High-throughput sequence analysis of Ciona intestinalis SL trans -spliced mRNAs: Alternative expression modes and gene function correlates

作者：Jun Matsumoto, Ken Dewar, Jessica Wasserscheid, Graham B. Wiley, Simone L. Macmil, Bruce A. Roe, Robert W. Zeller, Yutaka Satou, Kenneth E.M. Hastings · 发表于：Genome Research · 年份：2010 · DOI：10.1101/gr.100271.109 · 被引用次数：50 · 研究领域：RNA Research and Splicing、RNA and protein synthesis mechanisms、Marine Ecology and Invasive Species

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 approximately 250,000 high-quality reads corresponding to 8790 genes, approximately 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 approximately 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 approximately 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 ...