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Updated: Jun 20, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.
Amit N Khachane1, Paul M Harrison
1Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave, Montreal, QC, H3A 1B1 Canada. amit.khachane@mcgill.ca
BMC Genomics
|September 17, 2009
Summary
Researchers identified 1750 transcribed pseudogene annotations (TPAs) in the human genome. Of these, 68 show evolutionary conservation across mammals, suggesting potential regulatory functions for these pseudogenes.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Transcribed pseudogenes (TPAs) are gene copies with decay indicators but active transcription.
- Emerging evidence suggests TPAs may regulate homologous gene expression via antisense interference or small interfering RNAs (siRNAs).
- Assessing genomic evidence for functional TPAs in humans is crucial.
Purpose of the Study:
- To identify and characterize potentially functional transcribed pseudogenes in the human genome.
- To investigate evolutionary conservation and selection pressure on human TPAs.
- To pinpoint strong candidates for further functional studies.
Main Methods:
- Pooled and filtered pseudogene annotations from multiple sources.
- Identified sequences with mid-sequence disablements and full-length mRNA transcription.
- Assessed syntenic conservation of TPAs in various mammalian species (rhesus monkey, mouse, rat, dog, cow).
- Analyzed selection pressure indicators (GC content, substitution rates) and Ka/Ks ratios.
Main Results:
- Identified 1750 human TPAs (approx. 11.5% of all pseudogene annotations).
- Found significant conservation of TPAs in rhesus monkeys (approx. 50%) but limited conservation in mice (approx. 3%).
- TPAs conserved in rhesus monkeys showed evidence of selection pressure on GC content and substitution rates.
- Identified 68 human TPAs syntenically conserved in at least two other mammals.
- Observed three TPA sequences in dogs with characteristics of both protein-coding ability and pseudogenicity.
Conclusions:
- Evolutionary analysis identified candidate functional human transcribed pseudogenes.
- Pinpointed 68 strong candidates for further investigation.
- These conserved TPAs across mammals represent key targets for understanding pseudogene function.
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