Generic placeholder image

Current HIV Research

Editor-in-Chief

ISSN (Print): 1570-162X
ISSN (Online): 1873-4251

Review Article

HIV Preintegration Transcription and Host Antagonism

Author(s): Yuntao Wu*

Volume 21, Issue 3, 2023

Published on: 27 June, 2023

Page: [160 - 171] Pages: 12

DOI: 10.2174/1570162X21666230621122637

Price: $65

conference banner
Abstract

Retrovirus integration is an obligatory step for the viral life cycle, but large amounts of unintegrated DNA (uDNA) accumulate during retroviral infection. For simple retroviruses, in the absence of integration, viral genomes are epigenetically silenced in host cells. For complex retroviruses such as HIV, preintegration transcription has been found to occur at low levels from a large population of uDNA even in the presence of host epigenetic silencing mechanisms. HIV preintegration transcription has been suggested to be a normal early process of HIV infection that leads to the syntheses of all three classes of viral transcripts: multiply-spliced, singly-spliced, and unspliced genomic RNA; only viral early proteins such as Nef are selectively translated at low levels in blood CD4 T cells and macrophages, the primary targets of HIV. The initiation and persistence of HIV preintegration transcription have been suggested to rely on viral accessory proteins, particularly virion Vpr and de novo Tat generated from uDNA; both proteins have been shown to antagonize host epigenetic silencing of uDNA. In addition, stimulation of latently infected resting T cells and macrophages with cytokines, PKC activator, or histone deacetylase inhibitors has been found to greatly upregulate preintegration transcription, leading to low-level viral production or even replication from uDNA. Functionally, Nef synthesized from preintegration transcription is biologically active in modulating host immune functions, lowering the threshold of T cell activation, and downregulating surface CD4, CXCR4/CCR5, and HMC receptors. The early Tat activity from preintegration transcription antagonizes repressive minichromatin assembled onto uDNA. The study of HIV preintegration transcription is important to understanding virus-host interaction and antagonism, viral persistence, and the mechanism of integrase drug resistance. The application of unintegrated lentiviral vectors for gene therapy also offers a safety advantage for minimizing retroviral vector-mediated insertional mutagenesis.

