HIV gene expression from intact proviruses positioned in bacterial artificial chromosomes at integration sites previously identified in latently infected T cells

Virology

Volumn 410, Issue 1, 2011, Pages 151-160

  Eipers, Peter G ^a   Salazar Gonzalez, Jesus F ^b   Morrow, Casey D ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b University of Alabama at Birmingham   (United States)

Author keywords

Bacterial artificial chromosome; HIV; Integration site; Latent T cell

Indexed keywords

BASIC LEUCINE TRANSCRIPTION FACTOR 2; DNA METHYLTRANSFERASE 1; DNA TOPOISOMERASE (ATP HYDROLYSING); GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; NEF PROTEIN; TRANSCRIPTION FACTOR; TUMOR NECROSIS FACTOR ALPHA; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BINDING SITE; CELL STRAIN HEK293; CONTROLLED STUDY; EMBRYO; GENE EXPRESSION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; PROVIRUS; T LYMPHOCYTE; VIROGENESIS; VIRUS CELL INTERACTION; VIRUS GENE; VIRUS LATENCY; VIRUS REACTIVATION;

CELL LINE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; GENE EXPRESSION REGULATION, VIRAL; GREEN FLUORESCENT PROTEINS; HIV-1; HUMANS; PROVIRUSES; T-LYMPHOCYTES; VIRUS INTEGRATION;

BACTERIA (MICROORGANISMS); HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 78650743390     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2010.11.001     Document Type: Article

References (43)

