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.
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Certain retroviruses such as HIV tend to target gene-rich, transcriptionally active, euchromatic regions within the host chromosome for integration.
“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
The Introduction reports that a study of 61 HIV-1 integration sites found no preferential integration near or within transcription units, contrary to the claim that HIV tends to target gene-rich, transcriptionally active regions. It also reports that integration was disfavored in centromeric heterochromatin, but that narrower observation does not establish the claimed preference. (LLM, conf=0.86)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredIntegrating at a specific site can enhance or repress transcription of integrated proviral DNA; integration in transcriptionally active regions can favor viral gene expression, whereas integration in silent heterochromatin may not favor expression and may force transcriptional silence.
“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
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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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 893 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Verdin, E. M., Paras, P., & Lint, C. M. V. (1993) · The EMBO Journal · doi:10.1002/j.1460-2075.1993.tb05994.x · Cited by 515 · see citing works
Self-citationChromatin structure of endogenous retroviral genes and activation by an inhibitor of DNA methylation
Groudine, M. T., Eisenman, R. N., & Weintraub, H. M. (1981) · Nature · doi:10.1038/292311a0 · Cited by 461 · see citing works
HIV‐1 Tat transcriptional activity is regulated by acetylation
Kiernan, R. E., Vanhulle, C., Schiltz, L., Adam, E., Xiao, H., Maudoux, F., Calomme, C., Burny, A., Nakatani, Y., Jeang, K., et al. (1999) · The EMBO Journal · doi:10.1093/emboj/18.21.6106 · Cited by 416 · see citing works
Karn, J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3060 · Cited by 387 · see citing works
Farnet, C. M., & Bushman, F. D. (1997) · Cell · doi:10.1016/s0092-8674(00)81888-7 · Cited by 359 · see citing works
Acetylation of the HIV-1 Tat protein by p300 is important for its transcriptional activity
Ott, M., Schnölzer, M., Garnica, J., Fischle, W., Emiliani, S., Rackwitz, H., & Verdin, E. M. (1999) · Current Biology · doi:10.1016/s0960-9822(00)80120-7 · Cited by 276 · see citing works
Self-citationHighly preferred targets for retrovirus integration
Shih, C.-C., Stoye, J. P., & Coffin, J. M. (1988) · Cell · doi:10.1016/0092-8674(88)90569-7 · Cited by 259 · see citing works
Reactivation of silenced, virally transduced genes by inhibitors of histone deacetylase
Chen, W., Bailey, E. C., McCune, S. L., Dong, J.-Y., & Townes, T. M. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.11.5798 · Cited by 251 · see citing works
A chromatin insulator protects retrovirus vectors from chromosomal position effects
Emery, D. W., Yannaki, E., Tubb, J., & Stamatoyannopoulos, G. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.160159597 · Cited by 242 · see citing works
Pruss, D., Bushman, F. D., & Wolffe, A. P. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.13.5913 · Cited by 236 · see citing works
Kirchner, J., Connolly, C. M., & Sandmeyer, S. B. (1995) · Science · doi:10.1126/science.7878467 · Cited by 213 · see citing works
Immune Hyperactivation of HIV-1-Infected T Cells Mediated by Tat and the CD28 Pathway
Ott, M., Emiliani, S., Lint, C. M. V., Herbein, G., Lovett, J. L., Chirmule, N. B., McCloskey, T. W., Pahwa, S. G., & Verdin, E. M. (1997) · Science · doi:10.1126/science.275.5305.1481 · Cited by 211 · see citing works
Self-citationTy3 integrates within the region of RNA polymerase III transcription initiation.Preprint
Chalker, D. L., & Sandmeyer, S. B. (1992) · Genes & Development · doi:10.1101/gad.6.1.117 · Cited by 208 · see citing works
Müller, H. P., & Varmus, H. E. (1994) · The EMBO Journal · doi:10.1002/j.1460-2075.1994.tb06794.x · Cited by 202 · see citing works
Rivella, S., Callegari, J., May, C., Tan, C. W., & Sadelain, M. (2000) · Journal of Virology · doi:10.1128/jvi.74.10.4679-4687.2000 · Cited by 201 · see citing works
Zou, S., Ning, K., Kim, J. M., & Voytas, D. F. (1996) · Genes & Development · doi:10.1101/gad.10.5.634 · Cited by 191 · see citing works
Emiliani, S., Fischle, W., Ott, M., Lint, C. M. V., Amella, C. A., & Verdin, E. M. (1998) · Journal of Virology · doi:10.1128/jvi.72.2.1666-1670.1998 · Cited by 188 · see citing works
Self-citationGene silencing as a threat to the success of gene therapy
Bestor, T. H. (2000) · Journal of Clinical Investigation · doi:10.1172/jci9459 · Cited by 182 · see citing works
Histone acetyltransferases regulate HIV-1 enhancer activity in vitroPreprint
Sheridan, P. L., Mayall, T. P., Verdin, E. M., & Jones, K. A. (1997) · Genes & Development · doi:10.1101/gad.11.24.3327 · Cited by 179 · see citing works
Self-citationA point mutation in the HIV-1 Tat responsive element is associated with postintegration latency.
