Context-Dependent Function of the Splicing Factor hnRNP L

Based on the number of genes impacted (~95% of humans genes), alternative splicing is one of the most extensively used mechanisms for generating proteomic diversity and cellular complexity. Splicing of pre-mRNAs is carried out by a highly specialized, RNA-based macromolecular enzyme known as the spliceosome. The spliceosome is made up of 5 small nuclear RNP (snRNP) complexes (U1, U2, U4/U6, and U5), all of which consist of a uridine-rich snRNA and multiple proteins. Importantly, the spliceosome is not a pre-formed enzyme but instead forms through the step-wise assembly of the snRNP complexes on the pre-mRNA. Mechanistically, the selection of exons or splice sites during alternative splicing occurs by modulating the assembly of the spliceosome on a pre-mRNA. Ultimately, the decision to include or exclude an exon into the final mRNA is based on the integration of both the synergistic and antagonistic forces between groups of protein regulators and between protein regulators and the snRNP complexes. An excellent model system to illustrate the mechanisms of alternative splicing, as well as the physiologic significance of this mode of regulation, is the human CD45 gene. HnRNP L binds to a motif present in both CD45 variable exons 4 and 5 to affect their coordinate repression. Previously, it was shown that hnRNP L regulates exon 4 by stalling the U1 and U2 snRNPs in a non-permissive A-like exon-defined spliceosomal complex. Here, we show that, in contrast to its direct repression of exon 4, hnRNP L represses exon 5 by countering the activity of a neighboring splicing enhancer element. As the splice sites flanking exon 4 and 5 are distinct, we directly examined the effect of varying splice site strength on the mechanism of hnRNP L function. Remarkably, binding of hnRNP L to an exon represses strong splice sites but enhances weak splice sites. A model in which hnRNP L stabilizes snRNP-binding can explain both effects in a manner determined by the inherent snRNP-substrate affinity. Overall, these findings demonstrate that context can fundamentally alter the activity of a splicing regulatory protein and can therefore impact our predictions of splicing patterns and mechanisms of splicing regulation.