Mechanism of an alternative splicing switch mediated by cell-specific and general splicing regulators

Abstract

Alternative pre-mRNA splicing is regulated by RNA binding proteins (RBPs) that activate or repress regulated splice sites. Repressive RBPs bind stably to target RNAs via multivalent interactions, which can be achieved by both homo-oligomerization and by interactions with other RBPs mediated by intrinsically disordered regions (IDRs). Cell-specific splicing decisions commonly involve the action of widely expressed RBPs that can bind around target exons, but without effect in the absence of a key cell-specific regulator. To address how cell-specific regulators collaborate with constitutive RBPs in alternative splicing regulation we used the smooth-muscle specific regulator RBPMS. Recombinant RBPMS is sufficient to switch cell specific alternative splicing of Tpm1 exon 3 in cell free assays by remodelling ribonucleprotein complexes and preventing assembly of ATP-dependent splicing complexes. This activity depends upon its C-terminal IDR, which facilitates dynamic higher-order self-assembly, cooperative binding to multivalent RNA, and interactions with other splicing co-regulators, including MBNL1 and RBFOX2. Our data show how a cell-specific RBP can co-opt more widely expressed regulatory RBPs to facilitate cooperative assembly of stable cell-specific regulatory complexes.