H. Naif, Pathogenesis of HIV infection, Infectious Disease Reports, vol.5, issue.1S, p.2013, 2014.
DOI : 10.4081/idr.2013.s1.e6

L. Douce, V. Herbein, G. Rohr, O. Schwartz, and C. , Molecular mechanisms of HIV-1 persistence in the monocyte-macrophage lineage, Retrovirology, vol.7, issue.1, p.32, 2010.
DOI : 10.1186/1742-4690-7-32
URL : https://hal.archives-ouvertes.fr/inserm-00663900

A. Bergamaschi and G. Pancino, Host hindrance to HIV-1 replication in monocytes and macrophages, Retrovirology, vol.7, issue.1, p.31, 2010.
DOI : 10.1186/1742-4690-7-31

P. Gorry, N. Francella, S. Lewin, and R. Collman, HIV-1 envelope-receptor interactions required for macrophage infection and implications for current HIV-1 cure strategies, Journal of Leukocyte Biology, vol.95, issue.1, pp.71-81, 2014.
DOI : 10.1189/jlb.0713368

C. Guenzel, C. Hérate, and S. Benichou, HIV?1 Vpr?a still " enigmatic multitasker, Front Microbiol, vol.5, p.127, 2014.
URL : https://hal.archives-ouvertes.fr/inserm-01078252

R. Chen, E. Rouzic, J. Kearney, L. Mansky, and S. Benichou, Vpr-mediated Incorporation of UNG2 into HIV-1 Particles Is Required to Modulate the Virus Mutation Rate and for Replication in Macrophages, Journal of Biological Chemistry, vol.279, issue.27, pp.28419-28444, 2004.
DOI : 10.1074/jbc.M403875200

C. Guenzel, C. Hérate, L. Rouzic, E. Maidou?peindara, P. Sadler et al., Recruitment of the Nuclear Form of Uracil DNA Glycosylase into Virus Particles Participates in the Full Infectivity of HIV-1, Journal of Virology, vol.86, issue.5, pp.2533-2577, 2012.
DOI : 10.1128/JVI.05163-11

S. Priet, N. Gros, J. Navarro, J. Boretto, B. Canard et al., HIV-1-Associated Uracil DNA Glycosylase Activity Controls dUTP Misincorporation in Viral DNA and Is Essential to the HIV-1 Life Cycle, Molecular Cell, vol.17, issue.4, pp.479-90, 2005.
DOI : 10.1016/j.molcel.2005.01.016

K. Jones, M. Roche, M. Gantier, N. Begum, T. Honjo et al., X4 and R5 HIV-1 have distinct post-entry requirements for uracil DNA glycosylase during infection of primary cells, Journal of Biological Chemistry, vol.285, issue.24, pp.18603-18617, 2010.
DOI : 10.1074/jbc.M109.090126

S. Kaiser and M. Emerman, Uracil DNA Glycosylase Is Dispensable for Human Immunodeficiency Virus Type 1 Replication and Does Not Contribute to the Antiviral Effects of the Cytidine Deaminase Apobec3G, Journal of Virology, vol.80, issue.2, pp.875-82, 2006.
DOI : 10.1128/JVI.80.2.875-882.2006

B. Schrofelbauer, Q. Yu, S. Zeitlin, and N. Landau, Human Immunodeficiency Virus Type 1 Vpr Induces the Degradation of the UNG and SMUG Uracil-DNA Glycosylases, Journal of Virology, vol.79, issue.17, pp.10978-87, 2005.
DOI : 10.1128/JVI.79.17.10978-10987.2005

B. Yang, K. Chen, C. Zhang, S. Huang, and H. Zhang, Virion-associated Uracil DNA Glycosylase-2 and Apurinic/Apyrimidinic Endonuclease Are Involved in the Degradation of APOBEC3G-edited Nascent HIV-1 DNA, Journal of Biological Chemistry, vol.282, issue.16, pp.11667-75, 2007.
DOI : 10.1074/jbc.M606864200

M. Sousa, H. Krokan, and G. Slupphaug, DNA-uracil and human pathology, Molecular Aspects of Medicine, vol.28, issue.3-4, pp.276-306, 2007.
DOI : 10.1016/j.mam.2007.04.006

