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), the SL1 snRNP. This snRNP is structurally and functionally similar to the U snRNAs (U1, U2, U4, U5 and U6) that play key roles in intron removal and trans-splicing, except that the SL1 snRNP is consumed in the process. More than half of C. elegans pre-mRNAs are subject to SL1 trans-splicing, whereas ~30% are not trans-spliced. The remaining genes are trans-spliced by SL2, which is donated by a similar snRNP, the SL2 snRNP. SL2 recipients 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 ~100 nt further downstream. SL2 trans-splicing requires a sequence between the genes, the Ur element, that likely base pairs with the 5' splice site on the SL2 snRNP, in a manner analogous to the interaction between the 5' splice site in cis-splicing with the U1 snRNP. The key difference is that in trans-splicing, the snRNP contains the 5' splice site, whereas in cis-splicing the pre-mRNA does. Some operons, termed "hybrid operons", contain an additional promoter between two genes that can express the downstream gene or genes with a developmental profile that is different from that of the entire operon. The operons contain primarily genes required for rapid growth, including genes whose products are needed for mitochondrial function and the basic machinery of gene expression. Recent evidence suggests that RNA polymerase is poised at the promoters of growth genes, and operons allow more efficient recovery from growth-arrested states, resulting in reduction in the need for this cache of inactive RNA polymerase.
Highlights
About 70% of C. elegans mRNAs are trans-spliced to one of two 22 nucleotide spliced leaders
Trans-splicing mRNAs of ~70% of Caenorhabditis elegans genes begin with a 22 nucleotide sequence, the spliced leader or SL, which is not associated with the gene
The SL small nuclear ribonucleoprotein particle (snRNP) may be attracted to the outron by base pairing to the Ou element in a manner analogous to the base pairing between the SL2 snRNP 5’ splice site/Ur element base pairing of SL2 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 sequence, resembling the U1-5’ splice site base pairing. 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. Deep sequencing of RNA that has not been polyA selected should allow determination of promoter locations of many more trans-spliced genes
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