A. Jarmuz, A. Chester, J. Bayliss, J. Gisbourne, and I. Dunham, An Anthropoid-Specific Locus of Orphan C to U RNA-Editing Enzymes on Chromosome 22, Genomics, vol.79, issue.3, pp.285-296, 2002.
DOI : 10.1006/geno.2002.6718

R. Harris, K. Bishop, A. Sheehy, H. Craig, and S. Petersen-mahrt, DNA Deamination Mediates Innate Immunity to Retroviral Infection, Cell, vol.113, issue.6, pp.803-809, 2003.
DOI : 10.1016/S0092-8674(03)00423-9

D. Lecossier, F. Bouchonnet, F. Clavel, and A. Hance, Hypermutation of HIV-1 DNA in the Absence of the Vif Protein, Science, vol.300, issue.5622, p.1112, 2003.
DOI : 10.1126/science.1083338

M. Liddament, W. Brown, A. Schumacher, and R. Harris, APOBEC3F Properties and Hypermutation Preferences Indicate Activity against HIV-1 In Vivo, Current Biology, vol.14, issue.15, pp.1385-1391, 2004.
DOI : 10.1016/j.cub.2004.06.050

B. Mangeat, P. Turelli, G. Caron, M. Friedli, and L. Perrin, Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts, Nature, vol.424, issue.6944, pp.99-103, 2003.
DOI : 10.1038/nature01709

R. Mariani, D. Chen, B. Schrofelbauer, F. Navarro, and R. Konig, Species-Specific Exclusion of APOBEC3G from HIV-1 Virions by Vif, Cell, vol.114, issue.1, pp.21-31, 2003.
DOI : 10.1016/S0092-8674(03)00515-4

A. Sheehy, N. Gaddis, J. Choi, and M. Malim, Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein, Nature, vol.71, issue.6898, pp.646-650, 2002.
DOI : 10.1093/emboj/16.15.4531

H. Wiegand, B. Doehle, H. Bogerd, and B. Cullen, A second human antiretroviral factor, APOBEC3F, is suppressed by the HIV-1 and HIV-2 Vif proteins, The EMBO Journal, vol.67, issue.12, pp.2451-2458, 2004.
DOI : 10.1038/nature01707

H. Zhang, Y. B. Pomerantz, R. Zhang, C. Arunachalam, and S. , The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA, Nature, vol.424, issue.6944, pp.94-98, 2003.
DOI : 10.1038/nature01707

F. Delebecque, R. Suspene, S. Calattini, N. Casartelli, and A. Saib, Restriction of Foamy Viruses by APOBEC Cytidine Deaminases, Journal of Virology, vol.80, issue.2, pp.605-614, 2006.
DOI : 10.1128/JVI.80.2.605-614.2006
URL : https://hal.archives-ouvertes.fr/hal-00357984

M. Lochelt, F. Romen, P. Bastone, H. Muckenfuss, and N. Kirchner, The antiretroviral activity of APOBEC3 is inhibited by the foamy virus accessory Bet protein, Proceedings of the National Academy of Sciences, vol.102, issue.22, pp.7982-7987, 2005.
DOI : 10.1073/pnas.0501445102

C. Noguchi, H. Ishino, M. Tsuge, Y. Fujimoto, and M. Imamura, G to A hypermutation of hepatitis B virus, Hepatology, vol.4, issue.3, pp.626-633, 2005.
DOI : 10.1002/hep.20580

C. Rosler, J. Kock, M. Kann, M. Malim, and H. Blum, APOBEC-mediated interference with hepadnavirus production, Hepatology, vol.235, issue.2, pp.301-309, 2005.
DOI : 10.1002/hep.20801

R. Suspene, D. Guetard, M. Henry, P. Sommer, and S. Wain-hobson, Extensive editing of both hepatitis B virus DNA strands by APOBEC3 cytidine deaminases in vitro and in vivo, Proceedings of the National Academy of Sciences, vol.102, issue.23, pp.8321-8326, 2005.
DOI : 10.1073/pnas.0408223102
URL : https://hal.archives-ouvertes.fr/pasteur-00013744

P. Turelli, B. Mangeat, S. Jost, S. Vianin, and D. Trono, Inhibition of Hepatitis B Virus Replication by APOBEC3G, Science, vol.303, issue.5665, p.1829, 2004.
DOI : 10.1126/science.1092066

