J. C. Paillart, M. Dettenhofer, X. F. Yu, C. Ehresmann, B. Ehresmann et al., First snapshots of the HIV-1 RNA structure in infected cells and in virions, J. Biol. Chem, vol.279, pp.48397-48403, 2004.

B. Berkhout and J. L. Van-wamel, The leader of the HIV-1 RNA genome forms a compactly folded tertiary structure, RNA, vol.6, pp.282-295, 2000.

K. A. Wilkinson, R. J. Gorelick, S. M. Vasa, N. Guex, A. Rein et al., High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states, PLoS Biol, vol.6, p.96, 2008.

M. Mougel, F. Smagulova, J. Ramirez, and L. Houzet, RNA Packaging in MuLV and HIV-1 Retroviral Particles, Curr. Topics Virol, vol.4, pp.201-218, 2004.

V. D'souza and M. F. Summers, How retroviruses select their genomes, Nat. Rev. Microbiol, vol.3, pp.643-655, 2005.

N. Jouvenet, S. Laine´, L. Pessel-vivares, and M. Mougel, Cell biology of retroviral RNA packaging, RNA Biol, vol.8, pp.1-9, 2011.

D. Harrich, C. W. Hooker, and E. Parry, The human immunodeficiency virus type 1 TAR RNA upper stem-loop plays distinct roles in reverse transcription and RNA packaging, 2000.

, J. Virol, vol.74, pp.5639-5646

R. Song, J. Kafaie, and M. Laughrea, Role of the 5 0 TAR stem-loop and the U5-AUG duplex in dimerization of HIV-1 genomic RNA, Biochemistry, vol.47, pp.3283-3293, 2008.

M. S. Mcbride, M. D. Schwartz, and A. T. Panganiban, Efficient encapsidation of human immunodeficiency virus type 1 vectors and further characterization of cis elements required for encapsidation, J. Virol, vol.71, pp.4544-4554, 1997.

C. Helga-maria, M. L. Hammarskjold, and D. Rekosh, An intact TAR element and cytoplasmic localization are necessary for efficient packaging of human immunodeficiency virus type 1 genomic RNA, J. Virol, vol.73, pp.4127-4135, 1999.

A. T. Das, A. Harwig, M. M. Vrolijk, and B. Berkhout, The TAR hairpin of human immunodeficiency virus type 1 can be deleted when not required for Tat-mediated activation of transcription, J. Virol, vol.81, pp.7742-7748, 2007.

B. Berkhout, Structure and function of the human immunodeficiency virus leader RNA, Prog. Nucleic Acid Res. Mol. Biol, vol.54, pp.1-34, 1996.

J. L. Clever, D. Mirandar, and T. G. Parslow, RNA structure and packaging signals in the 5 0 leader region of the human immunodeficiency virus type 1 genome, J. Virol, vol.76, pp.12381-12387, 2002.

R. S. Russell, J. Hu, M. Laughrea, M. A. Wainberg, and C. Liang, Deficient dimerization of human immunodeficiency virus type 1 RNA caused by mutations of the u5 RNA sequences, Virology, vol.303, pp.152-163, 2002.

R. N. De-guzman, Z. R. Wu, C. C. Stalling, L. Pappalardo, P. N. Borer et al., Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element, Science, vol.279, pp.384-388, 1998.

G. K. Amarasinghe, R. N. De-guzman, R. B. Turner, K. J. Chancellor, Z. R. Wu et al., NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition, J. Mol. Biol, vol.301, pp.491-511, 2000.

E. Chertova, O. Chertov, L. V. Coren, J. D. Roser, C. M. Trubey et al., Proteomic and biochemical analysis of purified, Nucleic Acids Research, vol.39, issue.20, p.8925, 2006.

, Virol, vol.80, pp.9039-9052, 2020.

J. L. Darlix, M. Lapadat-tapolsky, H. De-rocquigny, and B. P. Roques, First glimpses at structure-function relationships of the nucleocapsid protein of retroviruses, J. Mol. Biol, vol.254, pp.523-537, 1995.

J. G. Levin, J. Guo, I. Rouzina, and K. Musier-forsyth, Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism, Prog. Nucleic Acid Res. Mol. Biol, vol.80, pp.217-286, 2005.

D. Muriaux and J. L. Darlix, Properties and functions of the nucleocapsid protein in virus assembly, RNA Biol, vol.7, pp.744-753, 2010.