Emiliani, S., Lint, C. M. V., Fischle, W., Paras, P., Ott, M., Brady, J. N., & Verdin, E. M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.13.6377 · Cited by 166 · see citing works
Self-citationRetrovirus vector silencing is de novo methylase independent and marked by a repressive histone code
Pannell, D., Osborne, C. S., Yao, S., Sukonnik, T., Pasceri, P., Karaiskakis, A., Okano, M., Li, E., Lipshitz, H. D., & Ellis, J. (2000) · The EMBO Journal · doi:10.1093/emboj/19.21.5884 · Cited by 158 · see citing works
Hoeben, R. C., Migchielsen, A. A., van der Jagt, R. C., van Ormondt, H., & van der Eb, A. J. (1991) · Journal of Virology · doi:10.1128/jvi.65.2.904-912.1991 · Cited by 157 · see citing works
Inactivation of the HIV LTR by DNA CpG methylation: evidence for a role in latency.
Bednarik, D. P., Cook, J. A., & Pitha, P. M. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb08222.x · Cited by 150 · see citing works
Carteau, S., Hoffmann, C. J., & Bushman, F. D. (1998) · Journal of Virology · doi:10.1128/jvi.72.5.4005-4014.1998 · Cited by 144 · see citing works
Kharroubi, A. E., Piras, G., Zensen, R., & Martin, M. A. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.5.2535 · Cited by 134 · see citing works
Lorincz, M., Schübeler, D., Goeke, S. C., Walters, M. C., Groudine, M., & Martin, D. I. K. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.3.842-850.2000 · Cited by 132 · see citing works
Chen, W., & Townes, T. M. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.1.377 · Cited by 125 · see citing works
Distribution of targets for avian retrovirus DNA integration in vivo
Withers-Ward, E. S., Kitamura, Y., Barnes, J. P., & Coffin, J. M. (1994) · Genes & Development · doi:10.1101/gad.8.12.1473 · Cited by 125 · see citing works
Gold, M. O., Yang, X., Herrmann, C. H., & Rice, A. P. (1998) · Journal of Virology · doi:10.1128/jvi.72.5.4448-4453.1998 · Cited by 117 · see citing works
HIV-1 Tat: coping with negative elongation factors
Garber, M. E., & Jones, K. A. (1999) · Current Opinion in Immunology · doi:10.1016/s0952-7915(99)80077-6 · Cited by 110 · see citing works
Sequence analysis of the human DNA flanking sites of human immunodeficiency virus type 1 integration
Stevens, S. W., & Griffith, J. D. (1996) · Journal of Virology · doi:10.1128/jvi.70.9.6459-6462.1996 · Cited by 96 · see citing works
Trans‐activation of HIV‐1 LTR‐directed gene expression by tat requires protein kinase C.
Jakobovits, A., Rosenthal, A. S., & Capon, D. J. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb08223.x · Cited by 88 · see citing works
Stevens, S. W., & Griffith, J. D. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.12.5557 · Cited by 57 · see citing works
Zhu, Y., Zou, S., Wright, D. A., & Voytas, D. F. (1999) · Genes & Development · doi:10.1101/gad.13.20.2738 · Cited by 57 · see citing works
Host Sequences Flanking the Human T-Cell Leukemia Virus Type 1 Provirus In Vivo
Leclercq, I., Mortreux, F., Cavrois, M., Leroy, A., Antoine Gessain, A., Wain–Hobson, S., & Wattel, E. (2000) · Journal of Virology · doi:10.1128/jvi.74.5.2305-2312.2000 · Cited by 48 · see citing works
Variegation of retroviral vector gene expression in myeloid cells
Zentilin, L., Qin, G., Tafuro, S., Dinauer, M. C., Baum, C., & Giacca, M. (2000) · Gene Therapy · doi:10.1038/sj.gt.3301057 · Cited by 40 · see citing works
West, M. J., & Karn, J. (1999) · The EMBO Journal · doi:10.1093/emboj/18.5.1378 · Cited by 26 · see citing works
HIV Integration: Ini1 for integration?