H. Bogerd, H. Wiegand, A. Hulme, J. Garcia-perez, O. Shea et al., Cellular inhibitors of long interspersed element 1 and Alu retrotransposition, Proceedings of the National Academy of Sciences, vol.103, issue.23, pp.8780-8785, 2006.
DOI : 10.1073/pnas.0603313103

C. Esnault, O. Heidmann, F. Delebecque, M. Dewannieux, and D. Ribet, APOBEC3G cytidine deaminase inhibits retrotransposition of endogenous retroviruses, Nature, vol.16, issue.7024, pp.430-433, 2005.
DOI : 10.1093/nar/30.11.e49
URL : https://hal.archives-ouvertes.fr/pasteur-01372656

P. Jern, J. Stoye, and J. Coffin, Role of APOBEC3 in Genetic Diversity among Endogenous Murine Leukemia Viruses, PLoS Genetics, vol.104, issue.10, pp.2014-2022, 2007.
DOI : 10.1371/journal.pgen.0030183.st002

H. Muckenfuss, M. Hamdorf, U. Held, M. Perkovic, and J. Lower, APOBEC3 Proteins Inhibit Human LINE-1 Retrotransposition, Journal of Biological Chemistry, vol.281, issue.31, pp.22161-22172, 2006.
DOI : 10.1074/jbc.M601716200

A. Schumacher, G. Hache, D. Macduff, W. Brown, and R. Harris, The DNA Deaminase Activity of Human APOBEC3G Is Required for Ty1, MusD, and Human Immunodeficiency Virus Type 1 Restriction, Journal of Virology, vol.82, issue.6, pp.2652-2660, 2008.
DOI : 10.1128/JVI.02391-07

A. Schumacher, D. Nissley, and R. Harris, APOBEC3G hypermutates genomic DNA and inhibits Ty1 retrotransposition in yeast, Proceedings of the National Academy of Sciences, vol.102, issue.28, pp.9854-9859, 2005.
DOI : 10.1073/pnas.0501694102

S. Jonsson, G. Hache, M. Stenglein, S. Fahrenkrug, and V. Andresdottir, Evolutionarily conserved and non-conserved retrovirus restriction activities of artiodactyl APOBEC3F proteins, Nucleic Acids Research, vol.34, issue.19, pp.5683-5694, 2006.
DOI : 10.1093/nar/gkl721

C. Munk, T. Beck, J. Zielonka, A. Hotz-wagenblatt, and S. Chareza, Functions, structure, and read-through alternative splicing of feline APOBEC3 genes, Genome Biology, vol.9, issue.3, p.48, 2008.
DOI : 10.1186/gb-2008-9-3-r48

M. Ohainle, J. Kerns, M. Li, H. Malik, and M. Emerman, Antiretroelement Activity of APOBEC3H Was Lost Twice in Recent Human Evolution, Cell Host & Microbe, vol.4, issue.3, pp.249-259, 2008.
DOI : 10.1016/j.chom.2008.07.005

L. Betts, S. Xiang, S. Short, R. Wolfenden, C. Carter et al., Cytidine Deaminase. The 2??3 ?? Crystal Structure of an Enzyme: Transition-state Analog Complex, Journal of Molecular Biology, vol.235, issue.2, pp.635-656, 1994.
DOI : 10.1006/jmbi.1994.1018

T. Ko, J. Lin, C. Hu, Y. Hsu, and A. Wang, Crystal Structure of Yeast Cytosine Deaminase: INSIGHTS INTO ENZYME MECHANISM AND EVOLUTION, Journal of Biological Chemistry, vol.278, issue.21, pp.19111-19117, 2003.
DOI : 10.1074/jbc.M300874200

K. Xie, M. Sowden, G. Dance, A. Torelli, and H. Smith, The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1, Proceedings of the National Academy of Sciences, vol.101, issue.21, pp.8114-8119, 2004.
DOI : 10.1073/pnas.0400493101

E. Newman, R. Holmes, H. Craig, K. Klein, and J. Lingappa, Antiviral Function of APOBEC3G Can Be Dissociated from Cytidine Deaminase Activity, Current Biology, vol.15, issue.2, pp.166-170, 2005.
DOI : 10.1016/j.cub.2004.12.068

B. Gooch and B. Cullen, Functional domain organization of human APOBEC3G, Virology, vol.379, issue.1, pp.118-124, 2008.
DOI : 10.1016/j.virol.2008.06.013

