The DOI matches its Crossref record; 47 of the 48 references it cites were found in a registry or an index.
The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation
Open accessAbstract
Because of the heterogeneity of chromatin, the site of integration of human immunodeficiency virus (HIV) in the genome could have dramatic effects on its transcriptional activity. We have used an HIV-1-derived retroviral vector, in which the green fluorescent protein is under the control of the HIV promoter, to generate by infection 34 Jurkat clonal cell lines each containing a single integration of the HIV-1 vector. In the absence of Tat, a 75-fold difference in expression level between the highest and lowest expressing clones was observed. Basal promoter activity was low in 80% of the clones and moderate to high in the remaining 20% of clones. We found that differences in expression levels are due to the integration site and are not controlled by DNA methylation or histone acetylation. Tat activated transcription in each clone, and an inverse correlation was observed between basal transcriptional activity and inducibility by Tat. These observations demonstrate that the chromatin environment influences basal HIV gene expression and that the HIV Tat protein activates transcription independently of the chromatin environment.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source doesn’t support the claim as written.
In the citing paper
“However, it is now becoming clearer that certain retroviruses like HIV tend to target gene-rich, transcriptionally active, euchromatic regions within the host’s chromosome to integrate.”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Jordan et al. 2001
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“For example, proviral integration in the transcriptionally active regions could potentially favor expression of the viral genes, whereas integration in the transcriptionally silent regions (heterochromatin) may not be in favor of viral expression and may even force the virus to stay transcriptionally silent (Jordan et al. 2001, Lewinski et al. 2006, Einkauf et al. 2022, Teixeira et al. 2024).”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Jordan et al. 2001
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
A Third-Generation Lentivirus Vector with a Conditional Packaging System
Dull, T., Zufferey, R., Kelly, M., Mandel, R. J., Nguyen, M., Trono, D., & Naldini, L. (1998) · Journal of Virology · doi:10.1128/jvi.72.11.8463-8471.1998 · Cited by 3,341
Dissecting the regulatory circuitry of a eukaryotic genome
Holstege, F. C. P., Jennings, E. G., Wyrick, J. J., Lee, T. I., Hengartner, C. J., Green, M. R., Golub, T. R., Lander, E. S., & Young, R. A. (1998) · Cell · doi:10.1016/s0092-8674(00)81641-4 · Cited by 1,670
Ory, D., Neugeboren, B. I., & Mulligan, R. C. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.21.11400 · Cited by 926
Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product
Kao, S.-Y., Calman, A. F., Luciw, P. A., & Peterlin, B. M. (1987) · Nature · doi:10.1038/330489a0 · Cited by 908
HIV-1 Genome Nuclear Import Is Mediated by a Central DNA Flap
Zennou, V., Petit, C., Guétard, D., Nerhbass, U., Montagnier, L., & Charneau, P. (2000) · Cell · doi:10.1016/s0092-8674(00)80828-4 · Cited by 864
Miller, M. D., Farnet, C. M., & Bushman, F. D. (1997) · Journal of Virology · doi:10.1128/jvi.71.7.5382-5390.1997 · Cited by 620
Lint, C. M. V., Emiliani, S., Ott, M., & Verdin, E. M. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00449.x · Cited by 579
Self-citationP-TEFb kinase is required for HIV Tat transcriptional activation in vivo and in vitroPreprint
Mancebo, H. S. Y., Lee, G., Flygare, J. A., Tomassini, J. E., Luu, P., Zhu, Y., Peng, J., Blau, C., Hazuda, D. J., Price, D. H., et al. (1997) · Genes & Development · doi:10.1101/gad.11.20.2633 · Cited by 546
