A role for the Ψ-U mismatch in the recognition of the 5′ splice site of yeast introns by the U1 small nuclear ribonucleoprotein particle

The U1 small nuclear ribonucleoprotein particle (snRNP)/5' splice site (5'SS) interaction in yeast is essential for the splicing process and depends on the formation of a short RNA duplex between the 5' arm of U1 snRNA and the 1st intronic nucleotides. This RNA/RNA interaction is characterized by the presence of a mismatch that occurs with almost all yeast introns and concerns nucleotides 4 on the pre-mRNA (a U) and 5 on U1 snRNA (a P). The latter nucleotide is well conserved from yeast to vertebrates, but its role in yeast and the significance of the associated mismatch in the U1 snRNA/5'SS interaction have never been fully explained. We report here that the presence of this mismatch is a determinant of stability that mainly affects the off rate of the interaction. To our knowledge this is the first report assigning a function to this noncanonical interaction. We also performed SELEX (systematic evolution of ligands by exponential enrichment) experiments by immunoprecipitating U1 snRNP and the associated RNA. The artificial phylogeny derived from these experiments allows the isolation of the selective pressure due to U1 snRNP binding on the 5'SS of yeast introns.