ArticlePLoS computational biology2016
Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed, 29 citations in OpenAlex.
- Co-option of an endogenous retrovirus (LTR7-HERVH) in early human embryogenesis: becoming useful and going unnoticed.Mobile DNA · 2025Review
- Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations.Journal of molecular evolution · 2025Review
- Review
- Review
- Invasion and Amplification of Endogenous Retroviruses in Dasyuridae Marsupial Genomes.Molecular biology and evolution · 2024Article
- Current perspective on the impact of endogenous retroviruses in clear cell renal cell carcinoma.Kidney cancer journal : official journal of the Kidney Cancer Association · 2023Article
- The Immunological Conundrum of Endogenous Retroelements.Annual review of immunology · 2023Review
- The essential but enigmatic regulatory role of HERVH in pluripotency.Trends in genetics : TIG · 2022Review
- HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression.Nucleic acids research · 2020Article
- Human Endogenous Retrovirus K in Cancer: A Potential Biomarker and Immunotherapeutic Target.Viruses · 2020Review
- Human Endogenous Retroviruses in Clear Cell Renal Cell Carcinoma: Biological Functions and Clinical Values.OncoTargets and therapy · 2020Review
- Endogenous Retroviruses Activity as a Molecular Signature of Neurodevelopmental Disorders.International journal of molecular sciences · 2019Review
- Article
- Identification of human endogenous retrovirus transcripts in Hodgkin Lymphoma cells.Molecular biology reports · 2019Article
- Border collies of the genome: domestication of an autonomous retrovirus-like transposon.Current genetics · 2019Review
- Distribution of endogenous gammaretroviruses and variants of the Fv1 restriction gene in individual mouse strains and strain subgroups.PloS one · 2019Article
- The Exaptation of HERV-H: Evolutionary Analyses Reveal the Genomic Features of Highly Transcribed Elements.Frontiers in immunology · 2019Article
- Children With Autism Spectrum Disorder and Their Mothers Share Abnormal Expression of Selected Endogenous Retroviruses Families and Cytokines.Frontiers in immunology · 2019Article
- Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
About 8% of the human genome is made up of endogenous retroviruses (ERVs). Though most human endogenous retroviruses (HERVs) are thought to be irrelevant to our biology notable exceptions include members of the HERV-H family that are necessary for the correct functioning of stem cells. ERVs are commonly found in two forms, the full-length proviral form, and the more numerous solo-LTR form, thought to result from homologous recombination events. Here we introduce a phylogenetic framework to study ERV insertion and solo-LTR formation. We then apply the framework to site patterns sampled from a set of long alignments covering six primate genomes. Studying six categories of ERVs we quantitatively recapitulate patterns of insertional activity that are usually described in qualitative terms in the literature. A slowdown in most ERV groups is observed but we suggest that HERV-K activity may have increased in humans since they diverged from chimpanzees. We find that the rate of solo-LTR formation decreases rapidly as a function of ERV age and that an age dependent model of solo-LTR formation describes the history of ERVs more accurately than the commonly used exponential decay model. We also demonstrate that HERV-H loci are markedly less likely to form solo-LTRs than ERVs from other families. We conclude that the slower dynamics of HERV-H suggest a host role for the internal regions of these exapted elements and posit that in future it will be possible to use the relationship between full-length proviruses and solo-LTRs to help identify large scale co-options in distant vertebrate genomes.
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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.