Graphical Abstract

[1]
Schwartzberg P, Colicelli J, Goff SP. Construction and analysis of deletion mutations in the pol gene of moloney murine leukemia virus: A new viral function required for productive infection. Cell 1984; 37(3): 1043-52.
[http://dx.doi.org/10.1016/0092-8674(84)90439-2] [PMID: 6204767]
[2]
Donehower LA, Varmus HE. A mutant murine leukemia virus with a single missense codon in pol is defective in a function affecting integration. Proc Natl Acad Sci 1984; 81(20): 6461-5.
[http://dx.doi.org/10.1073/pnas.81.20.6461] [PMID: 6208550]
[3]
List J, Haase AT. Integration of visna virus DNA occurs and may be necessary for productive infection. Virology 1997; 237(2): 189-97.
[http://dx.doi.org/10.1006/viro.1997.8785] [PMID: 9356331]
[4]
Rein A. Murine leukemia viruses: objects and organisms. Adv Virol 2011; 2011: 1-14.
[http://dx.doi.org/10.1155/2011/403419] [PMID: 22312342]
[5]
Wang GZ, Wang Y, Goff SP. Histones are rapidly loaded onto unintegrated retroviral DNAs soon after nuclear entry. Cell Host Microbe 2016; 20(6): 798-809.
[http://dx.doi.org/10.1016/j.chom.2016.10.009] [PMID: 27866901]
[6]
Goff SP. Silencing of unintegrated retroviral DNAs. Viruses 2021; 13(11): 2248.
[http://dx.doi.org/10.3390/v13112248] [PMID: 34835055]
[7]
Malim MH, Emerman M. HIV-1 accessory proteins-ensuring viral survival in a hostile environment. Cell Host Microbe 2008; 3(6): 388-98.
[http://dx.doi.org/10.1016/j.chom.2008.04.008] [PMID: 18541215]
[8]
Shen Q, Wu C, Freniere C, Tripler TN, Xiong Y. Nuclear import of HIV-1. Viruses 2021; 13(11): 2242.
[http://dx.doi.org/10.3390/v13112242] [PMID: 34835048]
[9]
Sakai H, Kawamura M, Sakuragi J, et al. Integration is essential for efficient gene expression of human immunodeficiency virus type 1. J Virol 1993; 67(3): 1169-74.
[http://dx.doi.org/10.1128/jvi.67.3.1169-1174.1993] [PMID: 8437208]
[10]
Englund G, Theodore TS, Freed EO, Engelman A, Martin MA. Integration is required for productive infection of monocyte-derived macrophages by human immunodeficiency virus type 1. J Virol 1995; 69(5): 3216-9.
[http://dx.doi.org/10.1128/jvi.69.5.3216-3219.1995] [PMID: 7707554]
[11]
Ansari-Lari MA, Donehower LA, Gibbs RA. Analysis of human immunodeficiency virus type 1 integrase mutants. Virology 1995; 211(1): 332-5.
[http://dx.doi.org/10.1006/viro.1995.1412] [PMID: 7544046]
[12]
Kelly J, Beddall MH, Yu D, Iyer SR, Marsh JW, Wu Y. Human macrophages support persistent transcription from unintegrated HIV-1 DNA. Virology 2008; 372(2): 300-12.
[http://dx.doi.org/10.1016/j.virol.2007.11.007] [PMID: 18054979]
[13]
Wu Y, Marsh JW. Early transcription from nonintegrated DNA in human immunodeficiency virus infection. J Virol 2003; 77(19): 10376-82.
[http://dx.doi.org/10.1128/JVI.77.19.10376-10382.2003] [PMID: 12970422]
[14]
Wu Y, Marsh JW. Selective transcription and modulation of resting T cell activity by preintegrated HIV DNA. Science 2001; 293(5534): 1503-6.
[http://dx.doi.org/10.1126/science.1061548] [PMID: 11520990]
[15]
Stevenson M, Haggerty S, Lamonica CA, Meier CM, Welch SK, Wasiak AJ. Integration is not necessary for expression of human immunodeficiency virus type 1 protein products. J Virol 1990; 64(5): 2421-5.
[http://dx.doi.org/10.1128/jvi.64.5.2421-2425.1990] [PMID: 2157898]
[16]
Nakajima N, Lu R, Engelman A. Human immunodeficiency virus type 1 replication in the absence of integrase-mediated dna recombination: definition of permissive and nonpermissive T-cell lines. J Virol 2001; 75(17): 7944-55.
[http://dx.doi.org/10.1128/JVI.75.17.7944-7955.2001] [PMID: 11483739]
[17]
Cara A, Guarnaccia F, Reitz MS Jr, Gallo RC, Lori F. Self-limiting, cell type-dependent replication of an integrase-defective human immunodeficiency virus type 1 in human primary macrophages but not T lymphocytes. Virology 1995; 208(1): 242-8.
[http://dx.doi.org/10.1006/viro.1995.1148] [PMID: 11831706]
[18]
Wu Y. HIV-1 gene expression: lessons from provirus and non-integrated DNA. Retrovirology 2004; 1(1): 13.
[http://dx.doi.org/10.1186/1742-4690-1-13] [PMID: 15219234]
[19]
Siekevitz M, Josephs SF, Dukovich M, Peffer N, Wong-Staal F, Greene WC. Activation of the HIV-1 LTR by T cell mitogens and the trans-activator protein of HTLV-. iScience 1987; 238(4833): 1575-8.
[http://dx.doi.org/10.1126/science.2825351] [PMID: 2825351]
[20]
Zimmermann K, Dobrovnik M, Ballaun C, Bevec D, Hauber J, Böhnlein E. trans-Activation of the HIV-1 LTR by the HIV-1 tat and HTLV-I tax proteins is mediated by different cis-acting sequences. Virology 1991; 182(2): 874-8.
[http://dx.doi.org/10.1016/0042-6822(91)90633-M] [PMID: 2024503]
[21]
Rimsky L, Hauber J, Dukovich M, et al. Functional replacement of the HIV-1 rev protein by the HTLV-1 rex protein. Nature 1988; 335(6192): 738-40.
[http://dx.doi.org/10.1038/335738a0] [PMID: 3262832]
[22]
Felber BK, Derse D, Athanassopoulos A, Campbell M, Pavlakis GN. Cross-activation of the Rex proteins of HTLV-I and BLV and of the Rev protein of HIV-1 and nonreciprocal interactions with their RNA responsive elements. New Biol 1989; 1(3): 318-28.
[PMID: 2562124]
[23]