Miller, M. D., & Bushman, F. D. (1995) · Current Biology · doi:10.1016/s0960-9822(95)00074-1 · Cited by 19 · see citing works
Flagged first, then by citations
1 of the 48 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots
Schröder, A. R. W., Shinn, P., Chen, H., Berry, C., Ecker, J. R., & Bushman, F. (2002) · Cell · doi:10.1016/s0092-8674(02)00864-4 · Cited by 1,832 · see citing works
HIV reproducibly establishes a latent infection after acute infection of T cells in vitro
Jordan, A., Bisgrove, D., & Verdin, E. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg188 · Cited by 914 · see citing works
Self-citationWeinberger, L. S., Burnett, J., Toettcher, J. E., Arkin, A. P., & Schaffer, D. V. (2005) · Cell · doi:10.1016/j.cell.2005.06.006 · Cited by 616 · see citing works
Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus
Ebina, H., Misawa, N., Kanemura, Y., & Koyanagi, Y. (2013) · Scientific Reports · doi:10.1038/srep02510 · Cited by 565 · see citing works
HIV LatencyPreprint
Siliciano, R. F., & Greene, W. C. (2011) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a007096 · Cited by 509 · see citing works
Transcriptional burst frequency and burst size are equally modulated across the human genome
Dar, R. D., Razooky, B. S., Singh, A., Trimeloni, T. V., McCollum, J. M., Cox, C. D., Simpson, M. L., & Weinberger, L. S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1213530109 · Cited by 491 · see citing works
HIV-1 Integration Landscape during Latent and Active Infection
Cohn, L. B., da Silva, I. T., Oliveira, T. Y., Rosales, R., Parrish, E. H., Learn, G. H., Hahn, B. H., Czartoski, J., McElrath, M. J., Lehmann, C., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.020 · Cited by 438 · see citing works
Stevenson, M. (2003) · Nature Medicine · doi:10.1038/nm0703-853 · Cited by 438 · see citing works
Genome-wide analysis of retroviral DNA integration
Bushman, F., Lewinski, M., Ciuffi, A., Barr, S. D., Leipzig, J., Hannenhalli, S., & Hoffmann, C. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1263 · Cited by 456 · see citing works
Epigenetic Regulation of HIV-1 Latency by Cytosine Methylation
Kauder, S. E., Bosque, A., Lindkvist, A., Planelles, V., & Verdin, E. M. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000495 · Cited by 371 · see citing works
Self-citationMicroglial Cells: The Main HIV-1 Reservoir in the Brain
Wallet, C., Rovere, M. D., Assche, J. V., Daouad, F., Wit, S. D., Gautier, V., Mallon, P. W. G., Marcello, A., Lint, C. M. V., Rohr, O., et al. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00362 · Cited by 359 · see citing works
Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells
Tchasovnikarova, I. A., Timms, R. T., Matheson, N. J., Wals, K., Antrobus, R., Göttgens, B., Dougan, G., Dawson, M. A., & Lehner, P. J. (2015) · Science · doi:10.1126/science.aaa7227 · Cited by 360 · see citing works
Targeting the Latent Reservoir for HIV-1
Sengupta, S., & Siliciano, R. F. (2018) · Immunity · doi:10.1016/j.immuni.2018.04.030 · Cited by 333 · see citing works
Yukl, S. A., Kaiser, P. D., Kim, P., Telwatte, S., Joshi, S. K., Vu, M., Lampiris, H. W., & Wong, J. K. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aap9927 · Cited by 332 · see citing works
Expression of Latent HIV Induced by the Potent HDAC Inhibitor Suberoylanilide Hydroxamic Acid
Archin, N. M., Espeseth, A. S., Parker, D., Cheema, M., Hazuda, D. J., & Margolis, D. M. (2009) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2008.0191 · Cited by 336 · see citing works
CpG Methylation Controls Reactivation of HIV from Latency