M. Akbari, K. Solvang?garten, A. Hanssen?bauer, N. Lieske, H. Pettersen et al., Direct interaction between XRCC1 and UNG2 facilitates rapid repair of uracil in DNA by XRCC1 complexes, DNA Repair, vol.9, issue.7, pp.785-95, 2010.
DOI : 10.1016/j.dnarep.2010.04.002

S. Ali, J. Shin, S. Bae, B. Kim, and B. Choi, Replication protein A 32 interacts through a similar binding interface with TIPIN, XPA, and UNG2, The International Journal of Biochemistry & Cell Biology, vol.42, issue.7, pp.1210-1215, 2010.
DOI : 10.1016/j.biocel.2010.04.011

L. Hagen, B. Kavli, M. Sousa, K. Torseth, N. Liabakk et al., Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA, The EMBO Journal, vol.4, issue.1, pp.51-61, 2008.
DOI : 10.1038/sj.emboj.7601958

R. Ko and S. Bennett, Physical and functional interaction of human nuclear uracil-DNA glycosylase with proliferating cell nuclear antigen, DNA Repair, vol.4, issue.12, pp.1421-1452, 2005.
DOI : 10.1016/j.dnarep.2005.08.006

G. Mer, A. Bochkarev, R. Gupta, E. Bochkareva, L. Frappier et al., Structural Basis for the Recognition of DNA Repair Proteins UNG2, XPA, and RAD52 by Replication Factor RPA, Cell, vol.103, issue.3, pp.449-56, 2000.
DOI : 10.1016/S0092-8674(00)00136-7

T. Nagelhus, T. Haug, K. Singh, K. Keshav, F. Skorpen et al., A Sequence in the N-terminal Region of Human Uracil-DNA Glycosylase with Homology to XPA Interacts with the C-terminal Part of the 34-kDa Subunit of Replication Protein A, Journal of Biological Chemistry, vol.272, issue.10, pp.6561-6567, 1997.
DOI : 10.1074/jbc.272.10.6561

K. Torseth, B. Doseth, L. Hagen, C. Olaisen, N. Liabakk et al., The UNG2 Arg88Cys variant abrogates RPA-mediated recruitment of UNG2 to single-stranded DNA, DNA Repair, vol.11, issue.6, pp.559-69, 2012.
DOI : 10.1016/j.dnarep.2012.03.006

E. Fanning, V. Klimovich, and A. Nager, A dynamic model for replication protein A (RPA) function in DNA processing pathways, Nucleic Acids Research, vol.34, issue.15, pp.4126-4163, 2006.
DOI : 10.1093/nar/gkl550

G. Oakley and S. Patrick, Replication protein A: directing traffic at the intersection of replication and repair, Frontiers in Bioscience, vol.15, issue.1, pp.883-900, 2010.
DOI : 10.2741/3652

A. Matthews, S. Zheng, L. Dimenna, and J. Chaudhuri, Regulation of Immunoglobulin Class-Switch Recombination, Adv Immunol, vol.122, pp.1-57, 2014.
DOI : 10.1016/B978-0-12-800267-4.00001-8

D. Noia, J. Neuberger, and M. , Molecular Mechanisms of Antibody Somatic Hypermutation, Annual Review of Biochemistry, vol.76, issue.1, pp.1-22, 2007.
DOI : 10.1146/annurev.biochem.76.061705.090740

N. Begum, K. Kinoshita, N. Kakazu, M. Muramatsu, H. Nagaoka et al., Uracil DNA Glycosylase Activity Is Dispensable for Immunoglobulin Class Switch, Science, vol.305, issue.5687, pp.1160-1163, 2004.
DOI : 10.1126/science.1098444

N. Begum, N. Izumi, M. Nishikori, H. Nagaoka, R. Shinkura et al., Requirement of Non-canonical Activity of Uracil DNA Glycosylase for Class Switch Recombination, Journal of Biological Chemistry, vol.282, issue.1, pp.731-773, 2007.
DOI : 10.1074/jbc.M607439200

