F. La-bande-nommée-linear and . Au-produit-d, intégration concertée, sous forme linéaire (Figure 50A) Les produits d'auto-intégration (donneur-donneur) sont représentés par les bandes AutoIntegration ou AI (Figure 50A) La bande S de plus bas poids moléculaire

. Linding, Les résidus de la région ET (676-738) sont en italique. Les zones prédites comme désordonnées sont en bleu (781-793 et 812-836). Bas, Figure 53. Haut. Prédiction du désordre intrinsèque du CTD de l'isoforme 2 de Brd2 humain (666-836) avec le serveur Globplot, 2003.

P. La-souche-bactérienne-bl21-le-ctd-de-l-'in-de, Un des clones résultants a servi à inoculer la préculture (milieu LB supplémenté en kanamycine 50 ?g/ml) Après une nuit d'incubation à 37°C, la préculture a été versée dans un volume de milieu LB plus grand (culture) contenant de la kanamycine (50 ?g/ml), placé à 37°C, sous agitation (180 rpm)

J. Agapkina, M. Smolov, S. Barbe, E. Zubin, T. Zatsepin et al., Probing of HIV-1 Integrase/DNA Interactions Using Novel Analogs of Viral DNA, Journal of Biological Chemistry, vol.246, issue.17, pp.11530-11540, 2006.
DOI : 10.1074/jbc.M510628200
URL : https://hal.archives-ouvertes.fr/hal-00283458

A. Aiyar, P. Hindmarsh, A. Skalka, and J. Leis, Concerted integration of linear retroviral DNA by the avian sarcoma virus integrase in vitro: dependence on both long terminal repeat termini, J Virol, vol.70, pp.3571-3580, 1996.

S. Aiyer, G. Swapna, N. Malani, J. Aramini, W. Schneider et al., Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction, Nucleic Acids Research, vol.42, issue.9, pp.5917-5928, 2014.
DOI : 10.1093/nar/gku175

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

M. Andrake, J. Ramcharan, G. Merkel, X. Zhao, T. Burke et al., Comparison of metal-dependent catalysis by HIV-1 and ASV integrase proteins using a new and rapid, moderate throughput assay for joining activity in solution, AIDS Research and Therapy, vol.6, issue.1, p.14, 2009.
DOI : 10.1186/1742-6405-6-14

T. Arakawa and K. Tsumoto, The effects of arginine on refolding of aggregated proteins: not facilitate refolding, but suppress aggregation, Biochemical and Biophysical Research Communications, vol.304, issue.1, pp.148-152, 2003.
DOI : 10.1016/S0006-291X(03)00578-3

E. Arts and D. Hazuda, HIV-1 Antiretroviral Drug Therapy, Cold Spring Harbor Perspectives in Medicine, vol.2, issue.4, 2012.
DOI : 10.1101/cshperspect.a007161
URL : http://perspectivesinmedicine.cshlp.org/content/2/4/a007161.full.pdf

S. Assil, P. Bolze, M. Boukhali, C. Cariou, L. Chauveau et al., Retrovirus humain XMRV : la fin d'une histoire seduisante ?, Virologie, vol.15, pp.222-234, 2011.

I. Azran, Y. Schavinsky-khrapunsky, E. Priel, M. Huleihel, and M. Aboud, Implications of the evolution pattern of human T-cell leukemia retroviruses on their pathogenic virulence (Review), International Journal of Molecular Medicine, vol.14, pp.909-915, 2004.
DOI : 10.3892/ijmm.14.5.909

E. Balada, M. Vilardell-tarres, and J. Ordi-ros, Implication of Human Endogenous Retroviruses in the Development of Autoimmune Diseases, International Reviews of Immunology, vol.124, issue.4, pp.351-370, 2010.
DOI : 10.1111/j.0022-202X.2004.23504.x

M. Balakrishnan, S. Yant, L. Tsai, O. Sullivan, C. Bam et al., Non-Catalytic Site HIV-1 Integrase Inhibitors Disrupt Core Maturation and Induce a Reverse Transcription Block in Target Cells, PLoS ONE, vol.8, issue.9, p.74163, 2013.
DOI : 10.1371/journal.pone.0074163.s002

M. Balasubramaniam and E. Freed, New Insights into HIV Assembly and Trafficking, Physiology, vol.67, issue.4, pp.236-251, 2011.
DOI : 10.1038/415088a

A. Ballandras-colas, M. Brown, N. Cook, T. Dewdney, B. Demeler et al., Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function, Nature, vol.42, issue.7590, pp.358-361, 2016.
DOI : 10.1093/nar/gku316

A. Ballandras, K. Moreau, X. Robert, M. Confort, R. Merceron et al., A Crystal Structure of the Catalytic Core Domain of an Avian Sarcoma and Leukemia Virus Integrase Suggests an Alternate Dimeric Assembly, PLoS ONE, vol.68, issue.8, p.23032, 2011.
DOI : 10.1371/journal.pone.0023032.s003

D. Baltimore, Expression of animal virus genomes, Bacteriol Rev, vol.35, pp.235-241, 1971.

S. Baranova, F. Tuzikov, O. Zakharova, N. Tuzikova, C. Calmels et al., Small-angle X-ray characterization of the nucleoprotein complexes resulting from DNA-induced oligomerization of HIV-1 integrase, Nucleic Acids Research, vol.35, issue.3, pp.975-987, 2007.
DOI : 10.1093/nar/gkl1111
URL : https://hal.archives-ouvertes.fr/hal-00166177

F. Barre-sinoussi, J. Chermann, F. Rey, M. Nugeyre, S. Chamaret et al., Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS), Science, vol.220, issue.4599, pp.868-871, 1983.
DOI : 10.1126/science.6189183

M. Benleulmi, J. Matysiak, D. Henriquez, C. Vaillant, P. Lesbats et al., Intasome architecture and chromatin density modulate retroviral integration into nucleosome, Retrovirology, vol.12, issue.1, p.13, 2015.
DOI : 10.1101/gad.872801
URL : https://hal.archives-ouvertes.fr/pasteur-01416843

B. Bernstein, A. Meissner, and E. Lander, The Mammalian Epigenome, Cell, vol.128, issue.4, pp.669-681, 2007.
DOI : 10.1016/j.cell.2007.01.033
URL : https://doi.org/10.1016/j.cell.2007.01.033

M. Biasini, S. Bienert, A. Waterhouse, K. Arnold, G. Studer et al., SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information, Nucleic Acids Research, vol.42, issue.W1, pp.252-258, 2014.
DOI : 10.1093/nar/gku340
URL : https://academic.oup.com/nar/article-pdf/42/W1/W252/7438166/gku340.pdf

H. Birnboim and J. Doly, A rapid alkaline extraction procedure for screening recombinant plasmid DNA, Nucleic Acids Research, vol.7, issue.6, pp.1513-1523, 1979.
DOI : 10.1093/nar/7.6.1513

J. Blond, D. Lavillette, V. Cheynet, O. Bouton, G. Oriol et al., An Envelope Glycoprotein of the Human Endogenous Retrovirus HERV-W Is Expressed in the Human Placenta and Fuses Cells Expressing the Type D Mammalian Retrovirus Receptor, Journal of Virology, vol.74, issue.7, pp.3321-3329, 2000.
DOI : 10.1128/JVI.74.7.3321-3329.2000

R. Bojja, M. Andrake, S. Weigand, G. Merkel, O. Yarychkivska et al., Architecture of a Full-length Retroviral Integrase Monomer and Dimer, Revealed by Small Angle X-ray Scattering and Chemical Cross-linking, Journal of Biological Chemistry, vol.70, issue.19, pp.17047-17059, 2011.
DOI : 10.1107/S0021889807002853

B. Brenner and M. Wainberg, We need to use the best antiretroviral drugs worldwide to prevent HIV drug resistance, AIDS, vol.30, issue.17, pp.2725-2727, 2016.
DOI : 10.1097/QAD.0000000000001234

M. Briones, C. Dobard, and S. Chow, Role of Human Immunodeficiency Virus Type 1 Integrase in Uncoating of the Viral Core, Journal of Virology, vol.84, issue.10, pp.5181-5190, 2010.
DOI : 10.1128/JVI.02382-09

P. Brown, B. Bowerman, H. Varmus, and J. Bishop, Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein., Proceedings of the National Academy of Sciences, vol.86, issue.8, pp.2525-2529, 1989.
DOI : 10.1073/pnas.86.8.2525

R. Brown and J. Bennett, The miscellaneous botanical works of Robert Brown, 1866.

G. Bujacz, J. Alexandratos, Z. Qing, C. Clement-mella, and A. Wlodawer, The catalytic domain of human immunodeficiency virus integrase: ordered active site in the F185H mutant, FEBS Letters, vol.6, issue.2-3, pp.175-178, 1996.
DOI : 10.1016/S0263-7855(98)80040-4

M. Bukrinsky, A hard way to the nucleus, Mol Med, vol.10, pp.1-5, 2004.

F. Bushman and B. Wang, Rous sarcoma virus integrase protein: mapping functions for catalysis and substrate binding, J Virol, vol.68, pp.2215-2223, 1994.

