et al. 2002. A Drosophila full-length cDNA resource. Genome Biol. 3: research0080. 0081-0080.0088.
29. Stephens, R.M. and Schneider, T.D. 1992. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J. Mol. Biol. 228: 1124-1136.
30. Szathmary, E., Jordan, F., and Pal, C. 2001. Molecular biology and evolution. Can genes explain biological complexity? Science 292: 1315-1316.
31. Tacke, R. and Manley, J.L. 1995. The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J. 14: 3540-3551.
32. Tacke, R., Tohyama, M., Ogawa, S., and Manley, J. 1998. Human Tra2 proteins are sequence-specific activators of pre-mRNA splicing. Cell 93: 139-148.
33. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
34. 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.
35. Zavolan, M., van Nimwegen, E., and Gaasterland, T. 2002. Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome Res. 12: 1377-1385.