Abstract
About 70% of C. elegans mRNAs are trans-spliced to one of two 22 nucleotide spliced leaders. SL1 is used to trim off the 5' ends of pre-mRNAs and replace them with the SL1 sequence. This processing event is very closely related to cis-splicing, or intron removal. The SL1 sequence is donated by a 100 nt small nuclear ribonucleoprotein particle (snRNP). This snRNP is structurally and functionally related to the U snRNAs (U1, U2, U4, U5 and U6) that play key roles in intron removal and trans-splicing, except that it is consumed in the process of splicing. More than half of C. elegans pre-mRNAs are subject to SL1 trans-splicing. About 30% are not trans-spliced at all. The remaining genes are trans-spliced by SL2. These genes are all downstream genes in closely spaced gene clusters similar to bacterial operons. They are transcribed from a promoter at the 5' end of the cluster of between 2 and 8 genes. This transcription makes a polycistronic pre-mRNA that is co-transcriptionally processed by cleavage and polyadenylation at the 3' end of each gene, and this event is closely coupled to the SL2 trans-splicing event that occurs only approximately 100 nt further downstream. Recent studies on the mechanism of SL2 trans-splicing have revealed that one of the 3' end formation proteins, CstF, interacts with the only protein known to be specific to the SL2 snRNP. The operons contain primarily genes whose products are needed for mitochondrial function and the basic machinery of gene expression: transcription, splicing and translation. Many operons contain genes whose products are known to function together. This presumably provides co-regulation of these proteins by producing a single RNA that encodes both.
Highlights
Trans-splicing and operons primarily genes whose products are needed for mitochondrial function and the basic machinery of gene expression: transcription, splicing and translation
Trans-splicing mRNAs of ~70% of C. elegans genes begin with a 22 nucleotide sequence, the spliced leader or SL, which is not associated with the gene
The SL is donated by a 100 nucleotide RNA, SL RNA, by trans-splicing
Summary
The SL RNAs exist as snRNPs (Blumenthal and Steward, 1997; Hastings, 2005) They have a discrete secondary structure as do other snRNAs, they are bound to the Sm proteins, and they have a trimethylguanosine (TMG) cap like the U snRNAs. In the SL snRNPs the 5' splice sites are base paired to the upstream part of the SL. The signal for trans-splicing is the presence of intron-like sequence, the outron, at the 5' end of the mRNA, with no functional 5' splice site upstream (Conrad et al, 1995; Conrad et al, 1993; Conrad et al, 1991). Genes whose pre-mRNAs are subject to trans-splicing are distinguished from those that are by the presence of an outron. In a few cases the promoters of trans-spliced genes or start sites of outrons have been identified [e.g., col-13 has a 64 bp outron (Park and Kramer, 1990) and rol-6 has a 172 bp outron (Conrad et al, 1993) ]
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