Hope TJ, Bond BL, McDonald D, Klein NP, Parslow TG. Effector domains of human immunodeficiency virus type 1 Rev and human T-cell leukemia virus type I Rex are functionally interchangeable and share an essential peptide motif. J Virol 1991; 65(11): 6001-7.
[http://dx.doi.org/10.1128/jvi.65.11.6001-6007.1991] [PMID: 1920623]
[24]
Hanly SM, Rimsky LT, Malim MH, et al. Comparative analysis of the HTLV-I Rex and HIV-1 Rev trans-regulatory proteins and their RNA response elements. Genes Dev 1989; 3(10): 1534-44.
[http://dx.doi.org/10.1101/gad.3.10.1534] [PMID: 2482226]
[25]
Irwan ID, Cullen BR, Kirchhoff F. Tax induces the recruitment of NF-κB to unintegrated HIV-1 DNA To rescue viral gene expression and replication. J Virol 2021; 95(13): e00285-21.
[http://dx.doi.org/10.1128/JVI.00285-21] [PMID: 33883218]
[26]
Irwan ID, Karnowski HL, Bogerd HP, Tsai K, Cullen BR. Reversal of epigenetic silencing allows robust HIV-1 replication in the absence of integrase function. MBio 2020; 11(3): e01038-20.
[http://dx.doi.org/10.1128/mBio.01038-20] [PMID: 32487757]
[27]
Gelderblom HC, Vatakis DN, Burke SA, Lawrie SD, Bristol GC, Levy DN. Viral complementation allows HIV-1 replication without integration. Retrovirology 2008; 5(1): 60.
[http://dx.doi.org/10.1186/1742-4690-5-60] [PMID: 18613957]
[28]
Wu Y. The second chance story of HIV-1 DNA: Unintegrated? Not a problem! Retrovirology 2008; 5(1): 61.
[http://dx.doi.org/10.1186/1742-4690-5-61] [PMID: 18613958]
[29]
Gaur M, Leavitt AD. Mutations in the human immunodeficiency virus type 1 integrase D,D(35)E motif do not eliminate provirus formation. J Virol 1998; 72(6): 4678-85.
[http://dx.doi.org/10.1128/JVI.72.6.4678-4685.1998] [PMID: 9573231]
[30]
Wiskerchen M, Muesing MA. Human immunodeficiency virus type 1 integrase: effects of mutations on viral ability to integrate, direct viral gene expression from unintegrated viral DNA templates, and sustain viral propagation in primary cells. J Virol 1995; 69(1): 376-86.
[http://dx.doi.org/10.1128/jvi.69.1.376-386.1995] [PMID: 7983732]
[31]
Engelman A, Englund G, Orenstein JM, Martin MA, Craigie R. Multiple effects of mutations in human immunodeficiency virus type 1 integrase on viral replication. J Virol 1995; 69(5): 2729-36.
[http://dx.doi.org/10.1128/jvi.69.5.2729-2736.1995] [PMID: 7535863]
[32]
Kimpton J, Emerman M. Detection of replication-competent and pseudotyped human immunodeficiency virus with a sensitive cell line on the basis of activation of an integrated beta-galactosidase gene. J Virol 1992; 66(4): 2232-9.
[http://dx.doi.org/10.1128/jvi.66.4.2232-2239.1992] [PMID: 1548759]
[33]
Swingler S, Easton A, Morris A. Cytokine augmentation of HIV-1 LTR-driven gene expression in neural cells. AIDS Res Hum Retroviruses 1992; 8(4): 487-93.
[http://dx.doi.org/10.1089/aid.1992.8.487] [PMID: 1599755]
[34]
Aguilar-Cordova E, Chinen J, Donehower L, Lewis D, Belmont JW. A sensitive reporter cell line for HIV-1 tat activity, HIV-1 inhibitors, and T cell activation effects. AIDS Res Hum Retroviruses 1994; 10(3): 295-301.
[http://dx.doi.org/10.1089/aid.1994.10.295] [PMID: 8018390]
[35]
Garcia JA, Wu FK, Mitsuyasu R, Gaynor RB. Interactions of cellular proteins involved in the transcriptional regulation of the human immunodeficiency virus. EMBO J 1987; 6(12): 3761-70.
[http://dx.doi.org/10.1002/j.1460-2075.1987.tb02711.x] [PMID: 3428273]
[36]
Swingler S, Morris A, Easton A. Tumour necrosis factor alpha and interleukin-1 beta induce specific subunits of NFKB to bind the HIV-1 enhancer: characterisation of transcription factors controlling human immunodeficiency virus type 1 gene expression in neural cells. Biochem Biophys Res Commun 1994; 203(1): 623-30.
[http://dx.doi.org/10.1006/bbrc.1994.2228] [PMID: 8074713]
[37]
Akan E, Chang-Liu CM, Watanabe J, Ishizawa K, Woloschak GE. The effects of vinblastine on the expression of human immunodeficiency virus type 1 long terminal repeat. Leuk Res 1997; 21(5): 459-64.
[http://dx.doi.org/10.1016/S0145-2126(96)00125-7] [PMID: 9225075]
[38]
Sweet MJ, Hume DA. RAW264 macrophages stably transfected with an HIV-1 LTR reporter gene provide a sensitive bioassay for analysis of signalling pathways in macrophages stimulated with lipopolysaccharide, TNF-alpha or taxol. J Inflamm 1995; 45(2): 126-35.
[PMID: 7583358]
[39]
Kurata S. Sensitization of the HIV-1-LTR upon long term low dose oxidative stress. J Biol Chem 1996; 271(36): 21798-802.
[http://dx.doi.org/10.1074/jbc.271.36.21798] [PMID: 8702977]
[40]
Iordanskiy S, Van Duyne R, Sampey GC, et al. Therapeutic doses of irradiation activate viral transcription and induce apoptosis in HIV-1 infected cells. Virology 2015; 485: 1-15.
[http://dx.doi.org/10.1016/j.virol.2015.06.021] [PMID: 26184775]
[41]
Merzouki A, Patel P, Cassol S, et al. HIV-1 gp120/160 expressing cells upregulate HIV-1 LTR directed gene expression in a cell line transfected with HIV-1 LTR-reporter gene constructs. Cell Mol Biol 1995; 41(3): 445-52.
[PMID: 7580840]
[42]
Poon B, Chang MA, Chen ISY. Vpr is required for efficient Nef expression from unintegrated human immunodeficiency virus type 1 DNA. J Virol 2007; 81(19): 10515-23.