K. Busschots, J. Vercammen, S. Emiliani, R. Benarous, Y. Engelborghs et al., The Interaction of LEDGF/p75 with Integrase Is Lentivirus-specific and Promotes DNA Binding, Journal of Biological Chemistry, vol.70, issue.18, pp.17841-17847, 2005.
DOI : 10.1016/S0092-8674(02)00864-4

M. Bustin and R. Reeves, High-Mobility-Group Chromosomal Proteins: Architectural Components That Facilitate Chromatin Function, Prog Nucleic Acid Res Mol Biol, vol.54, pp.35-100, 1996.
DOI : 10.1016/S0079-6603(08)60360-8

M. Cai, R. Zheng, M. Caffrey, R. Craigie, G. Clore et al., Solution structure of the N-terminal zinc binding domain of HIV-1 integrase, Nature Structural Biology, vol.4, issue.7, pp.567-577, 1997.
DOI : 10.1107/S0021889892009944

C. Calmels, V. De-soultrait, A. Caumont, C. Desjobert, A. Faure et al., Biochemical and random mutagenesis analysis of the region carrying the catalytic E152 amino acid of HIV-1 integrase, Nucleic Acids Research, vol.32, issue.4, pp.1527-1538, 2004.
DOI : 10.1093/nar/gkh298

J. Carrington and W. Dougherty, A viral cleavage site cassette: identification of amino acid sequences required for tobacco etch virus polyprotein processing., Proceedings of the National Academy of Sciences, vol.85, issue.10, pp.3391-3395, 1988.
DOI : 10.1073/pnas.85.10.3391

S. Carteau, R. Gorelick, and F. Bushman, Coupled integration of human immunodeficiency virus type 1

J. Carter and V. Saunders, Virology : principles and applications, 2007.

C. Cellier, K. Moreau, K. Gallay, A. Ballandras, P. Gouet et al., In vitro functional analyses of the human immunodeficiency virus type 1 (HIV-1) integrase mutants give new insights into the intasome assembly, Virology, vol.439, issue.2, pp.97-104, 2013.
DOI : 10.1016/j.virol.2013.02.001

J. Chen, J. Krucinski, L. Miercke, J. Finer-moore, A. Tang et al., Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: A model for viral DNA binding, Proceedings of the National Academy of Sciences, vol.50, issue.Pt 5, pp.8233-8238, 2000.
DOI : 10.1107/S0907444994003112

P. Cherepanov, LEDGF/p75 interacts with divergent lentiviral integrases and modulates their enzymatic activity in vitro, Nucleic Acids Research, vol.35, issue.1, pp.113-124, 2007.
DOI : 10.1093/nar/gkl885

P. Cherepanov, A. Ambrosio, S. Rahman, T. Ellenberger, and A. Engelman, Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75, Proceedings of the National Academy of Sciences, vol.15, issue.4, pp.17308-17313, 2005.
DOI : 10.1093/bioinformatics/15.4.305

P. Cherepanov, E. Devroe, P. Silver, and A. Engelman, Identification of an Evolutionarily Conserved Domain in Human Lens Epithelium-derived Growth Factor/Transcriptional Co-activator p75 (LEDGF/p75) That Binds HIV-1 Integrase, Journal of Biological Chemistry, vol.73, issue.47, pp.48883-48892, 2004.
DOI : 10.1093/bioinformatics/15.4.305

P. Cherepanov, G. Maertens, P. Proost, B. Devreese, J. Van-beeumen et al., HIV-1 Integrase Forms Stable Tetramers and Associates with LEDGF/p75 Protein in Human Cells, Journal of Biological Chemistry, vol.40, issue.1, pp.372-381, 2003.
DOI : 10.1002/bms.1200111109

S. Chow, K. Vincent, V. Ellison, and P. Brown, Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus, Science, vol.255, issue.5045, pp.723-726, 1992.
DOI : 10.1126/science.1738845

F. Clavel, D. Guetard, F. Brun-vezinet, S. Chamaret, M. Rey et al., Isolation of a new human retrovirus from West African patients with AIDS, Science, vol.233, issue.4761, pp.343-346, 1986.
DOI : 10.1126/science.2425430

J. Coleman, S. Eaton, G. Merkel, A. Skalka, and T. Laue, Virus Integrase by Analytical Ultracentrifugation, Journal of Biological Chemistry, vol.8, issue.46, pp.32842-32846, 1999.
DOI : 10.1021/bi00519a023

B. Collins, R. Stevens, and R. Page, Crystallization Optimum Solubility Screening: using crystallization results to identify the optimal buffer for protein crystal formation, Acta Crystallographica Section F Structural Biology and Crystallization Communications, vol.61, issue.12, pp.1035-1038, 2005.
DOI : 10.1107/S1744309105035244

D. Cooper, B. Gollackner, and D. Sachs, Will the Pig Solve the Transplantation Backlog?, Annual Review of Medicine, vol.53, issue.1, pp.133-147, 2002.
DOI : 10.1146/annurev.med.53.082901.103900

B. Crowe, R. Larue, C. Yuan, S. Hess, M. Kvaratskhelia et al., Structure of the Brd4 ET domain bound to a C-terminal motif from ??-retroviral integrases reveals a conserved mechanism of interaction, Proceedings of the National Academy of Sciences, vol.16, issue.1, pp.2086-2091, 2016.
DOI : 10.1016/j.molcel.2015.10.033

C. Davey, D. Sargent, K. Luger, A. Maeder, and T. Richmond, Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9?? Resolution, Journal of Molecular Biology, vol.319, issue.5, pp.1097-1113, 2002.
DOI : 10.1016/S0022-2836(02)00386-8

D. Clercq, E. Li, and G. , SUMMARY, Clinical Microbiology Reviews, vol.29, issue.3, pp.695-747, 2016.
DOI : 10.1128/CMR.00102-15

J. De-rijck, C. De-kogel, J. Demeulemeester, S. Vets, E. Ashkar et al., The BET Family of Proteins Targets Moloney Murine Leukemia Virus Integration near Transcription Start Sites, Cell Reports, vol.5, issue.4, pp.886-894, 2013.
DOI : 10.1016/j.celrep.2013.09.040

Z. Debyser, F. Christ, D. Rijck, J. Gijsbers, and R. , Host factors for retroviral integration site selection, Trends in Biochemical Sciences, vol.40, issue.2, pp.108-116, 2015.
DOI : 10.1016/j.tibs.2014.12.001

W. Delano, The PyMOL Molecular Graphics System, 2008.

O. Delelis, K. Carayon, A. Saib, E. Deprez, and J. Mouscadet, Integrase and integration: biochemical activities of HIV-1 integrase, Retrovirology, vol.5, issue.1, p.114, 2008.
DOI : 10.1186/1742-4690-5-114

A. Demange, H. Yajjou-hamalian, K. Gallay, C. Luengo, V. Beven et al., Porcine endogenous retrovirus-A/C: biochemical properties of its integrase and susceptibility to raltegravir, Journal of General Virology, vol.96, issue.10, pp.3124-3130, 2015.
DOI : 10.1099/jgv.0.000236

J. Demeulemeester, P. Chaltin, A. Marchand, D. Maeyer, M. Debyser et al., LEDGINs, non-catalytic site inhibitors of HIV-1 integrase: a patent review (2006 ??? 2014), Expert Opinion on Therapeutic Patents, vol.15, issue.4, pp.609-632, 2006.
DOI : 10.1093/infdis/jis750

