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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene
Jun Matsumoto1, Ken Dewar, Jessica Wasserscheid
1Department of Neurology & Neurosurgery, McGill University, Montreal Neurological Institute, Montréal, Québec H3A 2B4, Canada.
Genome Research
|March 10, 2010
Summary
This study reveals that pre-mRNA 5' spliced-leader (SL) trans-splicing in Ciona intestinalis is more complex than previously thought. It identifies frequently and infrequently trans-spliced genes, challenging a simple binary classification.
Area of Science:
- Molecular Biology
- Genomics
- Developmental Biology
Background:
- Pre-mRNA 5' spliced-leader (SL) trans-splicing is a biological process found in some metazoans but not others.
- A comprehensive, genome-wide analysis of the trans-spliced mRNA population has not been previously reported for any metazoan.
Purpose of the Study:
- To perform a high-throughput characterization of the SL trans-spliced mRNA population in the ascidian Ciona intestinalis.
- To investigate the quantitative aspects of trans-splicing and identify novel categories of trans-spliced genes.
- To explore the mechanistic basis and functional implications of alternative trans-splice acceptor site usage.
Main Methods:
- High-throughput pyrosequencing (454 Life Sciences) of SL-PCR-amplified complementary DNA (cDNA) from Ciona intestinalis tailbud embryo RNA.
- Analysis of approximately 250,000 high-quality reads, representing 8790 genes (58% of the Ciona genome).
- Bioinformatic analysis to identify frequently and infrequently trans-spliced genes and assess alternative splice site usage.
Main Results:
- Identification of a significant class of "infrequently trans-spliced" genes (approximately 28% of represented genes) that produce both trans-spliced and non-trans-spliced mRNAs.
- Demonstration of significant use of closely spaced alternative trans-splice acceptor sites, supporting spliceosomal mechanisms over other factors.
- Discovery of correlations between trans-splicing status and gene function, with frequent trans-splicing associated with plasma/endomembrane systems, Ca(2+) homeostasis, and the actin cytoskeleton.
Conclusions:
- The dichotomy of trans-spliced versus non-trans-spliced genes should be replaced by a quantitative view including frequently and infrequently trans-spliced categories.
- Alternative trans-splice acceptor site usage is mechanistically similar to cis-splicing and driven by the spliceosome.
- Trans-splicing status is linked to specific gene functions, providing insights into cellular organization and homeostasis in Ciona intestinalis.
