RT Journal
A1 Matsumoto, Jun
A1 Dewar, Ken
A1 Wasserscheid, Jessica
A1 Wiley, Graham B.
A1 Macmil, Simone L.
A1 Roe, Bruce A.
A1 Zeller, Robert W.
A1 Satou, Yutaka
A1 Hastings, Kenneth E.M.
T1 High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: Alternative expression modes and gene function correlates
JF Genome Research 
JO Genome Research 
YR 2010 
FD May 01 
VO 20 
IS 5 
SP 636 
OP 645 
DO 10.1101/gr.100271.109 
UL http://genome.cshlp.org/content/20/5/636.abstract 
AB Pre-mRNA 5′ spliced-leader (SL) trans-splicing occurs in some metazoan groups but not in others. Genome-wide characterization of the trans-spliced mRNA subpopulation has not yet been reported for any metazoan. We carried out a high-throughput analysis of the SL trans-spliced mRNA population of the ascidian tunicate Ciona intestinalis by 454 Life Sciences (Roche) pyrosequencing of SL-PCR-amplified random-primed reverse transcripts of tailbud embryo RNA. We obtained ∼250,000 high-quality reads corresponding to 8790 genes, ∼58% of the Ciona total gene number. The great depth of this data revealed new aspects of trans-splicing, including the existence of a significant class of “infrequently trans-spliced” genes, accounting for ∼28% of represented genes, that generate largely non-trans-spliced mRNAs, but also produce trans-spliced mRNAs, in part through alternative promoter use. Thus, the conventional qualitative dichotomy of trans-spliced versus non-trans-spliced genes should be supplanted by a more accurate quantitative view recognizing frequently and infrequently trans-spliced gene categories. Our data include reads representing ∼80% of Ciona frequently trans-spliced genes. Our analysis also revealed significant use of closely spaced alternative trans-splice acceptor sites which further underscores the mechanistic similarity of cis- and trans-splicing and indicates that the prevalence of ±3-nt alternative splicing events at tandem acceptor sites, NAGNAG, is driven by spliceosomal mechanisms, and not nonsense-mediated decay, or selection at the protein level. The breadth of gene representation data enabled us to find new correlations between trans-splicing status and gene function, namely the overrepresentation in the frequently trans-spliced gene class of genes associated with plasma/endomembrane system, Ca2+ homeostasis, and actin cytoskeleton.