RNA Processing in C. elegans - Caenorhabditis Elegans: Molecular Genetics and Development - page 188

promoter deploys RNA polymerase to transcribe all of these genes at once,
making a polycistronic mRNA that is translated by repeated translation termi-
nation at the 3 0 ends of upstream coding sequences followed by reinitiation by
ribosomes at the 5 0 start site of downstream coding sequences ( McCarthy and
Gualerzi, 1990 ).
In eukaryotes there are several types of gene clusters that resemble operons. First,
in several species of yeast, genes involved in similar functions can sometimes be
found in close proximity ( Wong and Wolfe, 2005 ). Although the genes in this
arrangement, called a metabolic gene cluster, do not contain a common promoter,
their organization resembles that of an operon in other respects (reviewed in Osbourn
and Field, 2009 ). Second, dicistronic gene clusters resembling short operons have
been reported in plants, flies, and even mammals (reviewed in Blumenthal, 1998,
2004 ). Intron splicing of the pre-mRNA and 3 0 end formation of the downstream
transcript occur normally, and the dicistronic transcript is exported for translation,
which may occur via internal ribosomal entry sites between the coding sequences.
Often these genes encode metabolically related products. This latter type of poly-
cistronic cluster appears to be present, at least occasionally, in C. elegans (e.g., tin-
9.2 and exos-4.1), but it has not been studied there. Multigene transcription units of a
third type are prevalent in trypanosomes ( Muhich and Boothroyd, 1988 ), although
these have not been termed operons because there is no evidence for their transcrip-
tional regulation. Indeed, often these transcriptional units extend the length of an
entire chromosome (reviewed in Clayton, 2002 ). The vast majority of C. elegans
operons (to be discussed in a later section) are processed like those of trypanosomes,
by a concerted process of 3 0 end formation and trans-splicing just downstream. Many
animal phyla, including most or all nematodes, have operons of this type.
III. RNA Processing in C. elegans
A. Intron Splicing
1. C. elegans Introns
The splicing machinery and the process of intron removal have been highly
conserved in C. elegans. Most C. elegans genes have multiple introns, defined by
the core GT-AG splice sites ( The C. elegans Sequencing Consortium, 1998 ). Intron
splicing occurs cotranscriptionally and is directed by the well-characterized spliceo-
somal snRNAs U1, U2, U4, U5, and U6, along with their associated proteins
( Thomas et al., 1990 ). In many species including plants, flies, and vertebrates, there
exists a related, but distinct, group of introns, the removal of which is catalyzed by a
spliceosome, called the U12 type, with some different components (reviewed in Will
and Luhrmann, 2005 ). However, no U12-type introns or minor spliceosomal com-
ponent genes are present within the C. elegans genome, and it appears that all introns
have evolved to undergo splicing by the U2-type major spliceosome ( Burge et al.,
1998; Sheth et al., 2006 ).