Abstract
Nearly 15% of the ~20,000 C. elegans genes are contained in operons, multigene clusters controlled by a single promoter. The vast majority of these are of a type where the genes in the cluster are ~100 bp apart and the pre-mRNA is processed by 3' end formation accompanied by trans-splicing. A spliced leader, SL2, is specialized for operon processing. Here we summarize current knowledge on several variations on this theme including: (1) hybrid operons, which have additional promoters between genes; (2) operons with exceptionally long (> 1 kb) intercistronic regions; (3) operons with a second 3' end formation site close to the trans-splice site; (4) alternative operons, in which the exons are sometimes spliced as a single gene and sometimes as two genes; (5) SL1-type operons, which use SL1 instead of SL2 to trans-splice and in which there is no intercistronic space; (6) operons that make dicistronic mRNAs; and (7) non-operon gene clusters, in which either two genes use a single exon as the 3' end of one and the 5' end of the next, or the 3' UTR of one gene serves as the outron of the next. Each of these variations is relatively infrequent, but together they show a remarkable variety of tight-linkage gene arrangements in the C. elegans genome.
Highlights
Operons are polycistronic clusters of genes transcribed from a promoter at the 5’ end of the cluster
15% of the ~20,000 protein-coding genes in the C. elegans genome are organized into ~1250 operons, tight clusters of two to eight genes (Allen et al, 2011)
Almost all gene clusters in the C. elegans genome are of the type exemplified in Figure 1, in this case a four-gene operon
Summary
Operons are polycistronic clusters of genes transcribed from a promoter at the 5’ end of the cluster. SL1-type operons are mechanistically quite interesting since they have no intercistronic sequence; polyadenylation of the upstream gene occurs right at the trans-splice site of the downstream gene (Williams et al, 1999). In these operons, 3’ end formation may occur by SL1 trans-splicing of the downstream gene, resulting in a free 3’ end upstream that may be debranched and polyadenylated. 3’ end formation may occur by SL1 trans-splicing of the downstream gene, resulting in a free 3’ end upstream that may be debranched and polyadenylated In these cases, the same processing event at least sometimes may serve to create the 3’ end of the upstream gene mRNA and the 5’ end of the downstream gene mRNA. Examples of each kind of gene cluster are described, and tables with lists of known examples of each type are included
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