A. Mowat and J. Viney, The anatomical basis of intestinal immunity, Immunological Reviews, vol.39, issue.1, pp.145-166, 1997.
DOI : 10.1084/jem.183.6.2605

R. Veazey, K. Mansfield, I. Tham, A. Carville, and D. Shvetz, Dynamics of CCR5 Expression by CD4+ T Cells in Lymphoid Tissues during Simian Immunodeficiency Virus Infection, Journal of Virology, vol.74, issue.23, pp.11001-11007, 2000.
DOI : 10.1128/JVI.74.23.11001-11007.2000

R. Veazey, P. Marx, and A. Lackner, The mucosal immune system: primary target for HIV infection and AIDS, Trends in Immunology, vol.22, issue.11, pp.626-633, 2001.
DOI : 10.1016/S1471-4906(01)02039-7

C. Heise, C. Miller, A. Lackner, and S. Dandekar, Primary acute simian Influence du polymorphisme du promoteur des sous-types du VIH-1 sur la dynamique de la réplication virale in vivo BIBLIOGRAPHIE 169, 1994.

K. Khalili and A. Giordano, Regulatory functions of Cdk9 and of cyclin T1 in HIV tat transactivation pathway gene expression, J Cell Biochem, vol.75, pp.357-368, 1999.

J. Hiscott, Differential regulation of HIV-1, 2002.

B. Clade-specific, C. , and E. , long terminal repeats by NF-kappaB and the Tat transactivator, Virology, vol.296, pp.77-83

M. Boswell, S. L. Sax, P. E. Kalams, S. A. Walker, and B. D. , Vigorous HIV-1-specific CD4+ T cell responses associated with control of viremia, Science, vol.278, pp.1447-1450, 1997.

J. Ogunro, Virus-induced cytokines regulate circulating lymphocyte levels during primary SIV infections, Int Immunol, vol.9, pp.703-712, 1997.

R. Mcallister, J. J. Millhouse, S. Wigdahl, and B. , HIV-1 LTR C/EBP binding site sequence configurations preferentially encountered in brain lead to enhanced C/EBP factor binding and increased LTR-specific activity, J Neurovirol, vol.7, pp.235-249, 2001.

H. L. Ross, M. R. Nonnemacher, T. H. Hogan, S. J. Quiterio, A. Henderson et al., Interaction between CCAAT/enhancer binding protein and cyclic AMP response element binding protein 1 regulates human immunodeficiency virus type 1, 2001.

C. Rousseau, E. Abrams, M. Lee, R. Urbano, and M. C. King, Gene Variants of Human Immunodeficiency Virus Type 1 in Perinatally Infected Long-Term Survivors and Rapid Progressors, AIDS Research and Human Retroviruses, vol.13, issue.18, pp.1611-1623, 1997.
DOI : 10.1089/aid.1997.13.1611

R. , S. L. Dong, T. Dorrell, L. Ogg, G. Hansasuta et al., Broadly cross-reactive HIV-specific cytotoxic Tlymphocytes in highly-exposed persistently seronegative donors, Immunol Lett, vol.66, pp.9-14, 1999.

S. Roy, U. Delling, C. H. Chen, C. A. Rosen, and N. Sonenberg, A bulge structure in HIV, 1990.

S. Roy, N. T. Parkin, C. Rosen, J. Itovitch, and N. Sonenberg, Structural requirements for trans activation of human immunodeficiency virus type 1 long terminal repeat-directed gene expression by tat: importance of base pairing, loop sequence, and bulges in the tat-responsive sequence, J Virol, vol.64, pp.1402-1406, 1990.

