MBNL1 and RBFOX1 co-regulate alternative splicing events transcriptome-wide through a conserved buffering mechanism

Alternative splicing (AS) is an important component of RNA processing controlled by cis- and trans-acting component. Here we investigate modes and mechanisms of AS co-regulation by MBNL1 and RBFOX1. We generated two cell models (human and mouse) whereby the expression of both RBPs can be independently modulated and utilize these cell lines to perform RNAseq and transcriptome wide alternative splicing analysis. Categorization of alternative splicing outcomes of the impacts of RBFOX1 expression on MBNL1 splicing revealed a common co-regulatory mode whereby RBFOX1 buffers MBNL1 dose-dependent splicing regulation by reducing the total range of exon inclusion induced. Overall, our studies define a conserved co-regulatory mechanism through which RBFOX1 and MBNL1 can fine-tune and provide redundancy for AS outcomes. Analysis of alternative splicing changes in the presence or absence of MBNL1 and RBFOX1 in human embyonic kidney and mouse embryonic fibroblasts