@article{Allen01022011,
author = {Allen, Mary Ann and Hillier, LaDeana W. and Waterston, Robert H. and Blumenthal, Thomas}, 
title = {A global analysis of C. elegans trans-splicing},
volume = {21}, 
number = {2}, 
pages = {255-264}, 
year = {2011}, 
doi = {10.1101/gr.113811.110}, 
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.}, 
URL = {http://genome.cshlp.org/content/21/2/255.abstract}, 
eprint = {http://genome.cshlp.org/content/21/2/255.full.pdf+html}, 
journal = {Genome Research} 
}