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

Michael Brudno, Mikhail S. Gelfand, Sylvia Spengler, Manfred Zorn, Inna Dubchak, John G. Conboy

Research output: Contribution to journalArticlepeer-review

91 Citations (Scopus)


Alternative pre-mRNA splicing is a major cellular process by which functionally diverse proteins can be generated from the primary transcript of a single gene, often in tissue-specific patterns. The current study investigates the hypothesis that splicing of tissue-specific alternative exons is regulated in part by control sequences in adjacent introns and that such elements may be recognized via computational analysis of exons sharing a highly specific 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 analyze key features of these nucleotide sequences. By comparison to a control group of constitutive exons, brain-specific exons were often found to possess the following: divergent 5′ splice sites; highly pyrimidine-rich upstream introns; a paucity of GGG motifs in the downstream intron; a highly statistically significant over-representation of the hexanucleotide UGCAUG in the proximal downstream intron. UGCAUG was also found at a high frequency downstream of a smaller group of muscle-specific exons. Intriguingly, UGCAUG has been identified previously in a few intron splicing enhancers. Our results indicate that this element plays a much wider role than previously appreciated in the regulated tissue-specific splicing of many alternative exons.

Original languageEnglish
Pages (from-to)2338-2348
Number of pages11
JournalNucleic Acids Research
Issue number11
Publication statusPublished - 1 Jun 2001
Externally publishedYes


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