Blažková, J., Trejbalová, K., Gondois‐Rey, F., Halfon, P., Patrick, P., Guiguen, A., Verdin, E. M., Olive, D., Lint, C. M. V., Hejnar, J., et al. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000554 · Cited by 332 · see citing works
Self-citationHan, Y., Lassen, K. G., Monie, D., Sedaghat, A. R., Shimoji, S., Liu, X., Pierson, T. C., Margolick, J. B., Siliciano, R. F., & Siliciano, J. D. (2004) · Journal of Virology · doi:10.1128/jvi.78.12.6122-6133.2004 · Cited by 328 · see citing works
Craigie, R., & Bushman, F. D. (2012) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a006890 · Cited by 327 · see citing works
Prostratin Antagonizes HIV Latency by Activating NF-κB
Williams, S. A., Chen, L., Kwon, H., Fenard, D., Bisgrove, D. A., Verdin, E. M., & Greene, W. C. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m402124200 · Cited by 315 · see citing works
Self-citationLlano, M., Vanegas, M., Fregoso, O., Saenz, D., Chung, S., Peretz, M., & Poeschla, E. M. (2004) · Journal of Virology · doi:10.1128/jvi.78.17.9524-9537.2004 · Cited by 305 · see citing works
Charting HIV's remarkable voyage through the cell: Basic science as a passport to future therapy
Greene, W. C., & Peterlin, B. M. (2002) · Nature Medicine · doi:10.1038/nm0702-673 · Cited by 293 · see citing works
Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription
Lewinski, M. K., Bisgrove, D. A., Shinn, P., Chen, H., Hoffmann, C., Hannenhalli, S. S., Verdin, E. M., Berry, C. C., Ecker, J. R., & Bushman, F. D. (2005) · Journal of Virology · doi:10.1128/jvi.79.11.6610-6619.2005 · Cited by 270 · see citing works
Self-citationSingh, A., Razooky, B. S., Cox, C. D., Simpson, M. L., & Weinberger, L. S. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.03.001 · Cited by 241 · see citing works
Emiliani, S., Mousnier, A., Busschots, K., Maroun, M., Maele, B. V., Tempé, D., Vandekerckhove, L., Moisant, F., Benslama, L., Witvrouw, M., et al. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m501378200 · Cited by 243 · see citing works
Role of PSIP1/LEDGF/p75 in Lentiviral Infectivity and Integration Targeting
Marshall, H. M., Ronen, K., Berry, C., Llano, M., Sutherland, H., Saenz, D., Bickmore, W., Poeschla, E., & Bushman, F. D. (2007) · PLoS ONE · doi:10.1371/journal.pone.0001340 · Cited by 241 · see citing works
Reuse, S., Calao, M., Kabeya, K., Guiguen, A., Gatot, J., Quivy, V., Vanhulle, C., Lamine, A., Vaira, D., Demonté, D., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006093 · Cited by 239 · see citing works
The multifactorial nature of HIV-1 latency
Lassen, K. G., Han, Y., Zhou, Y., Siliciano, J. D., & Siliciano, R. F. (2004) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2004.09.006 · Cited by 233 · see citing works
Lesbats, P., Engelman, A., & Cherepanov, P. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00125 · Cited by 232 · see citing works
A Hardwired HIV Latency Program
Razooky, B. S., Pai, A., Aull, K. H., Rouzine, I. M., & Weinberger, L. S. (2015) · Cell · doi:10.1016/j.cell.2015.02.009 · Cited by 229 · see citing works
The gene product Murr1 restricts HIV-1 replication in resting CD4+ lymphocytes
Lakshmanan, G., Burstein, E., Guha-Niyogi, A., Louder, M. K., Mascola, J. R., Klomp, L. W. J., Wijmenga, C., Duckett, C. S., & Nabel, G. J. (2003) · Nature · doi:10.1038/nature02171 · Cited by 226 · see citing works
Reactivation of latent HIV by histone deacetylase inhibitors
Shirakawa, K., Chávez, L., Hakre, S., Calvanese, V., & Verdin, E. M. (2013) · Trends in Microbiology · doi:10.1016/j.tim.2013.02.005 · Cited by 214 · see citing works
Self-citationHan, Y., Lin, Y. B., An, W., Xu, J., Yang, H., O’Connell, K. A., Dordai, D. I., Boeke, J. D., Siliciano, J. D., & Siliciano, R. F. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.06.008 · Cited by 214 · see citing works
