Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing

Alternative pre-mRNA splicing is a major cellular process by which function ally diverse proteins can be generated from the primary transcript of a sin gle gene, often in tissue-specific patterns. The current study investigates the hypothesis that splicing of tissue-specific alternative exons is regul ated in part by control sequences in adjacent introns and that such element s may be recognized via computational analysis of exons sharing a highly sp ecific expression pattern. We have identified 25 brain-specific alternative cassette exons, compiled a dataset of genomic sequences encompassing these exons and their adjacent introns and used word contrast algorithms to anal yze key features of these nucleotide sequences. By comparison to a control group of constitutive exons, brain-specific exons were often found to posse ss the following: divergent 5' splice sites; highly pyrimidine-rich upstrea m introns; a paucity of GGG motifs in the downstream intron; a highly stati stically significant over-representation of the hexanucleotide UGCAUG in th e proximal downstream intron, UGCAUG was also found at a high frequency dow nstream of a smaller group of muscle-specific exons, Intriguingly, UGCAUG h as been identified previously in a few intron splicing enhancers. Our resul ts indicate that this element plays a much wider role than previously appre ciated in the regulated tissue-specific splicing of many alternative exons.