ArticleGenome research2016
The life history of retrocopies illuminates the evolution of new mammalian genes.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed, 154 citations in OpenAlex.
- Functional roles and clinical implications of pseudogenes signatures as emerging biomarkers in cancer.Discover oncology · 2026Review
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- The marsupial imprinted gene MLH1 has retrocopies in three marsupial families.Epigenetics & chromatin · 2026Article
- Elevated retrocopy burden and sloth-specific expansions illuminate mammalian genome evolution.BMC biology · 2026Article
- Article
- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- Multiple Retrotransposon-mediated NF-YA Gene Duplication Events Recurred in Diverse Groups of Mammals at Different Ancestry Levels.Genome biology and evolution · 2025Article
- Unveiling the functional nature of retrogenes in dinoflagellates.Open biology · 2025Article
- Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.Genome research · 2025Article
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- The Role of SARS-CoV-2 Spike Protein in Long-term Damage of Tissues and Organs, the Underestimated Role of Retrotransposons and Stem Cells, a Working Hypothesis.Endocrine, metabolic & immune disorders drug targets · 2025Review
- Article
- TheInternational journal of molecular sciences · 2024Article
- Genomic exploration of retrocopies in Insect pests of plants and their role in the expansion of heat shock proteins superfamily as evolutionary targets.BMC genomics · 2024Article
- Article
- Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.bioRxiv : the preprint server for biology · 2024Article
- RCPedia: a global resource for studying and exploring retrocopies in diverse species.Bioinformatics (Oxford, England) · 2024Article
- Evolution of retrocopies in the context of HUSH silencing.Biology direct · 2024Article
- Compensation of gene dosage on the mammalian X.Development (Cambridge, England) · 2024Review
- The roles of gene duplications in the dynamics of evolutionary conflicts.Proceedings. Biological sciences · 2024Review
27 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work established mRNA-derived gene duplicates, known as retrocopies, as models for the study of new gene origination. Here we combine mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some robustly expressed retrocopies are transcribed from preexisting promoters, most evolved new promoters from scratch or recruited proto-promoters in their genomic vicinity. In particular, many retrocopy promoters emerged from ancestral enhancers (or bivalent regulatory elements) or are located in CpG islands not associated with other genes. We detected 88-280 selectively preserved retrocopies per mammalian species, illustrating that these mechanisms facilitated the birth of many functional retrogenes during mammalian evolution. The regulatory evolution of originally monoexonic retrocopies was frequently accompanied by exon gain, which facilitated co-option of distant promoters and allowed expression of alternative isoforms. While young retrogenes are often initially expressed in the testis, increased regulatory and structural complexities allowed retrogenes to functionally diversify and evolve somatic organ functions, sometimes as complex as those of their parents. Thus, some retrogenes evolved the capacity to temporarily substitute for their parents during the process of male meiotic X inactivation, while others rendered parental functions superfluous, allowing for parental gene loss. Overall, our reconstruction of the "life history" of mammalian retrogenes highlights retroposition as a general model for understanding new gene birth and functional evolution.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.