ArticleGenome research2010
High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed, 49 citations in OpenAlex.
- Reference-free discovery with barcoded single-cell sequencing.Nature biotechnology · 2026Article
- Evolution of SL-RNA Genes and Their Splicing Targets in Parasitic Flatworms.Molecular biology and evolution · 2025Article
- Characterization ofNAR genomics and bioinformatics · 2024Article
- Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids.Nature communications · 2024Article
- slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences.Briefings in bioinformatics · 2023Article
- A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa.Open biology · 2022Article
- SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data.BMC bioinformatics · 2021Article
- SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem.BMC bioinformatics · 2020Article
- A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona.Genome biology and evolution · 2019Article
- Article
- Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni.Scientific reports · 2018Article
- ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.Nucleic acids research · 2018Article
- Evolutionary Insights into RNA trans-Splicing in Vertebrates.Genome biology and evolution · 2016Review
- Fibronectin contributes to notochord intercalation in the invertebrate chordate, Ciona intestinalis.EvoDevo · 2016Article
- Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis.Genome research · 2016Article
- Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.Nucleic acids research · 2015Article
- A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis.Developmental biology · 2015Article
- Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader.Development genes and evolution · 2015Article
- A directed approach for the identification of transcripts harbouring the spliced leader sequence and the effect of trans-splicing knockdown in Schistosoma mansoni.Memorias do Instituto Oswaldo Cruz · 2013Article
- Article
Corrections and comments
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Authors and funding
9 authors at 5 institutions in 3 countries.
Funding
Abstract
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 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, Ca(2+) homeostasis, and actin cytoskeleton.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.