ArticleCell cycle (Georgetown, Tex.)2015
New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome.
Article in Cell cycle (Georgetown, Tex.), 2015. 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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Who cites it
21 citing papers in PubMed, 28 citations in OpenAlex.
- RETRACTED: Endogenous Retroviruses as Regulators of Innate Immune Signaling and InflammationViruses · 2026Review
- Review
- Endogenous retroviruses and response to immune checkpoint inhibitors: mechanisms, clinical evidence, and therapeutic implications.Frontiers in immunology · 2026Review
- EEfinder, a general purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes.Computational and structural biotechnology journal · 2024Article
- Targeted Variant Assessments of Human Endogenous Retroviral Regions in Whole Genome Sequencing Data Reveal Retroviral Variants Associated with Papillary Thyroid Cancer.Microorganisms · 2024Article
- Activation of human endogenous retroviruses and its physiological consequences.Nature reviews. Molecular cell biology · 2024Review
- Beyond pathogens: the intriguing genetic legacy of endogenous retroviruses in host physiology.Frontiers in cellular and infection microbiology · 2024Review
- HERVs and Cancer-A Comprehensive Review of the Relationship of Human Endogenous Retroviruses and Human Cancers.Biomedicines · 2023Review
- Endogenous Retroviruses as Modulators of Innate Immunity.Pathogens (Basel, Switzerland) · 2023Review
- Metagenomic analysis of viral genes integrated in whole genome sequencing data of Thai patients with Brugada syndrome.Genomics & informatics · 2022Article
- FNC: An Advanced Anticancer Therapeutic or Just an Underdog?Frontiers in oncology · 2022Review
- Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species.BMC genomics · 2020Review
- Human Endogenous Retroviruses in Clear Cell Renal Cell Carcinoma: Biological Functions and Clinical Values.OncoTargets and therapy · 2020Review
- Article
- Article
- ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins.Frontiers in immunology · 2018Article
- Review
- Viral component of the human genome.Molecular biology · 2017Review
- Friends-Enemies: Endogenous Retroviruses Are Major Transcriptional Regulators of Human DNA.Frontiers in chemistry · 2017Review
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Endogenous retroviruses (ERVs) and LTR retrotransposons (LRs) occupy ∼8% of human genome. Deep sequencing technologies provide clues to understanding of functional relevance of individual ERVs/LRs by enabling direct identification of transcription factor binding sites (TFBS) and other landmarks of functional genomic elements. Here, we performed the genome-wide identification of human ERVs/LRs containing TFBS according to the ENCODE project. We created the first interactive ERV/LRs database that groups the individual inserts according to their familial nomenclature, number of mapped TFBS and divergence from their consensus sequence. Information on any particular element can be easily extracted by the user. We also created a genome browser tool, which enables quick mapping of any ERV/LR insert according to genomic coordinates, known human genes and TFBS. These tools can be used to easily explore functionally relevant individual ERV/LRs, and for studying their impact on the regulation of human genes. Overall, we identified ∼110,000 ERV/LR genomic elements having TFBS. We propose a hypothesis of "domestication" of ERV/LR TFBS by the genome milieu including subsequent stages of initial epigenetic repression, partial functional release, and further mutation-driven reshaping of TFBS in tight coevolution with the enclosing genomic loci.
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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.