ArticlePloS one2012
29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
43 citing papers in PubMed, 71 citations in OpenAlex.
- Genomic indicators of gene function: a systematic assessment of the human genome.G3 (Bethesda, Md.) · 2026Article
- CroCoNet: a framework for the quantitative comparison of gene regulatory networks across species.Genome biology · 2026Article
- Enrichment ofInternational journal of molecular sciences · 2024Article
- Neurodegenerative diseases reflect the reciprocal roles played by retroelements in regulating memory and immunity.Frontiers in neuroscience · 2024Article
- Cis-Regulatory Elements in Mammals.International journal of molecular sciences · 2023Review
- Review
- Mammalian genome innovation through transposon domestication.Nature cell biology · 2022Review
- Roles of transposable elements in the regulation of mammalian transcription.Nature reviews. Molecular cell biology · 2022Review
- Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements.Molecular biology and evolution · 2022Article
- Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes.Nature communications · 2020Article
- The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements.BioEssays : news and reviews in molecular, cellular and developmental biology · 2020Review
- Co-opted transposons help perpetuate conserved higher-order chromosomal structures.Genome biology · 2020Article
- Transposable elements in human genetic disease.Nature reviews. Genetics · 2019Review
- MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies.Mobile DNA · 2019Article
- Anthropoid primate-specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length.PLoS biology · 2018Article
- Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon.Cell systems · 2018Article
- Mammalian transposable elements and their impacts on genome evolution.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Review
- Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.Nucleic acids research · 2018Article
- Polymorphism in lncRNA AC008392.1 and its interaction with smoking on the risk of lung cancer in a Chinese population.Cancer management and research · 2018Article
- Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints.Molecular biology and evolution · 2017Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Recent research supports the view that changes in gene regulation, as opposed to changes in the genes themselves, play a significant role in morphological evolution. Gene regulation is largely dependent on transcription factor binding sites. Researchers are now able to use the available 29 mammalian genomes to measure selective constraint at the level of binding sites. This detailed map of constraint suggests that mammalian genomes co-opt fragments of mobile elements to act as gene regulatory sequence on a large scale. In the human genome we detect over 280,000 putative regulatory elements, totaling approximately 7 Mb of sequence, that originated as mobile element insertions. These putative regulatory regions are conserved non-exonic elements (CNEEs), which show considerable cross-species constraint and signatures of continued negative selection in humans, yet do not appear in a known mature transcript. These putative regulatory elements were co-opted from SINE, LINE, LTR and DNA transposon insertions. We demonstrate that at least 11%, and an estimated 20%, of gene regulatory sequence in the human genome showing cross-species conservation was co-opted from mobile elements. The location in the genome of CNEEs co-opted from mobile elements closely resembles that of CNEEs in general, except in the centers of the largest gene deserts where recognizable co-option events are relatively rare. We find that regions of certain mobile element insertions are more likely to be held under purifying selection than others. In particular, we show 6 examples where paralogous instances of an often co-opted mobile element region define a sequence motif that closely matches a transcription factor's binding profile.
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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.