M. Mougel, A. Cimarelli, and J. Darlix, Implications of the nucleocapsid and the microenvironment in retroviral reverse transcription, Viruses, vol.2, pp.939-960, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02322864

M. Mougel, L. Houzet, and J. L. Darlix, When is it time for reverse transcription to start and go?, Retrovirology, vol.6, p.24, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00420508

C. Liang, J. Hu, R. S. Russell, M. Kameoka, and M. A. Wainberg, Spliced human immunodeficiency virus type 1 RNA is reverse transcribed into cDNA within infected cells, AIDS Res. Hum. Retroviruses, vol.20, pp.203-211, 2004.

L. Houzet, Z. Morichaud, and M. Mougel, Fully-spliced HIV-1 RNAs are reverse transcribed with similar efficiencies as the genomic RNA in virions and cells, but more efficiently in AZT-treated cells, Retrovirology, vol.4, p.30, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00258943

S. Saurya, Z. Lichtenstein, and A. Karpas, Defective rev response element (RRE) and rev gene in HAART treated AIDS patients with discordance between viral load and CD4+ T-cell counts, J. Clin. Virol, vol.33, pp.324-327, 2005.

D. F. Purcell and M. A. Martin, Alternative splicing of human immunodeficiency virus type 1 mRNA modulates viral protein expression, replication, and infectivity, J. Virol, vol.67, pp.6365-6378, 1993.

R. Yi, H. P. Bogerd, and B. R. Cullen, Recruitment of the Crm1 nuclear export factor is sufficient to induce cytoplasmic expression of incompletely spliced human immunodeficiency virus mRNAs, J. Virol, vol.76, pp.2036-2042, 2002.

L. Houzet, J. C. Paillart, F. Smagulova, S. Maurel, Z. Morichaud et al., HIV controls the selective packaging of genomic, spliced viral and cellular RNAs into virions through different mechanisms, Nucleic Acids Res, vol.35, pp.2695-2704, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00142548

S. J. Rulli, . Jr, C. S. Hibbert, J. Mirro, T. Pederson et al., Selective and nonselective packaging of cellular RNAs in retrovirus particles, J. Virol, vol.81, pp.6623-6631, 2007.

A. A. Onafuwa-nuga, A. Telesnitsky, and S. R. King, , p.7, 2006.

, RNA, but not the 54-kd signal recognition particle protein, is an abundant component of both infectious HIV-1 and minimal virus-like particles, RNA, vol.12, pp.542-546

C. Tian, T. Wang, W. Zhang, and X. F. Yu, Virion packaging determinants and reverse transcription of SRP RNA in HIV-1 particles, Nucleic Acids Res, vol.35, pp.7288-7302, 2007.

K. E. Giles, M. Caputi, and K. L. Beemon, Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes, RNA, vol.10, pp.299-307, 2004.

D. Bach, S. Peddi, B. Mangeat, A. Lakkaraju, K. Strub et al., , 2008.

, RNA. Retrovirology, vol.5, p.54

M. A. Khan, R. Goila-gaur, S. Opi, E. Miyagi, H. Takeuchi et al., Analysis of the contribution of cellular and viral RNA to the packaging of APOBEC3G into HIV-1 virions, Retrovirology, vol.4, p.48, 2007.

K. Strebel and M. A. Khan, APOBEC3G encapsidation into HIV-1 virions: which RNA is it?, Retrovirology, vol.5, p.55, 2008.

K. Verhoef, G. Marzio, W. Hillen, H. Bujard, and B. Berkhout, Strict control of human immunodeficiency virus type 1 replication by a genetic switch: Tet for Tat, J. Virol, vol.75, pp.979-987, 2001.

V. Tanchou, D. Decimo, C. Pechoux, D. Lener, V. Rogemond et al., Role of the N-terminal zinc finger of human immunodeficiency virus type 1 nucleocapsid protein in virus structure and replication, J. Virol, vol.72, pp.4442-4447, 1998.

B. Grigorov, D. Decimo, F. Smagulova, C. Pechoux, M. Mougel et al., Intracellular HIV-1 Gag localization is impaired by mutations in the nucleocapsid zinc fingers, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00258941

L. Berthoux, C. Pechoux, M. Ottmann, G. Morel, and J. L. Darlix, Mutations in the N-terminal domain of human immunodeficiency virus type 1 nucleocapsid protein affect virion core structure and proviral DNA synthesis, J. Virol, vol.71, pp.6973-6981, 1997.

