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only in certain tissues or developmental stages (such as transcription factors and
collagens) are rarely found in operons (
Blumenthal and Gleason, 2003
). Thus, operons
may have evolved in nematodes not to coordinate expression of similarly regulated
genes, but to ensure universal expression of continuously needed gene products
(
Blumenthal, 2004
). It has been proposed that in C. elegans operons serve to allow
rapid response to global signals (
Blumenthal and Gleason, 2003
). In support of this
idea, it has recently been shown that operons serve to respond to a need for growth
following starvation or during development (
Zaslaver et al., 2011
).
Several studies have shown that the transcripts from genes in operons are not
always present in equal amounts (
Blumenthal, 2005; Cutter et al., 2009
). This could
be due to a variety of causes. For example the individual mRNAs might have
different stabilities; processing sites might have differential or even regulated effi-
ciencies, resulting in failure to make stable downstream mRNAs or even termination
of transcription. Recently, it has been demonstrated that some operons contain
internal promoters (
Huang et al., 2007; Whittle et al., 2008
). Hybrid operons feature
an upstream promoter, which drives expression of all genes in the cluster, but they
also contain an additional internal promoter, located within the operon. Presumably,
such a system allows transcription of all genes from the promoter at the 5
0
end of the
complex, while allowing transcription of specific genes in the operon during various
periods of alternative metabolic requirements. Recent transcriptome evidence sug-
gests that the promoters within the operons tend to be differentially regulated
compared to those at the operon 5
0
ends (
Allen et al., 2011
).
4. Elements Controlling SL2 Trans-Splicing
The mechanism that controls SL2 specificity is incompletely understood,
although intensive study of the process since its discovery has resolved some ques-
tions. During processing, a polycistronic pre-mRNA must be divided into separate
genes, each competent for nuclear export and translation. At the 3
0
end of every gene,
several signals have been identified that signal the RNA processing machinery to
cleave the nascent RNA from the polymerase and polyadenylate it (
Mandel et al.,
2008
). Key among these signals is the polyadenylation signal, AAUAAA (
Wickens
and Stephenson, 1984
). The machinery of 3
0
processing will be discussed in a later
section. Typically, 3
0
processing in some way signals the RNA polymerase to termi-
nate transcription (
Rosonina et al., 2006
), and this must be prevented at 3
0
end
formation sites within operons. There are currently two models to describe how
termination might occur: the allosteric model and the torpedo model. According to
the allosteric model, interaction with the 3
0
processing machinery induces a confor-
mational shift in the RNA polymerase, resulting in weaker binding to DNA, reduced
processivity, and termination (
Logan et al., 1987
). The torpedo model proposes that
the uncapped RNA produced downstream of the 3
0
cleavage site is subject to rapid
5
0
!
3
0
degradation (
Connelly and Manley, 1988; Kim et al., 2004; West et al., 2004
).
The exonuclease responsible for this eventually catches up to the polymerase, knock-
ing it off the DNA. A hybrid termination model combines features of both of these
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