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genome contains more than 1000 such operons. The polycistronic pre-mRNA is
processed into individual gene-encoding mRNAs by coordinated upstream 3
0
end
formation and downstream trans-splicing. An intercistronic RNA sequence, the Ur
element, plays a key role in specifying downstream trans-splicing.
I. Introduction
During and after transcription, pre-mRNA is processed into mature mRNA. In
C. elegans, several different types of canonical RNA processing occur. Shortly
after transcription begins, the nascent RNA is capped with a 7-methylguanosine
nucleotide. As transcription proceeds, introns are recognized and removed from
the pre-mRNA by spliceosomes, which contain the snRNAs and associated splic-
ing factors found in other metazoans. Cleavage at the 3
0
end of the RNA is
executed by orthologs of the mammalian CPSF and CstF complexes.
Additionally, novel RNA-processing events in Caenorhabditis elegans result from
gene structures and chromosomal gene arrangements not found in other model
organisms. Many nascent RNA molecules are trans-spliced: a capped 22 nt RNA
leader sequence is spliced to an acceptor site near the 5
0
end of the pre-mRNA. Trans-
splicing has permitted the evolution of operons throughout the nematode genome,
since a single pre-mRNA encoding multiple genes can be processed into single-gene
units by coordinated 3
0
end formation and trans-splicing. Downstream genes in an
operon are uniquely identified by a special family of spliced-leader sequences. This
chapter will examine each of these processing activities with emphasis on aspects of
gene expression that are special to C. elegans and other nematodes.
II. RNA Processing in Other Organisms
Many of the RNA features and processing events studied in C. elegans have also
been examined in other organisms. Most eukaryote RNA contains introns, and their
removal is conducted by a conserved cellular machinery that has been extensively
studied. Likewise, the basic mechanism of 3
0
end formation is highly conserved
among the eukaryotes in which it has been studied. This section reviews what is
known about these processing events in these other systems. The subsequent section
describes the differences in common processing events and the unique events
observed in C. elegans and other nematodes.
A. Eukaryotic Pre-mRNA Processing
As pre-mRNA is transcribed, its introns are identified and removed by a large,
dynamic RNP complex, the spliceosome. This complex is composed of five core
small nuclear RNAs (snRNAs) - U1, U2, U4, U5, and U6 - as well as hundreds of
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