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in nematode species outside the Rhabditina clade DITTO that use SL1 or SL1
variants to trans-splice downstream gene mRNAs (Liu et al., 2009).
C. Operons
1. Operon Architecture
The C. elegans genome contains more than 1000 operons, in which several closely
clustered genes are transcribed from a single, upstream promoter, and the resulting
polycistronic pre-mRNA is cut into monocistronic units by 3 0 end formation and
trans-splicing, before the individual mRNAs exit the nucleus for translation
( Blumenthal, 2005; Nilsen, 1994; Spieth et al., 1993 ). Unlike bacterial operons,
these operon genes usually encode metabolically unrelated products.
2. Discovery of C. elegans Operons
The discovery of operons in C. elegans ( Spieth et al., 1993 )( Fig. 5a ) was facil-
itated by identification of the SL2 spliced-leader attached to only a subset of
mRNAs. As SL2 trans-spliced mRNAs were identified, it was observed that they
were always transcribed from genes located in the same orientation and immediately
downstream of other genes, usually with only 100 bp separating the 3 0 end of the
Fig. 5 Typical C. elegans operons. A single promoter (arrow) drives expression of both genes, in which
exons are depicted as colored boxes and introns are shown as chevrons. Each gene contains an independent
3 0 end formation signal (AATAAA). (a) An SL2-type operon. An intercistronic region (ICR) averaging
approximately 100 nt (shown as a bold line) separates the genes within the operon. As 3 0 end formation
occurs in the upstream gene, the downstream gene is trans-spliced with an SL2 spliced leader and the ICR
is excised as a Y-branched molecule on the used SL2 snRNP. (b) An SL1-type operon. This type of operon
contains no ICR and trans-splicing of the downstream genes is conducted by the SL1 snRNP. Studies
have shown that 3 0 end formation of the upstream gene can occur by the canonical mechanism, in which
case RNA cleavage destroys the trans-splice site of the downstream gene. Alternately, trans-splicing of the
downstream gene can inhibit canonical 3 0 end formation of the upstream gene. New evidence suggests,
however, that downstream trans-splicing in this type of operon may simultaneously act as an alternate 3 0
end processing pathway in the upstream gene, allowing both genes in the operon to be expressed. (For
color version of this figure, the reader is referred to the web version of this topic.)
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