ArticleNucleic acids research2021
rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 29 citations in OpenAlex.
- intmap: fast and flexible mapping of mobile DNA integration for basic and translational research.Bioinformatics (Oxford, England) · 2026Article
- Relationship between the distribution of LEDGF along genes and positions of HIV-1 DNA integration.mBio · 2026Article
- Clonal dynamics of HIV-infected and uninfected T cells.EBioMedicine · 2026Article
- HIV-1 Integration Site Determines the Transcriptional Fate and Persistence of Integrated Proviruses.bioRxiv : the preprint server for biology · 2026Article
- Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions.Nature microbiology · 2025Article
- CPSF6 promotes HIV-1 preintegration complex function.Journal of virology · 2025Article
- TAR RNA Mimicry of INI1 and Its Influence on Non-Integration Function of HIV-1 Integrase.Viruses · 2025Review
- The nuclear localization signal of CPSF6 governs post-nuclear import steps of HIV-1 infection.PLoS pathogens · 2025Article
- HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration.Nucleic acids research · 2024Article
- Brief Histories of Retroviral Integration Research and Associated International Conferences.Viruses · 2024Review
- The cell biology of HIV-1 latency and rebound.Retrovirology · 2024Review
- Viral and host mediators of non-suppressible HIV-1 viremia.Nature medicine · 2023Article
- Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster.Nucleic acids research · 2023Article
- New insights into transcription elongation control of HIV-1 latency and rebound.Trends in immunology · 2023Review
- HIV-1 Preintegration Complex Preferentially Integrates the Viral DNA into Nucleosomes Containing Trimethylated Histone 3-Lysine 36 Modification and Flanking Linker DNA.Journal of virology · 2022Article
- Allosteric Integrase Inhibitor Influences on HIV-1 Integration and Roles of LEDGF/p75 and HDGFL2 Host Factors.Viruses · 2022Article
- Potential multi-modal effects of provirus integration on HIV-1 persistence: lessons from other viruses.Trends in immunology · 2022Review
- Article
- Review
- Integration features of intact latent HIV-1 in CD4+ T cell clones contribute to viral persistence.The Journal of experimental medicine · 2021Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
HIV-1 integration favors recurrent integration gene (RIG) targets and genic proviruses can confer cell survival in vivo. However, the relationship between initial RIG integrants and how these evolve in patients over time are unknown. To address these shortcomings, we built phenomenological models of random integration in silico, which were used to identify 3718 RIGs as well as 2150 recurrent avoided genes from 1.7 million integration sites across 10 in vitro datasets. Despite RIGs comprising only 13% of human genes, they harbored 70% of genic HIV-1 integrations across in vitro and patient-derived datasets. Although previously reported to associate with super-enhancers, RIGs tracked more strongly with speckle-associated domains. While depletion of the integrase cofactor LEDGF/p75 significantly reduced recurrent HIV-1 integration in vitro, LEDGF/p75 primarily occupied non-speckle-associated regions of chromatin, suggesting a previously unappreciated dynamic aspect of LEDGF/p75 functionality in HIV-1 integration targeting. Finally, we identified only six genes from patient samples-BACH2, STAT5B, MKL1, MKL2, IL2RB and MDC1-that displayed enriched integration targeting frequencies and harbored proviruses that likely contributed to cell survival. Thus, despite the known preference of HIV-1 to target cancer-related genes for integration, we conclude that genic proviruses play a limited role to directly affect cell proliferation in vivo.
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