HnRNP L and HnRNP A1 Induce Extended U1 snRNA Interactions with an Exon to Repress Spliceosome Assembly

Pre-mRNA splicing is catalyzed through the activity of the spliceosome, a dynamic enzymatic complex. Forcing aberrant interactions within the spliceosome can reduce splicing efficiency and alter splice site choice; however, it is unknown whether such alterations are naturally exploited mechanisms of splicing regulation. Here, we demonstrate that hnRNP L represses CD45 exon 4 by recruiting hnRNP A1 to a sequence upstream of the 5′ splice site. Together, hnRNP L and A1 induce extended contacts between the 5′ splice site-bound U1 snRNA and neighboring exonic sequences that, in turn, inhibit stable association of U6 snRNA and subsequent catalysis. Importantly, analysis of several exons regulated by hnRNP L shows a clear relationship between the potential for binding of hnRNP A1 and U1 snRNA and the effect of hnRNP L on splicing. Together, our results demonstrate that conformational perturbations within the spliceosome are a naturally occurring and generalizable mechanism for controlling alternative splicing decisions. [Display omitted] ► HnRNP L recruits hnRNP A1 and U1 snRNA to sequences upstream of the 5′ splice site ► HnRNP L-induced extended base pairing of U1 snRNA inhibits exchange for U6 snRNA ► Local traps in spliceosome assembly are naturally exploited mechanisms of regulation ► Extended base pairing of U1 may account for much of regulation by hnRNPs L and A1