Interplay between AAUAAA and the trans-splice site in processing of a Caenorhabditis elegans operon pre-mRNA

About half of Caenorhabditis elegans genes have a 1-2 bp mismatch to the ca nonical AAUAAA hexamer that signals 3' end formation. One rare variant, AGU AAA, is found at the 3' end of the mai-l gene, the first gene in an operon also containing gpd-2 and gpd-3. When we expressed this operon under heat s hock control, 3' end formation dependent on the AGUAAA was very inefficient , but could be rescued by a single bp change to create a perfect AAUAAA. Wh en AGUAAA was present, most 3' ends formed at a different site, 100 bp fart her downstream, right at the gpd-2 trans-splice site. Surprisingly, 3' end formation at this site did not require any observable match to the AAUAAA c onsensus. It is possible that 3' end formation at this site occurs by a nov el mechanism-trans-splicing-dependent cleavage-as deletion of the trans-spl ice site prevented 3' end formation here. Changing the AGUAAA to AAUAAA als o influenced the trans-splicing process: with AGUAAA, most of the gpd-2 pro duct was trans-spliced to SL1, rather than SL2, which is normally used at d ownstream operon trans-splice sites. However, with AAUAAA, SL2 trans-splici ng of gpd-2 was increased. Our results imply that (1) the AAUAAA consensus controls 3' end formation frequency in C. elegans; (2) the AAUAAA is import ant in determining SL2 trans-splicing events more than 100 bp downstream; e nd (3) in some circumstances, 3' end formation may occur by a trans-splicin g-dependent mechanism.