Binding and Stimulation of HIV-1 Integrase by a Human Homolog of Yeast Transcription Factor SNF5
Kalpana, G. V., Marmon, S., Wang, W., Crabtree, G. R., & Goff, S. P. (1994) · Science · doi:10.1126/science.7801128 · Cited by 530
Verdin, E. M., Paras, P., & Lint, C. M. V. (1993) · The EMBO Journal · doi:10.1002/j.1460-2075.1993.tb05994.x · Cited by 520
Self-citation
Cited by
Sorted by citations
Items 401–468 of 468
Long Terminal Repeats of Gammaretroviruses Retain Stable Expression after Integration Retargeting
Miklík, D., Slavková, M., Kučerová, D., Mekadim, C., Mrázek, J., & Hejnar, J. (2024) · Viruses · doi:10.3390/v16101518 · Cited by 2
Retroviral Integration Target Site Selection
Ciuffi, A., & Bushman, F. D. (2011) · Wiley eBooks · doi:10.1002/9781118015377.ch5 · Cited by 2
Ruess, H., Lee, J., Guzman, C., Malladi, V. S., & D’Orso, I. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.01.072231 · Cited by 2
Implications of HIV persistence and pathogenesis in microglia
Zuidmeer, N., Symons, J., & Nijhuis, M. (2026) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000001044 · Cited by 1
Cell heterogeneity contributes to the variable response of HIV-1 to latency-reversing agents
Topno, R., Karaki, H., Mazzarda, F., Pourcelot, O., Philippe, M., Zibara, K., Radulescu, O., & Bertrand, É. (2026) · Science Advances · doi:10.1126/sciadv.aeb1435 · Cited by 1
White, C., Moesker, B., Ciuffi, A., & Beliakova‐Bethell, N. (2016) · World Journal of Clinical Infectious Diseases · doi:10.5495/wjcid.v6.i2.6 · Cited by 1
The complexity of genome integration process in human lentivirus
García‐Vallejo, F. (2016) · Revista de la Academia Colombiana de Ciencias Exactas Físicas y Naturales · doi:10.18257/raccefyn.364
Boehm, D., & Ott, M. (2017) · BIO-PROTOCOL · doi:10.21769/bioprotoc.2314 · Cited by 1
Tyagi, P., & Tyagi, M. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-99744-7.00007-9 · Cited by 1
Lagadec, F., Singh, P. K., Calmels, C., Lapaillerie, D., Lindemann, D., Parissi, V., Cherepanov, P., Engelman, A., & Lesbats, P. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf449 · Cited by 1
Systemic Approach to the Genome Integration Process of Human Lentivirus
García‐Vallejo, F., & Cecilia, M. D. (2012) · InTech eBooks · doi:10.5772/52885 · Cited by 1
Molecular Mechanisms of HIV-1 Infection in Neonatal Target Cells
Ahmad, N. (2012) · Future Virology · doi:10.2217/fvl.12.26 · Cited by 1
Wellensiek, B. P. (2007) · UA Campus Repository (The University of Arizona) · Cited by 1
Quantifying the dynamics of viruses and the cellular immune response of the host
Althaus, C. L. (2005) · Utrecht University Repository (Utrecht University)
Weinberger, L. S., Burnett, J. C., Toettcher, J. E., Arkin, A. P., & Schaffer, D. V. (2006) · arXiv (Cornell University) · doi:10.48550/arxiv.q-bio/0608003
Hammer, D. (2006) · University of Regensburg Publication Server (University of Regensburg) · doi:10.5283/epub.10447
MESSA A PUNTO DI TEST ALTERNATIVI PER LO SCREENING DI POTENZIALI INIBITORI DELLA PROTEASI DI HIV-1
Parolin, D. (2014) · Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) · doi:10.13130/parolin-debora_phd2014-02-03
Quantitative analysis of adenoviral vector modification of a cytokine-mediated cell death decision
Miller, K. E. (2006) · DSpace@MIT (Massachusetts Institute of Technology)
ASPECTS ON LATENCY IN HIV-1 INFECTION
Lindkvist, A. (2010) · Figshare
Control of HIV-1C Replication Both in Vivo and in Vitro
Xie, W. (2015) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
Características do genoma humano associadas à integração do HIV - análise bioinformática
Gonçalves, J. (2014) · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)