[http://dx.doi.org/10.1128/JVI.00947-07] [PMID: 17652391]
[43]
Poon B, Chen ISY. Human immunodeficiency virus type 1 (HIV-1) Vpr enhances expression from unintegrated HIV-1 DNA. J Virol 2003; 77(7): 3962-72.
[http://dx.doi.org/10.1128/JVI.77.7.3962-3972.2003] [PMID: 12634356]
[44]
Rampersad S, Tennant P. Replication and Expression Strategies of Viruses Viruses. Cambridge, USA: Academic Press 2018; pp. 55-82.
[http://dx.doi.org/10.1016/B978-0-12-811257-1.00003-6]
[45]
Meltzer B, Dabbagh D, Guo J, Kashanchi F, Tyagi M, Wu Y. Tat controls transcriptional persistence of unintegrated HIV genome in primary human macrophages. Virology 2018; 518: 241-52.
[http://dx.doi.org/10.1016/j.virol.2018.03.006] [PMID: 29549786]
[46]
Gillim-Ross L, Cara A, Klotman ME. Nef expressed from human immunodeficiency virus type 1 extrachromosomal DNA downregulates CD4 on primary CD4+ T lymphocytes: implications for integrase inhibitors. J Gen Virol 2005; 86(3): 765-71.
[http://dx.doi.org/10.1099/vir.0.80570-0] [PMID: 15722538]
[47]
Sloan RD, Donahue DA, Kuhl BD, Bar-Magen T, Wainberg MA. Expression of Nef from unintegrated HIV-1 DNA downregulates cell surface CXCR4 and CCR5 on T-lymphocytes. Retrovirology 2010; 7(1): 44.
[http://dx.doi.org/10.1186/1742-4690-7-44] [PMID: 20465832]
[48]
Wu Y, Beddall MH, Marsh JW. Rev-dependent lentiviral expression vector. Retrovirology 2007; 4(1): 12.
[http://dx.doi.org/10.1186/1742-4690-4-12] [PMID: 17286866]
[49]
Yuntao Wu, Beddall MH, Marsh JW. Rev-dependent indicator T cell line. Curr HIV Res 2007; 5(4): 394-402.
[http://dx.doi.org/10.2174/157016207781024018] [PMID: 17627502]
[50]
Sloan RD, Kuhl BD, Donahue DA, Roland A, Bar-Magen T, Wainberg MA. Transcription of preintegrated HIV-1 cDNA modulates cell surface expression of major histocompatibility complex class I via Nef. J Virol 2011; 85(6): 2828-36.
[http://dx.doi.org/10.1128/JVI.01854-10] [PMID: 21209113]
[51]
Stevenson M, Stanwick TL, Dempsey MP, Lamonica CA. HIV-1 replication is controlled at the level of T cell activation and proviral integration. EMBO J 1990; 9(5): 1551-60.
[http://dx.doi.org/10.1002/j.1460-2075.1990.tb08274.x] [PMID: 2184033]
[52]
Benkirane M, Chun RF, Xiao H, et al. Activation of integrated provirus requires histone acetyltransferase. p300 and P/CAF are coactivators for HIV-1 Tat. J Biol Chem 1998; 273(38): 24898-905.
[http://dx.doi.org/10.1074/jbc.273.38.24898] [PMID: 9733796]
[53]
Iyer SR, Yu D, Biancotto A, Margolis LB, Wu Y. Measurement of human immunodeficiency virus type 1 preintegration transcription by using Rev-dependent Rev-CEM cells reveals a sizable transcribing DNA population comparable to that from proviral templates. J Virol 2009; 83(17): 8662-73.
[http://dx.doi.org/10.1128/JVI.00874-09] [PMID: 19553325]
[54]
Shuck-Lee D, Chang H, Sloan EA, Hammarskjold ML, Rekosh D. Single-nucleotide changes in the HIV Rev-response element mediate resistance to compounds that inhibit Rev function. J Virol 2011; 85(8): 3940-9.
[http://dx.doi.org/10.1128/JVI.02683-10] [PMID: 21289114]
[55]
Sigal A, Kim JT, Balazs AB, et al. Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy. Nature 2011; 477(7362): 95-8.
[http://dx.doi.org/10.1038/nature10347] [PMID: 21849975]
[56]
Yoder A, Guo J, Yu D, Cui Z, Zhang XE, Wu Y. Effects of microtubule modulators on HIV-1 infection of transformed and resting CD4 T cells. J Virol 2011; 85(6): 3020-4.
[http://dx.doi.org/10.1128/JVI.02462-10] [PMID: 21209111]
[57]
Guo J, Wang W, Yu D, Wu Y. Spinoculation triggers dynamic actin and cofilin activity that facilitates HIV-1 infection of transformed and resting CD4 T cells. J Virol 2011; 85(19): 9824-33.
[http://dx.doi.org/10.1128/JVI.05170-11] [PMID: 21795326]
[58]
Svarovskaia ES, Barr R, Zhang X, et al. Azido-containing diketo acid derivatives inhibit human immunodeficiency virus type 1 integrase in vivo and influence the frequency of deletions at two-long-terminal-repeat-circle junctions. J Virol 2004; 78(7): 3210-22.
[http://dx.doi.org/10.1128/JVI.78.7.3210-3222.2004] [PMID: 15016842]
[59]
Pauza CD, Galindo JE, Richman DD. Reinfection results in accumulation of unintegrated viral DNA in cytopathic and persistent human immunodeficiency virus type 1 infection of CEM cells. J Exp Med 1990; 172(4): 1035-42.
[http://dx.doi.org/10.1084/jem.172.4.1035] [PMID: 2212939]
[60]
Shaw GM, Hahn BH, Arya SK, Groopman JE, Gallo RC, Wong-Staal F. Molecular characterization of human T-cell leukemia (lymphotropic) virus type III in the acquired immune deficiency syndrome. Science 1984; 226(4679): 1165-71.
[http://dx.doi.org/10.1126/science.6095449] [PMID: 6095449]
[61]
Bukrinsky MI, Stanwick TL, Dempsey MP, Stevenson M. Quiescent T lymphocytes as an inducible virus reservoir in HIV-1 infection. Science 1991; 254(5030): 423-7.
[http://dx.doi.org/10.1126/science.1925601] [PMID: 1925601]
[62]
Pang S, Koyanagi Y, Miles S, Wiley C, Vinters HV, Chen ISY. High levels of unintegrated HIV-1 DNA in brain tissue of AIDS dementia patients. Nature 1990; 343(6253): 85-9.
[http://dx.doi.org/10.1038/343085a0] [PMID: 2296295]
[63]
