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lin-15B, but also terminates transcription upstream of lin-15A. The combined
absence of both of these gene products results in an easily identifiable synthetic
phenotype, characterized by several vulvae protruding from the side of the mutant
animals. When these animals were subjected to a genome-wide RNAi screen, the
multivulva phenotype was suppressed by the inactivation of genes responsible for
(among other things) 3 0 end formation or transcription termination.
In addition to identifying several of the genes producing components of the CPSF
and CstF complexes, this screen implicated the genes cids-1, cids-2, nrd-1, and rsp-6
in these processes. The cids-1 gene is an ortholog of the S. cerevisiae gene RTT103.
In yeast, Rtt103p is a member of a complex, also containing Rat1p and Rai1p, that
have a role in transcription termination ( Kim et al., 2004 ). The cids-2 gene is a
paralog of cids-1 and has no similarity to any other known gene. Even within
C. elegans, similarity between the genes is restricted to a single region known to
interact with the C-terminal domain of RNA polymerase II, the CIDmotif. The nrd-1
gene is an ortholog of the yeast gene NRD1, known to play a role in the termination
of small nuclear RNAs and of cryptic unstable transcripts (CUTs) ( Arigo et al., 2006;
Thiebaut et al., 2006 ). It also contains a CID motif, but has not been previously
linked with cids-1 or cids-2. Finally, rsp-6 encodes the SR protein SRp20, known to
have a role in alternative splicing ( de la Mata and Kornblihtt, 2006; Longman et al.,
2000 ).
Additional analysis indicated that both CIDS-1 and CIDS-2 are involved in 3 0 end
cleavage, but the specific nature of their roles is still unclear. Likewise, NRD-1 may
help stimulate 3 0 end cleavage, although its role in terminating CUTs may have also
been a factor in its identification as a suppressor of 3 0 end formation and transcrip-
tion termination. Finally, SRp20 functions in transcription termination without
affecting 3 0 end cleavage, although its mechanism of action remains undetermined
( Cui et al., 2008 ).
3. A Summary of RNA Processing in C. elegans
As in other eukaryotes, RNA processing in C. elegans occurs primarily during
transcription. Intron splicing is conducted by the canonical spliceosomal machinery,
but the 3 0 splice-site consensus sequence is markedly different from that found in
other splicing organisms. Additionally, the splicing machinery is occasionally capa-
ble of splicing at noncanonical sites. These features have allowed C. elegans introns
to be unusually short, when compared with the introns of other organisms.
C. elegans RNA is also processed in several other unique ways. The 5 0 region of
approximately 70% of transcripts is replaced by a common 22 nt capped leader
sequence through trans-splicing, catalyzed by the specialized SL1 snRNP. The
discarded 5 0 piece of RNA, the outron, is removed and degraded during this process,
making it difficult to identify the promoter and transcriptional start site for these
C. elegans genes. Trans-splicing has also facilitated the evolution of operons, since
this process allows a polycistronic pre-mRNA to be divided into several capped
monocistronic transcripts.
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