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Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes


Reference:

Warnecke, T., Parmley, J. L. and Hurst, L. D., 2008. Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes. Genome Biology, 9 (2), R29.

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    Official URL:

    http://dx.doi.org/10.1186/gb-2008-9-2-r29

    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.

    Details

    Item Type Articles
    CreatorsWarnecke, T., Parmley, J. L. and Hurst, L. D.
    DOI10.1186/gb-2008-9-2-r29
    DepartmentsFaculty of Science > Biology & Biochemistry
    Publisher Statementgb-2008-9-2-r29.pdf: © 2008 Warnecke et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    RefereedYes
    StatusPublished
    ID Code3405
    Additional InformationID number: ISI:000254659300011

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