Barichievy, S. (2010) · University of the Witwatersrand, Johannesburg Institutional Repository on DSpace (University of the Witwatersrand, Johannesburg)
Hui, T. (2013) · National University of Singapore
LGIT In Vitro Latency Model in Primary and T Cell Lines to Test HIV-1 Reactivation Compounds
Jung, U., Takahashi, M. M., Rossi, J. J., & Burnett, J. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3046-3_17
Pearson, R. D. (2009) · OhioLink ETD Center (Ohio Library and Information Network)
Lentiviral Biology and Cell Death
Poeschla, E. M. (2005) · CRC Press eBooks · doi:10.1201/9781420038156.sec1
Provirus Silencing in Stem Cells: The Forbidden Regulators of Cell Fate
Satapathy, S. (2016) · Signal Transduction Insights · doi:10.4137/sti.s12311
Efficacy Trials and Progress of HIV Vaccines
Asif, D. F., & Irshad, M. (2017) · Journal of Cell Science & Therapy · doi:10.4172/2157-7013.1000265
Exploring HIV latency using transcription profiling
Telwatte, S., & Yukl, S. A. (2017) · Microbiology Australia · doi:10.1071/ma17050
The role of RhoA signaling pathways in regulating HIV-1 replication
Loomis, R. J. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/nwcm-q546
An HIV Feedback-Resistor: Auto-Regulatory Circuit Deactivator and Noise BufferPreprint
Weinberger, L. S., & Shenk, T. E. (2007) · arXiv (Cornell University) · doi:10.48550/arxiv.q-bio/0701015
μ-Lat: A Mouse Model to Evaluate Human Immunodeficiency Virus Eradication StrategiesPreprint
Sperber, H. S., Togarrati, P. P., Raymond, K. A., Bouzidi, M. S., Gilfanova, R., Gutierrez, A. G., Muench, M. O., & Pillai, S. K. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.18.955492
Comparative analysis of CpG islands in equine infectious anemia virus strains
Liu, Q., Yu, Y.-Y., & Wang, H. (2020) · Virus Genes · doi:10.1007/s11262-020-01749-1
Greene, W. C., Peterlin, B. M., & Stremlau, M. H. (2012) · Elsevier eBooks · doi:10.1016/b978-1-4557-0695-2.00003-1
Vpr shapes the proviral landscape and polyclonal HIV-1 reactivation patterns in cultured cellsPreprint
Atindaana, E., Emery, S. B., Burnett, C., Pitcher, J., Kidd, J. M., & Telesnitsky, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.08.463623
(2014) · ASM Press eBooks · doi:10.1128/9781555815653.refs
Battistini, A., & Sgarbanti, M. (2003) · Informa Healthcare eBooks · doi:10.1201/9780824748401.ch10
(2017) · Microbiology Australia · doi:10.1071/mav38n3
Use molecular barcodes to study emerging infectious diseasesPreprint
Chen, H. (2022) · doi:10.22541/au.165285401.15076943/v1
Lê-Bury, G., Chen, Y., Rhen, J. M., Grenier, J. K., Singhal, A., Russell, D. G., & Boliar, S. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.10.503487
Mkhize, Z. (2023) · ResearchSpace (University of KwaZulu-Natal) · doi:10.29086/10413/23002
Miklík, D., Slavková, M., Kučerová, D., Mekadim, C., Mrázek, J., & Hejnar, J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.30.596639
Maikoo, S., Palstra, R.-J. T. S., Dong, K. L., Mahmoudi, T., Ndung’u, T., & Madlala, P. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.02.606371
Li, S., Lund-Andersen, P. K., Wang, S., Ytreberg, F. M., Naik, M. T., Patel, J. S., & Rowley, P. A. (2025) · Journal of General Virology · doi:10.1099/jgv.0.002104
Zhang, Q., Wu, Y., Yang, J., Zhou, K., Manoharan, E. N. E. A., Wentz, T., Su, L., Yu, A., Wang, H., Bruhn, L., et al. (2025) · Blood Immunology & Cellular Therapy · doi:10.1016/j.bict.2025.100019
RNA splicing patterns contribute to burst size variation among HIV-1-infected Jurkat cell clones
Gopal, K., Burnett, C., Kharytonchyk, S., Emery, A., Atindaana, E., Swanstrom, R. I., Kidd, J. M., & Telesnitsky, A. (2025) · Journal of Virology · doi:10.1128/jvi.01334-25
Jadlowsky, J. K. (2009) · OhioLink ETD Center (Ohio Library and Information Network)
Murugavelu, P., Glebko, H., Rani, J., Tickotsky, N., Levin, L., Kuzmina, A., & Taube, R. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.10.705011
