CLONING OF CAENORHABDITIS U2AF(65) - AN ALTERNATIVELY SPLICED RNA CONTAINING A NOVEL EXON

The U2 small nuclear ribonucleoprotein particle (snRNP) auxiliary fact or, U2AF, is an essential splicing factor required for recognition of the polypyrimidine tract and subsequent U2 snRNP assembly at the branc h point. Because Caenorhabditis elegans introns lack both polypyrimidi ne tract and branch point consensus Sequences but have a very highly c onserved UUUUCAG/R consensus at their 3' splice sites, we hypothesized that U2AF might serve to recognize this sequence and thus promote int ron recognition in C. elegans. Here we report the cloning of the gene for the large subunit of U2AF, uaf-1. Three classes of cDNA were ident ified. In the most abundant class the open reading frame is similar to that for the U2AF(65) from mammals and flies. The remaining two class es result from an alternative splicing event in which an exon containi ng an in-frame stop codon is inserted near the beginning of the second RNA recognition motif. However, this alternative mRNA is apparently n ot translated. Interestingly, the inserted exon contains 10 matches to the 3' splice site consensus. To determine whether this feature is co nserved, we sequenced uaf-1 from the related nematode Caenorhabditis b riggsae, It is composed of six exons, including an alternatively splic ed third exon interrupting the gene at the same location as in C. eleg ans. uaf-1 is contained in an operon with the rab-18 gene in both spec ies. Although the alternative exons from the two species are not highl y conserved and would not encode related polypeptides, the C. briggsae alternative exon has 18 matches to the 3' splice site consensus. We h ypothesize that the array of 3' splice site-like sequences in the pre- mRNA and alternatively spliced exon may have a regulatory role. The al ternatively spliced RNA accumulates at high levels following starvatio n, suggesting that this RNA may represent an adaption for reducing U2A F(65) levels when pre-mRNA levels are low.