G. Denis, M. Mccomb, D. Faller, A. Sinha, P. Romesser et al., Identification of Transcription Complexes that Contain the Double Bromodomain Protein Brd2 and Chromatin Remodeling Machines, Journal of Proteome Research, vol.5, issue.3, pp.502-511, 2006.
DOI : 10.1021/pr050430u

S. Desfarges, S. Filippo, J. Fournier, M. Calmels, C. Caumont-sarcos et al., Chromosomal integration of LTR-flanked DNA in yeast expressing HIV-1 integrase: down regulation by RAD51, Nucleic Acids Research, vol.34, issue.21, pp.6215-6224, 2006.
DOI : 10.1093/nar/gkl843
URL : https://hal.archives-ouvertes.fr/hal-00166159

M. Dewannieux, D. Ribet, and T. Heidmann, Risks linked to endogenous retroviruses for vaccine production: A??general overview, Biologicals, vol.38, issue.3, pp.366-370, 2010.
DOI : 10.1016/j.biologicals.2010.01.006

A. Dey, F. Chitsaz, A. Abbasi, T. Misteli, and K. Ozato, The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis, Proceedings of the National Academy of Sciences, vol.111, issue.3, pp.8758-8763, 2003.
DOI : 10.1016/S0092-8674(02)01005-X

C. Dobard, M. Briones, and S. Chow, Molecular Mechanisms by Which Human Immunodeficiency Virus Type 1 Integrase Stimulates the Early Steps of Reverse Transcription, Journal of Virology, vol.81, issue.18, pp.10037-10046, 2007.
DOI : 10.1128/JVI.00519-07

R. Drapkin, A. Merino, and D. Reinberg, Regulation of RNA polymerase II transcription, Current Opinion in Cell Biology, vol.5, issue.3, pp.469-476, 1993.
DOI : 10.1016/0955-0674(93)90013-G

F. Dyda, A. Hickman, T. Jenkins, A. Engelman, R. Craigie et al., Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases, Science, vol.266, issue.5193, 1994.
DOI : 10.1126/science.7801124

T. Eickbush and H. Malik, Origins and Evolution of Retrotransposons, Mobile DNA II, pp.1111-1144, 2002.
DOI : 10.1128/9781555817954.ch49

J. Eidahl, B. Crowe, J. North, C. Mckee, N. Shkriabai et al., Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes, Nucleic Acids Research, vol.41, issue.6, pp.3924-3936, 2013.
DOI : 10.1093/nar/gkt074

A. Eijkelenboom, F. Van-den-ent, A. Vos, J. Doreleijers, K. Hard et al., The solution structure of the amino-terminal HHCC domain of HIV-2 integrase: a three-helix bundle stabilized by zinc, Current Biology, vol.7, issue.10, pp.739-746, 1997.
DOI : 10.1016/S0960-9822(06)00332-0

S. Emiliani, A. Mousnier, K. Busschots, M. Maroun, B. Van-maele et al., Integrase Mutants Defective for Interaction with LEDGF/p75 Are Impaired in Chromosome Tethering and HIV-1 Replication, Journal of Biological Chemistry, vol.280, issue.27, pp.25517-25523, 2005.
DOI : 10.1074/jbc.M501378200

A. Engelman, In Vivo Analysis of Retroviral Integrase Structure and Function, Adv Virus Res, vol.52, pp.411-426, 1999.
DOI : 10.1016/S0065-3527(08)60309-7

A. Engelman and P. Cherepanov, The Lentiviral Integrase Binding Protein LEDGF/p75 and HIV-1 Replication, PLoS Pathogens, vol.4, issue.3, p.1000046, 2008.
DOI : 10.1371/journal.ppat.1000046.g004
URL : https://doi.org/10.1371/journal.ppat.1000046

A. Engelman and P. Cherepanov, The structural biology of HIV-1: mechanistic and therapeutic insights, Nature Reviews Microbiology, vol.6, issue.4, pp.279-290, 2012.
DOI : 10.1038/nrd2336

A. Engelman, K. Mizuuchi, and R. Craigie, HIV-1 DNA integration: Mechanism of viral DNA cleavage and DNA strand transfer, Cell, vol.67, issue.6, pp.1211-1221, 1991.
DOI : 10.1016/0092-8674(91)90297-C

D. Esposito and R. Craigie, Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction, The EMBO Journal, vol.17, issue.19, pp.5832-5843, 1998.
DOI : 10.1093/emboj/17.19.5832

C. Farnet and W. Haseltine, Integration of human immunodeficiency virus type 1 DNA in vitro., Proceedings of the National Academy of Sciences, vol.87, issue.11, pp.4164-4168, 1990.
DOI : 10.1073/pnas.87.11.4164

V. Parissi, HIV-1 integrase crosslinked oligomers are active in vitro, Nucleic Acids Res, vol.33, pp.977-986, 2005.

Y. Feng, T. Baig, R. Love, and L. Chelico, Suppression of APOBEC3-mediated restriction of HIV-1 by Vif, Frontiers in Microbiology, vol.86, issue.e33495, p.450, 2014.
DOI : 10.1128/JVI.06957-11

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. Smith et al., Selective inhibition of BET bromodomains, Nature, vol.4, issue.7327, pp.1067-1073, 2010.
DOI : 10.1016/S0002-9440(10)63049-0

W. Fischle, Y. Wang, and C. Allis, Histone and chromatin cross-talk, Current Opinion in Cell Biology, vol.15, issue.2, pp.172-183, 2003.
DOI : 10.1016/S0955-0674(03)00013-9

B. Florence and D. Faller, You bet-cha: a novel family of transcriptional regulators, Front Biosci, vol.6, pp.1008-1018, 2001.

E. Freed, HIV-1 assembly, release and maturation, Nature Reviews Microbiology, vol.343, issue.8, pp.484-496, 2015.
DOI : 10.1126/science.1247786

E. Freed, HIV-1 replication, Somatic Cell and Molecular Genetics, vol.26, issue.1/6, pp.13-33, 2001.
DOI : 10.1023/A:1021070512287

K. Gao, R. Gorelick, D. Johnson, and F. Bushman, Cofactors for Human Immunodeficiency Virus Type 1 cDNA Integration In Vitro, Journal of Virology, vol.77, issue.2, pp.1598-1603, 2003.
DOI : 10.1128/JVI.77.2.1598-1603.2003

H. Ge, Y. Si, and R. Roeder, Isolation of cDNAs encoding novel transcription coactivators p52 and p75 reveals an alternate regulatory mechanism of transcriptional activation, The EMBO Journal, vol.17, issue.22, pp.6723-6729, 1998.
DOI : 10.1093/emboj/17.22.6723

J. Gerton and P. Brown, The Core Domain of HIV-1 Integrase Recognizes Key Features of Its DNA Substrates, Journal of Biological Chemistry, vol.13, issue.41, pp.25809-25815, 1997.
DOI : 10.1074/jbc.270.7.3320

Y. Goldgur, R. Craigie, G. Cohen, T. Fujiwara, T. Yoshinaga et al., Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: A platform for antiviral drug design, Proceedings of the National Academy of Sciences, vol.95, issue.9, pp.13040-13043, 1999.
DOI : 10.1073/pnas.95.9.4831

Y. Goldgur, F. Dyda, A. Hickman, T. Jenkins, R. Craigie et al., Three new structures of the core domain of HIV-1 integrase: An active site that binds magnesium, Proceedings of the National Academy of Sciences, vol.272, issue.29, pp.9150-9154, 1998.
DOI : 10.1074/jbc.272.29.18161

P. Gouet, X. Robert, C. E. Espript, and /. Endscript, ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins, Nucleic Acids Research, vol.31, issue.13, pp.3320-3323, 2003.
DOI : 10.1093/nar/gkg556
URL : https://hal.archives-ouvertes.fr/hal-00314281

D. Grandgenett, A. Vora, and R. Schiff, 000-dalton nucleic acid-binding protein from avian retravirus cores possesses DNA endonuclease activity, Virology, vol.32, issue.89, pp.119-132, 1978.
DOI : 10.1016/0042-6822(78)90046-6