Teo I, Veryard C, Barnes H, et al. Circular forms of unintegrated human immunodeficiency virus type 1 DNA and high levels of viral protein expression: association with dementia and multinucleated giant cells in the brains of patients with AIDS. J Virol 1997; 71(4): 2928-33.
[http://dx.doi.org/10.1128/jvi.71.4.2928-2933.1997] [PMID: 9060651]
[64]
Chun TW, Carruth L, Finzi D, et al. Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection. Nature 1997; 387(6629): 183-8.
[http://dx.doi.org/10.1038/387183a0] [PMID: 9144289]
[65]
Spina CA, Guatelli JC, Richman DD. Establishment of a stable, inducible form of human immunodeficiency virus type 1 DNA in quiescent CD4 lymphocytes in vitro. J Virol 1995; 69(5): 2977-88.
[http://dx.doi.org/10.1128/jvi.69.5.2977-2988.1995] [PMID: 7707524]
[66]
Butler SL, Hansen MST, Bushman FD. A quantitative assay for HIV DNA integration in vivo. Nat Med 2001; 7(5): 631-4.
[http://dx.doi.org/10.1038/87979] [PMID: 11329067]
[67]
Vandegraaff N, Kumar R, Burrell CJ, Li P. Kinetics of human immunodeficiency virus type 1 (HIV) DNA integration in acutely infected cells as determined using a novel assay for detection of integrated HIV DNA. J Virol 2001; 75(22): 11253-60.
[http://dx.doi.org/10.1128/JVI.75.22.11253-11260.2001] [PMID: 11602768]
[68]
O’Doherty U, Swiggard WJ, Jeyakumar D, McGain D, Malim MH. A sensitive, quantitative assay for human immunodeficiency virus type 1 integration. J Virol 2002; 76(21): 10942-50.
[http://dx.doi.org/10.1128/JVI.76.21.10942-10950.2002] [PMID: 12368337]
[69]
Varmus HE, Guntaka RV, Deng CT, Bishop JM. Synthesis, structure and function of avian sarcoma virus-specific DNA in permissive and nonpermissive cells. Cold Spring Harb Symp Quant Biol 1975; 39(Pt 2): 987-96.
[PMID: 50903]
[70]
Guntaka RV, Mahy BWJ, Bishop JM, Varmus HE. Ethidium bromide inhibits appearance of closed circular viral DNA and integration of virus-specific DNA in duck cells infected by avian sarcoma virus. Nature 1975; 253(5492): 507-11.
[http://dx.doi.org/10.1038/253507a0] [PMID: 163973]
[71]
Gianni AM, Smotkin D, Weinberg RA. Murine leukemia virus: detection of unintegrated double-stranded DNA forms of the provirus. Proc Natl Acad Sci USA 1975; 72(2): 447-51.
[http://dx.doi.org/10.1073/pnas.72.2.447] [PMID: 1054828]
[72]
Shank PR, Hughes SH, Kung HJ, et al. Mapping unintegrated avian sarcoma virus DNA: Termini of linear DNA bear 300 nucleotides present once or twice in two species of circular DNA. Cell 1978; 15(4): 1383-95.
[http://dx.doi.org/10.1016/0092-8674(78)90063-6] [PMID: 215324]
[73]
Yoshimura FK, Weinberg RA. Restriction endonuclease cleavage of linear and closed circular murine leukemia viral DNAS: Discovery of a smaller circular form. Cell 1979; 16(2): 323-32.
[http://dx.doi.org/10.1016/0092-8674(79)90009-6] [PMID: 455438]
[74]
Guntaka RV, Richards OC, Shank PR, et al. Covalently closed circular DNA of avian sarcoma virus: Purification from nuclei of infected quail tumor cells and measurement by electron microscopy and gel electrophoresis. J Mol Biol 1976; 106(2): 337-57.
[http://dx.doi.org/10.1016/0022-2836(76)90090-5] [PMID: 185393]
[75]
Bukrinsky MI, Sharova N, Dempsey MP, et al. Active nuclear import of human immunodeficiency virus type 1 preintegration complexes. Proc Natl Acad Sci USA 1992; 89(14): 6580-4.
[http://dx.doi.org/10.1073/pnas.89.14.6580] [PMID: 1631159]
[76]
Brown PO, Bowerman B, Varmus HE, Bishop JM. Correct integration of retroviral DNA in vitro. Cell 1987; 49(3): 347-56.
[http://dx.doi.org/10.1016/0092-8674(87)90287-X] [PMID: 3032450]
[77]
Lobel LI, Murphy JE, Goff SP. The palindromic LTR-LTR junction of Moloney murine leukemia virus is not an efficient substrate for proviral integration. J Virol 1989; 63(6): 2629-37.
[http://dx.doi.org/10.1128/jvi.63.6.2629-2637.1989] [PMID: 2724412]
[78]
Ellis J, Bernstein A. Retrovirus vectors containing an internal attachment site: evidence that circles are not intermediates to murine retrovirus integration. J Virol 1989; 63(6): 2844-6.
[http://dx.doi.org/10.1128/jvi.63.6.2844-2846.1989] [PMID: 2724414]
[79]
Bukrinsky M, Sharova N, Stevenson M. Human immunodeficiency virus type 1 2-LTR circles reside in a nucleoprotein complex which is different from the preintegration complex. J Virol 1993; 67(11): 6863-5.
[http://dx.doi.org/10.1128/jvi.67.11.6863-6865.1993] [PMID: 8411390]
[80]
Shoemaker C, Goff S, Gilboa E, Paskind M, Mitra SW, Baltimore D. Structure of a cloned circular Moloney murine leukemia virus DNA molecule containing an inverted segment: implications for retrovirus integration. Proc Natl Acad Sci USA 1980; 77(7): 3932-6.
[http://dx.doi.org/10.1073/pnas.77.7.3932] [PMID: 6449003]
[81]
Katz RA, Omer CA, Weis JH, Mitsialis SA, Faras AJ, Guntaka RV. Restriction endonuclease and nucleotide sequence analyses of molecularly cloned unintegrated avian tumor virus DNA: structure of large terminal repeats in circle junctions. J Virol 1982; 42(1): 346-51.
[http://dx.doi.org/10.1128/jvi.42.1.346-351.1982] [PMID: 6283156]
[82]
Farnet CM, Haseltine WA. Circularization of human immunodeficiency virus type 1 DNA in vitro. J Virol 1991; 65(12): 6942-52.