N. Sachsenberg, A. S. Perelson, S. Yerly, G. A. Schockmel, D. Leduc et al., T Lymphocytes in HIV-1 Infection as Measured by Ki-67 Antigen, The Journal of Experimental Medicine, vol.375, issue.8, pp.1295-1303, 1998.
DOI : 10.1038/375196a0

J. T. Safrit and R. A. Koup, The immunology of primary HIV infection: which immune responses control HIV replication?, Current Opinion in Immunology, vol.7, issue.4, pp.456-461, 1995.
DOI : 10.1016/0952-7915(95)80088-3

H. Saito, Y. Kanamori, T. Takemori, H. Nariuchi, E. Kubota et al., Generation of Intestinal T Cells from Progenitors Residing in Gut Cryptopatches, Science, vol.280, issue.5361, pp.275-278, 1998.
DOI : 10.1126/science.280.5361.275

M. Sala, S. Wain-hobson, and F. Schaeffer, Human immunodeficiency virus type 1, 1995.

S. Ayehunie, D. Gotte, P. Leinikki, D. S. Burke, and F. E. Mccutchan, Full-length sequence of an ethiopian human immunodeficiency virus type 1 (HIV-1) isolate of genetic subtype C, AIDS Res Hum Retroviruses, vol.12, pp.1329-1339, 1996.

P. J. Sansonetti, War and peace at mucosal surfaces, Nature Reviews Immunology, vol.67, issue.12, pp.953-964, 2004.
DOI : 10.1016/j.it.2003.10.007

C. Lackner and A. A. , Induction of lymphocyte proliferation and severe gastrointestinal disease in macaques by a nef gene variant SIVmac239, Am J Pathol, vol.149, pp.163-176, 1996.

M. Schindler, S. Wurfl, P. Benaroch, T. C. Greenough, R. Daniels et al., Down-Modulation of Mature Major Histocompatibility Complex Class II and Up-Regulation of Invariant Chain Cell Surface Expression Are Well-Conserved Functions of Human and Simian Immunodeficiency Virus nef Alleles, Journal of Virology, vol.77, issue.19, pp.10548-10556, 2003.
DOI : 10.1128/JVI.77.19.10548-10556.2003

J. E. Schmitz, M. J. Kuroda, S. Santra, V. G. Sasseville, M. A. Simon et al., Control of Viremia in Simian Immunodeficiency Virus Infection by CD8+ Lymphocytes, Science, vol.283, issue.5403, pp.857-860, 1999.
DOI : 10.1126/science.283.5403.857

J. E. Schmitz, R. S. Veazey, M. J. Kuroda, D. B. Levy, A. Seth et al., Simian immunodeficiency virus (SIV)-specific cytotoxic T lymphocytes in gastrointestinal tissues of chronically SIV-infected rhesus monkeys, Blood, vol.98, issue.13, pp.3757-3761, 2001.
DOI : 10.1182/blood.V98.13.3757

M. L. Schmitz and P. A. Baeuerle, Multi-Step Activation of NF-??B/Rel Transcription Factors, Immunobiology, vol.193, issue.2-4, pp.116-127, 1995.
DOI : 10.1016/S0171-2985(11)80534-6

T. Schneider, H. U. Jahn, W. Schmidt, E. O. Riecken, M. Zeitz et al., Loss of CD4 T lymphocytes in patients infected with human immunodeficiency virus type 1 is more pronounced in the duodenal mucosa than in the peripheral blood. Berlin Diarrhea/Wasting Syndrome Study Group., Gut, vol.37, issue.4, pp.524-529, 1995.
DOI : 10.1136/gut.37.4.524

T. Schneider, R. Ullrich, C. Bergs, W. Schmidt, E. O. Riecken et al., Abnormalities in subset distribution, activation, and differentiation of T ceils isolated from large intestine biopsies in HIV infection, Clinical & Experimental Immunology, vol.10, issue.Suppl.l, pp.430-435, 1994.
DOI : 10.1111/j.1365-2249.1994.tb07014.x

H. Salzman, N. P. Fauci, and A. S. , The reservoir for HIV-1 in human peripheral blood is a T cell that maintains expression of CD4, Science, vol.245, pp.305-308, 1989.

C. Schwartz, F. Canonne-hergaux, D. Aunis, and E. Schaeffer, Characterization of nuclear proteins that bind to the regulatory TGATTGGC motif in the human immunodeficiency virus type 1, 1997.

