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SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements.
Britta Mersch1, Noa Sela, Gil Ast
1Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany. b.mersch@dkfz.de
BMC Genetics
|November 8, 2007
Summary
Transposed elements can create new gene versions called isoforms. Our study developed SERpredict to find tissue-specific isoforms generated by these elements in humans and mice.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Transposed elements (TEs) influence organism transcriptomes by generating novel exons (exonization) or inserting into existing ones.
- Exonization events can lead to tissue-specific isoforms or disease-associated transcripts, highlighting their significant biological impact.
Purpose of the Study:
- To identify novel tissue- or tumor-specific isoforms originating from transposed element exonization in human and mouse genomes.
- To develop and validate an automated computational pipeline for detecting such specific exonized retroelements.
Main Methods:
- Development of SERpredict (Specific Exonized Retroelement predictor), an automated analysis pipeline.
- Utilization of Bayesian Statistics within the SERpredict pipeline for robust detection of exonized TEs.
- Application of SERpredict to human and mouse genomic data to identify tissue- or tumor-specific isoforms.
Main Results:
- SERpredict successfully identified multiple genes containing transposed elements that form tissue- or tumor-specific isoforms.
- The analysis confirmed the role of exonized TEs in generating transcriptomic diversity in both human and mouse genomes.
- A higher prevalence of TE-driven transcriptomic shaping was observed in humans compared to mice.
Conclusions:
- The SERpredict pipeline is effective in identifying biologically relevant, specific exonized retroelements.
- Transposed elements play a crucial role in shaping the transcriptomes of both humans and mice.
- Primate-specific Alu elements significantly contribute to the greater impact of TEs on the human transcriptome compared to the mouse transcriptome.
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