Understanding HIV Latency: The Road to an HIV Cure
Dahabieh, M. S., Battivelli, E., & Verdin, E. M. (2015) · Annual Review of Medicine · doi:10.1146/annurev-med-092112-152941 · Cited by 215 · see citing works
Self-citationDequiedt, F., Kasler, H. G., Fischle, W., Kiermer, V., Weinstein, M., HERNDIER, B. G., & Verdin, E. M. (2003) · Immunity · doi:10.1016/s1074-7613(03)00109-2 · Cited by 212 · see citing works
Self-citationExperimental approaches to the study of HIV-1 latency
Han, Y., Wind‐Rotolo, M., Yang, H., Siliciano, J. D., & Siliciano, R. F. (2007) · Nature Reviews Microbiology · doi:10.1038/nrmicro1580 · Cited by 207 · see citing works
Transient-mediated fate determination in a transcriptional circuit of HIV
Weinberger, L. S., Dar, R. D., & Simpson, M. L. (2007) · Nature Genetics · doi:10.1038/ng.116 · Cited by 191 · see citing works
Molecular mechanisms of HIV-1 persistence in the monocyte-macrophage lineage
Douce, V. L., Herbein, G., Rohr, O., & Schwartz, C. (2010) · Retrovirology · doi:10.1186/1742-4690-7-32 · Cited by 191 · see citing works
Molecular Characterization, Reactivation, and Depletion of Latent HIV
Brooks, D. G., Hamer, D. H., Arlen, P. A., Gao, L., Bristol, G., Ramirez, C. M., Berger, E. A., & Zack, J. A. (2003) · Immunity · doi:10.1016/s1074-7613(03)00236-x · Cited by 192 · see citing works
The transcriptional cycle of HIV-1 in real-time and live cells
Boireau, S., Maiuri, P., Basyuk, E., de la Mata, M., Knezevich, A., Pradet-Balade, B., Bäcker, V., Kornblihtt, A., Marcello, A., & Bertrand, E. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200706018 · Cited by 191 · see citing works
Repressive LTR Nucleosome Positioning by the BAF Complex Is Required for HIV Latency
Rafati, H., Parra, M., Hakre, S., Moshkin, Y. M., Verdin, E. M., & Mahmoudi, T. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001206 · Cited by 188 · see citing works
Self-citationHermankova, M., Siliciano, J. D., Zhou, Y., Monie, D., Chadwick, K. R., Margolick, J. B., Quinn, T. C., & Siliciano, R. F. (2003) · Journal of Virology · doi:10.1128/jvi.77.13.7383-7392.2003 · Cited by 185 · see citing works
Basics of the virology of HIV-1 and its replication
Sierra, S., Kupfer, B., & Kaiser, R. (2005) · Journal of Clinical Virology · doi:10.1016/j.jcv.2005.09.004 · Cited by 183 · see citing works
Battivelli, E., Dahabieh, M. S., Abdel‐Mohsen, M., Svensson, J. P., da Silva, I. T., Cohn, L. B., Gramatica, A., Deeks, S. G., Greene, W. C., Pillai, S. K., et al. (2018) · eLife · doi:10.7554/elife.34655 · Cited by 185 · see citing works
Self-citationPerera, S. A., Li, D., Shimamura, T., Raso, M. G., Ji, H., Chen, L., Borgman, C. L., Zaghlul, S., Brandstetter, K. A., Kubo, S., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808930106 · Cited by 185 · see citing works
Swiggard, W. J., Baytop, C., Yu, J. J., Dai, J., Li, C., Schretzenmair, R., Theodosopoulos, T., & O'Doherty, U. (2005) · Journal of Virology · doi:10.1128/jvi.79.22.14179-14188.2005 · Cited by 182 · see citing works
The SWI/SNF Chromatin-remodeling Complex Is a Cofactor for Tat Transactivation of the HIV Promoter
Mahmoudi, T., Parra, M., Vries, R. G. J., Kauder, S. E., Verrijzer, C. P., Ott, M., & Verdin, E. M. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m603336200 · Cited by 182 · see citing works
Self-citationTréand, C., du Chéné, I., Brès, V., Kiernan, R. E., Bénarous, R., Benkirane, M., & Emiliani, S. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601074 · Cited by 178 · see citing works
Hide, shield and strike back: how HIV-infected cells avoid immune eradication
Peterlin, B. M., & Trono, D. (2003) · Nature reviews. Immunology · doi:10.1038/nri998 · Cited by 176 · see citing works
