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Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay
Published on: August 26, 2018
A study of alternative splicing in the pig
Ann-Britt Nygard1, Susanna Cirera, Michael J Gilchrist
1University of Copenhagen, Faculty of Life Sciences, Department of Basic Animal and Veterinary Sciences, Division of Genetics and Bioinformatics, Groennegaardsvej 3, 1870 Frederiksberg C, Denmark. mf@life.ku.dk.
BMC Research Notes
|May 7, 2010
Summary
Alternative splicing in pigs is prevalent, with about 30% of genes exhibiting this process. Many splice events show tissue specificity and some may be unique to pigs, impacting species differentiation.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Alternative pre-mRNA splicing significantly contributes to proteome complexity in mammals.
- Expressed sequence tags (ESTs) offer a valuable resource for identifying alternative splice forms.
- Over one million porcine ESTs provide a robust dataset for studying alternative splicing in pigs.
Purpose of the Study:
- To identify and characterize alternative splicing events in the domestic pig using EST data.
- To determine the prevalence and tissue specificity of alternative splicing in porcine genes.
- To assess the potential impact of alternative splicing on species differentiation.
Main Methods:
- Assembled and analyzed a comprehensive dataset of porcine ESTs using the Distiller package.
- Identified candidate alternative isoforms in EST clusters.
- Selected genes with distinct tissue-specific alternative splicing for experimental validation using quantitative PCR (qPCR).
Main Results:
- Identified 2,515 EST clusters with candidate alternative isoforms.
- Found that approximately 30% of contigs with over 50 ESTs show putative splice variants.
- Experimentally validated tissue-specific alternative splicing in 6 out of 10 selected genes, with 5 events appearing pig-specific.
Conclusions:
- Approximately 30% of porcine genes undergo alternative splicing, consistent with human and rodent studies.
- Demonstrated a strong correlation between in silico-predicted and experimentally validated tissue-specific splicing events.
- Identified an optimal EST cluster size of around 50 for detecting alternative splicing and suggested its significant role in species differentiation.
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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
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There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
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