The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
Abstract
Pseudogenes have long been considered to be 'dead', nonfunctional by-products of genome evolution. However, several lines of evidence now show that some pseudogenes are transcriptionally 'alive', and a few might even have biochemical roles. Therefore, the boundary between genes (often considered to be 'living') and pseudogenes (often considered to be 'dead') might be ambiguous and difficult to define. Here, we examine the evidence for and against pseudogene functionality, and we argue that the time is ripe for revising the definition of a pseudogene. Furthermore, we suggest a classification system to accommodate pseudogenes with various levels of functionality.
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Recent evidence suggests that some pseudogenes are actively transcribed and play critical roles in gene regulation.
“recent evidence suggests that some are actively transcribed and play critical roles in gene regulation (Zheng and Gerstein 2007; Muro et al. 2011; Poliseno 2012).”
From RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations (2014) · cites this paper as Zheng and Gerstein 2007
Cites
The <i>Xist</i> RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene
Duret, L., Chureau, C., Samain, S., Weissenbach, J., & Avner, P. (2006) · Science · doi:10.1126/science.1126316 · Cited by 418 · see citing works
Emergence of Young Human Genes after a Burst of Retroposition in Primates
Marques, A. C., Dupanloup, I., Vinckenbosch, N., Reymond, A., & Kaessmann, H. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030357 · Cited by 311 · see citing works
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Proto-genes and de novo gene birth
Carvunis, A.-R., Rolland, T., Wapinski, I., Calderwood, M. A., Yildirim, M. A., Simonis, N., Charloteaux, B., Hidalgo, C. A., Barbette, J., Santhanam, B., et al. (2012) · Nature · doi:10.1038/nature11184 · Cited by 669 · see citing works
Munger, S. C., Raghupathy, N., Choi, K., Simons, A. K., Gatti, D. M., Hinerfeld, D. A., Svenson, K. L., Keller, M. P., Attie, A. D., Hibbs, M. A., et al. (2014) · Genetics · doi:10.1534/genetics.114.165886 · Cited by 85 · see citing works
- Authors
- Zheng, D., & Gerstein, M. B.
- Affiliations
- Yale University (US)
- Corresponding author
- Zheng, Deyou
- Gerstein, Mark B.
- Venue
- Trends in Genetics
- Publisher
- Elsevier BV
- Published
- 2007-05
- Volume
- 23
- Issue
- 5
- Pages
- 219-224
- ISSN
- 0168-9525 (ISSN-L)
- OpenAlex
- W2003343781
- Cited by
- 113
- References
- 2
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 3 · 2023: 6 · 2022: 2 · 2021: 2 · 2020: 1 · 2019: 2 · 2018: 3 · 2017: 1 · 2016: 6 · 2015: 5 · 2014: 10 · 2013: 9 · 2012: 14
- FWCI
- 1.08
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Trends in Genetics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (P50HG002357, U01HG003156)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- pseudogenes, gene definition, transcriptional activity, genome evolution, pseudogene evolution
- MeSH terms
- Animals, Genes, Humans, Molecular Sequence Data, Mutation, Terminology as Topic, Promoter Regions, Genetic, Pseudogenes, Transcription, Genetic, Genome, Mice
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