A dual role for RNA splicing signals.

gene expression in eukaryotes requires the excision of introns from pre-mrNas by splicing, which eliminates intervening sequences that interrupt the translation open-reading frame in mrNas. the spliceosome—a complex of small rNas and proteins—recognizes and acts on sequences at the exon–intron junctions—5'-splice site [SS] and 3'-SS—and at the branchpoint (Fig 1). Splicing is traditionally considered to be highly accurate and efficient because of the spliceosome’s specific recognition of these three splicing signals. However, there is growing evidence that the splicing of many pre-mrNas is suboptimal and that unspliced precursors can be detected after inhibition of rNa degradation activities (He et al, 1993; Jaillon et al, 2008; Mitrovich & anderson, 2000; Sayani et al, 2008). these observations bring to light the concept that quality control mechanisms exist to eliminate rNa molecules that have escaped the splicing process. in the absence of rNa quality control, unspliced rNas would accumulate and could be translated at high efficiency. Because intronic sequences are not usually constrained to preserve the open-reading frame in unspliced rNas, there is a high chance of the occurrence of a premature stop codon in the intron. translation of unspliced rNas would thus generate truncated polypeptides with potential dominant-negative functions and deleterious consequences for cellular pathways. Nonsense-mediated mrNa decay (NMD) is an rNa turnover mechanism that eliminates transcripts containing premature termination codons (isken & Maquat, 2007) and thus provides an efficient mechanism to degrade most unspliced rNas if they reach the cytoplasm. indeed, NMD has been implicated in discarding a large number of unspliced mrNas (Farlow et al, 2010; He et al, 1993; Jaillon et al, 2008; Mitrovich & anderson, 2000; Sayani et al, 2008). Elimination of unspliced rNas by NMD might also have contributed to intron gain during the evolution of genomes, as it minimizes the negative impact of inefficiently spliced transcripts (Farlow et al, 2010). the ability of NMD to degrade unspliced rNas relies on the presence of a stop codon that is recognized as premature (isken & Maquat, 2007). Strikingly, intronic signals recognized by the spliceosome to mediate rNa splicing also coincide with sequences that have the potential to trigger translation termination (Fig 1). For instance, one of the two optimal 3'-SS sequences, uag, corres ponds to a translation termination codon (Fig 1). the typical branchpoint sequence in fungi uacuaac also contains a uaa stop codon (Fig 1). recent work on the yeast Yarrowia lipolytica has shown that this phenomenon is widespread and that all three splicing signals in this species (5'-SS, branchpoint and 3'-SS) contain sequences that have the potential to induce translation termi nation if the introns are inserted into a particular frame (Mekouar et al, 2010). this includes the consensus 5'-SS gugagu (Fig 1), which differs from that of other fungi and includes a uga stop codon. the presence of a stop codon in the 5'-SS is also prominent in other species such as Drosophila (Farlow et al, 2010). thus, all three splicing signals can potentially mediate premature translation termination and NMD degradation. this prominence of stop codons within splicing signals provides a way to ensure the cytoplasmic degradation of unspliced rNas by NMD, regardless of the remainder of the intronic sequence. these observations suggest that the splicing signals have been specifically selected or have co-evolved with the translation machinery to maximize the likelihood of degradation of unspliced or aberrantly spliced rNas by NMD. the fact that splicing signals coincide with stop codons was noted previously (Senapathy, 1988), but was interpreted as evidence that splicing signals originated from stop codons. in the light of the widespread involvement of NMD in degrading unspliced precursors, and its potential evolutionary impact on genome building (Farlow et al, 2010), it is striking to consider that splicing signals play a dual role in the life and death of rNa molecules. they are essential to generate correctly spliced rNas, but also to mediate the destruction of rNas that have escaped the splicing machinery. Whether this is a coincidence or reflects a more direct evolutionary relationship remains to be established. A dual role for RNA splicing signals