Trans-splicing of one of two short leader RNAs, SL1 or SL2, occurs at the 5' 
ends of pre-mRNAs of many C. elegans genes. We have exploited RNA-sequencing 
data from the modENCODE project to analyze the transcriptome of C. elegans for 
patterns of trans-splicing. Transcripts of ∼70% of genes are trans-spliced, 
similar to earlier estimates based on analysis of far fewer genes. The mRNAs of 
most trans-spliced genes are spliced to either SL1 or SL2, but most genes are 
not trans-spliced to both, indicating that SL1 and SL2 trans-splicing use 
different underlying mechanisms. SL2 trans-splicing occurs in order to separate 
the products of genes in operons genome wide. Shorter intercistronic distance is 
associated with greater use of SL2. Finally, increased use of SL1 trans-splicing 
to downstream operon genes can indicate the presence of an extra promoter in the 
intercistronic region, creating what has been termed a "hybrid" operon. Within 
hybrid operons the presence of the two promoters results in the use of the two 
SL classes: Transcription that originates at the promoter upstream of another 
gene creates a polycistronic pre-mRNA that receives SL2, whereas transcription 
that originates at the internal promoter creates transcripts that receive SL1. 
Overall, our data demonstrate that >17% of all C. elegans genes are in operons.