N. Begum, A. Stanlie, T. Doi, Y. Sasaki, H. Jin et al., Further evidence for involvement of a noncanonical function of uracil DNA glycosylase in class switch recombination, Proceedings of the National Academy of Sciences, vol.106, issue.8, pp.2752-2759, 2009.
DOI : 10.1073/pnas.0813252106

A. Yamane, D. Robbiani, W. Resch, A. Bothmer, H. Nakahashi et al., RPA Accumulation during Class Switch Recombination Represents 5??????3??? DNA-End Resection during the S???G2/M Phase of the Cell Cycle, Cell Reports, vol.3, issue.1, pp.138-185, 2013.
DOI : 10.1016/j.celrep.2012.12.006

M. Langlois and M. Neuberger, Human APOBEC3G Can Restrict Retroviral Infection in Avian Cells and Acts Independently of both UNG and SMUG1, Journal of Virology, vol.82, issue.9, pp.4660-4664, 2008.
DOI : 10.1128/JVI.02469-07

L. Mansky, S. Preveral, L. Selig, R. Benarous, and S. Benichou, The Interaction of Vpr with Uracil DNA Glycosylase Modulates the Human Immunodeficiency Virus Type 1 In Vivo Mutation Rate, Journal of Virology, vol.74, issue.15, pp.7039-7086, 2000.
DOI : 10.1128/JVI.74.15.7039-7047.2000

P. Eldin, N. Chazal, D. Fenard, E. Bernard, J. Guichou et al., Vpr expression abolishes the capacity of HIV-1 infected cells to repair uracilated DNA, Nucleic Acids Research, vol.42, issue.3, pp.1698-710, 2013.
DOI : 10.1093/nar/gkt974
URL : https://hal.archives-ouvertes.fr/hal-00911312

J. Fischer, S. Muller?weeks, and S. Caradonna, Proteolytic degradation of the nuclear isoform of uracil-DNA glycosylase occurs during the S phase of the cell cycle, DNA Repair, vol.3, issue.5, pp.505-518, 2004.
DOI : 10.1016/j.dnarep.2004.01.012

A. Weil, D. Ghosh, Y. Zhou, L. Seiple, M. Mcmahon et al., Uracil DNA glycosylase initiates degradation of HIV-1 cDNA containing misincorporated dUTP and prevents viral integration, Proceedings of the National Academy of Sciences, vol.110, issue.6, pp.448-57, 2013.
DOI : 10.1073/pnas.1219702110

M. Otterlei, E. Warbrick, T. Nagelhus, T. Haug, G. Slupphaug et al., Post-replicative base excision repair in replication foci, The EMBO Journal, vol.18, issue.13, pp.3834-3878, 1999.
DOI : 10.1093/emboj/18.13.3834

M. Bouhamdan, Y. Xue, Y. Baudat, B. Hu, J. Sire et al., Diversity of HIV-1 Vpr Interactions Involves Usage of the WXXF Motif of Host Cell Proteins, Journal of Biological Chemistry, vol.273, issue.14, pp.8009-8025, 1998.
DOI : 10.1074/jbc.273.14.8009

M. Park, D. Ludwig, E. Stigger, and S. Lee, Physical Interaction between Human RAD52 and RPA Is Required for Homologous Recombination in Mammalian Cells, Journal of Biological Chemistry, vol.271, issue.31, pp.18996-9000, 1996.
DOI : 10.1074/jbc.271.31.18996

T. Sugiyama and N. Kantake, Dynamic Regulatory Interactions of Rad51, Rad52, and Replication Protein-A in Recombination Intermediates, Journal of Molecular Biology, vol.390, issue.1, pp.45-55, 2009.
DOI : 10.1016/j.jmb.2009.05.009

M. Demott, S. Zigman, and R. Bambara, Replication Protein A Stimulates Long Patch DNA Base Excision Repair, Journal of Biological Chemistry, vol.273, issue.42, pp.27492-27500, 1998.
DOI : 10.1074/jbc.273.42.27492

A. Bochkarev, E. Bochkareva, L. Frappier, and A. Edwards, The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single-stranded DNA binding, The EMBO Journal, vol.18, issue.16, pp.4498-504, 1999.
DOI : 10.1093/emboj/18.16.4498

