U1 snRNP can influence 3′-splice site selection as well as 5′-splice site selection

To address the mechanisms that underlie splice site selection and splice site partner assignment, we analyzed the splicing of yeast (Saccharomyces cerevisiae) transcripts containing splice site region duplications. When the 5′-splice site region was duplicated, both sites were utilized to the same extent, indicating little or no influence of proximity on 5′-splice site choice. However, the effect of a 5′-mutant site was greatly enhanced by the presence of an adjacent wild-type site, and this effect was reversed by the restoration of base-pairing with U1 snRNA. 3′-Splice site choice was apparently influenced by proximity, as the site closest to the 5′-splice site was greatly preferred. Studies with strains carrying some U1 snRNA mutations showed an increase in the use of the distal 3′-splice site, indicating a role for U1 snRNP in 3′-splice site selection. The data are compared with those from mammalian splice site choice experiments and suggest mechanisms that influence differential splice site choice as well as exon skipping.