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upstream gene and the site of SL2 trans-splicing at the 5
0
end of the downstream
gene. Furthermore, attempts to identify upstream promoters conferring SL2 speci-
ficity to transcripts from these downstream genes were unsuccessful (
Blumenthal,
1995
). Ultimately, the identification of cDNA containing the last exon of an
upstream gene followed by a short intercistronic region (ICR) and the downstream
gene indicated that both genes were transcribed together from a common upstream
promoter (
Spieth et al., 1993
).
However, the strongest evidence for operons comes from the almost perfect
correlation between SL2 trans-splicing and the location of the trans-splice site at a
downstream position in a tight gene cluster (
Blumenthal et al., 2002
). For this reason,
these operons have been named SL2-type operons. Recently this evidence has been
extended to the entire genome by analysis of the transcriptome by deep sequencing
(
Allen et al., 2011
). This analysis demonstrates that SL1 and SL2 trans-splicing
occur on different genes and that frequent SL2 trans-splicing is almost perfectly
correlated with downstream genes spaced about 100 bp from the 3
0
end of a gene
upstream.
Around 15% of the genes in C. elegans are arranged in operons (
Blumenthal and
Gleason, 2003
). These operons are concentrated within the central region of the
autosomes and there is a paucity of operons on the X chromosome
(
Blumenthal et al., 2002
). Each operon contains from two to eight genes, usually
transcribed from a single upstream promoter, although some operons also contain
internal promoters (
Huang et al., 2007
). Although operons in nematodes do share
some similarities with bacterial operons, they are evolutionarily unrelated. Instead,
they evolved independently, presumably after the development of trans-splicing.
Trans-splicing can isolate translatable single-gene units from a polycistronic pre-
mRNA. These capped and spliced monocistronic mRNAs can then be exported from
the nucleus for translation. The RNA transcribed from the first genes in operons is
not always trans-spliced, but when trans-splicing does occur, it is to SL1, as occurs in
transcripts from genes not in operons.
3. Functional Relationships of Operon Genes
Often the genes within a single C. elegans operon appear functionally unrelated,
although numerous instances of related genes being expressed in a single operon
have been observed. For example, an operon has been identified that contains genes
encoding U2AF
35
and SF1/BBP, proteins involved in 3
0
splice-site recognition,
along with a third gene, cyn-13, the human ortholog of which is also spliceosome-
associated. Indeed, groupings similar to this one have been found to occur more
frequently than expected by chance (
Blumenthal and Gleason, 2003
). It has also been
observed that genes expressed preferentially in the female germ line occur in operons
significantly more frequently than expected by chance (
Reinke and Cutter, 2009
).
These tend to be genes encoding proteins involved in universal processes such as gene
expression (the basic machinery of transcription, RNA degradation, splicing, and
translation) or mitochondrial function. Conversely, genes encoding proteins expressed
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