L. Zou and S. Elledge, Sensing DNA Damage Through ATRIP Recognition of RPA-ssDNA Complexes, Science, vol.300, issue.5625, pp.1542-1550, 2003.
DOI : 10.1126/science.1083430

Z. Xu, H. Zan, E. Pone, T. Mai, and P. Casali, Immunoglobulin class-switch DNA recombination: induction, targeting and beyond, Nature Reviews Immunology, vol.449, issue.7, pp.517-548, 2012.
DOI : 10.1038/nri3216

C. Rada, D. Noia, J. Neuberger, and M. , Mismatch Recognition and Uracil Excision Provide Complementary Paths to Both Ig Switching and the A/T-Focused Phase of Somatic Mutation, Molecular Cell, vol.16, issue.2, pp.163-71, 2004.
DOI : 10.1016/j.molcel.2004.10.011

A. Yousif, A. Stanlie, S. Mondal, T. Honjo, and N. Begum, Differential regulation of S-region hypermutation and class-switch recombination by noncanonical functions of uracil DNA glycosylase, Proceedings of the National Academy of Sciences, vol.111, issue.11, pp.1016-1040, 2014.
DOI : 10.1073/pnas.1402391111

S. Zeitlin, B. Chapados, N. Baker, C. Tai, G. Slupphaug et al., Uracil DNA N-Glycosylase Promotes Assembly of Human Centromere Protein A, PLoS ONE, vol.9, issue.3, p.17151, 2011.
DOI : 10.1371/journal.pone.0017151.s005

I. Tikhanovich and H. Nasheuer, Host-Specific Replication of BK Virus DNA in Mouse Cell Extracts Is Independently Controlled by DNA Polymerase ??-Primase and Inhibitory Activities, Journal of Virology, vol.84, issue.13, pp.6636-6680, 2010.
DOI : 10.1128/JVI.00527-10

A. Nicolas, N. Alazard?dany, C. Biollay, L. Arata, N. Jolinon et al., Identification of Rep-Associated Factors in Herpes Simplex Virus Type 1-Induced Adeno-Associated Virus Type 2 Replication Compartments, Journal of Virology, vol.84, issue.17, pp.8871-87, 2010.
DOI : 10.1128/JVI.00725-10
URL : https://hal.archives-ouvertes.fr/hal-00709365

K. Mohni, C. Livingston, D. Cortez, and S. Weller, ATR and ATRIP Are Recruited to Herpes Simplex Virus Type 1 Replication Compartments Even though ATR Signaling Is Disabled, Journal of Virology, vol.84, issue.23, pp.12152-64, 2010.
DOI : 10.1128/JVI.01643-10

A. Kudoh, S. Iwahori, Y. Sato, S. Nakayama, H. Isomura et al., Homologous Recombinational Repair Factors Are Recruited and Loaded onto the Viral DNA Genome in Epstein-Barr Virus Replication Compartments, Journal of Virology, vol.83, issue.13, pp.6641-51, 2009.
DOI : 10.1128/JVI.00049-09

M. Su, I. Liu, C. Wu, S. Chang, C. Tsai et al., Uracil DNA glycosylase BKRF3 contributes to EBV DNA replication through physical interactions with proteins in viral DNA replication complex, J Virol

X. Wang, C. Helfer, N. Pancholi, J. Bradner, and J. You, Recruitment of Brd4 to the Human Papillomavirus Type 16 DNA Replication Complex Is Essential for Replication of Viral DNA, Journal of Virology, vol.87, issue.7, pp.3871-84, 2013.
DOI : 10.1128/JVI.03068-12

A. Blackford, R. Bruton, O. Dirlik, G. Stewart, A. Taylor et al., A Role for E1B-AP5 in ATR Signaling Pathways during Adenovirus Infection, Journal of Virology, vol.82, issue.15, pp.7640-52, 2008.
DOI : 10.1128/JVI.00170-08

