Structure and expression of novel spliced leader RNA genes in Caenorhabditis elegans

Approximately 25% of Caenorhabditis elegans genes are organized as operons. Polycistronic transcripts are converted to monocistronic mRNAs by 3' cleavage/polyadenylation and 5' trans-splicing with untranslated, 5'-terminal exons called spliced leaders, (SLs). The 5' termini of mRNAs encoded by downstream genes in operons are acceptors for ≥7 recently discovered 'novel' SLs and a classical SL (SL2). Diversity in SL exons is now partly explained by the discovery and characterization of five novel genes that encode C. elegans SL RNAs. These novel SL RNAs contain a 22- or 23-nucleotide SL followed by conserved splice donor and downstream sequences that are essential for catalysis of trans-splicing reactions. The SL3α, SL4, and SL5 RNA genes are tightly clustered on chromosome III; their 114-nucleotide transcripts deliver three distinct SLs to mRNAs. The SL3β and SL3γ RNA genes are on chromosome I, but are not tightly linked. SL RNAs 3α, 3β, and 3γ, provide identical 5' leader exons, although their 3' sequences diverge. Transcription of SL 3-5 RNA genes appears to be driven by flanking DNA elements that are homologous with segments of promoters for the C. elegans SL2 RNA and small nuclear RNA genes. RNase protection assays demonstrated that novel SL RNAs are transcribed in vivo and accumulate in the poly(A^-) RNA pool. SL3 exons are transferred to mRNAs as frequently as SL2 exons. In contrast, SL4 is appended to mRNAs 10% as frequently as SL3. The abundance of SL4 RNA increased 6-fold during postembryonic development, and the SL4 RNA gene promoter is active principally in hypodermal cells.