T. Seshamma, O. Bagasra, D. Trono, D. Baltimore, and R. J. Pomerantz, Blocked early-stage latency in the peripheral blood cells of certain individuals infected with human immunodeficiency virus type 1., Proceedings of the National Academy of Sciences, vol.89, issue.22, pp.10663-10667, 1992.
DOI : 10.1073/pnas.89.22.10663

B. L. Shacklett, C. A. Cox, J. K. Sandberg, N. H. Stollman, M. A. Jacobson et al., Trafficking of Human Immunodeficiency Virus Type 1-Specific CD8+ T Cells to Gut-Associated Lymphoid Tissue during Chronic Infection, Journal of Virology, vol.77, issue.10, pp.5621-5631, 2003.
DOI : 10.1128/JVI.77.10.5621-5631.2003

S. K. Shaw and M. B. Brenner, The beta 7, 1995.

M. H. Sieweke, H. Tekotte, U. Jarosch, and T. Graf, Cooperative interaction of Ets-1 with USF-1 required for HIV-1 enhancer activity in T cells, The EMBO Journal, vol.17, issue.6, pp.1728-1739, 1998.
DOI : 10.1093/emboj/17.6.1728

K. Simons and S. D. Fuller, Cell Surface Polarity in Epithelia, Annual Review of Cell Biology, vol.1, issue.1, 1985.
DOI : 10.1146/annurev.cb.01.110185.001331

B. A. Smith, S. Gartner, Y. Liu, A. S. Perelson, N. I. Stilianakis et al., Persistence of Infectious HIV on Follicular Dendritic Cells, The Journal of Immunology, vol.166, issue.1, pp.690-696, 2001.
DOI : 10.4049/jimmunol.166.1.690

P. D. Smith, L. Li, and G. Meng, Mucosal Events in the Pathogenesis of Human Immunodeficiency Virus Type 1 Infection, The Journal of Infectious Diseases, vol.179, issue.s3, pp.436-440, 1999.
DOI : 10.1086/314812

P. D. Smith, G. Meng, J. F. Salazar-gonzalez, and G. M. Shaw, Macrophage HIV-1 infection and the gastrointestinal tract reservoir, Journal of Leukocyte Biology, vol.74, issue.5, 2003.
DOI : 10.1189/jlb.0503219

S. Shaw and G. M. , Biological parameters of HIV-1 infection in primary intestinal lymphocytes and macrophages, J Leukoc Biol, vol.68, pp.360-365, 2000.

P. Sommer, J. P. Vartanian, M. Wachsmuth, M. Henry, D. Guetard et al., Anti-termination by SIV Tat Requires Flexibility of the Nascent TAR Structure, Journal of Molecular Biology, vol.344, issue.1, pp.11-28, 2004.
DOI : 10.1016/j.jmb.2004.09.042

URL : https://hal.archives-ouvertes.fr/pasteur-00850259

S. Sopper, D. Nierwetberg, A. Halbach, U. Sauer, C. Scheller et al., Impact of simian immunodeficiency virus (SIV) infection on lymphocyte numbers and T-cell turnover in different organs of rhesus monkeys, Blood, vol.101, issue.4, pp.1213-1219, 2003.
DOI : 10.1182/blood-2002-06-1644

L. E. Soto-ramirez, B. Renjifo, M. F. Mclane, R. Marlink, C. O-'hara et al., HIV-1 Langerhans' Cell Tropism Associated with Heterosexual Transmission of HIV, Science, vol.271, issue.5253, pp.1291-1293, 1996.
DOI : 10.1126/science.271.5253.1291

J. Sprent, Lifespans of naive, memory and effector lymphocytes, Current Opinion in Immunology, vol.5, issue.3, pp.433-438, 1993.
DOI : 10.1016/0952-7915(93)90065-Z

C. Stahl-hennig, R. M. Steinman, K. Tenner-racz, M. Pope, N. Stolte et al., Rapid Infection of Oral Mucosal-Associated Lymphoid Tissue with Simian Immunodeficiency Virus, Science, vol.285, issue.5431, pp.1261-1265, 1999.
DOI : 10.1126/science.285.5431.1261

M. Stevenson, HIV-1 pathogenesis, Nature Medicine, vol.9, issue.7, pp.853-860, 2003.
DOI : 10.1038/nm0703-853

H. Dandekar and S. , Development of malabsorption and nutritional complications in simian immunodeficiency virus-infected rhesus macaques, Aids, vol.8, pp.1245-1256, 1994.

