Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution
Figure 2
Increased sequence conservation upstream of tissue- and developmentally-regulated NAGNAGs.
(A) NAGNAG ψ estimates are highly consistent in brain RNA-Seq data from the mouse strains DBA/2J and C57BL/6J. Only NAGNAGs with both isoforms expressed at ≥5% in either strain are shown. The 75th percentile of the deviation from the line y = x is shown in gray. (B) NAGNAG ψ estimates are quantitatively conserved between human and mouse brain. Only NAGNAGs with both isoforms expressed at ≥5% in either species and satisfying |proximal 3′ splice site score – distal 3′ splice site score|≤0.5 bits are plotted (splice sites scored by MaxEnt model [36]). Deviation from y = x shown as in (A). (C) Sequence conservation of human NAGNAGs, where all NAGNAGs are aligned by their 3′ splice site junctions and grouped by switch score. Mean (solid line) and standard error of the mean (shaded area about solid line) of phastCons score [50] shown by position (averaged over a 2 nt sliding window) for each switch score category. Analysis restricted to human NAGNAGs for which the two AGs were conserved at the sequence level in mouse. (D) As in (C), but grouped by switch score in mouse and restricted to mouse NAGNAGs for which the two AGs were conserved at the sequence level in human. (E) As in (D), but for NAGNAGs in Drosophila melanogaster, with switch score defined across developmental stages rather than between tissues. Analysis restricted to D. melanogaster NAGNAGs for which the two AGs were conserved at the sequence level in D. yakuba.
