Polycistronic pre-mRNAs in C. elegans are processed into monocistronic mRNAs by 3' end formation and SL2-specific trans-splicing. We are studying the mechanism of this type of RNA processing in vivo, using a heat-shock driven transgenic
gpd-2/gpd-3 operon. We have identified a U-rich sequence (Ur) located within the intercistronic region, 75 bp upstream of the
gpd-3 trans-splice site, but nevertheless required for trans-splicing of
gpd-3. A Ur mutation (DELTAUr) weakly inhibits 3' end formation, resulting in some polycistronic RNA accumulation, but more dramatically prevents the accumulation of trans-spliced
gpd-3 mRNA. In the absence of the Ur sequence and 3' end formation of
gpd-2 , trans-spliced
gpd-3 mRNA accumulates, but is only spliced to SL1. Insertion of a 10 base oligo(U) tract in place of the normal Ur sequence (DELTAUr/pU) partially rescues SL2 trans-splicing and completely restores 3' end formation. Under extreme heat-shock conditions that inhibit trans-splicing, we detect a primer extension product that extends from
gpd-3 into the intercistronic region and ends just upstream of the Ur sequence. Accumulation of this product requires an intact Ur region and is strongly enhanced by 3' end formation. In the DELTAUr/pU mutant, multiple primer extension products that map within and just upstream of the inserted poly(U) accumulate. These products do not appear to represent a Y-branch intermediate (with the Ur sequence playing a role as a polypyrimidine tract) since it is stable to debranching treatment with S100 extract. Instead, we hypothesize that the Ur sequence may act to prevent transcription termination following 3' end formation of the upstream mRNA by protecting the uncapped downstream product from degradation