S. Graslund, P. Nordlund, J. Weigelt, B. Hallberg, J. Bray et al., Protein production and purification, Nature Methods, vol.62, issue.2, pp.135-146, 2008.
DOI : 10.1128/MCB.3.12.2156

W. Greene, Z. Debyser, Y. Ikeda, E. Freed, E. Stephens et al., Novel targets for HIV therapy, Antiviral Research, vol.80, issue.3, pp.251-265, 2008.
DOI : 10.1016/j.antiviral.2008.08.003

K. Gupta, J. Curtis, S. Krueger, Y. Hwang, P. Cherepanov et al., Solution Conformations of Prototype Foamy Virus Integrase and Its Stable Synaptic Complex with U5 Viral DNA, Structure, vol.20, issue.11, pp.1918-1928, 2012.
DOI : 10.1016/j.str.2012.08.023

K. Gupta, V. Turkki, S. Sherrill-mix, Y. Hwang, G. Eilers et al., Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase, PLOS Biology, vol.78, issue.3, p.1002584, 2016.
DOI : 10.1371/journal.pbio.1002584.s009

S. Gupta, T. Maetzig, G. Maertens, A. Sharif, M. Rothe et al., Bromo- and Extraterminal Domain Chromatin Regulators Serve as Cofactors for Murine Leukemia Virus Integration, Journal of Virology, vol.87, issue.23, pp.12721-12736, 2013.
DOI : 10.1128/JVI.01942-13
URL : http://jvi.asm.org/content/87/23/12721.full.pdf

O. Haffar, S. Popov, L. Dubrovsky, I. Agostini, H. Tang et al., Two nuclear localization signals in the HIV-1 matrix protein regulate nuclear import of the HIV-1 pre-integration complex 1 1Edited by M. Gottesman, Journal of Molecular Biology, vol.299, issue.2, pp.359-368, 2000.
DOI : 10.1006/jmbi.2000.3768

S. Hare, D. Nunzio, F. Labeja, A. Wang, J. Engelman et al., Structural Basis for Functional Tetramerization of Lentiviral Integrase, PLoS Pathogens, vol.331, issue.7, p.1000515, 2009.
DOI : 10.1371/journal.ppat.1000515.s007
URL : https://hal.archives-ouvertes.fr/pasteur-01536181

S. Hare, S. Gupta, E. Valkov, A. Engelman, and P. Cherepanov, Retroviral intasome assembly and inhibition of DNA strand transfer, Nature, vol.25, issue.7286, pp.232-236, 2010.
DOI : 10.1038/nature08784

S. Hare, G. Maertens, and P. Cherepanov, 3'-processing and strand transfer catalysed by retroviral integration in crystallo, EMBO J, pp.3020-3028, 2012.

W. Hayward, B. Neel, and S. Astrin, Activation of a cellular onc gene by promoter insertion in ALV-induced lymphoid leukosis, Nature, vol.98, issue.5806, pp.475-480, 1981.
DOI : 10.1016/0005-2787(76)90307-5

P. Hindmarsh, T. Ridky, R. Reeves, M. Andrake, A. Skalka et al., HMG protein family members stimulate human immunodeficiency virus type 1 and avian sarcoma virus concerted DNA integration in vitro, J Virol, vol.73, pp.2994-3003, 1999.

J. Hnilicova, S. Hozeifi, E. Stejskalova, E. Duskova, I. Poser et al., The C-terminal domain of Brd2 is important for chromatin interaction and regulation of transcription and alternative splicing, Molecular Biology of the Cell, vol.24, issue.22, pp.3557-3568, 2013.
DOI : 10.1091/mbc.E13-06-0303

B. Huang, X. Yang, M. Zhou, K. Ozato, and L. Chen, Brd4 Coactivates Transcriptional Activation of NF-??B via Specific Binding to Acetylated RelA, Molecular and Cellular Biology, vol.29, issue.5, pp.1375-1387, 2009.
DOI : 10.1128/MCB.01365-08

T. Ikeda, H. Nishitsuji, X. Zhou, N. Nara, T. Ohashi et al., Evaluation of the Functional Involvement of Human Immunodeficiency Virus Type 1 Integrase in Nuclear Import of Viral cDNA during Acute Infection, Journal of Virology, vol.78, issue.21, pp.11563-11573, 2004.
DOI : 10.1128/JVI.78.21.11563-11573.2004

T. Jacks, K. Townsley, H. Varmus, and J. Majors, Two efficient ribosomal frameshifting events are required for synthesis of mouse mammary tumor virus gag-related polyproteins., Proceedings of the National Academy of Sciences, vol.84, issue.12, pp.4298-4302, 1987.
DOI : 10.1073/pnas.84.12.4298

J. Jacque and M. Stevenson, The inner-nuclear-envelope protein emerin regulates HIV-1 infectivity, Nature, vol.418, issue.7093, pp.641-645, 2006.
DOI : 10.1038/nature00896

J. Jancarik, R. Pufan, C. Hong, S. Kim, and R. Kim, Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins, Acta Crystallographica Section D Biological Crystallography, vol.60, issue.9, pp.1670-1673, 2004.
DOI : 10.1107/S0907444904010972

J. Janin and M. Delepierre, Biologie structurale : Principes et méthodes biophysiques, 1997.

M. Jaskolski, J. Alexandratos, G. Bujacz, and A. Wlodawer, Piecing together the structure of retroviral integrase, an important target in AIDS therapy, FEBS Journal, vol.25, issue.Suppl. 1, pp.2926-2946, 2009.
DOI : 10.1046/j.1365-4624.1997.00026.x

T. Jenkins, A. Engelman, R. Ghirlando, and R. Craigie, A Soluble Active Mutant of HIV-1 Integrase, Journal of Biological Chemistry, vol.267, issue.13, pp.7712-7718, 1996.
DOI : 10.1006/jmbi.1995.0556

K. Jones, J. Kadonaga, P. Rosenfeld, T. Kelly, and R. Tjian, A cellular DNA-binding protein that activates eukaryotic transcription and DNA replication, Cell, vol.48, issue.1, pp.79-89, 1987.
DOI : 10.1016/0092-8674(87)90358-8

K. Jones, J. Coleman, G. Merkel, T. Laue, and A. Skalka, Retroviral integrase functions as a multimer and can turn over catalytically, J Biol Chem, vol.267, pp.16037-16040, 1992.

G. Kalpana, S. Marmon, W. Wang, G. Crabtree, and S. Goff, Binding and stimulation of HIV-1 integrase by a human homolog of yeast transcription factor SNF5, Science, vol.266, issue.5193, pp.2002-2006, 1994.
DOI : 10.1126/science.7801128

G. Kalpana, A. Reicin, G. Cheng, M. Sorin, S. Paik et al., Isolation and Characterization of an Oligomerization-Negative Mutant of HIV-1 Integrase, Virology, vol.259, issue.2, pp.274-285, 1999.
DOI : 10.1006/viro.1999.9767

V. Kalyanaraman, M. Sarngadharan, M. Robert-guroff, I. Miyoshi, D. Golde et al., A new subtype of human T-cell leukemia virus (HTLV-II) associated with a T-cell variant of hairy cell leukemia, Science, vol.218, issue.4572, pp.571-573, 1982.
DOI : 10.1126/science.6981847

R. Katz and A. Skalka, A C-terminal domain in the avian sarcoma-leukosis virus pol gene product is not essential for viral replication, J Virol, vol.62, pp.528-533, 1988.

M. Katzman and M. Sudol, Nonspecific alcoholysis, a novel endonuclease activity of human immunodeficiency virus type 1 and other retroviral integrases, J Virol, vol.70, pp.2598-2604, 1996.

