A U-rich tract enhances usage of an alternative 3' splice site in yeast

There has been a long-standing belief that the mechanisms of mammalian and yeast splicing differ fundamentally in their requirement for a pyrimidine-rich motif preceding the 3' splice site. Using an in vivo assay, we have tested the influence of uridine content on competition between alternative 3' splice sites in yeast. We find that a uridine-rich tract preceding a PyAG greatly enhances its ability to compete as a splice acceptor. Moreover, a proximal PyAG is often overlooked if a more distal PyAG occurs in a superior sequence context; this observation cannot be accounted for by simple scanning models. Finally, we show that a distal (greater than 30 nucleotide) 3' splice site that is not preceded by uridines is a poor substrate for the second step of splicing; this argues that recognition of a uridine-rich motif is required for effective identification and utilization of distant splice sites.