Kwon, H., Brent, M. M., Getachew, R., Jayakumar, P., Chen, L., Schnölzer, M., McBurney, M. W., Marmorstein, R., Greene, W. C., & Ott, M. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.02.002 · Cited by 172 · see citing works
Hultquist, J. F., Schumann, K., Woo, J. M., Manganaro, L., McGregor, M. J., Doudna, J., Simon, V., Krogan, N. J., & Marson, A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.09.080 · Cited by 170 · see citing works
Position effects influence HIV latency reversal
Chen, H., Martínez, J. P., Zorita, E. V., Meyerhans, A., & Filion, G. J. P. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3328 · Cited by 164 · see citing works
Latency in Human Immunodeficiency Virus Type 1 Infection: No Easy Answers
Persaud, D., Zhou, Y., Siliciano, J. D., & Siliciano, R. F. (2003) · Journal of Virology · doi:10.1128/jvi.77.3.1659-1665.2003 · Cited by 165 · see citing works
Lassen, K. G., Bailey, J. R., & Siliciano, R. F. (2004) · Journal of Virology · doi:10.1128/jvi.78.17.9105-9114.2004 · Cited by 154 · see citing works
Vigna, E., Cavalieri, S., Ailles, L., Geuna, M., Loew, R., Bujard, H., & Naldini, L. (2002) · Molecular Therapy · doi:10.1006/mthe.2002.0542 · Cited by 147 · see citing works
HIV integration site distributions in resting and activated CD4 + T cells infected in culture
Brady, T., Agosto, L. M., Malani, N., Berry, C. C., O’Doherty, U., & Bushman, F. D. (2009) · AIDS · doi:10.1097/qad.0b013e32832caf28 · Cited by 143 · see citing works
Ramezani, A., Hawley, T., & Hawley, R. (2003) · Blood · doi:10.1182/blood-2002-09-2991 · Cited by 143 · see citing works
Regulation of HIV-1 gene transcription: from lymphocytes to microglial cells
Rohr, O., Marban, C., Aunis, D., & Schaeffer, E. (2003) · Journal of Leukocyte Biology · doi:10.1189/jlb.0403180 · Cited by 142 · see citing works
McNamara, R. P., Reeder, J. E., McMillan, E. A., Bacon, C. W., McCann, J. L., & D’Orso, I. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.11.004 · Cited by 138 · see citing works
Retroviral DNA Integration—Mechanism and Consequences
Lewinski, M. K., & Bushman, F. D. (2005) · Advances in genetics · doi:10.1016/s0065-2660(05)55005-3 · Cited by 137 · see citing works
Stochastic gene expression as a molecular switch for viral latency
Singh, A., & Weinberger, L. S. (2009) · Current Opinion in Microbiology · doi:10.1016/j.mib.2009.06.016 · Cited by 130 · see citing works
Ikeda, T., Shibata, J., Yoshimura, K., Koito, A., & Matsushita, S. (2007) · The Journal of Infectious Diseases · doi:10.1086/510915 · Cited by 123 · see citing works
Latency: the hidden HIV-1 challenge
Marcello, A. (2006) · Retrovirology · doi:10.1186/1742-4690-3-7 · Cited by 126 · see citing works
Orthogonal control of expression mean and variance by epigenetic features at different genomic loci
Dey, S. S., Foley, J. E., Limsirichai, P., Schaffer, D. V., & Arkin, A. P. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145704 · Cited by 119 · see citing works
HIV-1 gene expression: lessons from provirus and non-integrated DNA
Wu, Y. (2004) · Retrovirology · doi:10.1186/1742-4690-1-13 · Cited by 124 · see citing works
Regulation of HIV-1 latency by T-cell activation
Williams, S. A., & Greene, W. C. (2007) · Cytokine · doi:10.1016/j.cyto.2007.05.017 · Cited by 122 · see citing works
Acetylation of Tat Defines a CyclinT1-Independent Step in HIV Transactivation
Kaehlcke, K., Dorr, A., Hetzer‐Egger, C., Kiermer, V., Henklein, P., Schnoelzer, M., Loret, E. P., Cole, P. A., Verdin, E. M., & Ott, M. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00245-4 · Cited by 121 · see citing works
Self-citationRetroviral DNA integration: HIV and the role of LEDGF/p75.
