STRUCTURE AND EXPRESSION OF NOVEL SPLICED LEADER RNA GENES IN CAENORHABDITIS-ELEGANS

Approximately 25% of Caenorhabditis elegans genes are organized as ope rons. Polycistronic transcripts are converted to monocistronic mRNAs b y 3' cleavage/polyadenylation and 5' trans-splicing with untranslated, 5'-terminal exons called spliced leaders, (SLs). The 5' termini of mR NAs encoded by downstream genes in operons are accepters for greater t han or equal to 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 RN As. 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 SL3 alpha, SL4, and SL5 RN A genes are tightly clustered on chromosome III; their 114-nucleotide transcripts deliver three distinct SLs to mRNAs. The SL3 beta and SL3 gamma RNA genes are on chromosome I, but are not tightly linked. SL RN As 3 alpha, 3 beta, and 3 gamma provide identical 5' leader exons, alt hough their 3' sequences diverge. Transcription of SL 3-5 RNA genes ap pears to be driven by flanking DNA elements that are homologous with s egments of promoters for the C. elegans SL2 RNA and small nuclear RNA genes. RNase protection assays demonstrated that novel SL RNAs are tra nscribed 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 RN A increased 6-fold during postembryonic development, and the SL4 RNA g ene promoter is active principally in hypodermal cells.