The Arabidopsis U1 snRNP regulates mRNA 3'-end processing

Abstract

The removal of introns by the spliceosome is a key gene regulatory mechanism in eukaryotes, with the U1 snRNP subunit playing a crucial role in the early stages of splicing. Studies in metazoans show that the U1 snRNP also conducts splicing-independent functions, but the lack of genetic tools and knowledge about U1 snRNP-associated proteins have limited the study of such splicing-independent functions in plants. Here we describe an RNA-centric approach that identified more than 200 proteins associated with the Arabidopsis U1 snRNP and revealed a tight link to mRNA cleavage and polyadenylation factors. Interestingly, we found that the U1 snRNP protects mRNAs against premature cleavage and polyadenylation within introns—a mechanism known as telescripting in metazoans—while also influencing alternative polyadenylation site selection in 3′-UTRs. Overall, our work provides a comprehensive view of U1 snRNP interactors and reveals novel functions in regulating mRNA 3′-end processing in Arabidopsis, laying the groundwork for understanding non-canonical functions of plant U1 snRNPs.