C. Sune and M. A. Garcia-blanco, Sp1 transcription factor is required for in vitro basal and, 1995.

V. M. Tesmer and M. Bina, Regulation of HIV-1 Gene Expression by NF-IL6, Journal of Molecular Biology, vol.262, issue.3, pp.327-335, 1996.
DOI : 10.1006/jmbi.1996.0516

V. M. Tesmer, A. Rajadhyaksha, J. Babin, and M. Bina, NF-IL6-mediated transcriptional activation of the long terminal repeat of the human immunodeficiency virus type 1., Proceedings of the National Academy of Sciences, vol.90, issue.15, 1993.
DOI : 10.1073/pnas.90.15.7298

E. Tschachler, V. Groh, M. Popovic, D. L. Mann, K. Konrad et al., Epidermal Langerhans Cells-A Target for HTLV-III/LAV Infection, Journal of Investigative Dermatology, vol.88, issue.2, pp.233-237, 1987.
DOI : 10.1111/1523-1747.ep12525402

S. G. Turville, P. U. Cameron, A. Handley, G. Lin, S. Pohlmann et al., Diversity of receptors binding HIV on dendritic cell subsets, Nature Immunology, vol.3, issue.10, pp.975-983, 2002.
DOI : 10.1038/ni841

D. Kitchen, S. Schmid, I. Zack, J. A. Hays, and E. F. , Differential tropism of HIV-1 isolates for distinct thymocyte subsets in vitro, Aids, vol.10, 1996.

R. Ullrich, M. Zeitz, W. Heise, M. L-'age, G. Hoffken et al., Small Intestinal Structure and Function in Patients Infected with Human Immunodeficiency Virus (HIV): Evidence for HIV-Induced Enteropathy, Annals of Internal Medicine, vol.111, issue.1, pp.15-21, 1989.
DOI : 10.7326/0003-4819-111-1-15

D. Unutmaz, V. N. Kewalramani, S. Marmon, and D. R. Littman, Cytokine Signals Are Sufficient for HIV-1 Infection of Resting Human T Lymphocytes, The Journal of Experimental Medicine, vol.156, issue.11, pp.1735-1746, 1999.
DOI : 10.1006/smim.1998.0134

M. Vajdy, R. Veazey, I. Tham, C. Debakker, S. Westmoreland et al., Early Immunologic Events in Mucosal and Systemic Lymphoid Tissues after Intrarectal Inoculation with Simian Immunodeficiency Virus, The Journal of Infectious Diseases, vol.184, issue.8, 2001.
DOI : 10.1086/323615

M. Vajdy, R. S. Veazey, H. K. Knight, A. A. Lackner, and M. R. Neutra, Differential Effects of Simian Immunodeficiency Virus Infection on Immune Inductive and Effector Sites in the Rectal Mucosa of Rhesus Macaques, The American Journal of Pathology, vol.157, issue.2, pp.485-495, 2000.
DOI : 10.1016/S0002-9440(10)64560-9

L. Van-der-hoek, C. J. Sol, F. Snijders, J. F. Bartelsman, R. Boom et al., Human immunodeficiency virus type 1, 1996.

T. Jie and E. Verdin, Transcription factor binding sites downstream of the human immunodeficiency virus type 1 transcription start site are important for virus infectivity, J Virol, vol.71, pp.6113-6127, 1997.

