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Spliced leader (SL)  trans -splicing in  Caenorhabditis elegans  attaches a 22-nucleotide (nt) exon onto the 5′ end of many mRNAs. A particular class of SL, SL2, splices mRNAs of downstream operon genes. Here we use an embryonic extract-based in vitro splicing system to show that SL2 specificity information is encoded within the polycistronic pre-mRNA, and that  trans -splicing specificity is recapitulated in vitro. We define an RNA sequence required for SL2  trans -splicing, the U-rich (Ur) element, through mutational analysis and bioinformatics as a short stem–loop followed by a sequence motif, UAYYUU, located ∼50 nt upstream of the  trans -splice site. Furthermore, this element is predicted in intercistronic regions of numerous operons of  C. elegans  and other species that use SL2  trans -splicing. We propose that the UAYYUU motif hybridizes with the 5′ splice site on the SL2 RNA to recruit the SL to the pre-mRNA. In this way, the UAYYUU motif in the pre-mRNA would serve an analogous function to the similar sequence in the U1 snRNA, which binds to the 5′ splice site of introns, effectively reversing the roles of snRNP and pre-mRNA in  trans -splicing.

Polycistronic pre-mRNA processing in vitro: snRNP and pre-mRNA role reversal in trans-splicing