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(
Graber et al., 2007
). Subsequent study has shown that the Ur element contains a
highly conserved hairpin of variable sequence, followed closely by a UAYYUU
consensus sequence (
Lasda et al., 2010
). Both of these elements are required for
downstream SL2 trans-splicing in vitro. Interestingly, the UAYYUU sequence is
complementary to the sequence surrounding the donor splice site on the SL2 snRNP,
indicating that the same type of interaction may occur here as occurs between the U1
snRNP and the 5
0
splice site during cis-splicing, except that in trans-splicing, the
splice site is on the snRNP and the site that binds it is on the pre-mRNA.
These observations have produced the following current, albeit incomplete, model
of SL2 trans-splicing to downstream genes in operons. Transcription proceeds
through the first gene, and 3
0
end formation factors are recruited to cleave and
polyadenylate the mRNA. The polymerase continues to transcribe the operon, but
termination is inhibited, possibly by CstF-facilitated recruitment of the SL2 snRNP
to the Ur element. This protects the uncapped RNA downstream from this cleavage
event from degradation and inhibits the torpedoing of the polymerase. The SL2
snRNP then interacts with the trans-splice site of the downstream gene, initiating
spliceosome formation. Once trans-splicing occurs, the downstream RNA is capped
and safe from degradation so the polymerase can continue to transcribe without
premature termination.
As noted previously, there are several different species of SL2 spliced leader
(
MacMorris et al., 2007; Ross et al., 1995
). Any additional specificity rendered
by these variant SL2s has not been discovered, although they could be involved in
spatial or temporal regulation of gene expression.
5. SL1-Type Operons
There is a second type of operon in C. elegans, the SL1-type operon (
Fig. 5b
). This
class of operon does not contain a canonical 100 nt ICR between its genes. Instead,
the polyadenylation signal of the first gene immediately precedes the trans-splice
site of the second gene; that is there is no ICR at all. Initially, the overlap between
these two sites led researchers to suggest that trans-splicing of the downstream gene
would leave a free 3
0
end on the upstream mRNA that could then be polyadenylated,
instructed by the polyadenylation signal that is present just upstream of the trans-
splice site. However, experiments with one SL1-type operon suggested that, at least
in this case, formation of the 3
0
end of the upstreammRNA is not dependent on trans-
splicing of the downstreammRNA (
Williams et al., 1999
). It was concluded that any
given pre-mRNA from an SL1-type operon could give rise to either a functional
mRNA for the upstream gene or the downstream gene, but not both, since 3
0
cleavage
for the upstream mRNA would destroy the trans-splice site of the downstream
mRNA. Conversely, trans-splicing of the downstream mRNA would leave a
branched upstream mRNA, which might or might not allow formation of the
upstream mRNA. This would result in a rather interesting regulatory situation.
Recently, processing of this type of operon has been reexamined. As the results of
various transcriptional deep-sequencing projects have been reported, it has been
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