A global analysis of C. elegans trans-splicing

Genome Res. 2011 Feb;21(2):255-64. doi: 10.1101/gr.113811.110. Epub 2010 Dec 22.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Caenorhabditis elegans / genetics*
  • DNA, Intergenic / genetics
  • Gene Deletion
  • Male
  • Molecular Sequence Annotation
  • Operon / genetics
  • Promoter Regions, Genetic
  • RNA Precursors / genetics
  • RNA Precursors / metabolism
  • RNA Splice Sites / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Spliced Leader / genetics
  • RNA, Spliced Leader / metabolism
  • Trans-Splicing / genetics*


  • DNA, Intergenic
  • RNA Precursors
  • RNA Splice Sites
  • RNA, Messenger
  • RNA, Spliced Leader