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Genome-wide assembly and analysis of alternative transcripts in mouse
Alexei A Sharov1, Dawood B Dudekula, Minoru S H Ko
1Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
Genome Research
|May 4, 2005
Summary
Researchers developed a novel algorithm and pipeline to create a comprehensive mouse gene index, identifying numerous alternative transcription/splicing (ATS) events. This new resource significantly expands our understanding of gene expression complexity and aids in designing advanced molecular tools.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Understanding alternative transcription/splicing (ATS) is crucial for comprehending gene expression complexity.
- Existing mouse gene databases have limitations in comprehensively cataloging ATS events.
Purpose of the Study:
- To develop an algorithm and automated pipeline for building a comprehensive mouse gene index with extensive ATS coverage.
- To identify and characterize novel ATS units and their prevalence in protein-coding genes.
Main Methods:
- Developed a computational pipeline for transcript assembly from expressed sequences aligned to the genome.
- Compared the generated gene index with existing databases (TIGR, UniGene, DoTS, ESTGenes).
- Analyzed transcript structures to identify and classify different types of ATS units.
Main Results:
- Identified 191,946 genomic loci, including 27,497 protein-coding genes and 11,906 gene candidates.
- The new gene index contains more transcripts, exons, introns, and longer ORFs compared to existing databases.
- Discovered 23 types of ATS units, with 14 novel types of alternative splicing, alternative starts, and alternative termination.
- Observed significant percentages of protein-coding genes exhibiting alternative splicing (47%), alternative starts (18%), and alternative terminations (14%).
Conclusions:
- The developed gene index provides the most comprehensive coverage of ATS in mice to date.
- This resource will facilitate research into the mechanisms of ATS and the design of accurate exon-based DNA microarrays.
- The identified ATS units offer new insights into the regulatory mechanisms of gene expression.