ArticleGenome research2023
Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 25 citations in OpenAlex.
- Single-cell analysis of HIV expression and integration sites reveals robust viral expression across diverse chromatin environments.Microbiology spectrum · 2026Article
- A Leap Forward in Vaccination - the Epigenetic Silencing of HIV by cVacc.Current HIV/AIDS reports · 2026Review
- Is the molecular microenvironment of the latent HIV reservoir predictable using deep learning approaches?Journal of virology · 2026Review
- HERV-K HML-2 transcriptional profiling and splicing pattern unveiled by direct single-molecule long-read RNA sequencing.Mobile DNA · 2026Article
- Transcription of HIV-1 is heterogenous among authentic latent CD4+ T cell clones.The Journal of experimental medicine · 2026Article
- Review
- Article
- iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm.Briefings in bioinformatics · 2026Article
- Development and validation of HIV SMRTcap for the characterization of HIV-1 reservoirs across tissues and subtypes.PLoS pathogens · 2026Article
- Transcription factor BACH2 shapes tissue-resident memory T cell programs to promote HIV-1 persistence.Immunity · 2025Article
- Using single cell technologies to understand HIV latency models.Current opinion in HIV and AIDS · 2025Review
- Advances in Single-Cell Sequencing for Infectious Diseases: Progress and Perspectives.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Medications for opioid use disorder shape immune responses during chronic HIV infection.Cell reports. Medicine · 2025Article
- Impact of chromatin on HIV-1 latency: a multi-dimensional perspective.Epigenetics & chromatin · 2025Review
- HIV-1 control in vivo is related to the number but not the fraction of infected cells with viral unspliced RNA.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Transcription of HIV-1 at sites of intact latent provirus integration.The Journal of experimental medicine · 2024Article
- HIV-1 control in vivo is related to the number but not the fraction of infected cells with viral unspliced RNA.bioRxiv : the preprint server for biology · 2024Article
- Specific quantification of inducible HIV-1 reservoir by RT-LAMP.Communications medicine · 2024Article
- Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation.Genomics, proteomics & bioinformatics · 2024Article
- Transcription of HIV-1 at sites of intact latent provirus integration.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
HIV-1 integration introduces ectopic transcription factor binding sites into host chromatin. We postulate that the integrated provirus serves as an ectopic enhancer that recruits additional transcription factors to the integration locus, increases chromatin accessibility, changes 3D chromatin interactions, and enhances both retroviral and host gene expression. We used four well-characterized HIV-1-infected cell line clones having unique integration sites and low to high levels of HIV-1 expression. Using single-cell DOGMA-seq, which captured the heterogeneity of HIV-1 expression and host chromatin accessibility, we found that HIV-1 transcription correlated with HIV-1 accessibility and host chromatin accessibility. HIV-1 integration increased local host chromatin accessibility within an ∼5- to 30-kb distance. CRISPRa- and CRISPRi-mediated HIV-1 promoter activation and inhibition confirmed integration site-dependent HIV-1-driven changes of host chromatin accessibility. HIV-1 did not drive chromatin confirmation changes at the genomic level (by Hi-C) or the enhancer connectome (by H3K27ac HiChIP). Using 4C-seq to interrogate HIV-1-chromatin interactions, we found that HIV-1 interacted with host chromatin ∼100-300 kb from the integration site. By identifying chromatin regions having both increased transcription factor activity (by ATAC-seq) and HIV-1-chromatin interaction (by 4C-seq), we identified enrichment of ETS, RUNT, and ZNF-family transcription factor binding that may mediate HIV-1-host chromatin interactions. Our study has found that HIV-1 promoter activity increases host chromatin accessibility, and HIV-1 interacted with host chromatin within the existing chromatin boundaries in an integration site-dependent manner.
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