ArticlePLoS genetics2013
The majority of primate-specific regulatory sequences are derived from transposable elements.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 215 papers, 1 of them a synthesis that pooled it.
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Who cites it
215 citing papers in PubMed, 1 synthesis or guideline pooled it, 373 citations in OpenAlex.
- Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance.Genome medicine · 2021Pooled it
- Regulatory Evolution and the Genetic Basis of Human Brain Expansion.Journal of molecular evolution · 2026Review
- Gene regulatory innovations from transposable elements in primate cerebellum development.Nature communications · 2026Article
- Long-read sequencing maps transposable element variation and its regulatory and epigenetic effects in the human brain.bioRxiv : the preprint server for biology · 2026Article
- Transposable element regulation in mammalian germ cells and other contexts: multilayered repression, fertility, and regulated activation.Epigenomics · 2026Review
- Mechanisms coordinating exit from the stem cell state in mammals.Genes & development · 2026Review
- Transposable elements impact the human regulatory landscape through cell type specific epigenomic associations.Nature communications · 2026Article
- Genome architecture shapes the evolutionary origins of redundant enhancers in fly and mouse.bioRxiv : the preprint server for biology · 2026Article
- Comparative genomics reveals LINE-1 recombination with diverse RNAs.Cell genomics · 2026Article
- Transposable elements shape stemness in normal and leukemic hematopoiesis.Nature genetics · 2026Article
- Deciphering the Evolution Pattern of Structural Variations Overlapped With Repetitive Sequence During Cattle Evolution.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Transposable element-mediated evolutionary expansion of Sox2- and Brn2-binding regulatory modules for mammalian neural-cell differentiation.Genome biology · 2026Article
- Epigenetic Deregulation of Transposable Elements Links Developmental Processes and Tumorigenesis.International journal of molecular sciences · 2026Review
- Transposable Elements Seed Transcription Factor Binding Sites to Sequence-Specific Double-Stranded DNA Binding TF Networks Contributing to Governance of Primate Brain Evolution.Journal of molecular evolution · 2026Article
- Architectural and evolutionary features of TE-derived TSSs shape tissue-specific promoter activity in the human genome.Nature communications · 2026Article
- Expression spectrum of TE-driven transcripts in human adult tissues.Genome biology · 2026Article
- Dissecting the contribution of transposable elements to interphase chromosome structure.Genome biology · 2026Article
- PervasivebioRxiv : the preprint server for biology · 2025Article
- Derepression of transposable elements in the mouse prefrontal cortex disrupts social behavior.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Retroviral insertions contributed to the divergence of human and chimpanzee brains.bioRxiv : the preprint server for biology · 2025Article
155 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
Although emerging evidence suggests that transposable elements (TEs) have contributed novel regulatory elements to the human genome, their global impact on transcriptional networks remains largely uncharacterized. Here we show that TEs have contributed to the human genome nearly half of its active elements. Using DNase I hypersensitivity data sets from ENCODE in normal, embryonic, and cancer cells, we found that 44% of open chromatin regions were in TEs and that this proportion reached 63% for primate-specific regions. We also showed that distinct subfamilies of endogenous retroviruses (ERVs) contributed significantly more accessible regions than expected by chance, with up to 80% of their instances in open chromatin. Based on these results, we further characterized 2,150 TE subfamily-transcription factor pairs that were bound in vivo or enriched for specific binding motifs, and observed that TEs contributing to open chromatin had higher levels of sequence conservation. We also showed that thousands of ERV-derived sequences were activated in a cell type-specific manner, especially in embryonic and cancer cells, and we demonstrated that this activity was associated with cell type-specific expression of neighboring genes. Taken together, these results demonstrate that TEs, and in particular ERVs, have contributed hundreds of thousands of novel regulatory elements to the primate lineage and reshaped the human transcriptional landscape.
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Registered trials
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.