RNA-based gene duplication: Mechanistic and evolutionary insights
Open accessAbstract
Gene copies that stem from the mRNAs of parental source genes have long been viewed as evolutionary dead-ends with little biological relevance. Here we review a range of recent studies that have unveiled a significant number of functional retroposed gene copies in both mammalian and some non-mammalian genomes. These studies have not only revealed previously unknown mechanisms for the emergence of new genes and their functions but have also provided fascinating general insights into molecular and evolutionary processes that have shaped genomes. For example, analyses of chromosomal gene movement patterns via RNA-based gene duplication have shed fresh light on the evolutionary origin and biology of our sex chromosomes.
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Retrocopies initially lack introns and native regulatory sequences, but may occasionally acquire functional promoters and become expressed.
“Genes arising through this mechanism, known as retrocopies, initially lack introns and native regulatory sequences, but may occasionally acquire functional promoters and become expressed [13].”
From Origin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications (2025) · cites this paper as [13]
The “Mechanisms of retroposition” section describes retrocopies as copies of fully processed mRNA, supporting their initial lack of introns. “Sources of regulatory elements” describes ways retrocopies can gain promoters and become expressed, but also says they may inherit parental promoters, potentially rather frequently. Thus, the claim that they initially lack native regulatory sequences is too absolute. Page numbers are not available in our copy. (LLM, conf=0.85)
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The evolution of gene expression levels in mammalian organs
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., et al. (2011) · Nature · doi:10.1038/nature10532 · Cited by 1,248 · see citing works
Self-citationThe evolutionary origin of orphan genes
Tautz, D., & Domazet-Lošo, T. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3053 · Cited by 764 · see citing works
New genes as drivers of phenotypic evolution
Chen, S., Krinsky, B. H., & Long, M. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3521 · Cited by 428 · see citing works
Self-citationParker, H. G., VonHoldt, B. M., Quignon, P., Margulies, E. H., Shao, S., Mosher, D. S., Spady, T. C., Elkahloun, A., Cargill, M., Jones, P. G., et al. (2009) · Science · doi:10.1126/science.1173275 · Cited by 342 · see citing works
Recent de novo origin of human protein-coding genes
Knowles, D. G., & McLysaght, A. (2009) · Genome Research · doi:10.1101/gr.095026.109 · Cited by 291 · see citing works
Accelerated Recruitment of New Brain Development Genes into the Human Genome
Zhang, Y. E., Landback, P., Vibranovski, M. D., & Long, M. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001179 · Cited by 164 · see citing works
Self-citationBrosch, M., Saunders, G. I., Frankish, A., Collins, M. O., Yu, L., Wright, J., Verstraten, R., Adams, D. J., Harrow, J., Choudhary, J. S., et al. (2011) · Genome Research · doi:10.1101/gr.114272.110 · Cited by 130 · see citing works
Origin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications
Saccone, S., Brancato, D., Bruno, F., Coniglio, E., Sturiale, V., & Federico, C. (2025) · Genes · doi:10.3390/genes16060702 · Cited by 17 · see citing works
“Genes arising through this mechanism, known as retrocopies, initially lack introns and native regulatory sequences, but may occasionally acquire functional promoters and become expressed [13].”
- Authors
- Kaessmann, H., Vinckenbosch, N., & Long, M.
- Affiliations
- University of Lausanne (CH)
- University of Chicago (US)
- Corresponding author
- Kaessmann, Henrik
- Venue
- Nature Reviews Genetics
- Published
- 2009-01
- Volume
- 10
- Issue
- 1
- Pages
- 19-31
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC3690669
- OpenAlex
- W2028190503
- Cited by
- 449
- References
- 107
- Citations by year
- 2026: 20 · 2025: 9 · 2024: 31 · 2023: 30 · 2022: 32 · 2021: 44 · 2020: 14 · 2019: 23 · 2018: 23 · 2017: 30 · 2016: 28 · 2015: 16 · 2014: 23 · 2013: 33 · 2012: 31
- FWCI
- 1.76
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- IRIS (submittedVersion)
- SERVAL (Université de Lausanne) (submittedVersion, other-oa)
- Funders
- National Science Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (140404)
- National Institutes of Health
- U.S. Public Health Service (R0IGM078070-01A1)
- National Institute of General Medical Sciences (R01GM078070)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- retroposition, retrocopies, reverse transcription, genome evolution, sex chromosome evolution, mammalian genomes
- MeSH terms
- Animals, Humans, Models, Genetic, Phylogeny, RNA, RNA, Messenger, Sex Chromosomes, Retroelements, Evolution, Molecular, Genes, Duplicate, Gene Duplication, Regulatory Elements, Transcriptional
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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