C. J. Van-noesel, R. A. Gruters, F. G. Terpstra, P. T. Schellekens, R. A. Van-lier et al., Functional and phenotypic evidence for a selective loss of memory T cells in asymptomatic human immunodeficiency virus-infected men., Journal of Clinical Investigation, vol.86, issue.1, pp.293-299, 1990.
DOI : 10.1172/JCI114698

T. Van-opijnen, R. E. Jeeninga, M. C. Boerlijst, G. P. Pollakis, V. Zetterberg et al., Human Immunodeficiency Virus Type 1 Subtypes Have a Distinct Long Terminal Repeat That Determines the Replication Rate in a Host-Cell-Specific Manner, Journal of Virology, vol.78, issue.7, pp.3675-3683, 2004.
DOI : 10.1128/JVI.78.7.3675-3683.2004

T. Van-opijnen, J. Kamoschinski, R. E. Jeeninga, and B. Berkhout, The Human Immunodeficiency Virus Type 1 Promoter Contains a CATA Box Instead of a TATA Box for Optimal Transcription and Replication, Journal of Virology, vol.78, issue.13, pp.6883-6890, 2004.
DOI : 10.1128/JVI.78.13.6883-6890.2004

J. P. Vartanian, P. Sommer, and S. Wain-hobson, Death and the retrovirus, Trends in Molecular Medicine, vol.9, issue.10, pp.409-413, 2003.
DOI : 10.1016/j.molmed.2003.08.008

URL : https://hal.archives-ouvertes.fr/pasteur-00850260

R. Veazey and A. Lackner, The mucosal immune system and HIV-1 infection, AIDS Rev, vol.5, pp.245-252, 2003.

R. S. Veazey, M. Demaria, L. V. Chalifoux, D. E. Shvetz, D. R. Pauley et al., Gastrointestinal Tract as a Major Site of CD4+ T Cell Depletion and Viral Replication in SIV Infection, Science, vol.280, issue.5362, pp.427-431, 1998.
DOI : 10.1126/science.280.5362.427

R. S. Veazey, M. C. Gauduin, K. G. Mansfield, I. C. Tham, J. D. Altman et al., Emergence and Kinetics of Simian Immunodeficiency Virus-Specific CD8+ T Cells in the Intestines of Macaques during Primary Infection, Journal of Virology, vol.75, issue.21, pp.10515-10519, 2001.
DOI : 10.1128/JVI.75.21.10515-10519.2001

R. S. Veazey, J. D. Lifson, I. Pandrea, J. Purcell, M. Piatak et al., Simian Immunodeficiency Virus Infection in Neonatal Macaques, Journal of Virology, vol.77, issue.16, pp.8783-8792, 2003.
DOI : 10.1128/JVI.77.16.8783-8792.2003

R. S. Veazey, K. G. Mansfield, I. C. Tham, A. C. Carville, D. E. Shvetz et al., Dynamics of CCR5 Expression by CD4+ T Cells in Lymphoid Tissues during Simian Immunodeficiency Virus Infection, Journal of Virology, vol.74, issue.23, pp.11001-11007, 2000.
DOI : 10.1128/JVI.74.23.11001-11007.2000

R. S. Veazey, P. A. Marx, and A. A. Lackner, The mucosal immune system: primary target for HIV infection and AIDS, Trends in Immunology, vol.22, issue.11, pp.626-633, 2001.
DOI : 10.1016/S1471-4906(01)02039-7

R. S. Veazey, P. A. Marx, and A. A. Lackner, T Cells Express High Levels of CCR5 and Are Rapidly Depleted in Simian Immunodeficiency Virus Infection, The Journal of Infectious Diseases, vol.187, issue.5, pp.769-776, 2003.
DOI : 10.1086/368386

K. Verhoef, R. W. Sanders, V. Fontaine, S. Kitajima, and B. Berkhout, Evolution of the human immunodeficiency virus type 1 long terminal repeat promoter by conversion of an NFkappaB enhancer element into a GABP binding site, J Virol, vol.73, pp.1331-1340, 1999.

C. P. Verrijzer and R. Tjian, TAFs mediate transcriptional activation and promoter selectivity, Trends in Biochemical Sciences, vol.21, issue.9, pp.338-342, 1996.
DOI : 10.1016/0968-0004(96)10044-X

V. Gegerfelt, A. Albert, J. Morfeldt-manson, L. Broliden, K. Fenyo et al., Isolate-specific neutralizing antibodies in patients with progressive HIV-1-related disease, Virology, vol.185, issue.1, pp.162-168, 1991.
DOI : 10.1016/0042-6822(91)90764-3