Novel potent antiviral molecules targeting the nucleocapsid protein of the HIV-1 virus
Basta, B. (2012) · theses.fr (ABES) · doi:10.70675/151cc823z1197z4e3azbfd9z27dadc35fe11
Antagonism of HUSH restriction by lentiviral Vpx and Vpr proteins
Chougui, G. (2018) · theses.fr (ABES) · doi:10.70675/a8f60021z4ac1z485az94c1za6a503874720
Identification of specific phylogenetic properties of HIV-1 M and O integrases
Toccafondi, E. (2022) · theses.fr (ABES) · doi:10.70675/2facab6ezc20az472dz8350z9fb6e718e1d4 · Cited by 1
Efficacité et évolution de la réponse lymphocytaire T CD8 au cours de l'infection par VIH-1
White, E. (2022) · theses.fr (ABES) · doi:10.70675/46537244ze125z43e1z9c39z92cf9f645f78
Conflit moléculaire entre les protéines Vpr et Vpx des virus HIV/SIV et les facteurs HUSH et SAMHD1
Larrous, P. (2023) · theses.fr (ABES) · doi:10.70675/fc16267dzad68z4beczb28bz9a828aba2035
Said, M. A. (2023) · theses.fr (ABES) · doi:10.70675/a9c4a87dz9e77z48d7zbd35z5893bdb5df28
Chen, H. (2026) · Journal of Virology · doi:10.1128/jvi.00175-26
Jansen, J., Man, S., Kootstra, F., van Nuenen, A. C., van Dort, K. A., Zamperini, C., Houck, C. W., Kootstra, N. A., & Geijtenbeek, T. B. H. (2026) · Pathogens · doi:10.3390/pathogens15060575
Phan, T., Mavigner, M., Dashti, A., Chahroudi, A., Ribeiro, R. M., Ke, R., & Perelson, A. S. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.01.729198
Jackson-Jones, K. A., Loh, H. X., Tarcan, A., Arif, R., Duckett, K., Fu, R., Hird, C., Ferguson, C., Castelló, A., & Sloan, R. D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.21.739879
Virus-informed targeting of HIV reservoirs: Rev-dependent HIV Immunotherapy (RHIT)
Wu, Y. (2026) · Retrovirology · doi:10.1186/s12977-026-00682-9
Murugavelu, P., Rani, J., Glebko, H., Ambiel, I., Tibroni, N., Tickotsky, N., Heyn, F., Schommers, P., Levin, L., Kuzmina, A., et al. (2026) · EMBO Molecular Medicine · doi:10.1038/s44321-026-00536-z
Anti-HIV-1 Activities and Cytotoxicity Studies of Fadogia ancylantha ExtractsPreprint
Ng'weshemi, K., Makangara, J., Banyikwa, A. T., & Madulu, D. (2026) · Research Square · doi:10.21203/rs.3.rs-11008860/v1
Metadata
- Authors
- Jordan, A., Defechereux, P., & Verdin, E.
- Affiliations
- University of California, San Francisco (US)
- Corresponding author
- Verdin, Eric
- Venue
- The EMBO Journal
- Published
- 2001-04-02
- Volume
- 20
- Issue
- 7
- Pages
- 1726-1738
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC145503
- OpenAlex
- W1964660012
- Cited by
- 467
- References
- 48
- Citations by year
- 2026: 13 · 2025: 21 · 2024: 19 · 2023: 18 · 2022: 15 · 2021: 15 · 2020: 21 · 2019: 21 · 2018: 20 · 2017: 26 · 2016: 25 · 2015: 27 · 2014: 14 · 2013: 15 · 2012: 14
- FWCI
- 6.25
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The EMBO Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Belgian American Educational Foundation
- National Institutes of Health
- National Institute of General Medical Sciences (GM51671-05A2, R01GM051671)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- Tat transactivation, basal transcription, chromatin environment, HIV-1 promoter, retroviral vectors, Jurkat cells, DNA methylation, histone acetylation, HIV gene expression
- MeSH terms
- Binding Sites, Cell Line, Transformed, Genetic Vectors, HeLa Cells, Humans, Hydroxamic Acids, Promoter Regions, Genetic, Tetradecanoylphorbol Acetate, Transcription, Genetic, HIV-1, Transcriptional Activation, Gene Products, tat, Genome, Human, Gene Expression Regulation, Viral, HIV Long Terminal Repeat, Virus Integration, Cyclin-Dependent Kinases, Jurkat Cells, DNA Methylation, Cyclin-Dependent Kinase 9, tat Gene Products, Human Immunodeficiency Virus, Histone Deacetylase Inhibitors
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
