Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution
Figure 5
NAGNAGs are associated with accelerated protein evolution at exon-exon boundaries.
(A) Alignment of portions of exons 10 and 11 of TRIM28 gene from three mammals, illustrating a shift in the upstream boundary of exon 11 between human and rodents. Exonic sequence shown in capitals; intronic sequence in lower case. (B) Gain/loss of exonic sequence between human and mouse occurs preferentially at 3′ splice sites (p<10−6, permutation test). The fraction of aligned orthologous human and mouse exons with gaps at each position is shown; the background level (mean fraction across the indicated region excluding the 3′ splice site) is shown by the dotted yellow line; the right-hand axis shows enrichment relative to this background. (C) As in (B), but restricted to gaps of length three bases. Preferential occurrence at 3′ splice sites was highly significant (p<10−6, permutation test). (D) Similar to (C), but based on alignments of orthologous D. melanogaster and D. yakuba exons. Preferential occurrence at 3′ splice sites was highly significant (p<10−6, permutation test). (E) Similar to (C), but based on alignments of orthologous C. elegans and C. briggsae exons. Preferential occurrence at 3′ splice sites was highly significant (p<10−6, permutation test). (F) Residual NAG motif at exons whose boundaries changed in the rodent lineage. Orthologous mouse and rat exons were classified as unchanged (top), expanded by three bases (middle), or contracted by three bases(bottom) based on comparison to an outgroup (human, cow, chicken, or Xenopus laevis), aligned to the inferred location of the ancestral 3′ splice site (dotted line). Information content of each position is shown relative to a uniform background composition. (G) Exons whose 3′ splice site boundaries differ by three bases between rat and mouse are 7.5 times as likely to have a NAGNAG in the human ortholog as exons whose boundaries did not change (p-value for difference<10−24 by Fisher's exact test). Error bars indicate the 95% binomial confidence interval. (H) Rodent exons orthologous to alternatively spliced human NAGNAG exons (left) are much more likely to exhibit exon boundary changes of three base pairs than those orthologous to constitutively spliced human NAGNAGs (right) (p-value for difference<10−10 by Fisher's exact test). Blue and gray bars in (H) represent subsets of blue and gray bars in (G), respectively. Error bars indicate the 95% binomial confidence interval. (I) Frequency of encoded amino acids that occur opposite gaps at the 3′ splice site in alignments of human and mouse exons is plotted above, overall (pink) and separately by the phase of the upstream intron (i.e., the number of bases, if any, in the last incomplete codon of the upstream exon); amino acid frequency at background positions (4 codons downstream of the 3′ splice site) is shown below. The Shannon entropy (a measure of randomness) of each amino acid frequency distribution is also shown.