S. Luster and A. D. , Beta-chemokines are released from HIV-1-specific cytolytic T-cell granules complexed to proteoglycans, Nature, vol.391, issue.6670, pp.908-911, 1998.
DOI : 10.1038/36129

S. Wain-hobson, P. Sonigo, O. Danos, S. Cole, and M. And-alizon, Nucleotide sequence of the AIDS virus, LAV, Cell, vol.40, issue.1, pp.9-17, 1985.
DOI : 10.1016/0092-8674(85)90303-4

S. Wain-hobson, J. P. Vartanian, M. Henry, N. Chenciner, R. Cheynier et al., LAV revisited: origins of the early HIV-1 isolates from Institut Pasteur, Science, vol.252, issue.5008, 1991.
DOI : 10.1126/science.2035026

C. M. Walker, D. J. Moody, D. P. Stites, and J. A. Levy, CD8+ lymphocytes can control HIV infection in vitro by suppressing virus replication, Science, vol.234, issue.4783, pp.1563-1566, 1986.
DOI : 10.1126/science.2431484

H. Ishii, Interleukin 7 is produced by human intestinal epithelial cells and regulates the Influence du polymorphisme du promoteur des sous-types du VIH-1 sur la dynamique de la réplication virale in vivo BIBLIOGRAPHIE 176, 1995.

K. Osthoff, R. Frank, M. Kraft, M. Los, P. H. Krammer et al., HIV-1 Tat potentiates TNF-induced NFkappa B activation and cytotoxicity by altering the cellular redox state, Embo J, vol.14, pp.546-554, 1995.

R. D. Williams, B. A. Lee, S. P. Jackson, and N. J. Proudfoot, Activation Domains of Transcription Factors Mediate Replication Dependent Transcription from a Minimal HIV-1 Promoter, Nucleic Acids Research, vol.24, issue.4, pp.549-557, 1996.
DOI : 10.1093/nar/24.4.549

X. N. Xu, B. Laffert, G. R. Screaton, M. Kraft, D. Wolf et al., Induction of Fas Ligand Expression by HIV Involves the Interaction of Nef with the T Cell Receptor ?? Chain, The Journal of Experimental Medicine, vol.72, issue.9, pp.1489-1496, 1999.
DOI : 10.1084/jem.186.1.1

Y. Yasutomi, K. A. Reimann, C. I. Lord, M. D. Miller, and N. L. Letvin, Simian immunodeficiency virus-specific CD8+ lymphocyte response in acutely infected rhesus monkeys, J Virol, vol.67, pp.1707-1711, 1993.

V. S. Yedavalli, M. Benkirane, and K. T. Jeang, Tat and Trans-activation-responsive (TAR) RNA-independent Induction of HIV-1 Long Terminal Repeat by Human and Murine Cyclin T1 Requires Sp1, Journal of Biological Chemistry, vol.278, issue.8, pp.6404-6410, 2003.
DOI : 10.1074/jbc.M209162200

V. Zacharova, M. L. Becker, V. Zachar, P. Ebbesen, and A. S. Goustin, DNA sequence analysis of the long terminal repeat of the C subtype of human immunodeficiency virus type 1, 1997.

S. Haislip, A. , C. , and I. S. , HIV-1 entry into quiescent primary lymphocytes: molecular analysis reveals a labile, latent viral structure, Cell, vol.61, pp.213-222, 1990.

H. Smith, D. Grey, P. Suzuki, K. Carr, A. Goh et al., Increased turnover of CCR5+ and redistribution of CCR5-CD4 T lymphocytes during primary human immunodeficiency virus type 1 infection, J Infect Dis, vol.183, pp.736-743, 2001.

M. Zeitz, W. C. Greene, N. J. Peffer, J. , and S. P. , Lymphocytes isolated from the intestinal lamina propria of normal nonhuman primates have increased expression of genes associated with T-cell activation, Gastroenterology, vol.94, issue.3, pp.647-655, 1988.
DOI : 10.1016/0016-5085(88)90235-1

S. T. Smale, HIV-1 core promoter lacks a simple initiator element but contains a bipartite activator at the transcription start site, J Biol Chem, vol.268, pp.15823-15832, 1993.