Systematic evaluation of isoform function in literature reports of alternative splicing

Shamsuddin A. Bhuiyan, Sophia Ly, Minh Phan, Brandon Huntington, Ellie Hogan, Chao Chun Liu, James Liu, Paul Pavlidis

Although most genes in mammalian genomes have multiple isoforms, an ongoing debate is whether these isoforms are all functional as well as the extent to which they increase the functional repertoire of the genome. To ground this debate in data, it would be helpful to have a corpus of experimentally-verified cases of genes which have functionally distinct splice isoforms (FDSIs). We established a curation framework for evaluating experimental evidence of FDSIs, and analyzed over 700 human and mouse genes, strongly biased towards genes that are prominent in the alternative splicing literature. Despite this bias, we found experimental evidence meeting the classical definition for functionally distinct isoforms for ~ 5% of the curated genes. If we relax our criteria for inclusion to include weaker forms of evidence, the fraction of genes with evidence of FDSIs remains low (~ 13%). We provide evidence that this picture will not change substantially with further curation and conclude there is a large gap between the presumed impact of splicing on gene function and the experimental evidence. Furthermore, many functionally distinct isoforms were not traceable to a specific isoform in Ensembl, a database that forms the basis for much computational research. We conclude that the claim that alternative splicing vastly increases the functional repertoire of the genome is an extrapolation from a limited number of empirically supported cases. We also conclude that more work is needed to integrate experimental evidence and genome annotation databases. Our work should help shape research around the role of splicing on gene function from presuming large general effects to acknowledging the need for stronger experimental evidence.