Y. Lei, Y. Tian, H. Ding, B. Wang, and Y. Yang, N-terminal and C-terminal cytosine deaminase domain of APOBEC3G inhibit hepatitis B virus replication, World Journal of Gastroenterology, vol.12, issue.46, pp.7488-7496, 2006.
DOI : 10.3748/wjg.v12.i46.7488

M. Janini, M. Rogers, D. Birx, and F. Mccutchan, Human Immunodeficiency Virus Type 1 DNA Sequences Genetically Damaged by Hypermutation Are Often Abundant in Patient Peripheral Blood Mononuclear Cells and May Be Generated during Near-Simultaneous Infection and Activation of CD4+ T Cells, Journal of Virology, vol.75, issue.17, pp.7973-7986, 2001.
DOI : 10.1128/JVI.75.17.7973-7986.2001

V. Petit, D. Guétard, R. M. Keriel, A. Sitbon, and M. , Murine APOBEC1 Is a Powerful Mutator of Retroviral and Cellular RNA In Vitro and In Vivo, Journal of Molecular Biology, vol.385, issue.1, 2008.
DOI : 10.1016/j.jmb.2008.10.043
URL : https://hal.archives-ouvertes.fr/pasteur-00363408

J. Vartanian, U. Plikat, M. Henry, R. Mahieux, and L. Guillemot, HIV genetic variation is directed and restricted by DNA precursor availability, Journal of Molecular Biology, vol.270, issue.2, pp.139-151, 1997.
DOI : 10.1006/jmbi.1997.1104

C. Biebricher and M. Eigen, The error threshold, Virus Research, vol.107, issue.2, pp.117-127, 2005.
DOI : 10.1016/j.virusres.2004.11.002

L. Mansky and H. Temin, Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase, J Virol, vol.69, pp.5087-5094, 1995.

J. 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

K. Bishop, R. Holmes, and M. Malim, Antiviral Potency of APOBEC Proteins Does Not Correlate with Cytidine Deamination, Journal of Virology, vol.80, issue.17, pp.8450-8458, 2006.
DOI : 10.1128/JVI.00839-06

D. Nguyen, S. Gummuluru, and J. Hu, Deamination-Independent Inhibition of Hepatitis B Virus Reverse Transcription by APOBEC3G, Journal of Virology, vol.81, issue.9, pp.4465-4472, 2007.
DOI : 10.1128/JVI.02510-06

R. Suspène, M. Henry, S. Guillot, S. Wain-hobson, and J. Vartanian, Recovery of APOBEC3-edited human immunodeficiency virus G->A hypermutants by differential DNA denaturation PCR, Journal of General Virology, vol.86, issue.1, pp.125-129, 2005.
DOI : 10.1099/vir.0.80426-0

M. Bonvin, F. Achermann, I. Greeve, D. Stroka, and A. Keogh, Interferon-inducible expression of APOBEC3 editing enzymes in human hepatocytes and inhibition of hepatitis B virus replication, Hepatology, vol.203, issue.6, pp.1364-1374, 2006.
DOI : 10.1002/hep.21187
URL : https://hal.archives-ouvertes.fr/pasteur-00683855

C. Noguchi, N. Hiraga, N. Mori, M. Tsuge, and M. Imamura, Dual effect of APOBEC3G on Hepatitis B virus, Journal of General Virology, vol.88, issue.2, pp.432-440, 2007.
DOI : 10.1099/vir.0.82319-0

R. Harris and M. Liddament, Retroviral restriction by APOBEC proteins, Nature Reviews Immunology, vol.92, issue.11, pp.868-877, 2004.
DOI : 10.1046/j.1523-1747.1999.00682.x

M. Stenglein, H. Matsuo, and R. Harris, Two Regions within the Amino-Terminal Half of APOBEC3G Cooperate To Determine Cytoplasmic Localization, Journal of Virology, vol.82, issue.19, pp.9591-9599, 2008.
DOI : 10.1128/JVI.02471-07

M. Ohainle, J. Kerns, H. Malik, and M. Emerman, Adaptive Evolution and Antiviral Activity of the Conserved Mammalian Cytidine Deaminase APOBEC3H, Journal of Virology, vol.80, issue.8, pp.3853-3862, 2006.
DOI : 10.1128/JVI.80.8.3853-3862.2006