1. Bokhoven M., Stephen S.L., Knight S., Gevers E.F., Robinson I.C., Takeuchi Y., Collins M.K. Insertional gene activation by lentiviral and gammaretroviral vectors. J. Virol. 2009, 83(1):283-294.
2. Brady T., Agosto L.M., Malani N., Berry C.C., O'Doherty U., Bushman F. HIV integration site distributions in resting and activated CD4+ T cells infected in culture. AIDS 2009, 23(12):1461-1471.
3. Bushman F., Lewinski M., Ciuffi A., Barr S., Leipzig J., Hannenhalli S., Hoffmann C. Genome-wide analysis of retroviral DNA integration. Nat. Rev. Microbiol. 2005, 3(11):848-858.
4. Chang L.J., Chen C.H., Urlacher V., Lee T.Z. Differential apoptosis effects of primate lentiviral Vpr and Vpx in mammalian cells. J. Biomed. Sci. 2000, 7(4):322-333.
5. Chun T.W., Stuyver L., Mizell S.B., Ehler L.A., Mican J.A., Baseler M., Lloyd A.L., Nowak M.A., Fauci A.S. Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy. Proc. Natl. Acad. Sci. (U S A) 1997, 94(24):13193-13197.
6. Falck J., Jensen P.B., Sehested M. Evidence for repressional role of an inverted CCAAT box in cell cycle-dependent transcription of the human DNA topoisomerase IIalpha gene. J. Biol. Chem. 1999, 274(26):18753-18758.
7. Giraldo P., Montoliu L. Size matters: use of YACs, BACs and PACs in transgenic animals. Transgenic Res. 2001, 10(2):83-103.
8. Gong S., Yang X.W., Li C., Heintz N. Highly efficient modification of bacterial artificial chromosomes (BACs) using novel shuttle vectors containing the R6Kγ origin of replication. Genome Res. 2002, 12(12):1992-1998.
9. Han Y., Lassen K., Monie D., Sedaghat A.R., Shirnoji S., Liu X., Pierson T.C., Margolick J.B., Siliciano R.F., Siliciano J.D. Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. J. Virol. 2004, 78(12):6122-6133.
10. Han Y., Lin Y.B., An W., Xu J., Yang H.-C., O'Connell K., Dordai D., Boeke J.D., Siliciano J.D., Siliciano R.F. Orientation-dependent regulation of integrated HIV-1 expression by host gene transcriptional readthrough. Cell Host Microbe 2008, 4(2):134-146.
11. Han Y., Wind-Rotolo M., Yang H.-C., Siliciano J.D., Siliciano R.F. Experimental approaches to the study of HIV-1 latency. Nat. Rev. Microbiol. 2007, 5(2):95-106.
12. Ikeda T., Shibata J., Yoshimura K., Koito A., Matsushita S. Recurrent HIV-1 integration at the BACH2 locus in resting CD4+ T cell populations during effective highly active antiretroviral therapy. J. Infect. Dis. 2007, 195(5):716-725.
13. Jacobson K.K., Morrison L.E., Henderson B.T., Blondin B.A., Wilber K.A., Legator M.S., O'Hare A., Van Stedum S.C., Proffitt J.H., Seelig S.A., Coon J.S. Gene copy mapping of the ERBB2/TOP2A region in breast cancer. Genes Chromosom. Cancer 2004, 40(1):19-31.
14. Jones K.A., Peterlin B.M. Control of RNA initiation and elongation at the HIV-1 promoter. Annu. Rev. Biochem. 1994, 63:717-743.
15. Jordan A., Bisgrove D., Verdin E. HIV reproducibly establishes a latent infection after acute infection of T cells in vitro. EMBO J. 2003, 22(8):1868-1877.
16. Jordan A., Defechereux P., Verdin E. The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation. EMBO J. 2001, 20(7):1726-1738.
17. Kuiken C., Leitner T., Foley B., Hahn B., Marx P., McMCutchan F., Wolinsky S., Korber B. HIV Sequence Compendium 2009 2009.
18. Lee E.-C., Yu D., de Velasco J.M., Tessarollo L., Swing D.A., Court D.L., Jenkins N.A., Copeland N.G. A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 2001, 73(1):56-65.
19. Lee G., Saito I. Role of nucleotide sequences of loxP spacer regionin Cre-mediated recombination. Gene 1998, 216(1):55-65.
20. Lenasi T., Contreras X., Peterlin B.M. Transcriptional interference antagonizes proviral gene expression to promote HIV latency. Cell Host Microbe 2008, 4(2):123-133.
21. Levy D.N., Aldrovandi G.M., Kutsch O., Shaw G.M. Dynamics of HIV-1 recombination in its natural target cells. Proc. Natl. Acad. (USA) 2004, 101(12):4204-4209.
22. Lewinski M.K., Bisgrove D., Shinn P., Chen H., Hoffmann C., Hannenhalli S., Verdin E., Berry C.C., Ecker J.R., Bushman F.D. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. J. Virol. 2005, 79(11):6610-6619.
23. Mok H.P., Javed S., Lever A. Stable gene expression occurs from a minority of integrated HIV-1-based vectors: transcriptional silencing is present in the majority. Gene Ther. 2007, 14:741-751.
24. Moore-Rigdon K.L., Kosloff B.R., Kirkman R.L., Morrow C.D. Preferences for the selection of unique tRNA primers revealed from analysis of HIV-1 replication in peripheral blood mononuclear cells. Retrovirology 2005, 2:21.
25. Muyrers J.P.P., Zhang Y., Testa G., Stewart A.F. Rapid modification of bacterial artificial chromosomes by ET-recombination. Nucleic Acids Res. 1999, 27(6):1555-1557.
26. Quivy V., De Walque S., Van Lint C. Chromatin-associated regulation of HIV-1 transcription: implications for the development of therapeutic strategies. Subcell. Biochem. 2007, 41:371-396.
27. Richman D.D., Margolis D.M., Delaney M., Greene W.C., Hazuda D., Pomerantz R.J. The challenge of finding a cure for HIV infection. Science 2009, 323(5919):1304-1307.
28. Sambrook J., Russell D.W. Molecular Cloning: A Laboratory Manual 2001, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Third Edition.
29. Sawitzke J.A., Thomason L.C., Costatino N., Bubunenko M., Bubunenko M., Datta S., Court D.L. Recombineering: in vivo genetic engineering in E. coli, S. enterica, and beyond. Proc. Natl. Acad. Sci. (USA) 2007, 421:171-199.
30. Schreck R., Rieber P., Baeuerle P.A. Reactive oxygen intermediates as apparently widely used messengers in the activation of the NF-kappa B transcription factor and HIV-1. EMBO J. 1991, 10(8):2247-2258.
31. Schroder A.R.W., Shinn P., Chen H., Berry C., Ecker J.R., Bushman F. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 2002, 110:521-529.
32. Schubeler D., Maass K., Bode J. Retargeting of retroviral integration sites for the predictable expression of transgenes and the analysis of cis-acting sequences. Biochemistry 1998, 37(34):11907-11914.
33. Sharan S.K., Thomason L.C., Kuznetsov S.G., Court D.L. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 2009, 4(2):206-223.
34. Sorrell D.A., Kolb A.F. Targeted modification of mammalian genomes. Biotechnol. Adv. 2005, 23:431-469.
35. Stewart S.A., Poon B., Jowett J.B.M., Xie Y., Chen I.S.Y. Lentiviral delivery of HIV-1 Vpr protein induces apoptosis in transformed cells. Proc. Natl Acad. Sci. USA 1999, 96:12039-12043.
36. Strehlow A.N.T., Li J.Z., Myers R.M. Wild-type huntingtin participates in protein trafficking between the Golgi and the extracellular space. Hum. Mol. Genet. 2007, 16(4):391-409.
37. Szyf M., Bozovic V., Tanigawa G. Growth regulation of mouse DNA methyltransferase gene expression. J. Biol. Chem. 1991, 266(16):10027-10030.
38. Testa G., Zhang Y., Vintersten K., Benes V., Pijnappel W.W., Chambers I., Smith A.J., Smith A.G., Stewart A.F. Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles. Nat. Biotechnol. 2003, 21(4):443-447.
39. Vatakis D.N., Kim S., Kim N., Chow S.A., Zack J.A. HIV integration efficiency and site selection in quiescent CD4+ T cells. J. Virol. 2009, 83(12):6222-6233.
40. Vintersten K., Testa G., Naumann R., Anastassiadis K., Stewart A.F. Bacterial artificial chromosome transgenesis through pronuclear injection of fertilized mouse oocytes. Meth. Mol. Biol. 2008, 415:83-100.
41. Wang G.P., Ciuffi A., Leipzig J., Berry C.C., Bushman F.D. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res. 2007, 17(8):1186-1194.
42. Yang Y., Seed B. Site-specific gene targeting in mouse embryonic stem cells with intact bacterial artificial chromosomes. Nat. Biotechnol. 2003, 21(4):447-451.
43. Zhang Y., Buchholz F., Muyrers J.P.P., Stewart A.F. A new logic for DNA engineering using recombination in Escherichia coli. Nat. Genet. 1998, 20(2):123-128.