ArticleGenome research2007
The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 183 papers.
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183 citing papers in PubMed.
- Transposable elements as evolutionary catalysts of ant macrodiversity.Science advances · 2026Article
- Human Alu loci gain enhancer-type epigenetic modifications in monocytes during response to bacterial LPS.Epigenetics & chromatin · 2026Article
- Genomic sequence evolution underlying human neocortical interareal diversification.Genome biology · 2026Article
- Evolutionary genomic basis of mimicry diversity of Epicopeiidae moths.Molecular biology and evolution · 2026Article
- Retrotransposition Events Shape the Evolution of the Ataxin-3 Gene Family in Primates.Genome biology and evolution · 2026Article
- Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.International journal of molecular sciences · 2026Article
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- Evolution of Repetitive Genomic Content and Gene Families Over Geo-Climatic Gradients in Brassicaceae.Ecology and evolution · 2025Article
- Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice.Nature communications · 2025Article
- Transcriptional and post-transcriptional regulation of transposable elements and their roles in development and disease.Nature reviews. Molecular cell biology · 2025Review
- Emerging Functions of the Repeat Genome in Nuclear Structure: A View from the Human Karyotype.Annual review of genomics and human genetics · 2025Review
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- Exploration of gene presence/absence variations inOpen biology · 2025Article
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors.bioRxiv : the preprint server for biology · 2024Article
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- Evolution of Repetitive Elements, Their Roles in Homeostasis and Human Disease, and Potential Therapeutic Applications.Biomolecules · 2024Review
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- Regulatory transposable elements in the encyclopedia of DNA elements.Nature communications · 2024Article
- Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective.Annual review of genomics and human genetics · 2024Review
123 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Class 2, or DNA transposons, make up approximately 3% of the human genome, yet the evolutionary history of these elements has been largely overlooked and remains poorly understood. Here we carried out the first comprehensive analysis of the activity of human DNA transposons over the course of primate evolution using three independent computational methods. First, we conducted an exhaustive search for human DNA transposons nested within L1 and Alu elements known to be primate specific. Second, we assessed the presence/absence of 794 human DNA transposons at orthologous positions in 10 mammalian species using sequence data generated by The ENCODE Project. These two approaches, which do not rely upon sequence divergence, allowed us to classify DNA transposons into three different categories: anthropoid specific (40-63 My), primate specific (64-80 My), and eutherian wide (81-150 My). Finally, we used this data to calculate the substitution rates of DNA transposons for each category and refine the age of each family based on the average percent divergence of individual copies to their consensus. Based on these combined methods, we can confidently estimate that at least 40 human DNA transposon families, representing approximately 98,000 elements ( approximately 33 Mb) in the human genome, have been active in the primate lineage. There was a cessation in the transpositional activity of DNA transposons during the later phase of the primate radiation, with no evidence of elements younger than approximately 37 My. This data points to intense activity of DNA transposons during the mammalian radiation and early primate evolution, followed, apparently, by their mass extinction in an anthropoid primate ancestor.
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