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Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking
Paul M Harrison1, Deyou Zheng, Zhaolei Zhang
1Department of Biology, McGill University Stewart Biology Building, 1205 Dr. Penfield Avenue, Montreal, Quebec, Canada H3A 1B1. paul.harrison@mcgill.ca
Nucleic Acids Research
|April 30, 2005
Summary
Researchers identified transcribed processed pseudogenes (TPPSigs), which are disabled but transcribed gene copies. These TPPSigs, comprising 4-6% of pseudogenes, are lineage-specific and may influence gene expression.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Pseudogenes are non-functional gene copies, with processed pseudogenes (PPGs) arising from retrotransposition of mRNA.
- Thousands of human PPGs exist, alongside some complete retrotransposed genes.
- Transcribed processed pseudogenes (TPPSigs) are disabled yet transcribed entities, potentially impacting paralogous gene expression.
Purpose of the Study:
- To identify and characterize human transcribed processed pseudogenes (TPPSigs).
- To investigate the potential regulatory roles of TPPSigs in gene expression.
- To determine the genomic distribution and evolutionary conservation of TPPSigs.
Main Methods:
- Mapping expressed sequences to processed pseudogenes (PPGs) and extracting TPPSigs from known mRNAs.
- Filtering PPGs for homology to non-mammalian proteins or structured domains, requiring identical coding-sequence disablements.
- Verifying expression using oligonucleotide microarray data.
Main Results:
- Identified 166–233 human TPPSigs, representing approximately 4–6% of all PPGs.
- TPPSigs are frequently located near the 5' and 3' ends of genes, suggesting promoter co-option or untranslated region insertion.
- TPPSigs exhibit significant lineage specificity, with only 5% having mouse orthologs, likely due to lineage-specific SINE/LINE activity.
Conclusions:
- TPPSigs represent a distinct class of pseudogenes with potential regulatory functions.
- Their genomic location and lineage-specific nature highlight unique evolutionary dynamics.
- Further research into TPPSig function is warranted to understand their impact on gene regulation.