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Splice junctions are constrained by protein disorder.

Smithers B, Oates ME, Gough J - Nucleic Acids Res. (2015)

Bottom Line: Thus we infer that it is the positions of splice junctions in the gene that must be under constraint by the local protein environment.Examining exonic splicing enhancers found near the splice junction in the gene, reveals that these (short DNA motifs) are more prevalent in exons that encode disordered protein regions than exons encoding structured regions.Thus we also conclude that local protein features constrain efficient splicing more in structure than in disorder.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK ben.smithers@bristol.ac.uk.

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Selected examples of the distribution of rho values for the correlation in amino acid usage with distance from splice junction in exons from six taxonomic groups of eukaryotic genomes. Groups are ordered by the number of genomes they contain. (I) Correlation of Serine usage at the start of exons. (II) Correlation of Serine usage at the end of exons. (III) Correlation of Lysine usage at the end of exons. (IV) Correlation of Proline usage at the end of exons. For full results, see http://bioinformatics.bris.ac.uk/people/ben_smithers/splicing.
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Figure 6: Selected examples of the distribution of rho values for the correlation in amino acid usage with distance from splice junction in exons from six taxonomic groups of eukaryotic genomes. Groups are ordered by the number of genomes they contain. (I) Correlation of Serine usage at the start of exons. (II) Correlation of Serine usage at the end of exons. (III) Correlation of Lysine usage at the end of exons. (IV) Correlation of Proline usage at the end of exons. For full results, see http://bioinformatics.bris.ac.uk/people/ben_smithers/splicing.

Mentions: We compared the amino acids that are preferred or avoided near splice junctions between six different taxonomic groups and found that most trends are consistent, with some notable exceptions. Figure 6 shows some illustrative examples of the distribution of correlation coefficients for each taxonomic grouping; results for all amino acids and each exon class can be found online at http://bioinformatics.bris.ac.uk/people/ben_smithers/splicing.


Splice junctions are constrained by protein disorder.

Smithers B, Oates ME, Gough J - Nucleic Acids Res. (2015)

Selected examples of the distribution of rho values for the correlation in amino acid usage with distance from splice junction in exons from six taxonomic groups of eukaryotic genomes. Groups are ordered by the number of genomes they contain. (I) Correlation of Serine usage at the start of exons. (II) Correlation of Serine usage at the end of exons. (III) Correlation of Lysine usage at the end of exons. (IV) Correlation of Proline usage at the end of exons. For full results, see http://bioinformatics.bris.ac.uk/people/ben_smithers/splicing.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4446445&req=5

Figure 6: Selected examples of the distribution of rho values for the correlation in amino acid usage with distance from splice junction in exons from six taxonomic groups of eukaryotic genomes. Groups are ordered by the number of genomes they contain. (I) Correlation of Serine usage at the start of exons. (II) Correlation of Serine usage at the end of exons. (III) Correlation of Lysine usage at the end of exons. (IV) Correlation of Proline usage at the end of exons. For full results, see http://bioinformatics.bris.ac.uk/people/ben_smithers/splicing.
Mentions: We compared the amino acids that are preferred or avoided near splice junctions between six different taxonomic groups and found that most trends are consistent, with some notable exceptions. Figure 6 shows some illustrative examples of the distribution of correlation coefficients for each taxonomic grouping; results for all amino acids and each exon class can be found online at http://bioinformatics.bris.ac.uk/people/ben_smithers/splicing.

Bottom Line: Thus we infer that it is the positions of splice junctions in the gene that must be under constraint by the local protein environment.Examining exonic splicing enhancers found near the splice junction in the gene, reveals that these (short DNA motifs) are more prevalent in exons that encode disordered protein regions than exons encoding structured regions.Thus we also conclude that local protein features constrain efficient splicing more in structure than in disorder.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK ben.smithers@bristol.ac.uk.

Show MeSH