M. Ottmann, C. Gabus, and J. L. Darlix, The central globular domain of the nucleocapsid protein of human immunodeficiency virus type 1 is critical for virion structure and infectivity, J. Virol, vol.69, pp.1778-1784, 1995.

Y. Huang, A. Khorchid, J. Wang, M. A. Parniak, J. L. Darlix et al., Effect of mutations in the nucleocapsid protein (NCp7) upon Pr160(gag-pol) and tRNA(Lys) incorporation into human immunodeficiency virus type 1, 1997.

, J. Virol, vol.71, pp.4378-4384

F. Smagulova, S. Maurel, Z. Morichaud, C. Devaux, M. Mougel et al., The highly structured encapsidation signal of MuLV RNA is involved in the nuclear export of its unspliced RNA, J. Mol. Biol, vol.354, pp.1118-1128, 2005.

T. E. Abbink and B. Berkhout, A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon, J. Biol. Chem, vol.278, pp.11601-11611, 2003.

C. K. Damgaard, E. S. Andersen, B. Knudsen, J. Gorodkin, and J. Kjems, RNA interactions in the 5 0 region of the HIV-1 genome, J. Mol. Biol, vol.336, pp.369-379, 2004.

S. Spriggs, L. Garyu, R. Connor, and M. F. Summers, Potential intra-and intermolecular interactions involving the unique-5' region of the HIV-1 5 0 -UTR, Biochemistry, vol.47, pp.13064-13073, 2008.

M. M. Vrolijk, M. Ooms, A. Harwig, A. T. Das, and B. Berkhout, Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA, Nucleic Acids Res, vol.36, pp.4352-4363, 2008.

U. Geigenmuller and M. L. Linial, Specific binding of human immunodeficiency virus type 1 (HIV-1) Gag-derived proteins to a 5 0 HIV-1 genomic RNA sequence, J. Virol, vol.70, pp.667-671, 1996.

A. M. Lever, HIV-1 RNA packaging, Adv. Pharmacol, vol.55, pp.1-32, 2007.

S. S. Athavale, W. Ouyang, M. P. Mcpike, B. S. Hudson, and P. N. Borer, Effects of the nature and concentration of salt on the interaction of the HIV-1 nucleocapsid protein with SL3 RNA, Biochemistry, vol.49, pp.3525-3533, 2011.

Y. Mely, N. Jullian, N. Morellet, H. De-rocquigny, C. Z. Dong et al., Spatial proximity of the HIV-1 nucleocapsid protein zinc fingers investigated by time-resolved fluorescence and fluorescence resonance energy transfer, Biochemistry, vol.33, pp.12085-12091, 1994.

N. Morellet, H. De-rocquigny, Y. Mely, N. Jullian, H. Demene et al., Conformational behaviour of the active and inactive forms of the nucleocapsid NCp7 of HIV-1 studied by 1H NMR, J. Mol. Biol, vol.235, pp.287-301, 1994.

N. Morellet, N. Jullian, H. De-rocquigny, B. Maigret, J. L. Darlix et al., Determination of the structure of the nucleocapsid protein NCp7 from the human immunodeficiency virus type 1 by 1H NMR, EMBO J, vol.11, pp.3059-3065, 1992.

B. Berkhout, Multiple biological roles associated with the repeat (R) region of the HIV-1 RNA genome, Adv. Pharmacol, vol.48, pp.29-73, 2000.

L. Houzet, Z. Morichaud, L. Didierlaurent, D. Muriaux, J. L. Darlix et al., Nucleocapsid mutations turn HIV-1 into a DNA-containing virus, Nucleic Acids Res, vol.36, pp.2311-2319, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00273826

H. Demene, C. Z. Dong, M. Ottmann, M. C. Rouyez, N. Jullian et al., 1H NMR structure and biological studies of the His23->Cys mutant nucleocapsid protein of HIV-1 indicate that the conformation of the first zinc finger is critical for virus infectivity, Biochemistry, vol.33, pp.11707-11716, 1994.

R. J. Gorelick, T. D. Gagliardi, W. J. Bosche, T. A. Wiltrout, L. V. Coren et al., Strict conservation of the retroviral nucleocapsid protein zinc finger is strongly influenced by its role in viral infection processes: characterization of HIV-1 particles containing mutant nucleocapsid zinc-coordinating sequences, Virology, vol.256, pp.92-104, 1999.