Y. Koh, K. Matreyek, and A. Engelman, Differential Sensitivities of Retroviruses to Integrase Strand Transfer Inhibitors, Journal of Virology, vol.85, issue.7, pp.3677-3682, 2011.
DOI : 10.1128/JVI.02541-10

R. Kornberg and J. Thomas, Chromatin Structure: Oligomers of the Histones, Science, vol.184, issue.4139, pp.865-868, 1974.
DOI : 10.1126/science.184.4139.865

T. Kouzarides, Chromatin Modifications and Their Function, Cell, vol.128, issue.4, pp.693-705, 2007.
DOI : 10.1016/j.cell.2007.02.005
URL : https://doi.org/10.1016/j.cell.2007.02.005

M. Kozin and D. Svergun, Automated matching of high- and low-resolution structural models, Journal of Applied Crystallography, vol.34, issue.1, pp.33-41, 2001.
DOI : 10.1107/S0021889800014126

L. Krishnan and A. Engelman, Retroviral Integrase Proteins and HIV-1 DNA Integration, Journal of Biological Chemistry, vol.6, issue.49, pp.40858-40866, 2012.
DOI : 10.1128/AAC.00717-12
URL : http://www.jbc.org/content/287/49/40858.full.pdf

J. Kulkosky, K. Jones, R. Katz, J. Mack, and A. Skalka, Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases., Molecular and Cellular Biology, vol.12, issue.5, pp.2331-2338, 1992.
DOI : 10.1128/MCB.12.5.2331

J. Kulkosky, R. Katz, G. Merkel, and A. Skalka, Activities and substrate specificity of the evolutionarily conserved central domain of retroviral integrase, Virology, vol.206, issue.1, pp.448-456, 1995.
DOI : 10.1016/S0042-6822(95)80060-3

R. Kurth, N. Bannert, M. Kvaratskhelia, A. Sharma, R. Larue et al., Retroviruses: Molecular Biology, Genomics and Pathogenesis Molecular mechanisms of retroviral integration site selection, Nucleic Acids Res, vol.42, pp.10209-10225, 2010.

U. Laemmli, Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4, Nature, vol.244, issue.5259, pp.680-685, 1970.
DOI : 10.1101/SQB.1963.028.01.053

L. Grice and S. , Human Immunodeficiency Virus Reverse Transcriptase: 25 Years of Research, Drug Discovery, and Promise, Journal of Biological Chemistry, vol.17, issue.49, pp.40850-40857, 2012.
DOI : 10.1016/j.str.2009.09.016

C. Amadori, J. Brias, S. Vomscheid, S. Eiler, N. Levy et al., Dual inhibition of HIV-1 replication by integrase- LEDGF allosteric inhibitors is predominant at the post-integration stage, Retrovirology, vol.10, pp.1186-1742, 2013.
URL : https://hal.archives-ouvertes.fr/inserm-00914180

M. Lee and R. Craigie, A previously unidentified host protein protects retroviral DNA from autointegration, Proceedings of the National Academy of Sciences, vol.88, issue.4, pp.1528-1533, 1998.
DOI : 10.1016/S0092-8674(00)81888-7

S. Lee, M. Potempa, and R. Swanstrom, The Choreography of HIV-1 Proteolytic Processing and Virion Assembly, Journal of Biological Chemistry, vol.11, issue.49, pp.40867-40874, 2012.
DOI : 10.1073/pnas.70.6.1734

G. Leroy, B. Rickards, and S. Flint, The Double Bromodomain Proteins Brd2 and Brd3 Couple Histone Acetylation to Transcription, Molecular Cell, vol.30, issue.1, pp.51-60, 2008.
DOI : 10.1016/j.molcel.2008.01.018

P. Lesbats, Y. Botbol, G. Chevereau, C. Vaillant, C. Calmels et al., Functional Coupling between HIV-1 Integrase and the SWI/SNF Chromatin Remodeling Complex for Efficient in vitro Integration into Stable Nucleosomes, PLoS Pathogens, vol.16, issue.2, p.1001280, 2011.
DOI : 10.1371/journal.ppat.1001280.s010
URL : https://hal.archives-ouvertes.fr/hal-00594715

P. Lesbats, M. Metifiot, C. Calmels, S. Baranova, G. Nevinsky et al., In vitro initial attachment of HIV-1 integrase to viral ends: control of the DNA specific interaction by the oligomerization state, Nucleic Acids Research, vol.36, issue.22, pp.7043-7058, 2008.
DOI : 10.1093/nar/gkn796
URL : https://hal.archives-ouvertes.fr/hal-00426343

A. Levin, Z. Hayouka, A. Friedler, and A. Loyter, Transportin 3 and importin ?? are required for effective nuclear import of HIV-1 integrase in virus-infected cells, Nucleus, vol.66, issue.5, pp.422-431, 2010.
DOI : 10.1038/87979

N. Levy, S. Eiler, K. Pradeau-aubreton, B. Maillot, F. Stricher et al., Production of unstable proteins through the formation of stable core complexes, Nature Communications, vol.404, p.10932, 2016.
DOI : 10.1016/j.ab.2010.04.039

S. Lieberman-blum, H. Fung, and J. Bandres, Maraviroc: A CCR5-receptor antagonist for the treatment of HIV-1 infection, Clinical Therapeutics, vol.30, issue.7, pp.1228-1250, 2008.
DOI : 10.1016/S0149-2918(08)80048-3

R. Linding, R. Russell, V. Neduva, and T. Gibson, GlobPlot: exploring protein sequences for globularity and disorder, Nucleic Acids Research, vol.31, issue.13, pp.3701-3708, 2003.
DOI : 10.1093/nar/gkg519
URL : https://academic.oup.com/nar/article-pdf/31/13/3701/9487141/gkg519.pdf

M. Llano, S. Delgado, M. Vanegas, and E. Poeschla, Lens Epithelium-derived Growth Factor/p75 Prevents Proteasomal Degradation of HIV-1 Integrase, Journal of Biological Chemistry, vol.72, issue.53, pp.55570-55577, 2004.
DOI : 10.1126/science.1083413
URL : http://www.jbc.org/content/279/53/55570.full.pdf

M. Llano, D. Saenz, A. Meehan, P. Wongthida, M. Peretz et al., An Essential Role for LEDGF/p75 in HIV Integration, Science, vol.314, issue.5798, pp.461-464, 2006.
DOI : 10.1126/science.1132319

P. Lodi, J. Ernst, J. Kuszewski, A. Hickman, A. Engelman et al., Solution Structure of the DNA Binding Domain of HIV-1 Integrase, Biochemistry, vol.34, issue.31, pp.9826-9833, 1995.
DOI : 10.1021/bi00031a002

K. Luger, A. Mader, R. Richmond, D. Sargent, and T. Richmond, Crystal structure of the nucleosome core particle at 2.8????? resolution, Nature, vol.74, issue.6648, pp.251-260, 1997.
DOI : 10.1073/pnas.74.3.864

R. Lutzke and R. Plasterk, Structure-based mutational analysis of the C-terminal DNA-binding domain of human immunodeficiency virus type 1 integrase: critical residues for protein oligomerization and DNA binding, J Virol, vol.72, pp.4841-4848, 1998.

Z. Lv, Y. Chu, and Y. Wang, HIV protease inhibitors: a review of molecular selectivity and toxicity, HIV AIDS, vol.7, pp.95-104, 2015.

G. Maertens, S. Hare, and P. Cherepanov, The mechanism of retroviral integration from X-ray structures of its key intermediates, Nature, vol.14, issue.7321, pp.326-329, 2010.
DOI : 10.1038/nature09517

T. Mahmood and P. Yang, Western blot: technique, theory, and trouble shooting, N Am J Med Sci, vol.4, pp.429-434, 2012.

S. Maignan, J. Guilloteau, Q. Zhou-liu, C. Clement-mella, and V. Mikol, Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases 1 1Edited by R. Huber, Journal of Molecular Biology, vol.282, issue.2, pp.359-368, 1998.
DOI : 10.1006/jmbi.1998.2002

B. Maillot, N. Levy, S. Eiler, C. Crucifix, F. Granger et al., Structural and Functional Role of INI1 and LEDGF in the HIV-1 Preintegration Complex, PLoS ONE, vol.296, issue.4, p.60734, 2013.
DOI : 10.1371/journal.pone.0060734.s012
URL : https://hal.archives-ouvertes.fr/hal-00839158

D. Mandal and V. Prasad, Analysis of 2-LTR Circle Junctions of Viral DNA in Infected Cells, Methods Mol Biol, vol.485, pp.73-85, 2009.
DOI : 10.1007/978-1-59745-170-3_6