K. Bishop, R. Holmes, A. Sheehy, N. Davidson, and S. Cho, Cytidine Deamination of Retroviral DNA by Diverse APOBEC Proteins, Current Biology, vol.14, issue.15, pp.1392-1396, 2004.
DOI : 10.1016/j.cub.2004.06.057

M. Langlois, R. Beale, S. Conticello, and M. Neuberger, Mutational comparison of the single-domained APOBEC3C and double-domained APOBEC3F/G anti-retroviral cytidine deaminases provides insight into their DNA target site specificities, Nucleic Acids Research, vol.33, issue.6, pp.1913-1923, 2005.
DOI : 10.1093/nar/gki343

Y. Zheng, D. Irwin, T. Kurosu, K. Tokunaga, and T. Sata, Human APOBEC3F Is Another Host Factor That Blocks Human Immunodeficiency Virus Type 1 Replication, Journal of Virology, vol.78, issue.11, pp.6073-6076, 2004.
DOI : 10.1128/JVI.78.11.6073-6076.2004

S. Conticello, C. Thomas, S. Petersen-mahrt, and M. Neuberger, Evolution of the AID/APOBEC Family of Polynucleotide (Deoxy)cytidine Deaminases, Molecular Biology and Evolution, vol.22, issue.2, pp.367-377, 2005.
DOI : 10.1093/molbev/msi026

S. Sawyer, M. Emerman, and H. Malik, Ancient Adaptive Evolution of the Primate Antiviral DNA-Editing Enzyme APOBEC3G, PLoS Biology, vol.78, issue.9, p.275, 2004.
DOI : 10.1371/journal.pbio.0020275.st001

R. Xu, X. Zhang, W. Zhang, Y. Fang, and S. Zheng, Association of human APOBEC3 cytidine deaminases with the generation of hepatitis virus B x antigen mutants and hepatocellular carcinoma, Hepatology, vol.281, issue.6, pp.1810-1820, 2007.
DOI : 10.1002/hep.21893

N. Watts, J. Conway, N. Cheng, S. Stahl, and D. Belnap, The morphogenic linker peptide of HBV capsid protein forms a mobile array on the interior surface, The EMBO Journal, vol.21, issue.5, pp.876-884, 2002.
DOI : 10.1093/emboj/21.5.876

R. Suspène, P. Sommer, M. Henry, S. Ferris, and D. Guetard, APOBEC3G is a single-stranded DNA cytidine deaminase and functions independently of HIV reverse transcriptase, Nucleic Acids Research, vol.32, issue.8, pp.2421-2429, 2004.
DOI : 10.1093/nar/gkh554

J. Benjamin, B. Ganser-pornillos, W. Tivol, W. Sundquist, and G. Jensen, Three-dimensional Structure of HIV-1 Virus-like Particles by Electron Cryotomography, Journal of Molecular Biology, vol.346, issue.2, pp.577-588, 2005.
DOI : 10.1016/j.jmb.2004.11.064

H. Xu, E. Chertova, J. Chen, D. Ott, and J. Roser, Stoichiometry of the antiviral protein APOBEC3G in HIV-1 virions, Virology, vol.360, issue.2, pp.247-256, 2007.
DOI : 10.1016/j.virol.2006.10.036

L. Holden, C. Prochnow, Y. Chang, R. Bransteitter, and L. Chelico, Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications, Nature, vol.279, issue.7218, pp.121-124, 2008.
DOI : 10.1038/nature07357

Y. Chiu, V. Soros, J. Kreisberg, K. Stopak, and W. Yonemoto, Cellular APOBEC3G restricts HIV-1 infection in resting CD4+ T cells, Nature, vol.70, issue.7038, pp.108-114, 2005.
DOI : 10.1038/nature02171

Y. Chiu, H. Witkowska, S. Hall, M. Santiago, and V. Soros, High-molecular-mass APOBEC3G complexes restrict Alu retrotransposition, Proceedings of the National Academy of Sciences, vol.103, issue.42, pp.15588-15593, 2006.
DOI : 10.1073/pnas.0604524103

S. Petersen-mahrt and M. Neuberger, In Vitro Deamination of Cytosine to Uracil in Single-stranded DNA by Apolipoprotein B Editing Complex Catalytic Subunit 1 (APOBEC1), Journal of Biological Chemistry, vol.278, issue.22, pp.19583-19586, 2003.
DOI : 10.1074/jbc.C300114200

R. Larue, V. Andresdottir, Y. Blanchard, S. Conticello, and D. Derse, Guidelines for Naming Non-Primate APOBEC3 Genes and Proteins, J Virol, 2008.

