C. elegans sequences that control trans-splicing and operon pre-mRNA processing Journal Article uri icon



  • Many mRNAs in Caenorhabditis elegans are generated through a trans-splicing reaction that adds one of two classes of spliced leader RNA to an independently transcribed pre-mRNA. SL1 leaders are spliced mostly to pre-mRNAs from genes with outrons, intron-like sequences at the 5′-ends of the pre-mRNAs. In contrast, SL2 leaders are nearly exclusively trans-spliced to genes that occur downstream in polycistronic pre-mRNAs produced from operons. Operon pre-mRNA processing requires separation into individual transcripts, which is accomplished by 3′-processing of upstream genes and spliced leader trans-splicing to the downstream genes. We used a novel computational analysis, based on nonnegative matrix factorization, to identify and characterize significant differences in the cis-acting sequence elements that differentiate various types of functional site, including internal versus terminal 3′-processing sites, and SL1 versus SL2 trans-splicing sites. We describe several key elements, including the U-rich (Ur) element that couples 3′-processing with SL2 trans-splicing, and a novel outron (Ou) element that occurs upstream of SL1 trans-splicing sites. Finally, we present models of the distinct classes of trans-splicing reaction, including SL1 trans-splicing at the outron, SL2 trans-splicing in standard operons, competitive SL1-SL2 trans-splicing in operons with large intergenic separation, and SL1 trans-splicing in SL1-type operons, which have no intergenic separation.

publication date

  • September 1, 2007

has restriction

  • bronze

Date in CU Experts

  • April 24, 2014 9:49 AM

Full Author List

  • Graber JH; Salisbury J; Hutchins LN; Blumenthal T

author count

  • 4

published in

  • RNA  Journal

Other Profiles

International Standard Serial Number (ISSN)

  • 1355-8382

Electronic International Standard Serial Number (EISSN)

  • 1469-9001

Additional Document Info

start page

  • 1409

end page

  • 1426


  • 13


  • 9