Projects per year
Abstract
Background: In mammals, splice-regulatory domains impose marked trends on the relative abundance of certain amino acids near exon-intron boundaries. Is this a mammalian particularity or symptomatic of exonic splicing regulation across taxa? Are such trends more common in species that a priori have a harder time identifying exon ends, that is, those with pre-mRNA rich in intronic sequence? We address these questions surveying exon composition in a sample of phylogenetically diverse genomes. Results: Biased amino acid usage near exon-intron boundaries is common throughout the metazoa but not restricted to the metazoa. There is extensive cross-species concordance as to which amino acids are affected, and reduced/elevated abundances are well predicted by knowledge of splice enhancers. Species expected to rely on exon definition for splicing, that is, those with a higher ratio of intronic to coding sequence, more introns per gene and longer introns, exhibit more amino acid skews. Notably, this includes the intron-rich basidiomycete Cryptococcus neoformans, which, unlike intron-poor ascomycetes (Schizosaccharomyces pombe, Saccharomyces cerevisiae), exhibits compositional biases reminiscent of the metazoa. Strikingly, 5 prime ends of nematode exons deviate radically from normality: amino acids strongly preferred near boundaries are strongly avoided in other species, and vice versa. This we suggest is a measure to avoid attracting trans-splicing machinery. Conclusion: Constraints on amino acid composition near exon-intron boundaries are phylogenetically widespread and characteristic of species where exon localization should be problematic. That compositional biases accord with sequence preferences of splice-regulatory proteins and are absent in ascomycetes is consistent with selection on exonic splicing regulation.
Original language | English |
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Article number | R29 |
Journal | Genome Biology |
Volume | 9 |
Issue number | 2 |
DOIs | |
Publication status | Published - 7 Feb 2008 |
Bibliographical note
ID number: ISI:000254659300011Fingerprint
Dive into the research topics of 'Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes'. Together they form a unique fingerprint.Projects
- 1 Finished
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COOPERATIVE GROUP IN ORGANOGENESIS, GROWTH AND REGENERATION
Ward, A. (PI), Holman, G. (CoI), Hurst, L. (CoI), Kelsh, R. (CoI), Slack, J. (CoI) & Tosh, D. (CoI)
21/06/04 → 20/06/09
Project: Research council