R. Larue, S. Jonsson, K. Silverstein, M. Lajoie, and D. Bertrand, The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals, BMC Molecular Biology, vol.9, issue.1, p.104, 2008.
DOI : 10.1186/1471-2199-9-104

J. Kidd, T. Newman, E. Tuzun, R. Kaul, and E. Eichler, Population Stratification of a Common APOBEC Gene Deletion Polymorphism, PLoS Genetics, vol.296, issue.4, p.63, 2007.
DOI : 10.1371/journal.pgen.0030063.st007

M. Ortiz, G. Bleiber, R. Martinez, H. Kaessmann, and A. Telenti, Patterns of evolution of host proteins involved in retroviral pathogenesis, Retrovirology, vol.3, issue.1, p.11, 2006.
DOI : 10.1186/1742-4690-3-11

J. Vartanian, D. Guetard, M. Henry, and S. Wain-hobson, Evidence for Editing of Human Papillomavirus DNA by APOBEC3 in Benign and Precancerous Lesions, Science, vol.320, issue.5873, pp.230-233, 2008.
DOI : 10.1126/science.1153201
URL : https://hal.archives-ouvertes.fr/pasteur-00363398

W. Stunkel and H. Bernard, The chromatin structure of the long control region of human papillomavirus type 16 represses viral oncoprotein expression, J Virol, vol.73, pp.1918-1930, 1999.

Y. Endo, H. Marusawa, K. Kinoshita, T. Morisawa, and T. Sakurai, Expression of activation-induced cytidine deaminase in human hepatocytes via NF-??B signaling, Oncogene, vol.296, issue.38, pp.5587-5595, 2007.
DOI : 10.1038/sj.onc.1210344

Y. Endo, H. Marusawa, T. Kou, H. Nakase, and S. Fujii, Activation-Induced Cytidine Deaminase Links Between Inflammation and the Development of Colitis-Associated Colorectal Cancers, Gastroenterology, vol.135, issue.3, pp.889-898, 2008.
DOI : 10.1053/j.gastro.2008.06.091

K. Machida, K. Cheng, V. Sung, S. Shimodaira, and K. Lindsay, Hepatitis C virus induces a mutator phenotype: Enhanced mutations of immunoglobulin and protooncogenes, Proceedings of the National Academy of Sciences, vol.101, issue.12, pp.4262-4267, 2004.
DOI : 10.1073/pnas.0303971101

Y. Matsumoto, H. Marusawa, K. Kinoshita, Y. Endo, and T. Kou, Helicobacter pylori infection triggers aberrant expression of activation-induced cytidine deaminase in gastric epithelium, Nature Medicine, vol.290, issue.4, pp.470-476, 2007.
DOI : 10.1038/nm1566

T. Morisawa, H. Marusawa, Y. Ueda, A. Iwai, and I. Okazaki, Organ-specific profiles of genetic changes in cancers caused by activation-induced cytidine deaminase expression, International Journal of Cancer, vol.31, issue.12, pp.2735-2740, 2008.
DOI : 10.1002/ijc.23853

I. Okazaki, H. Hiai, N. Kakazu, S. Yamada, and M. Muramatsu, Constitutive Expression of AID Leads to Tumorigenesis, The Journal of Experimental Medicine, vol.194, issue.9, pp.1173-1181, 2003.
DOI : 10.1016/S1097-2765(02)00742-6

S. Yamanaka, M. Balestra, L. Ferrell, J. Fan, and K. Arnold, Apolipoprotein B mRNA-editing protein induces hepatocellular carcinoma and dysplasia in transgenic animals., Proceedings of the National Academy of Sciences, vol.92, issue.18, pp.8483-8487, 1995.
DOI : 10.1073/pnas.92.18.8483

A. Adachi, H. Gendelman, S. Koenig, T. Folks, and R. Willey, Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone, J Virol, vol.59, pp.284-291, 1986.

J. Thompson, T. Gibson, F. Plewniak, F. Jeanmougin, and D. Higgins, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Research, vol.25, issue.24, pp.4876-4882, 1997.
DOI : 10.1093/nar/25.24.4876

S. Kumar, K. Tamura, and M. Nei, MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment, Briefings in Bioinformatics, vol.5, issue.2, pp.150-163, 2004.
DOI : 10.1093/bib/5.2.150