The Evolutionarily Conserved AU-Dinucleotide at the 5’ End of U1 snRNA is Critical for the Biogenesis and Functionality of U1 snRNP

Splicing is initiated by a productive interaction of pre-mRNA and the U1 snRNP, which dictates the formation a short RNA duplex between the 5’ splice site of a pre-mRNA and the 5’ end of the U1 snRNA. A long-standing puzzle has been why the AU dincucleotide at the 5’-end of the U1 snRNA shows strict conservation, despite the absence of an apparent role in duplex formation. To explore this conundrum, we varied this AU dinucleotide into to all possible permutations and analyzed the resulting molecular, biochemical, and physiological consequences. This led to the findings that the AU dinucleotide governs the precision of transcription start site, the methylation status of the U1 snRNA 5’-cap, appropriate maturation of a functional U1 snRNP, and its subsequent utilization in the splicing pathway. Our data also provide an insight as to why the identity of the AU dinucleotide is strongly favored during evolution. Splicing sensitive microarrays for S. cerevisiae (Agilent AMADID #: 019521) were used to monitor global changes in splicing in the background of U1 snRNA (snR19) variant compared to wild type