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11:52
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
Published on: August 4, 2016
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Improved definition of the mouse transcriptome via targeted RNA sequencing
Giovanni Bussotti1, Tommaso Leonardi1, Michael B Clark2
1EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom;
Genome Research
|May 20, 2016
Summary
Targeted RNA sequencing reveals a more complex mouse transcriptome than previously understood. This approach refines gene models and identifies novel long noncoding RNA isoforms with open reading frames.
Area of Science:
- Genomics
- Transcriptomics
- Molecular Biology
Background:
- The mouse transcriptome's complexity is not fully characterized.
- Existing transcript annotations may be incomplete or inaccurate.
Purpose of the Study:
- To refine transcript annotations in the murine GRCm38 assembly using targeted RNA sequencing.
- To identify novel long noncoding RNA (lncRNA) isoforms and improve gene models.
Main Methods:
- Applied CaptureSeq (targeted RNA sequencing) across five mouse tissues and three brain subregions.
- Selected over 23,000 putative lncRNA regions and 154,281 splicing junction sites for sequencing.
- Developed a novel filtering pipeline to identify high-quality, unannotated transcript isoforms.
Main Results:
- Demonstrated a significantly more complex mouse transcriptome than previously known.
- Assembled more complete transcript isoforms, expanded transcript boundaries, and connected fragmented read data.
- Condensed 911 GENCODE neighboring genes into 400 expanded gene models and identified 594 lncRNAs acquiring an open reading frame (ORF).
Conclusions:
- CaptureSeq significantly enhances transcript annotation accuracy and completeness in the mouse genome.
- The study reveals novel lncRNA isoforms and refines existing gene models, contributing to a deeper understanding of the transcriptome.
- Findings were validated using FANTOM and Mouse ENCODE resources.
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