E. Schmalzbauer, B. Strack, J. Dannull, S. Guehmann, and K. Moelling, Mutations of basic amino acids of NCp7 of human immunodeficiency virus type 1 affect RNA binding in vitro, J. Virol, vol.70, pp.771-777, 1996.

D. T. Poon, J. Wu, and A. Aldovini, Charged amino acid residues of human immunodeficiency virus type 1 nucleocapsid p7 protein involved in RNA packaging and infectivity, J. Virol, vol.70, pp.6607-6616, 1996.

S. Cen, Y. Huang, A. Khorchid, J. L. Darlix, M. A. Wainberg et al., The role of Pr55(gag) in the annealing of tRNA3Lys to human immunodeficiency virus type 1 genomic RNA, J. Virol, vol.73, pp.4485-4488, 1999.

J. Kafaie, R. Song, L. Abrahamyan, A. J. Mouland, and M. Laughrea, Mapping of nucleocapsid residues important for HIV-1 genomic RNA dimerization and packaging, Virology, vol.375, pp.592-610, 2008.

M. Laughrea, N. Shen, L. Jette, J. L. Darlix, L. Kleiman et al., Role of distal zinc finger of nucleocapsid protein in genomic RNA dimerization of human immunodeficiency virus type 1; no role for the palindrome crowning the R-U5 hairpin, Virology, vol.281, pp.109-116, 2001.

A. Cimarelli, S. Sandin, S. Hoglund, and J. Luban, Basic residues in human immunodeficiency virus type 1 nucleocapsid promote virion assembly via interaction with RNA, J. Virol, vol.74, pp.3046-3057, 2000.
URL : https://hal.archives-ouvertes.fr/hal-02323109

T. Wang, C. Tian, W. Zhang, K. Luo, P. T. Sarkis et al., 7SL RNA mediates virion packaging of the antiviral cytidine deaminase APOBEC3G, J. Virol, vol.81, pp.13112-13124, 2007.

T. Wang, C. Tian, W. Zhang, P. T. Sarkis, and X. F. Yu, Interaction with 7SL RNA but not with HIV-1 genomic RNA or P bodies is required for APOBEC3F virion packaging, J. Mol. Biol, vol.375, pp.1098-1112, 2008.

S. E. Keene, S. R. King, and A. Telesnitsky, 7SL RNA is retained in HIV-1 minimal virus-like particles as an S-domain fragment, J. Virol, vol.84, pp.9070-9077, 2010.

M. A. Khan, C. Aberham, S. Kao, H. Akari, R. Gorelick et al., Human immunodeficiency virus type 1 Vif protein is packaged into the nucleoprotein complex through an interaction with viral genomic RNA, J. Virol, vol.75, pp.7252-7265, 2001.

H. Zhang, R. J. Pomerantz, G. Dornadula, and Y. Sun, Human immunodeficiency virus type 1 Vif protein is an integral component of an mRNP complex of viral RNA and could be involved in the viral RNA folding and packaging process, 2000.

, J. Virol, vol.74, pp.8252-8261

A. J. Mouland, J. Mercier, M. Luo, L. Bernier, L. Desgroseillers et al., The double-stranded RNA-binding protein Staufen is incorporated in human immunodeficiency virus type 1: evidence for a role in genomic RNA encapsidation, J. Virol, vol.74, pp.5441-5451, 2000.

J. R. Lingappa, J. E. Dooher, M. A. Newman, P. K. Kiser, and K. C. Klein, Basic residues in the nucleocapsid domain of Gag are required for interaction of HIV-1 gag with ABCE1 (HP68), a cellular protein important for HIV-1 capsid assembly, J. Biol. Chem, vol.281, pp.3773-3784, 2006.

S. Popov, E. Popova, M. Inoue, and H. G. Gottlinger, Human immunodeficiency virus type 1 Gag engages the Bro1 domain of ALIX/AIP1 through the nucleocapsid, J. Virol, vol.82, pp.1389-1398, 2008.

S. P. Goff, Host factors exploited by retroviruses, Nat. Rev. Microbiol, vol.5, pp.253-263, 2007.

R. Berkowitz, J. Fisher, and S. P. Goff, RNA packaging, Curr. Top. Microbiol. Immunol, vol.214, pp.177-218, 1996.

J. L. Clever and T. G. Parslow, Mutant human immunodeficiency virus type 1 genomes with defects in RNA dimerization or encapsidation, J. Virol, vol.71, pp.3407-3414, 1997.