F. Mantovani, J. Drost, P. Voorhoeve, D. Sal, G. Agami et al., Gene regulation and tumor suppression by the bromodomain-containing protein BRD7, Cell Cycle, vol.9, issue.14, pp.2777-2781, 2010.
DOI : 10.4161/cc.9.14.12309

C. Marchand, A. Johnson, R. Karki, G. Pais, X. Zhang et al., Metal-Dependent Inhibition of HIV-1 Integrase by ??-Diketo Acids and Resistance of the Soluble Double-Mutant (F185K/C280S), Molecular Pharmacology, vol.64, issue.3, pp.600-609, 2003.
DOI : 10.1124/mol.64.3.600

G. Martin, The road to Src, Oncogene, vol.23, issue.48, pp.7910-7917, 2004.
DOI : 10.1073/pnas.73.2.447

D. Maskell, R. L. Serrao, E. Lesbats, P. Matadeen, R. Hare et al., Structural basis for retroviral integration into nucleosomes, Nature, vol.14, issue.7560, pp.366-369, 2015.
DOI : 10.1101/gr.849004
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530500/pdf

Y. Matuo, S. Matsui, N. Nishi, F. Wada, and A. Sandberg, Quantitative solubilization of nonhistone chromosomal proteins without denaturation using zwitterionic detergents, Analytical Biochemistry, vol.150, issue.2, pp.337-344, 1985.
DOI : 10.1016/0003-2697(85)90520-2

L. Mcguffin, K. Bryson, and D. Jones, The PSIPRED protein structure prediction server, Bioinformatics, vol.16, issue.4, pp.404-405, 2000.
DOI : 10.1093/bioinformatics/16.4.404

M. Metifiot, C. Marchand, and Y. Pommier, HIV Integrase Inhibitors, Adv Pharmacol, vol.67, pp.75-105, 2013.
DOI : 10.1016/B978-0-12-405880-4.00003-2
URL : https://hal.archives-ouvertes.fr/hal-01101093

S. Mi, X. Lee, X. Li, G. Veldman, H. Finnerty et al., Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis, Nature, vol.101, issue.1, pp.785-789, 2000.
DOI : 10.1007/BF00355363

F. Michel, C. Crucifix, F. Granger, S. Eiler, J. Mouscadet et al., Structural basis for HIV-1 DNA integration in the human genome, role of the LEDGF/P75 cofactor, The EMBO Journal, vol.269, issue.7, pp.980-991, 2009.
DOI : 10.1073/pnas.93.24.13659
URL : https://hal.archives-ouvertes.fr/inserm-00384501

R. Mitchell, B. Beitzel, A. Schroder, P. Shinn, H. Chen et al., Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences, PLoS Biology, vol.100, issue.8, p.234, 2004.
DOI : 10.1371/journal.pbio.0020234.sd002
URL : http://doi.org/10.1371/journal.pbio.0020234

Y. Moalic, Y. Blanchard, H. Felix, and A. Jestin, Porcine Endogenous Retrovirus Integration Sites in the Human Genome: Features in Common with Those of Murine Leukemia Virus, Journal of Virology, vol.80, issue.22, pp.10980-10988, 2006.
DOI : 10.1128/JVI.00904-06

V. Molteni, J. Greenwald, D. Rhodes, Y. Hwang, W. Kwiatkowski et al., Identification of a small-molecule binding site at the dimer interface of the HIV integrase catalytic domain, Acta Crystallographica Section D Biological Crystallography, vol.57, issue.4, pp.536-544, 2001.
DOI : 10.1107/S0907444901001652

K. Moreau, C. Faure, S. Violot, P. Gouet, G. Verdier et al., Mutational analyses of the core domain of Avian Leukemia and Sarcoma Viruses integrase: critical residues for concerted integration and multimerization, Virology, vol.318, issue.2, pp.566-581, 2004.
DOI : 10.1016/j.virol.2003.09.037
URL : https://hal.archives-ouvertes.fr/hal-00314279

K. Moreau, C. Faure, S. Violot, G. Verdier, and C. Ronfort, Mutations in the C-terminal domain of ALSV (Avian Leukemia and Sarcoma Viruses) integrase alter the concerted DNA integration process in vitro, European Journal of Biochemistry, vol.26, issue.22
DOI : 10.1073/pnas.181024498

J. Moriniere, S. Rousseaux, U. Steuerwald, M. Soler-lopez, S. Curtet et al., Cooperative binding of two acetylation marks on a histone tail by a single bromodomain, Nature, vol.54, issue.7264, pp.664-668, 2009.
DOI : 10.1107/S0907444998003254
URL : https://hal.archives-ouvertes.fr/cea-00909643

L. Mulder, L. Chakrabarti, and M. Muesing, The SET complex acts as a barrier to autointegration of HIV-1, J Biol Chem, vol.5, pp.27489-27493, 2002.

K. Mullis, F. Faloona, S. Scharf, R. Saiki, G. Horn et al., Specific Enzymatic Amplification of DNA In Vitro: The Polymerase Chain Reaction, Cold Spring Harbor Symposia on Quantitative Biology, vol.51, issue.0, pp.263-273, 1986.
DOI : 10.1101/SQB.1986.051.01.032

Y. Nakamura, T. Umehara, K. Nakano, M. Jang, M. Shirouzu et al., Crystal Structure of the Human BRD2 Bromodomain: INSIGHTS INTO DIMERIZATION AND RECOGNITION OF ACETYLATED HISTONE H4, Journal of Biological Chemistry, vol.282, issue.6, pp.4193-4201, 2007.
DOI : 10.1074/jbc.M605971200

M. Navia, P. Fitzgerald, B. Mckeever, C. Leu, J. Heimbach et al., Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1, Nature, vol.337, issue.6208, pp.615-620, 1989.
DOI : 10.1038/337615a0

N. Neamati and W. B. , HIV-1 Integrase: Mechanism and Inhibitor Design, 2011.
DOI : 10.1002/9781118015377

S. Nisole, J. Stoye, and A. Saib, TRIM family proteins: retroviral restriction and antiviral defence, Nature Reviews Microbiology, vol.3, issue.10, pp.799-808, 2005.
DOI : 10.1128/JVI.75.13.6204-6208.2001

L. Ornstein, DISC ELECTROPHORESIS-I BACKGROUND AND THEORY*, Annals of the New York Academy of Sciences, vol.57, issue.2, pp.321-349, 1964.
DOI : 10.3181/00379727-108-27047
URL : http://www.pipeline.com/~lenornst/DiscEle1.pdf

I. Oz, O. Avidan, and A. Hizi, Inhibition of the integrases of human immunodeficiency viruses type 1 and type 2 by reverse transcriptases, Biochemical Journal, vol.361, issue.3, pp.557-566, 2002.
DOI : 10.1042/bj3610557

C. Pace, F. Vajdos, L. Fee, G. Grimsley, and T. Gray, How to measure and predict the molar absorption coefficient of a protein, Protein Science, vol.33, issue.11, pp.2411-2423, 1995.
DOI : 10.1093/oxfordjournals.jbchem.a127246

C. Patience, Y. Takeuchi, and R. Weiss, Infection of human cells by an endogenous retrovirus of pigs, Nature Medicine, vol.34, issue.3, pp.282-286, 1997.
DOI : 10.1038/bjc.1976.144

M. Petoukhov, D. Franke, A. Shkumatov, G. Tria, A. Kikhney et al., program package for small-angle scattering data analysis, Journal of Applied Crystallography, vol.36, issue.2, pp.342-350, 2012.
DOI : 10.1107/S0021889812007662/fs5015sup1.pdf

E. Poeschla, H. Integrase, and . Replication, Integrase, LEDGF/p75 and HIV replication, Cellular and Molecular Life Sciences, vol.65, issue.9, pp.1403-1424, 2008.
DOI : 10.1007/s00018-008-7540-5
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902792/pdf

B. Poiesz, F. Ruscetti, A. Gazdar, P. Bunn, J. Minna et al., Detection and isolation of type C retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma, Proceedings of the National Academy of Sciences, vol.77, issue.12, pp.7415-7419, 1980.
DOI : 10.1038/227680a0

J. Porath, J. Carlsson, I. Olsson, and G. Belfrage, Metal chelate affinity chromatography, a new approach to protein fractionation, Nature, vol.70, issue.5536, pp.598-599, 1975.
DOI : 10.1038/258598a0

S. Primrose, R. Twyman, R. Reeves, F. Bushman, and A. Wolffe, Principles of Gene Manipulation and Genomics The influence of DNA and nucleosome structure on integration events directed by HIV integrase, J Biol Chem, vol.269, pp.25031-25041, 1994.

