Does Conservation Account for Splicing Patterns?

A computational model is presented that predicts absolute (though not tissue-differential) percent-spliced-in of cassette exons more accurately than previous models. Nearly identical performance is achieved using only the conservation score (mammalian phastCons) of each splice junction normalized by average conservation over 100 bp of the corresponding flanking intron. Evidence is provided that splicing regulation occurs predominantly in these averaging regions, and that conserved elements there are splicing regulators, predominantly inhibitors. Among conserved cassette exons, increased conservation of flanking introns is associated with reduced inclusion, suggesting one mechanism for the evolutionary transition from constitutive to alternative splicing is the emergence of cis-acting splicing inhibitors. A new definition is proposed for intronic splicing regulatory elements (ISREs) that is independent of conservation. Most ISREs do not match known binding sites or splicing factors despite being predictive of percent-spliced-in, suggesting the existence of novel RNA-binding proteins and novel splicing roles for known RNA-binding proteins.M.A.S