M. K. Hill, M. Shehu-xhilaga, S. M. Campbell, P. Poumbourios, S. M. Crowe et al., The dimer initiation sequence stem-loop of human immunodeficiency virus type 1 is dispensable for viral replication in peripheral blood mononuclear cells, 2003.

, J. Virol, vol.77, pp.8329-8335

B. B. Roy, R. S. Russell, D. Turner, and C. Liang, The T12I mutation within the SP1 region of Gag restricts packaging of spliced viral RNA into human immunodeficiency virus type 1 with mutated RNA packaging signals and mutated nucleocapsid sequence, Virology, vol.344, pp.304-314, 2006.

R. S. Russell, A. Roldan, M. Detorio, J. Hu, M. A. Wainberg et al., Effects of a single amino acid substitution within the p2 region of HIV-1 on packaging of spliced viral RNA, J. Virol, vol.77, pp.12986-12995, 2003.

D. E. Ott, L. V. Coren, and T. D. Gagliardi, Redundant roles for nucleocapsid and matrix RNA-binding sequences in human immunodeficiency virus type 1 assembly, J. Virol, vol.79, pp.13839-13847, 2005.

N. Ristic and M. P. Chin, Mutations in matrix and SP1 repair the packaging specificity of a Human Immunodeficiency Virus Type 1 mutant by reducing the association of Gag with spliced viral RNA, Retrovirology, vol.7, p.73, 2010.

A. T. Das, B. Klaver, and B. Berkhout, The 5 0 and 3 0 TAR elements of human immunodeficiency virus exert effects at several points in the virus life cycle, J. Virol, vol.72, pp.9217-9223, 1998.

J. C. Paillart, E. Skripkin, B. Ehresmann, C. Ehresmann, and R. Marquet, In vitro evidence for a long range pseudoknot in the 5 0 -untranslated and matrix coding regions of HIV-1 genomic RNA, J. Biol. Chem, vol.277, pp.5995-6004, 2002.

C. K. Damgaard, H. Dyhr-mikkelsen, and J. Kjems, Mapping the RNA binding sites for human immunodeficiency virus type-1 gag and NC proteins within the complete HIV-1 and -2 untranslated leader regions, Nucleic Acids Res, vol.26, pp.3667-3676, 1998.

L. Didierlaurent, L. Houzet, Z. Morichaud, J. L. Darlix, and M. Mougel, The conserved N-terminal basic residues and zinc-finger motifs of HIV-1 nucleocapsid restrict the viral cDNA synthesis during virus formation and maturation, Nucleic Acids Res, vol.36, pp.4745-4753, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00311686

J. A. Thomas, W. J. Bosche, T. L. Shatzer, D. G. Johnson, and R. J. Gorelick, Mutations in human immunodeficiency virus type 1 nucleocapsid protein zinc fingers cause premature reverse transcription, J. Virol, vol.82, pp.9318-9328, 2008.

L. Sinck, D. Richer, J. Howard, M. Alexander, D. F. Purcell et al., vitro dimerization of human immunodeficiency virus type 1 (HIV-1), 2007.
URL : https://hal.archives-ouvertes.fr/hal-00200856

, RNA, vol.13, pp.2141-2150

E. Poole, P. Strappe, H. P. Mok, R. Hicks, and A. M. Lever, HIV-1 Gag-RNA interaction occurs at a perinuclear/centrosomal site; analysis by confocal microscopy and FRET, Traffic, vol.6, pp.741-755, 2005.

N. Jouvenet, S. M. Simon, and P. D. Bieniasz, Imaging the interaction of HIV-1 genomes and Gag during assembly of individual viral particles, Proc. Natl Acad. Sci. USA, vol.106, pp.19114-19119, 2009.

I. Kemler, A. Meehan, and E. M. Poeschla, Live-cell coimaging of the genomic RNAs and Gag proteins of two lentiviruses, J. Virol, vol.84, pp.6352-6366, 2010.

M. D. Moore, O. A. Nikolaitchik, J. Chen, M. L. Hammarskjold, D. Rekosh et al., Probing the HIV-1 genomic RNA trafficking pathway and dimerization by genetic recombination and single virion analyses, PLoS Pathog, vol.5, p.1000627, 2009.