The Alternative Choice of Constitutive Exons throughout Evolution

TL;DR

This study uncovers an evolutionary pathway where constitutive exons become alternative splicing variants through splice site relaxation and ESR fixation, increasing transcriptome diversity across species.

Contribution

It reveals a novel mechanism of exon evolution involving splice site relaxation and ESR fixation, expanding understanding of splicing evolution.

Findings

Relaxation of 5' splice site facilitates exon transition to alternative splicing.

ESR fixation controls exon inclusion levels post-transition.

Conservation of ESR effects from fish to humans.

Abstract

Alternative cassette exons are known to originate from two processes exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced exons become alternative cassette exons during evolution. We compiled a dataset of orthologous exons from human and mouse that are constitutively spliced in one species but alternatively spliced in the other. Examination of these exons suggests that the common ancestors were constitutively spliced. We show that relaxation of the 59 splice site during evolution is one of the molecular mechanisms by which exons shift from constitutive to alternative splicing. This shift is associated with the fixation of exonic splicing regulatory sequences (ESRs) that are essential for exon definition and control the inclusion level only after the transition to alternative splicing. The effect of each ESR on splicing and the combinatorial effects between two ESRs are conserved from fish to human. Our results uncover an evolutionary pathway that increases transcriptome diversity by shifting exons from constitutive to alternative splicing