P. Pryciak, H. Varmus, and . Nucleosomes, Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection, Cell, vol.69, issue.5, pp.769-780, 1992.
DOI : 10.1016/0092-8674(92)90289-O

C. Putnam, M. Hammel, G. Hura, and J. Tainer, X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution, Quarterly Reviews of Biophysics, vol.52, issue.03, pp.191-285, 2007.
DOI : 10.1016/j.str.2007.02.007

K. Reddy, P. Singh, and S. Singh, Blocking the interaction between HIV-1 integrase and human LEDGF/p75: mutational studies, virtual screening and molecular dynamics simulations, Molecular BioSystems, vol.52, issue.Suppl 7, pp.526-536, 2014.
DOI : 10.1021/ci300361e

S. Rety, L. Reaeabkova, B. Dubanchet, J. Silhan, P. Legrand et al., Structural studies of the catalytic core of the primate foamy virus (PFV-1) integrase, Acta Crystallographica Section F Structural Biology and Crystallization Communications, vol.37, issue.8, pp.881-886, 2010.
DOI : 10.1107/S1744309110022852

P. Rice and T. Baker, Comparative architecture of transposase and integrase complexes, Nature Structural Biology, vol.8, issue.4, pp.302-307, 2001.
DOI : 10.1038/86166

P. Rous, A SARCOMA OF THE FOWL TRANSMISSIBLE BY AN AGENT SEPARABLE FROM THE TUMOR CELLS, Journal of Experimental Medicine, vol.13, issue.4, pp.397-411, 1911.
DOI : 10.1084/jem.13.4.397

K. Ruprecht, J. Mayer, M. Sauter, K. Roemer, and N. Mueller-lantzsch, Endogenous retroviruses, Cellular and Molecular Life Sciences, vol.65, issue.21, pp.3366-3382, 2008.
DOI : 10.1007/s00018-008-8496-1

D. Sachs, The pig as a potential xenograft donor, Veterinary Immunology and Immunopathology, vol.43, issue.1-3, pp.185-191, 1994.
DOI : 10.1016/0165-2427(94)90135-X

A. Sali, L. Potterton, F. Yuan, H. Van-vlijmen, and M. Karplus, Evaluation of comparative protein modeling by MODELLER, Proteins: Structure, Function, and Genetics, vol.270, issue.3, pp.318-326, 1995.
DOI : 10.1002/prot.340230306

F. Sanger, S. Nicklen, and A. Coulson, DNA sequencing with chain-terminating inhibitors, Proceedings of the National Academy of Sciences, vol.74, issue.12, pp.5463-5467, 1977.
DOI : 10.1073/pnas.74.12.5463
URL : http://www.pnas.org/content/74/12/5463.full.pdf

U. Scherdin, K. Rhodes, and M. Breindl, Transcriptionally active genome regions are preferred targets for retrovirus integration, J Virol, vol.64, pp.907-912, 1990.

T. Schmidt and A. Skerra, The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins, Nature Protocols, vol.31, issue.6, pp.1528-1535, 2007.
DOI : 10.1074/jbc.M410466200

A. Schroder, P. Shinn, H. Chen, C. Berry, J. Ecker et al., HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots, Cell, vol.110, issue.4, pp.521-529, 2002.
DOI : 10.1016/S0092-8674(02)00864-4

E. Semenova, C. Marchand, and Y. Pommier, HIV???1 Integrase Inhibitors: Update and Perspectives, Adv Pharmacol, vol.56, pp.199-228, 2008.
DOI : 10.1016/S1054-3589(07)56007-2

E. Serrao and A. Engelman, Sites of retroviral DNA integration: From basic research to clinical applications, Critical Reviews in Biochemistry and Molecular Biology, vol.64, issue.1, pp.26-42, 2016.
DOI : 10.1016/0378-1119(94)90091-4

P. Sherman and J. Fyfe, Human immunodeficiency virus integration protein expressed in Escherichia coli possesses selective DNA cleaving activity., Proceedings of the National Academy of Sciences, vol.87, issue.13, pp.5119-5123, 1990.
DOI : 10.1073/pnas.87.13.5119
URL : http://www.pnas.org/content/87/13/5119.full.pdf

K. Shi, K. Pandey, S. Bera, A. Vora, D. Grandgenett et al., A Possible Role for the Asymmetric C-Terminal Domain Dimer of Rous Sarcoma Virus Integrase in Viral DNA Binding, PLoS ONE, vol.75, issue.2, p.56892, 2013.
DOI : 10.1371/journal.pone.0056892.s004

D. Singh, A. Kimura, L. Chylack, J. Shinohara, and T. , Lens epithelium-derived growth factor (LEDGF/p75) and p52 are derived from a single gene by alternative splicing, Gene, vol.242, issue.1-2, pp.265-273, 2000.
DOI : 10.1016/S0378-1119(99)00506-5

P. Singh, M. Plumb, A. Ferris, J. Iben, X. Wu et al., LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes, Genes & Development, vol.29, issue.21, pp.2287-2297, 2015.
DOI : 10.1101/gad.267609.115
URL : http://genesdev.cshlp.org/content/29/21/2287.full.pdf

D. Smith and K. Johnson, Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase, Gene, vol.67, issue.1, pp.31-40, 1988.
DOI : 10.1016/0378-1119(88)90005-4

F. Studier, Protein production by auto-induction in high-density shaking cultures, Protein Expression and Purification, vol.41, issue.1, pp.207-234, 2005.
DOI : 10.1016/j.pep.2005.01.016

F. Studier and B. Moffatt, Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes, Journal of Molecular Biology, vol.189, issue.1, pp.113-130, 1986.
DOI : 10.1016/0022-2836(86)90385-2

W. Sundquist and H. Krausslich, HIV-1 assembly, budding, and maturation. Cold Spring Harb Perspect Med, p.6924, 2012.
DOI : 10.1101/cshperspect.a015420
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385941/pdf

Y. Suzuki and R. Craigie, The road to chromatin ??? nuclear entry of retroviruses, Nature Reviews Microbiology, vol.5, issue.3, pp.187-196, 2007.
DOI : 10.1007/978-3-642-56114-6_2

D. Svergun and M. Koch, Small-angle scattering studies of biological macromolecules in solution, Reports on Progress in Physics, vol.66, issue.10, pp.1735-1782, 2003.
DOI : 10.1088/0034-4885/66/10/R05

R. Tarlinton, J. Meers, and P. Young, Retroviral invasion of the koala genome, Nature, vol.42, issue.7098, pp.79-81, 2006.
DOI : 10.1073/pnas.73.4.1260

S. Taverna, H. Li, A. Ruthenburg, C. Allis, and D. Patel, How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers, Nature Structural & Molecular Biology, vol.14, issue.11, pp.1025-1040, 2007.
DOI : 10.1126/science.1145801
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691843/pdf

R. Taylor, D. Walker, and R. E. Mcinnes, host strains significantly affect the quality of small scale plasmid DNA preparations used for sequencing, Nucleic Acids Research, vol.21, issue.7, pp.1677-1678, 1993.
DOI : 10.1093/nar/21.7.1677

H. Tegel, J. Ottosson, and S. Hober, Enhancing the protein production levels in Escherichia???coli with a strong promoter, FEBS Journal, vol.46, issue.5, pp.729-739, 2011.
DOI : 10.1016/j.pep.2005.12.010

H. Temin and S. Mizutani, Viral RNA-dependent DNA Polymerase: RNA-dependent DNA Polymerase in Virions of Rous Sarcoma Virus, Nature, vol.37, issue.5252, pp.1211-1213, 1970.
DOI : 10.1515/znb-1966-0513

K. Terpe, Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems, Applied Microbiology and Biotechnology, vol.60, issue.5, pp.523-533, 2003.
DOI : 10.1007/s00253-002-1158-6

