Calarco et al 2007 - University of Toronto

Downloaded from genesdev.cshlp.org on June 10, 2013 - Published by Cold Spring Harbor Laboratory PressCalarco et al.Figure 2. Quantitative alternative splicing microarray profilingreveals the extent of alternative splicing differences betweenhuman and chimpanzee orthologous exons, as well as the degreeof divergence between splicing patterns over different evolutionarytime periods. (A) Color spectrum plots indicating thenumber and magnitude of alternative splicing differences betweenhuman and chimpanzee frontal cortex and heart tissues.The Y-axes indicate the number of alternative splicing eventsprofiled; these are sorted according to the magnitude of the absolutevalue of the percent exon inclusion level (%in) differencebetween the human and chimpanzee tissue being compared.The magnitude of the percentage inclusion difference is indicatedby the color scale on the right. (B) Cumulative distributionplot displaying the distribution of percentage inclusion differenceswhen comparing microarray data for 217 conservedalternative splicing events between the following pairs of tissues:human and chimpanzee frontal cortex (blue line), humanand chimpanzee heart (red line), human frontal cortex andmouse cortex (green line), and human and mouse heart (purpleline). (C) Spearman correlation coefficients are shown for pairwisecomparisons between alternative splicing levels (blacknumbers) and transcript levels (purple numbers) for the set of217 orthologous genes analyzed in human, chimpanzee, andmouse tissues in B. Double arrows indicate the pairs of speciescompared. (Hs) Homo sapiens; (Pt) Pan troglodytes; (Mm) Musmusculus.despite the remarkable degree of conservation betweenthe coding regions of the human and chimpanzee genomes,a substantial number of alternative exons thatare not associated with high substitution rates in thealternative exons and flanking intron regions displaypronounced splicing level differences between the twospecies.Evidence for stabilizing selection pressure acting topreserve the majority of splicing levels of orthologoushuman, chimpanzee, and mouse alternative exonsThe similarity between the splicing levels for the majorityof the profiled orthologous exons could reflect stabilizingselection pressure acting to conserve the inclusionlevels of most human and chimpanzee orthologous exons.However, it is also possible that insufficient evolutionarytime has accumulated to result in a higher incidenceof pronounced inclusion level differences than observedabove. To investigate these possibilities, wecompared the extent of divergence between alternativesplicing profiles representing a longer evolutionary timespan, namely the 80- to 90-million-year period separatingthe common ancestor of human or chimpanzee andmouse. Percent inclusion values for 217 alternativesplicing events conserved between humans and themouse were obtained from RT–PCR-validated, quantitativealternative splicing microarray profiling data frommouse heart and brain cortex tissues (Fagnani et al. 2007)and compared with percent inclusion values from thehuman and chimpanzee datasets described above (Fig.2B,C; see the Supplemental Material).Notably, although the splicing levels of the mouse exonsare also very similar to the orthologous exons in thecorresponding human and chimpanzee tissues, they havediverged to a significantly greater extent in both tissues(P