Ciuffi, A., & Bushman, F. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.05.006 · Cited by 134 · see citing works
Hide-and-Seek: The Challenge of Viral Persistence in HIV-1 Infection
Geeraert, L., Kraus, G., & Pomerantz, R. J. (2007) · Annual Review of Medicine · doi:10.1146/annurev.med.59.062806.123001 · Cited by 117 · see citing works
Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy
Lian, X., Seiger, K. W., Parsons, E. M., Gao, C., Sun, W., Gladkov, G. T., Roseto, I. C., Einkauf, K. B., Osborn, M. R., Chevalier, J. M., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2022.12.002 · Cited by 116 · see citing works
Quivy, V., Adam, E., Collette, Y., Demonté, D., Chariot, A., Vanhulle, C., Berkhout, B., Castellano, R., de Launoit, Y., Burny, A., et al. (2002) · Journal of Virology · doi:10.1128/jvi.76.21.11091-11103.2002 · Cited by 117 · see citing works
Shen, A., Zink, M. C., Mankowski, J. L., Chadwick, K. R., Margolick, J. B., Carruth, L. M., Li, M., Clements, J. E., & Siliciano, R. F. (2003) · Journal of Virology · doi:10.1128/jvi.77.8.4938-4949.2003 · Cited by 116 · see citing works
Vranckx, L. S., Demeulemeester, J., Saleh, S., Boll, A., Vansant, G., Schrijvers, R., Weydert, C., Battivelli, E., Verdin, E., Cereseto, A., et al. (2016) · EBioMedicine · doi:10.1016/j.ebiom.2016.04.039 · Cited by 113 · see citing works
Self-citationInfluence of Host Gene Transcription Level and Orientation on HIV-1 Latency in a Primary-Cell Model
Shan, L., Yang, H., Rabi, S. A., Bravo, H. C., Shroff, N. S., Irizarry, R. A., Zhang, H., Margolick, J. B., Siliciano, J. D., & Siliciano, R. F. (2011) · Journal of Virology · doi:10.1128/jvi.02536-10 · Cited by 114 · see citing works
HIV latency and integration site placement in five cell-based models
Sherrill-Mix, S. A., Lewinski, M. K., Famiglietti, M., Bosque, A., Malani, N., Ocwieja, K. E., Berry, C. C., Looney, D. J., Shan, L., Agosto, L. M., et al. (2013) · Retrovirology · doi:10.1186/1742-4690-10-90 · Cited by 111 · see citing works
Kolossov, E., Lu, Z., Drobinskaya, I., Gassanov, N., Duan, Y., Sauer, H., Manzke, O., Bloch, W., Bohlen, H., Hescheler, J., et al. (2005) · The FASEB Journal · doi:10.1096/fj.03-1451fje · Cited by 111 · see citing works
Effect of SWI/SNF chromatin remodeling complex on HIV-1 Tat activated transcription
Agbottah, E. T., Deng, L., Dannenberg, L. O., Pumfery, A. M., & Kashanchi, F. (2006) · Retrovirology · doi:10.1186/1742-4690-3-48 · Cited by 110 · see citing works
Determinants of the Establishment of Human Immunodeficiency Virus Type 1 Latency
Duverger, A. E., Jones, J., May, J. E., Bibollet‐Ruche, F., Wagner, F. A., Cron, R. Q., & Kutsch, O. (2009) · Journal of Virology · doi:10.1128/jvi.02058-08 · Cited by 109 · see citing works
Telwatte, S., Lee, S. A., Somsouk, M., Hatano, H., Baker, C. A. R., Kaiser, P. D., Kim, P., Chen, T., Milush, J. M., Hunt, P. W., et al. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1007357 · Cited by 107 · see citing works
Establishment of latent HIV-1 reservoirs: what do we really know?