G. Trobridge, D. Miller, M. Jacobs, J. Allen, H. Kiem et al., Foamy virus vector integration sites in normal human cells, Proceedings of the National Academy of Sciences, vol.79, issue.17, pp.1498-1503, 2006.
DOI : 10.1128/JVI.79.17.11434-11442.2005

F. Turlure, E. Devroe, P. Silver, and A. Engelman, Human cell proteins and human immunodeficiency virus DNA integration, Frontiers in Bioscience, vol.9, issue.1-3, pp.3187-3208, 2004.
DOI : 10.2741/1472

F. Turlure, G. Maertens, S. Rahman, P. Cherepanov, and A. Engelman, A tripartite DNA-binding element, comprised of the nuclear localization signal and two AT-hook motifs, mediates the association of LEDGF/p75 with chromatin in vivo, Nucleic Acids Research, vol.34, issue.5, pp.1653-1665, 2006.
DOI : 10.1093/nar/gkl052

T. Umehara, Y. Nakamura, M. Jang, K. Nakano, A. Tanaka et al., Structural Basis for Acetylated Histone H4 Recognition by the Human BRD2 Bromodomain, Journal of Biological Chemistry, vol.15, issue.10, pp.7610-7618, 2010.
DOI : 10.1093/bioinformatics/8.2.189

B. Van-maele, K. Busschots, L. Vandekerckhove, F. Christ, and Z. Debyser, Cellular co-factors of HIV-1 integration, Trends in Biochemical Sciences, vol.31, issue.2, pp.98-105, 2006.
DOI : 10.1016/j.tibs.2005.12.002

N. Vandegraaff, E. Devroe, F. Turlure, P. Silver, and A. Engelman, Biochemical and genetic analyses of integrase-interacting proteins lens epithelium-derived growth factor (LEDGF)/p75 and hepatoma-derived growth factor related protein 2 (HRP2) in preintegration complex function and HIV-1 replication, Virology, vol.346, issue.2, pp.415-426, 2006.
DOI : 10.1016/j.virol.2005.11.022

C. Vink, R. Lutzke, and R. Plasterk, Formation of a stable complex between the human immunodeficiency virus integrase protein and viral DNA, Nucleic Acids Research, vol.22, issue.20, pp.4103-4110, 1994.
DOI : 10.1093/nar/22.20.4103

S. Violot, S. Hong, D. Rakotobe, C. Petit, B. Gay et al., The Human Polycomb Group EED Protein Interacts with the Integrase of Human Immunodeficiency Virus Type 1, Journal of Virology, vol.77, issue.23, pp.12507-12522, 2003.
DOI : 10.1128/JVI.77.23.12507-12522.2003
URL : https://hal.archives-ouvertes.fr/hal-00119648

L. Vranckx, J. Demeulemeester, S. Saleh, A. Boll, G. Vansant et al., LEDGIN-mediated Inhibition of Integrase- LEDGF, 2016.
DOI : 10.1016/j.ebiom.2016.04.039
URL : https://doi.org/10.1016/j.ebiom.2016.04.039

F. Wang, H. Liu, W. Blanton, A. Belkina, N. Lebrasseur et al., disruption in mice causes severe obesity without Type??2 diabetes, Biochemical Journal, vol.255, issue.1, pp.71-83, 2009.
DOI : 10.1007/BF00316069
URL : http://www.biochemj.org/content/ppbiochemj/425/1/71.full.pdf

J. Wang, H. Ling, W. Yang, and R. Craigie, Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein, The EMBO Journal, vol.20, issue.24, pp.7333-7343, 2001.
DOI : 10.1093/emboj/20.24.7333

M. Weidner-glunde, M. Ottinger, and T. Schulz, WHAT do viruses BET on?, Frontiers in Bioscience, vol.15, issue.1, pp.537-549, 2010.
DOI : 10.2741/3632

R. Weiss, The discovery of endogenous retroviruses, Retrovirology, vol.3, issue.1, p.67, 2006.
DOI : 10.1186/1742-4690-3-67

R. Weiss and P. Vogt, 100 years of Rous sarcoma virus, The Journal of Experimental Medicine, vol.50, issue.12, pp.2351-2355, 2011.
DOI : 10.1073/pnas.79.6.2031

A. Wensing, V. Calvez, H. Gunthard, V. Johnson, R. Paredes et al., Update of the drug resistance mutations in HIV-1, Top Antivir Med, vol.22, pp.642-650, 2014.

L. Whitmore and B. Wallace, DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data, Nucleic Acids Research, vol.32, issue.Web Server, pp.668-673, 2004.
DOI : 10.1093/nar/gkh371
URL : https://academic.oup.com/nar/article-pdf/32/suppl_2/W668/6208083/gkh371.pdf

J. Wielens, I. Crosby, and D. Chalmers, A Three-dimensional Model of the Human Immunodeficiency Virus Type 1 Integration Complex, Journal of Computer-Aided Molecular Design, vol.76, issue.5, pp.301-317, 2005.
DOI : 10.1080/07391102.1998.10508285

C. Wilen, J. Tilton, and R. Doms, HIV: cell binding and entry. Cold Spring Harb Perspect Med, 2012.
DOI : 10.1101/cshperspect.a006866
URL : http://perspectivesinmedicine.cshlp.org/content/2/8/a006866.full.pdf

T. Wilkinson, S. Chow, and N. Neamati, Functional Interaction between Human Immunodeficiency Virus Type 1 Reverse Transcriptase and Integrase, HIV-1 Integrase, Mechanism and Inhibitor Design, pp.95-103, 2011.
DOI : 10.1074/jbc.M414679200

A. Wlodawer and J. Erickson, Structure-Based Inhibitors of HIV-1 Protease, Annual Review of Biochemistry, vol.62, issue.1, pp.543-585, 1993.
DOI : 10.1146/annurev.bi.62.070193.002551

K. Wright, AIDS therapy: First tentative signs of therapeutic promise, Nature, vol.323, issue.6086, p.283, 1986.
DOI : 10.1038/323283a0

S. Wu and C. Chiang, The Double Bromodomain-containing Chromatin Adaptor Brd4 and Transcriptional Regulation, Journal of Biological Chemistry, vol.15, issue.18, pp.13141-13145, 2007.
DOI : 10.1242/jcs.03262

M. Yamashita and M. Emerman, Retroviral infection of non-dividing cells: Old and new perspectives, Virology, vol.344, issue.1, pp.88-93, 2006.
DOI : 10.1016/j.virol.2005.09.012

F. Yang and M. Roth, Assembly and Catalysis of Concerted Two-End Integration Events by Moloney Murine Leukemia Virus Integrase, Journal of Virology, vol.75, issue.20, pp.9561-9570, 2001.
DOI : 10.1128/JVI.75.20.9561-9570.2001

Z. Yang, T. Mueser, F. Bushman, and C. Hyde, Crystal structure of an active two-domain derivative of rous sarcoma virus integrase 1 1Edited by I. A. Wilson, Journal of Molecular Biology, vol.296, issue.2, pp.535-548, 2000.
DOI : 10.1006/jmbi.1999.3463

Z. Yin, K. Shi, S. Banerjee, K. Pandey, S. Bera et al., Crystal structure of the Rous sarcoma virus intasome, Nature, vol.289, issue.7590, pp.362-366, 2016.
DOI : 10.1074/jbc.M114.573311

V. Zennou, C. Petit, D. Guetard, U. Nerhbass, L. Montagnier et al., HIV-1 Genome Nuclear Import Is Mediated by a Central DNA Flap, Cell, vol.101, issue.2, pp.173-185, 2000.
DOI : 10.1016/S0092-8674(00)80828-4
URL : https://doi.org/10.1016/s0092-8674(00)80828-4

R. Zheng, T. Jenkins, and R. Craigie, Zinc folds the N-terminal domain of HIV-1 integrase, promotes multimerization, and enhances catalytic activity, Proceedings of the National Academy of Sciences, vol.35, issue.3, pp.13659-13664, 1996.
DOI : 10.1021/bi952056p

B. Zimm, The dependence of the scattering of light on angle and concentration in linear polymer solutions, J Phys Colloid Chem, vol.52, pp.260-267, 1948.