[http://dx.doi.org/10.1128/jvi.65.12.6942-6952.1991] [PMID: 1834863]
[83]
Swanstrom R, DeLorbe WJ, Bishop JM, Varmus HE. Nucleotide sequence of cloned unintegrated avian sarcoma virus DNA: viral DNA contains direct and inverted repeats similar to those in transposable elements. Proc Natl Acad Sci USA 1981; 78(1): 124-8.
[http://dx.doi.org/10.1073/pnas.78.1.124] [PMID: 6264426]
[84]
Dina D, Benz EW Jr. Structure of murine sarcoma virus DNA replicative intermediates synthesized in vitro. J Virol 1980; 33(1): 377-89.
[http://dx.doi.org/10.1128/jvi.33.1.377-389.1980] [PMID: 6245239]
[85]
Gilboa E, Goff S, Shields A, Yoshimura F, Mitra S, Baltimore D. In vitro synthesis of a 9 kbp terminally redundant DNA carrying the infectivity of moloney murine leukemia virus. Cell 1979; 16(4): 863-74.
[http://dx.doi.org/10.1016/0092-8674(79)90101-6] [PMID: 88264]
[86]
Junghans RP, Boone LR, Skalka AM. Products of reverse transcription in avian retrovirus analyzed by electron microscopy. J Virol 1982; 43(2): 544-54.
[http://dx.doi.org/10.1128/jvi.43.2.544-554.1982] [PMID: 6180182]
[87]
Pauza CD, Trivedi P, McKechnie TS, Richman DD, Graziano FM. 2-LTR circular viral DNA as a marker for human immunodeficiency virus type 1 infection in vivo. Virology 1994; 205(2): 470-8.
[http://dx.doi.org/10.1006/viro.1994.1667] [PMID: 7975248]
[88]
Panther LA, Coombs RW, Aung SA, dela Rosa C, Gretch D, Corey L. Unintegrated HIV-1 circular 2-LTR proviral DNA as a marker of recently infected cells: Relative effect of recombinant CD4, zidovudine, and saquinavir in vitro. J Med Virol 1999; 58(2): 165-73.
[http://dx.doi.org/10.1002/(SICI)1096-9071(199906)58:2<165:AID-JMV11>3.0.CO;2-1] [PMID: 10335865]
[89]
Zazzi M, Romano L, Catucci M, et al. Evaluation of the presence of 2-LTR HIV-1 unintegrated DNA as a simple molecular predictor of disease progression. J Med Virol 1997; 52(1): 20-5.
[http://dx.doi.org/10.1002/(SICI)1096-9071(199705)52:1<20:AID-JMV4>3.0.CO;2-T] [PMID: 9131453]
[90]
Butler SL, Johnson EP, Bushman FD. Human immunodeficiency virus cDNA metabolism: notable stability of two-long terminal repeat circles. J Virol 2002; 76(8): 3739-47.
[http://dx.doi.org/10.1128/JVI.76.8.3739-3747.2002] [PMID: 11907213]
[91]
Pierson TC, Kieffer TL, Ruff CT, Buck C, Gange SJ, Siliciano RF. Intrinsic stability of episomal circles formed during human immunodeficiency virus type 1 replication. J Virol 2002; 76(8): 4138-44.
[http://dx.doi.org/10.1128/JVI.76.8.4138-4144.2002] [PMID: 11907256]
[92]
Gillim-Ross L, Cara A, Klotman ME. HIV-1 extrachromosomal 2-LTR circular DNA is long-lived in human macrophages. Viral Immunol 2005; 18(1): 190-6.
[http://dx.doi.org/10.1089/vim.2005.18.190] [PMID: 15802963]
[93]
Cara A, Cereseto A, Lori F, Reitz MS Jr. HIV-1 protein expression from synthetic circles of DNA mimicking the extrachromosomal forms of viral DNA. J Biol Chem 1996; 271(10): 5393-7.
[http://dx.doi.org/10.1074/jbc.271.10.5393] [PMID: 8621393]
[94]
Brussel A, Sonigo P. Evidence for gene expression by unintegrated human immunodeficiency virus type 1 DNA species. J Virol 2004; 78(20): 11263-71.
[http://dx.doi.org/10.1128/JVI.78.20.11263-11271.2004] [PMID: 15452245]
[95]
Trinité B, Ohlson EC, Voznesensky I, et al. An HIV-1 replication pathway utilizing reverse transcription products that fail to integrate. J Virol 2013; 87(23): 12701-20.
[http://dx.doi.org/10.1128/JVI.01939-13] [PMID: 24049167]
[96]
Philippe S, Sarkis C, Barkats M, et al. Lentiviral vectors with a defective integrase allow efficient and sustained transgene expression in vitro and in vivo. Proc Natl Acad Sci USA 2006; 103(47): 17684-9.
[http://dx.doi.org/10.1073/pnas.0606197103] [PMID: 17095605]
[97]
Saenz DT, Loewen N, Peretz M, et al. Unintegrated lentivirus DNA persistence and accessibility to expression in nondividing cells: analysis with class I integrase mutants. J Virol 2004; 78(6): 2906-20.
[http://dx.doi.org/10.1128/JVI.78.6.2906-2920.2004] [PMID: 14990709]
[98]
Yáñez-Muñoz RJ, Balaggan KS, MacNeil A, et al. Effective gene therapy with nonintegrating lentiviral vectors. Nat Med 2006; 12(3): 348-53.
[http://dx.doi.org/10.1038/nm1365] [PMID: 16491086]
[99]
Chan CN, Trinité B, Lee CS, et al. HIV-1 latency and virus production from unintegrated genomes following direct infection of resting CD4 T cells. Retrovirology 2016; 13(1): 1.
[http://dx.doi.org/10.1186/s12977-015-0234-9] [PMID: 26728316]
[100]
Kantor B, Ma H, Webster-Cyriaque J, Monahan PE, Kafri T. Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection. Proc Natl Acad Sci USA 2009; 106(44): 18786-91.
[http://dx.doi.org/10.1073/pnas.0905859106] [PMID: 19843699]
[101]
Machida S, Depierre D, Chen HC, et al. Exploring histone loading on HIV DNA reveals a dynamic nucleosome positioning between unintegrated and integrated viral genome. Proc Natl Acad Sci USA 2020; 117(12): 6822-30.
[http://dx.doi.org/10.1073/pnas.1913754117] [PMID: 32161134]
[102]
Geis FK, Goff SP. Unintegrated HIV-1 DNAs are loaded with core and linker histones and transcriptionally silenced. Proc Natl Acad Sci USA 2019; 116(47): 23735-42.
[http://dx.doi.org/10.1073/pnas.1912638116] [PMID: 31685613]
[103]
