An anciently diverged family of RNA binding proteins maintain correct splicing of ultra-long exons through cryptic splice site repression

Abstract

AbstractWe previously showed that the germ cell specific nuclear protein RBMXL2 represses cryptic splicing patterns during meiosis and is required for male fertility. It has remained unknown whether RBMXL2 evolved its role in splicing repression to deal with the transcriptionally permissive environment of meiosis or might fulfil a function required in all cells. RBMXL2 evolved from the X-linked RBMX gene, which is silenced during meiosis due to sex chromosome inactivation. Here we find that like RBMXL2, RBMX primarily operates as a splicing repressor in somatic cells, and specifically regulates a distinct class of exons that exceed the median human exon size. RBMX protein-RNA interactions are enriched within ultra-long exons, particularly within genes involved in genome stability, and RBMX represses the selection of cryptic splice sites that would compromise gene function. These similarities in overall function suggested that RBMXL2 during meiosis might replace the otherwise ubiquitous RBMX protein. To test this prediction we carried out inducible expression of RBMXL2 and the more distantly related RBMY protein in somatic cells, finding each could rescue aberrant patterns of RNA processing in response to RBMX depletion. The C-terminal disordered domain of RBMXL2 is sufficient to rescue proper splicing control after RBMX depletion. Our data indicate that RBMXL2 replaces RBMX during meiosis, and these proteins have maintained parallel roles that must have been conserved over at least 200 million years of mammalian evolution. We propose RBMX family proteins are important for the splicing inclusion of ultra-long exons because these are particularly susceptible to disruption by cryptic splice site selection.