RNA Processing in C. elegans - Caenorhabditis Elegans: Molecular Genetics and Development - page 192

Fig. 2 Paired 3 0 splice site consensus sequences. The upstream 3 0 splice site has no consensus other
than a terminal AG. The downstream 3 0 splice site consists of the canonical C. elegans 3 0 consensus
sequence TTTTCAG, except with a G in place of the T at -7 due to the preponderance of 6 bp spacing
between the two splice sites. In introns, such sites are commonly observed separated by multiples of three
bases. At trans-splice sites, splice site separation is not constrained by reading frame. (For color version of
this figure, the reader is referred to the web version of this topic.)
cases there is a good match to the UUUUCAG/R consensus, which U2AF recognizes
as the intron border region. However, only some of the splicing actually occurs at this
sequence. The rest of it occurs at a short distance upstream at a much weaker match
to the consensus, often even at a non-AG site ( Fig. 2 ). Documented cases of this
phenomenon generally show 6, 9, or 12 nucleotides between the two splice sites,
presumably because splicing at other nearby sites results in a frameshift and would
not be detected due to RNA degradation by nonsense-mediated decay. Indeed, this
phenomenon also occurs at trans-splice sites (see below) upstream of the translation
initiation codon, and here the spacing between the sites does not occur in multiples of
3 (Blumenthal, unpublished).
B. Trans-Splicing
1. Components of the Trans-Splicing Reaction
During transcription of many C. elegans genes, the 5 0 ends of their pre-mRNAs are
replaced with a 22 nt trimethylguanosine-capped RNA leader sequence by trans-
splicing ( Krause and Hirsh, 1987 ). The mRNAs of approximately 70% of all genes
in the C. elegans genome are trans-spliced ( Blumenthal, 2005 ). Trans-splicing is
closely related to intron splicing and utilizes the same U2, U4, U5, and U6 snRNAs
found in the spliceosome, as well as their associated proteins. The U1 snRNP, however,
does not play a role in this process ( Hannon et al., 1991 ). Instead, a different snRNP,
the SL snRNP, is required for this reaction ( Bruzik et al., 1988; Thomas et al.,1988 ).
After transcription, some snRNA molecules are transported from the nucleus to
mature in the cytoplasm at a large protein assemblysome, the survival of motor
neurons (SMN) complex ( Patel and Bellini, 2008 ). Here, a heteroheptamer ring of
Sm proteins is assembled around its Sm-binding site, RAUUUUGR. During assem-
bly, the arginine residues of the D1 and D3 Sm proteins can be symmetrically
dimethylated by a protein arginine methyltransferase, such as PRMT-5. It is thought
that this modification increases the stability of the Sm protein heptamer by enhanc-
ing Sm affinity to the SMN complex. After addition of the Sm ring, the 7-methyl-
guanosine cap of the snRNA is hypermethylated into a 2,2,7-trimethylguanosine