A computational and experimental approach toward a priori identification of alternatively spliced exons

RNA

Volumn 10, Issue 12, 2004, Pages 1838-1844

  Philipps, Dana L ^a,b   Park, Jung W ^a   Graveley, Brenton R ^a  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

^b Cornell University ^*  (United States)

Author keywords

Alternative splicing; Bioinformatics; Comparative genomics; Drosophila

Indexed keywords

DNA; MESSENGER RNA; MESSENGER RNA PRECURSOR; PROTEOME;

ARTICLE; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA PSEUDOOBSCURA; EXON; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE EXPRESSION REGULATION; GENETIC CONSERVATION; GENOMICS; METAZOON; NONHUMAN; PRIORITY JOURNAL; PROTEIN VARIANT; RNA SPLICING;

ALTERNATIVE SPLICING; ANIMALS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DROSOPHILA; DROSOPHILA MELANOGASTER; EXONS; EXPRESSED SEQUENCE TAGS; FEMALE; GENOMICS; MALE; SPECIES SPECIFICITY;

DROSOPHILA MELANOGASTER; DROSOPHILA PSEUDOOBSCURA; MELANOGASTER; METAZOA;

EID: 9344228450     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7136104     Document Type: Article

References (22)

1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, I.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F., et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Black, D.L. 2000. Protein diversity from alternative splicing: A challenge for bioinformatics and post-genome biology. Cell 103: 367-370.
3. Delaunay, J., Le Mee, G., Ezzeddine, N., Labesse, G., Terzian, C., Capri, M., and Ait-Ahmed, O. 2004. The Drosophila Bruno paralogue Bru-3 specifically binds the EDEN translational repression element. Nucleic Acids Res. 32: 3070-3082.
4. Forch, P. and Valcarcel, J. 2003. Splicing regulation in Drosophila sex determination. Prog. Mol. Subcell. Biol. 31: 127-151.
5. Graveley, B.R. 2001. Alternative splicing: Increasing diversity in the proteomic world. Trends Genet. 17: 100-107.
6. Graveley, B.R., Kaur, A., Gunning, D., Zipursky, S.L., Rowen, L., and Clemens, J.C. 2004. The organization and evolution of the Dipteran and Hymenopteran Down syndrome cell adhesion molecule (Dscam) genes. RNA 10: 1499-1506.
7. Jackson, V.N., Cameron, J.M., Zammit, V.A., and Price, N.T. 1999. Sequencing and functional expression of the malonyl-CoA-sensitive carnitine palmitoyltransferase from Drosophila melanogaster. Biochem. J. 341: 483-489.
8. Johnson, J.M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P.M., Armour, C.D., Santos, R., Schadt, E.E., Stoughton, R., and Shoemaker, D.D. 2003. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302: 2141-2144.
9. Lewis, B.P., Green, R.E., and Brenner, S.E. 2003. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl. Acad. Sci. 100: 189-192.
10. Mayor, C., Brudno, M., Schwartz, J.R., Poliakov, A., Rubin, E.M., Frazer, K.A., Pachter, L.S., and Dubchak, I. 2000. VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16: 1046-1047.
11. Miki, H., Setou, M., Kaneshiro, K., and Hirokawa, N. 2001. All kinesin superfamily protein, KIF, genes in mouse and human. Proc. Natl. Acad. Sci. 98: 7004-7011.
12. Misra, S., Crosby, M.A., Mungall, C.J., Matthews, B.B., Campbell, K.S., Hradecky, P., Huang, Y., Kaminker, J.S., Millburn, G.H., Prochnik, S.E., et al. 2002. Annotation of the Drosophila melanogaster euchromatic genome: A systematic review. Genome Biol. 3: RESEARCH0083.
13. Modrek, B. and Lee, C.J. 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.
14. Modrek, B., Resch, A., Grasso, C., and Lee, C. 2001. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 29: 2850-2859.
15. Powell, J.R. 1997. Progress and prospects in evolutionary biology: The Drosophila model. Oxford University Press, NY.
16. Resch, A., Xing, Y., Alekseyenko, A., Modrek, B., and Lee C. 2004. Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Res. 32: 1261-1269.
17. Russo, C.A., Takezaki, N., and Nei, M. 1995. Molecular phylogeny and divergence times of drosophilid species. Mol. Biol. Evol. 12: 391-404.
18. Schmucker, D., Clemens, J.C., Shu, H., Worby, C.A., Xiao, J., Muda, M., Dixon, J.E., and Zipursky, S.L. 2000. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101:671-684.
19. Sorek, R. and Ast, G. 2003. Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res. 13: 1631-1637.
20. Sugnet, C.W., Kent, W.J., Ares Jr., M., and Haussler, D. 2004. Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac. Symp. Biocomput. 66-77.
21. Takeshima, H., Nishi, M., Iwabe, N., Miyata, T., Hosoya, T., Masai, I., and Hotta, Y. 1994. Isolation and characterization of a gene for a ryanodine receptor/calcium release channel in Drosophila melanogaster. FEBS Lett. 337: 81-87.
22. zur Lage, P., Shrimpton, A.D., Flavell, A.J., Mackay, T.F., and Brown, A.J. 1997. Genetic and molecular analysis of smooth, a quantitative trait locus affecting bristle number in Drosophila melanogaster. Genetics 146: 607-618.