Transiently depleting RNPS1 leads to perdurable changes in alternative splicing

Abstract

While robust regulatory mechanisms are expected to control the production of splice variants that confer distinct functions, a low level of stochasticity may be tolerated. To investigate stringency of regulation, we followed changes in the splicing of 192 alternative cassette exons after growth of cancer-derived HCT116 cells and embryonic colonocytes. In both cell lines approximately 15% of alternative splicing events changed by more than 10 percentage points over a 42-day period. We then carried out a cycle of transient depletions targeting RNPS1, a splicing regulator implicated in genomic stability. For alternative splicing units not regulated by RNPS1, the level of splicing changes was similar to the stochastic value obtained after normal growth. However, the frequency of perdurable changes was at least twice that value for splicing events regulated by RNPS1. A swap allele assay performed on four RNPS1-responsive units that underwent splicing changes indicated the presence of mutations mediating this effect. Specifically, a T to C mutation in a RNPS1-responsive exon of ADARB1 confered exon skipping. Our results suggest that fluctuations in the level of a splicing regulator preferentially impact the integrity of genes encoding transcripts that are regulated by this splicing factor to produce perdurable changes in alternative splicing. We discuss the potential implication of this process in human evolution.