Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes.
We previously reported a computational approach to infer alternative splicing patterns from Mus musculus full-length cDNA clones and microarray data. Although we predicted a large number of unreported splice variants, the general mechanisms regulating alternative splicing were yet unknown. In the present study, we compared alternative exons and constitutive exons in terms of splice-site strength and frequency of potential regulatory sequences. These regulatory features were further compared among five different species: Homo sapiens, M. musculus, Arabidopsis thaliana, Oryza sativa, and Drosophila melanogaster. Solid statistical validations of our comparative analyses indicated that alternative exons have (1) weaker splice sites and (2) more potential regulatory sequences than constitutive exons. Based on our observations, we propose a combinatorial model of alternative splicing mechanisms, which suggests that alternative exons contain weak splice sites regulated alternatively by potential regulatory sequences on the exons.
Itoh
Hitomi
H
Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan.
Washio
Takanori
T
Tomita
Masaru
M
D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D017124:Conserved Sequence; D018076:DNA, Complementary / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics; D005091:Exons / Q000235:genetics; D006801:Humans; D007438:Introns / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid; D013045:Species Specificity
D018076:DNA, Complementary