The current predicted mechanisms that describe RNA polymerase II (pol II) 
transcription termination downstream of protein expressing genes fail to 
adequately explain, how premature termination is prevented in eukaryotes that 
possess operon-like structures. Here we address this issue by analysing 
transcription termination at the end of single protein expressing genes and 
genes located within operons in the nematode Caenorhabditis elegans. By using a 
combination of RT-PCR and ChIP analysis we found that pol II generally 
transcribes up to 1 kb past the poly(A) sites into the 3' flanking regions of 
the nematode genes before it terminates. We also show that pol II does not 
terminate after transcription of internal poly(A) sites in operons. We provide 
experimental evidence that five randomly chosen C. elegans operons are 
transcribed as polycistronic pre-mRNAs. Furthermore, we show that cis-splicing 
of the first intron located in downstream positioned genes in these 
polycistronic pre-mRNAs is critical for their expression and may play a role in 
preventing premature pol II transcription termination.