Geis FK, Kelenis DP, Goff SP. Two lymphoid cell lines potently silence unintegrated HIV-1 DNAs. Retrovirology 2022; 19(1): 16.
[http://dx.doi.org/10.1186/s12977-022-00602-7] [PMID: 35810297]
[104]
Romani B, Kamali Jamil R, Hamidi-Fard M, et al. HIV-1 Vpr reactivates latent HIV-1 provirus by inducing depletion of class I HDACs on chromatin. Sci Rep 2016; 6(1): 31924.
[http://dx.doi.org/10.1038/srep31924] [PMID: 27550312]
[105]
Yurkovetskiy L, Guney MH, Kim K, et al. Primate immunodeficiency virus proteins Vpx and Vpr counteract transcriptional repression of proviruses by the HUSH complex. Nat Microbiol 2018; 3(12): 1354-61.
[http://dx.doi.org/10.1038/s41564-018-0256-x] [PMID: 30297740]
[106]
Forouzanfar F, Ali S, Wallet C, et al. HIV-1 Vpr mediates the depletion of the cellular repressor CTIP2 to counteract viral gene silencing. Sci Rep 2019; 9(1): 13154.
[http://dx.doi.org/10.1038/s41598-019-48689-x] [PMID: 31511615]
[107]
Zhou X, Monnie C, DeLucia M, Ahn J. HIV-1 Vpr activates host CRL4-DCAF1 E3 ligase to degrade histone deacetylase SIRT7. Virol J 2021; 18(1): 48.
[http://dx.doi.org/10.1186/s12985-021-01514-2] [PMID: 33648539]
[108]
Dupont L, Bloor S, Williamson JC, et al. The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr. Cell Host Microbe 2021; 29(5): 792-805.e6.
[http://dx.doi.org/10.1016/j.chom.2021.03.001] [PMID: 33811831]
[109]
Geis FK, Sabo Y, Chen X, Li Y, Lu C, Goff SP. CHAF1A/B mediate silencing of unintegrated HIV-1 DNAs early in infection. Proc Natl Acad Sci USA 2022; 119(4): e2116735119.
[http://dx.doi.org/10.1073/pnas.2116735119] [PMID: 35074917]
[110]
Marzio G, Tyagi M, Gutierrez MI, Giacca M. HIV-1 Tat transactivator recruits p300 and CREB-binding protein histone acetyltransferases to the viral promoter. Proc Natl Acad Sci USA 1998; 95(23): 13519-24.
[http://dx.doi.org/10.1073/pnas.95.23.13519] [PMID: 9811832]
[111]
Hottiger MO, Nabel GJ. Interaction of human immunodeficiency virus type 1 Tat with the transcriptional coactivators p300 and CREB binding protein. J Virol 1998; 72(10): 8252-6.
[http://dx.doi.org/10.1128/JVI.72.10.8252-8256.1998] [PMID: 9733868]
[112]
Kamine J, Elangovan B, Subramanian T, Coleman D, Chinnadurai G. Identification of a cellular protein that specifically interacts with the essential cysteine region of the HIV-1 Tat transactivator. Virology 1996; 216(2): 357-66.
[http://dx.doi.org/10.1006/viro.1996.0071] [PMID: 8607265]
[113]
Col E, Caron C, Seigneurin-Berny D, Gracia J, Favier A, Khochbin S. The histone acetyltransferase, hGCN5, interacts with and acetylates the HIV transactivator, Tat. J Biol Chem 2001; 276(30): 28179-84.
[http://dx.doi.org/10.1074/jbc.M101385200] [PMID: 11384967]
[114]
Okada M, Jeang KT. Differential requirements for activation of integrated and transiently transfected human T-cell leukemia virus type 1 long terminal repeat. J Virol 2002; 76(24): 12564-73.
[http://dx.doi.org/10.1128/JVI.76.24.12564-12573.2002] [PMID: 12438582]
[115]
Schneider WM, Wu D, Amin V, Aiyer S, Roth MJ. MuLV IN mutants responsive to HDAC inhibitors enhance transcription from unintegrated retroviral DNA. Virology 2012; 426(2): 188-96.
[http://dx.doi.org/10.1016/j.virol.2012.01.034] [PMID: 22365328]
[116]
Zhu Y, Wang GZ, Cingöz O, Goff SP. NP220 mediates silencing of unintegrated retroviral DNA. Nature 2018; 564(7735): 278-82.
[http://dx.doi.org/10.1038/s41586-018-0750-6] [PMID: 30487602]
[117]
Kinter A, Moorthy A, Jackson R, Fauci AS. Productive HIV infection of resting CD4+ T cells: role of lymphoid tissue microenvironment and effect of immunomodulating agents. AIDS Res Hum Retroviruses 2003; 19(10): 847-56.
[http://dx.doi.org/10.1089/088922203322493012] [PMID: 14585216]
[118]
Eckstein DA, Penn ML, Korin YD, et al. HIV-1 actively replicates in naive CD4(+) T cells residing within human lymphoid tissues. Immunity 2001; 15(4): 671-82.
[http://dx.doi.org/10.1016/S1074-7613(01)00217-5] [PMID: 11672548]
[119]
Unutmaz D. KewalRamani VN, Marmon S, Littman DR. Cytokine signals are sufficient for HIV-1 infection of resting human T lymphocytes. J Exp Med 1999; 189(11): 1735-46.
[http://dx.doi.org/10.1084/jem.189.11.1735] [PMID: 10359577]
[120]
Walmsley SL, Antela A, Clumeck N, et al. Dolutegravir plus abacavir-lamivudine for the treatment of HIV-1 infection. N Engl J Med 2013; 369(19): 1807-18.
[http://dx.doi.org/10.1056/NEJMoa1215541] [PMID: 24195548]
[121]
Clotet B, Feinberg J, van Lunzen J, et al. Once-daily dolutegravir versus darunavir plus ritonavir in antiretroviral-naive adults with HIV-1 infection (FLAMINGO): 48 week results from the randomised open-label phase 3b study. Lancet 2014; 383(9936): 2222-31.
[http://dx.doi.org/10.1016/S0140-6736(14)60084-2] [PMID: 24698485]
[122]
Raffi F, Jaeger H, Quiros-Roldan E, et al. Once-daily dolutegravir versus twice-daily raltegravir in antiretroviral-naive adults with HIV-1 infection (SPRING-2 study): 96 week results from a randomised, double-blind, non-inferiority trial. Lancet Infect Dis 2013; 13(11): 927-35.
[http://dx.doi.org/10.1016/S1473-3099(13)70257-3] [PMID: 24074642]
[123]
