title: A global analysis of C. elegans trans-splicing.
abstract: 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.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Colorado 80309, USA.
authors.forename: Mary Ann
authors.initials: MA
authors.lastname: Allen
authors.forename: LaDeana W
authors.initials: LW
authors.lastname: Hillier
authors.forename: Robert H
authors.initials: RH
authors.lastname: Waterston
authors.forename: Thomas
authors.initials: T
authors.lastname: Blumenthal
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics; D017353:Gene Deletion; D008297:Male; D058977:Molecular Sequence Annotation; D009876:Operon / Q000235:genetics; D011401:Promoter Regions, Genetic; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D022821:RNA Splice Sites / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D020038:RNA, Spliced Leader / Q000235:genetics / Q000378:metabolism; D020040:Trans-Splicing / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic; D012322:RNA Precursors; D022821:RNA Splice Sites; D012333:RNA, Messenger; D020038:RNA, Spliced Leader