Vanhamel, J., Bruggemans, A., & Debyser, Z. (2019) · Journal of Virus Eradication · doi:10.1016/s2055-6640(20)30275-2 · Cited by 112 · see citing works
Control of Stochastic Gene Expression by Host Factors at the HIV Promoter
Burnett, J., Miller‐Jensen, K., Shah, P. S., Arkin, A. P., & Schaffer, D. V. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000260 · Cited by 103 · see citing works
Identification of T cell-signaling pathways that stimulate latent HIV in primary cells
Brooks, D. G., Arlen, P. A., Gao, L., Ramirez, C. M., & Zack, J. A. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2233345100 · Cited by 104 · see citing works
Combinatorial Latency Reactivation for HIV-1 Subtypes and Variants
Burnett, J., Lim, K., Calafi, A., Rossi, J. J., Schaffer, D. V., & Arkin, A. P. (2010) · Journal of Virology · doi:10.1128/jvi.00161-10 · Cited by 104 · see citing works
Marban-Doran, C. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki529 · Cited by 103 · see citing works
RetractedSMYD2-Mediated Histone Methylation Contributes to HIV-1 Latency
Boehm, D., Jeng, M. Y., Camus, G., Gramatica, A., Schwarzer, R., Johnson, J. R., Hull, P. A., Montaño, M., Sakane, N., Pagans, S., et al. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.04.011 · Cited by 102 · see citing works
HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency
Skupsky, R., Burnett, J., Foley, J. E., Schaffer, D. V., & Arkin, A. P. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000952 · Cited by 99 · see citing works
Ensoli, B., Bellino, S., Tripiciano, A., Longo, O., Francavilla, V., Marcotullio, S., Cafaro, A., Picconi, O., Paniccia, G., Scoglio, A., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013540 · Cited by 97 · see citing works
Kwon, K. J., Timmons, A. E., Sengupta, S., Simonetti, F. R., Zhang, H., Hoh, R., Deeks, S. G., Siliciano, J. D., & Siliciano, R. F. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aax6795 · Cited by 93 · see citing works
Lian, X., Gao, C., Sun, X., Jiang, C., Einkauf, K. B., Seiger, K. W., Chevalier, J. M., Yuki, Y., Martin, M. P., Hoh, R., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abl4097 · Cited by 96 · see citing works
Lin, X., Irwin, D., Kanazawa, S., Huang, L., Romeo, J. M., Yen, T. S. B., & Peterlin, B. M. (2003) · Journal of Virology · doi:10.1128/jvi.77.15.8227-8236.2003 · Cited by 94 · see citing works
Berro, R., Kehn‐Hall, K., de la Fuente, C., Pumfery, A. M., Adair, R., Wade, J. D., Colberg‐Poley, A. M., Hiscott, J. B., & Kashanchi, F. (2006) · Journal of Virology · doi:10.1128/jvi.80.7.3189-3204.2006 · Cited by 92 · see citing works
Greenwood, E. J. D., Williamson, J. C., Sienkiewicz, A., Naamati, A., Matheson, N. J., & Lehner, P. J. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.025 · Cited by 91 · see citing works
Mechanisms of HIV Latency: an Emerging Picture of Complexity
Margolis, D. M. (2010) · Current HIV/AIDS Reports · doi:10.1007/s11904-009-0033-9 · Cited by 89 · see citing works
Tan, W., Dong, Z., Wilkinson, T. A., Barbas, C., & Chow, S. A. (2006) · Journal of Virology · doi:10.1128/jvi.80.4.1939-1948.2006 · Cited by 89 · see citing works
An HIV Feedback Resistor: Auto-Regulatory Circuit Deactivator and Noise Buffer
Weinberger, L. S., & Shenk, T. E. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0050009 · Cited by 89 · see citing works
Chromatin Reassembly Factors Are Involved in Transcriptional Interference Promoting HIV Latency
Gallastegui, E., Millán-Zambrano, G., Terme, J.-M., Chávez, S., & Jordan, A. (2011) · Journal of Virology · doi:10.1128/jvi.01920-10 · Cited by 85 · see citing works
Self-citationCuring HIV: Pharmacologic Approaches to Target HIV-1 Latency
Choudhary, S. K., & Margolis, D. M. (2011) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010510-100237 · Cited by 83 · see citing works
Althaus, C. L., & de Boer, R. J. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.4 · Cited by 84 · see citing works
MicroRNA-155 Reinforces HIV Latency
Ruelas, D. S., Chan, J. K., Oh, E., Heidersbach, A. J., Hebbeler, A. M., Chávez, L., Verdin, E. M., Rapé, M., & Greene, W. C. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.641837 · Cited by 84 · see citing works
Self-citationHIV-1 Latency: An Update of Molecular Mechanisms and Therapeutic Strategies
Battistini, A., & Sgarbanti, M. (2014) · Viruses · doi:10.3390/v6041715 · Cited by 79 · see citing works
Common Threads in Persistent Viral Infections
Kane, M., & Golovkina, T. (2009) · Journal of Virology · doi:10.1128/jvi.01905-09 · Cited by 88 · see citing works
- 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
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