Hazuda DJ, Young SD, Guare JP, et al. Integrase inhibitors and cellular immunity suppress retroviral replication in rhesus macaques. Science 2004; 305(5683): 528-32.
[http://dx.doi.org/10.1126/science.1098632] [PMID: 15247437]
[124]
Gandhi RT, Zheng L, Bosch RJ, et al. The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial. PLoS Med 2010; 7(8): e1000321.
[http://dx.doi.org/10.1371/journal.pmed.1000321] [PMID: 20711481]
[125]
Gandhi RT, Coombs RW, Chan ES, et al. No effect of raltegravir intensification on viral replication markers in the blood of HIV-1-infected patients receiving antiretroviral therapy. J Acquir Immune Defic Syndr 2012; 59(3): 229-35.
[http://dx.doi.org/10.1097/QAI.0b013e31823fd1f2] [PMID: 22083073]
[126]
Llibre JM, Buzón MJ, Massanella M, et al. Treatment intensification with raltegravir in subjects with sustained HIV-1 viraemia suppression: a randomized 48-week study. Antivir Ther 2012; 17(2): 355-64.
[http://dx.doi.org/10.3851/IMP1917] [PMID: 22290239]
[127]
White K, Kulkarni R, Miller MD. Analysis of early resistance development at the first failure timepoint in elvitegravir/cobicistat/emtricitabine/tenofovir disoproxil fumarate-treated patients. J Antimicrob Chemother 2015; 70(9): 2632-8.
[http://dx.doi.org/10.1093/jac/dkv149] [PMID: 26108607]
[128]
Fourati S, Charpentier C, Amiel C, et al. Cross-resistance to elvitegravir and dolutegravir in 502 patients failing on raltegravir: a French national study of raltegravir-experienced HIV-1-infected patients. J Antimicrob Chemother 2015; 70(5): 1507-12.
[http://dx.doi.org/10.1093/jac/dku535] [PMID: 25558077]
[129]
Malet I, Subra F, Charpentier C, et al. Mutations located outside the integrase gene can confer resistance to HIV-1 integrase strand transfer inhibitors. MBio 2017; 8(5): e00922-17.
[http://dx.doi.org/10.1128/mBio.00922-17] [PMID: 28951475]
[130]
Hikichi Y, Van Duyne R, Pham P, et al. Mechanistic analysis of the broad antiretroviral resistance conferred by HIV-1 envelope glycoprotein mutations. MBio 2021; 12(1): e03134-20.
[http://dx.doi.org/10.1128/mBio.03134-20] [PMID: 33436439]
[131]
Lau JW, Levy DN, Wodarz D. Contribution of HIV-1 genomes that do not integrate to the basic reproductive ratio of the virus. J Theor Biol 2015; 367: 222-9.
[http://dx.doi.org/10.1016/j.jtbi.2014.12.004] [PMID: 25496730]
[132]
Zack JA, Arrigo SJ, Weitsman SR, Go AS, Haislip A, Chen ISY. HIV-1 entry into quiescent primary lymphocytes: Molecular analysis reveals a labile, latent viral structure. Cell 1990; 61(2): 213-22.
[http://dx.doi.org/10.1016/0092-8674(90)90802-L] [PMID: 2331748]
[133]
Ott M, Emiliani S, Van Lint C, et al. Immune hyperactivation of HIV-1-infected T cells mediated by Tat and the CD28 pathway. Science 1997; 275(5305): 1481-5.
[http://dx.doi.org/10.1126/science.275.5305.1481] [PMID: 9045614]
[134]
Schrager JA, Marsh JW. HIV-1 Nef increases T cell activation in a stimulus-dependent manner. Proc Natl Acad Sci 1999; 96(14): 8167-72.
[http://dx.doi.org/10.1073/pnas.96.14.8167] [PMID: 10393966]
[135]
Wodarz D, Chan CN, Trinité B, Komarova NL, Levy DN. On the laws of virus spread through cell populations. J Virol 2014; 88(22): 13240-8.
[http://dx.doi.org/10.1128/JVI.02096-14] [PMID: 25187551]
[136]
Petitjean G, Al Tabaa Y, Tuaillon E, et al. Unintegrated HIV-1 provides an inducible and functional reservoir in untreated and highly active antiretroviral therapy-treated patients. Retrovirology 2007; 4(1): 60.
[http://dx.doi.org/10.1186/1742-4690-4-60] [PMID: 17727722]
[137]
King W, Patel MD, Lobel LI, Goff SP, Nguyen-Huu MC. Insertion mutagenesis of embryonal carcinoma cells by retroviruses. Science 1985; 228(4699): 554-8.
[http://dx.doi.org/10.1126/science.3838595] [PMID: 3838595]
[138]
Li Z, Düllmann J, Schiedlmeier B, et al. Murine leukemia induced by retroviral gene marking. Science 2002; 296(5567): 497.
[http://dx.doi.org/10.1126/science.1068893] [PMID: 11964471]
[139]
Vargas J Jr, Gusella GL, Najfeld V, Klotman ME, Cara A. Novel integrase-defective lentiviral episomal vectors for gene transfer. Hum Gene Ther 2004; 15(4): 361-72.
[http://dx.doi.org/10.1089/104303404322959515] [PMID: 15053861]
[140]
Vargas J Jr, Klotman M, Cara A. Conditionally replicating lentiviral-hybrid episomal vectors for suicide gene therapy. Antiviral Res 2008; 80(3): 288-94.
[http://dx.doi.org/10.1016/j.antiviral.2008.06.015] [PMID: 18647620]
[141]
Wang Z, Tang Z, Zheng Y, et al. Development of a nonintegrating Rev-dependent lentiviral vector carrying diphtheria toxin A chain and human TRAF6 to target HIV reservoirs. Gene Ther 2010; 17(9): 1063-76.
[http://dx.doi.org/10.1038/gt.2010.53] [PMID: 20410930]
[142]
Negri DRM, Michelini Z, Baroncelli S, et al. Successful immunization with a single injection of non-integrating lentiviral vector. Mol Ther 2007; 15(9): 1716-23.
[http://dx.doi.org/10.1038/sj.mt.6300241] [PMID: 17593926]
[143]
Bayer M, Kantor B, Cockrell A, et al. A large U3 deletion causes increasedin vivo expression from a nonintegrating lentiviral vector. Mol Ther 2008; 16(12): 1968-76.
[http://dx.doi.org/10.1038/mt.2008.199] [PMID: 18797449]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy