1The Hebrew University of Jerusalem, Jerusalem Israel; 2The Weizmann Institute of Science, Rehovot Israel Pre-mRNA splicing involves recognition of a consensus sequence at the 5’ splice site. However, only some of the many potential sites that conform to the consensus are true ones, while the majority remain silent and are not normally used for splicing. We noticed that in most cases the utilization of such a latent intronic 5’splice site for splicing would introduce an in frame stop codon into the resultant mRNAs. This suggested a link between splice site selection and maintenance of an open reading frame, which is manifested by suppressing splicing events that could lead to the inclusion of pre-mature termination codons in mRNAs. We have experimentally verified this suppression of splicing (SOS) idea and found that splicing events at latent sites are indeed activated by mutations that eliminate the interfering stop codons. Attributing the null phenotype of latent splicing to nonsense-mediated mRNA decay (NMD) can be excluded because SOS, unlike NMD, is independent on translation. Nonetheless, latent splicing can be activated by eliminating start codons, indicating that at least start-codon-recognition is required for SOS. Our findings imply that the reading frame of mRNAs can be recognized in the cell nucleus prior to splicing, presumably by a surveillance mechanism that resides in the pre-mRNA processing machine. This nuclear scanning mechanism is highly important for accurate gene expression, as perturbations that would lead to splicing at latent sites are expected to introduce in frame stop codons into the majority of mRNAs.