D. Singh, M. Islam, N. Choudhury, S. Karjee, and S. Mukherjee, The 32 kDa subunit of replication protein A (RPA) participates in the DNA replication of Mung bean yellow mosaic India virus (MYMIV) by interacting with the viral Rep protein, Nucleic Acids Research, vol.35, issue.3, pp.755-70, 2007.
DOI : 10.1093/nar/gkl1088

A. Lada, I. Waisertreiger, C. Grabow, A. Prakash, G. Borgstahl et al., Replication Protein A (RPA) Hampers the Processive Action of APOBEC3G Cytosine Deaminase on Single-Stranded DNA, PLoS ONE, vol.430, issue.9, p.24848, 2011.
DOI : 10.1371/journal.pone.0024848.s001

G. Fuentes, P. Fay, and R. Bambara, Relationship between Plus Strand DNA Synthesis and Removal of Downstream Segments of Rna by Human Immunodeficiency Virus, Murine Leukemia Virus and Avian Myeloblastoma Virus Reverse Transcriptases, Nucleic Acids Research, vol.24, issue.9, pp.1719-1745, 1996.
DOI : 10.1093/nar/24.9.1719

M. Amacker, M. Hottiger, R. Mossi, and U. Hübscher, HIV?1 nucleocapsid protein and replication protein A influence the strand displacement DNA synthe? sis of lentiviral reverse transcriptase, AIDS Lond Engl, vol.11, pp.534-540, 1997.

K. Kitamura, Z. Wang, S. Chowdhury, M. Simadu, M. Koura et al., Uracil DNA Glycosylase Counteracts APOBEC3G-Induced Hypermutation of Hepatitis B Viral Genomes: Excision Repair of Covalently Closed Circular DNA, PLoS Pathogens, vol.7, issue.1, p.1003361, 2013.
DOI : 10.1371/journal.ppat.1003361.s008

G. Liang, K. Kitamura, Z. Wang, G. Liu, S. Chowdhury et al., RNA editing of hepatitis B virus transcripts by activation-induced cytidine deaminase, Proceedings of the National Academy of Sciences, vol.110, issue.6, pp.2246-51, 2013.
DOI : 10.1073/pnas.1221921110

L. Selig, J. Pages, V. Tanchou, S. Prévéral, C. Berlioz?torrent et al., Interaction with the p6 domain of the gag precursor mediates incorpora? tion into virions of Vpr and Vpx proteins from primate lentiviruses, J Virol, vol.73, pp.592-600, 1999.

C. Langevin, P. Maidou?peindara, P. Aas, G. Jacquot, M. Otterlei et al., Human Immunodeficiency Virus Type 1 Vpr Modulates Cellular Expression of UNG2 via a Negative Transcriptional Effect, Journal of Virology, vol.83, issue.19, pp.10256-63, 2009.
DOI : 10.1128/JVI.02654-08

J. Bouchet, C. Hérate, C. Guenzel, C. Vérollet, A. Järviluoma et al., Single-Domain Antibody-SH3 Fusions for Efficient Neutralization of HIV-1 Nef Functions, Journal of Virology, vol.86, issue.9, pp.4856-67, 2012.
DOI : 10.1128/JVI.06329-11

J. Mazzolini, F. Herit, J. Bouchet, A. Benmerah, S. Benichou et al., Inhibition of phagocytosis in HIV-1-infected macrophages relies on Nef-dependent alteration of focal delivery of recycling compartments, Blood, vol.115, issue.21, pp.4226-4262, 2010.
DOI : 10.1182/blood-2009-12-259473

A. Bergamaschi, D. Ayinde, A. David, E. Rouzic, M. Morel et al., The Human Immunodeficiency Virus Type 2 Vpx Protein Usurps the CUL4A-DDB1DCAF1 Ubiquitin Ligase To Overcome a Postentry Block in Macrophage Infection, Journal of Virology, vol.83, issue.10, pp.4854-60, 2009.
DOI : 10.1128/JVI.00187-09

A. Brussel and P. Sonigo, Analysis of Early Human Immunodeficiency Virus Type 1 DNA Synthesis by Use of a New Sensitive Assay for Quantifying Integrated Provirus, Journal of Virology, vol.77, issue.18, pp.10119-10143, 2003.
DOI : 10.1128/JVI.77.18.10119-10124.2003