TY  - JOUR
A1  - Allen, Mary Ann
A1  - Hillier, LaDeana W.
A1  - Waterston, Robert H.
A1  - Blumenthal, Thomas
T1  - A global analysis of C. elegans trans-splicing
Y1  - 2011/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 255 
EP  - 264 
DO  - 10.1101/gr.113811.110 
VL  - 21 
IS  - 2 
UR  - http://genome.cshlp.org/content/21/2/255.abstract 
N2  - 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. 
ER  -