The nematode worm Caenorhabditis elegans and its relatives are unique among 
animals in having operons. Operons are regulated multigene transcription units, 
in which polycistronic pre-messenger RNA (pre-mRNA coding for multiple peptides) 
is processed to monocistronic mRNAs. This occurs by 3' end formation and 
trans-splicing using the specialized SL2 small nuclear ribonucleoprotein 
particle for downstream mRNAs. Previously, the correlation between downstream 
location in an operon and SL2 trans-splicing has been strong, but anecdotal. 
Although only 28 operons have been reported, the complete sequence of the C. 
elegans genome reveals numerous gene clusters. To determine how many of these 
clusters represent operons, we probed full-genome microarrays for SL2-containing 
mRNAs. We found significant enrichment for about 1,200 genes, including most of 
a group of several hundred genes represented by complementary DNAs that contain 
SL2 sequence. Analysis of their genomic arrangements indicates that >90% are 
downstream genes, falling in 790 distinct operons. Our evidence indicates that 
the genome contains at least 1,000 operons, 2 8 genes long, that contain about 
15% of all C. elegans genes. Numerous examples of co-transcription of genes 
encoding functionally related proteins are evident. Inspection of the operon 
list should reveal previously unknown functional relationships.