V. Achuthan, J. M. Perreira, G. A. Sowd, M. Puray-chavez, W. M. Mcdougall et al., Brass AL & Engelman AN, 2018.

, Trafficking to Sites of Viral DNA Integration, Cell Host Microbe, vol.24, pp.392-404

J. Arbona, S. Herbert, E. Fabre, and C. Zimmer, Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations, Genome Biol, vol.18, p.81, 2017.
URL : https://hal.archives-ouvertes.fr/inserm-01517883

V. Arfi, L. Rivière, L. Jarrosson-wuillème, C. Goujon, D. Rigal et al., Characterization of the Early Steps of Infection of Primary Blood Monocytes by Human Immunodeficiency Virus Type 1, J. Virol, vol.82, pp.6557-6565, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02322944

M. Balasubramaniam, J. Zhou, A. Addai, P. Martinez, J. Pandhare et al., PF74 Inhibits HIV-1 Integration by Altering the Composition of the Preintegration Complex, J. Virol, vol.93, 2019.

D. A. Bejarano, K. Peng, V. Laketa, K. Börner, K. L. Jost et al., HIV-1 nuclear import in macrophages is regulated by CPSF6-capsid interactions at the nuclear pore complex, vol.8, p.41800, 2019.

P. Bell, L. J. Montaner, and G. G. Maul, Accumulation and Intranuclear Distribution of Unintegrated Human Immunodeficiency Virus Type 1 DNA, J. Virol, vol.75, pp.7683-7691, 2001.

W. S. Blair, C. Pickford, S. L. Irving, D. G. Brown, M. Anderson et al., HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention, PLOS Pathog, vol.6, p.1001220, 2010.

G. Blanco-rodriguez, A. Gazi, B. Monel, S. Frabetti, V. Scoca et al., Remodeling of the core leads HIV-1 preintegration complex in the nucleus of human lymphocytes, J. Virol. Available at, 2020.
URL : https://hal.archives-ouvertes.fr/pasteur-02548457

S. Bøe, B. Bjørndal, B. Røsok, A. M. Szilvay, and K. Kalland, Subcellular Localization of Human Immunodeficiency Virus Type 1 RNAs, Rev, and the Splicing Factor SC-35, Virology, vol.244, pp.473-482, 1998.

C. Buffone, A. Martinez-lopez, T. Fricke, S. Opp, M. Severgnini et al., Nup153 Unlocks the Nuclear Pore Complex for HIV-1 Nuclear Translocation in Nondividing Cells, J. Virol, vol.92, pp.648-666, 2018.

R. C. Burdick, K. A. Delviks-frankenberry, J. Chen, S. K. Janaka, J. Sastri et al., Dynamics and regulation of nuclear import and nuclear movements of HIV-1 complexes, PLOS Pathog, vol.13, p.1006570, 2017.

R. C. Burdick, W. Hu, V. Pathak, R. C. Burdick, C. Li et al., Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes, Proc. Natl. Acad. Sci. U. S. A, vol.117, pp.5486-5493, 2013.

S. Cardinale, B. Cisterna, P. Bonetti, C. Aringhieri, M. Biggiogera et al., Subnuclear Localization and Dynamics of the Pre-mRNA 3? End Processing Factor Mammalian Cleavage Factor I 68-kDa Subunit, Mol. Biol. Cell, vol.18, p.1282, 2007.

D. Nunzio, F. Fricke, T. Miccio, A. Valle-casuso, J. C. Perez et al., Nup153 and Nup98 bind the HIV-1 core and contribute to the early steps of HIV-1 replication, Virology, vol.440, pp.8-18, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01536160

D. J. Dismuke and C. Aiken, Evidence for a functional link between uncoating of the human immunodeficiency virus type 1 core and nuclear import of the viral preintegration complex, J Virol, vol.80, pp.3712-3720, 2006.

A. H. Fox, Y. W. Lam, A. Leung, C. E. Lyon, J. Andersen et al., Paraspeckles: A Novel Nuclear Domain, Curr. Biol, vol.12, pp.13-25, 2002.

A. C. Francis and G. B. Melikyan, Single HIV-1 Imaging Reveals Progression of Infection through CA-Dependent Steps of Docking at the Nuclear Pore, Uncoating, and Nuclear Transport, Cell Host Microbe, vol.23, pp.536-548, 2018.

E. O. Freed, HIV-1 Replication, Somat. Cell Mol. Genet, vol.26, pp.13-33, 2001.

Y. Ganor, F. Real, A. Sennepin, C. Dutertre, L. Prevedel et al., HIV-1 reservoirs in urethral macrophages of patients under suppressive antiretroviral therapy, Nat. Microbiol, vol.4, p.633, 2019.
URL : https://hal.archives-ouvertes.fr/inserm-02019067

F. K. Geis and S. P. Goff, Unintegrated HIV-1 DNAs are loaded with core and linker histones and transcriptionally silenced, Proc. Natl. Acad. Sci. Available at, 2019.

H. C. Gelderblom, D. N. Vatakis, S. A. Burke, S. D. Lawrie, G. Bristol et al., Viral complementation allows HIV-1 replication without integration, Retrovirology, vol.5, p.60, 2008.

S. Gordon and P. R. Taylor, Monocyte and macrophage heterogeneity, Nat. Rev. Immunol, vol.5, p.953, 2005.

C. Goujon, O. Moncorgé, H. Bauby, T. Doyle, C. C. Ward et al., Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection, Nature, vol.502, pp.559-562, 2013.

F. B. Hamid, J. Kim, and C. Shin, Distribution and fate of HIV-1 unintegrated DNA species: a comprehensive update, AIDS Res. Ther, vol.14, p.9, 2017.

S. Heinz, L. Texari, M. Hayes, M. Urbanowski, M. W. Chang et al., Transcription Elongation Can Affect Genome 3D Structure. Cell, vol.174, pp.1522-1536, 2018.

J. B. Honeycutt, W. O. Thayer, C. E. Baker, R. M. Ribeiro, S. M. Lada et al., HIV persistence in tissue macrophages of humanized myeloid-only mice during antiretroviral therapy, Nat. Med, vol.23, pp.638-643, 2017.

W. Hu and S. H. Hughes, HIV-1 Reverse Transcription. Cold Spring Harb, Perspect. Med, vol.2, p.6882, 2012.

A. E. Hulme, O. Perez, and T. J. Hope, Complementary assays reveal a relationship between HIV-1 uncoating and reverse transcription, Proc Natl Acad Sci U A, vol.108, pp.9975-9980, 2011.

C. Y. Jao and A. Salic, Exploring RNA transcription and turnover in vivo by using click chemistry, Proc. Natl. Acad. Sci. U. S. A, vol.105, pp.15779-15784, 2008.

H. Koppensteiner, R. Brack-werner, and M. Schindler, Macrophages and their relevance in Human Immunodeficiency Virus Type I infection, Retrovirology, vol.9, p.82, 2012.

N. Laguette, B. Sobhian, N. Casartelli, M. Ringeard, C. Chable-bessia et al., SAMHD1 is the dendritic-and myeloidcell-specific HIV-1 restriction factor counteracted by Vpx, Nature, vol.474, pp.654-657, 2011.

X. Lahaye, M. Gentili, A. Silvin, C. Conrad, L. Picard et al., NONO Detects the Nuclear HIV Capsid to Promote cGAS-Mediated Innate Immune Activation, Colleaux L & Manel N, vol.175, pp.488-501, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02087780

A. I. Lamond and D. L. Spector, Nuclear speckles: a model for nuclear organelles, Nat. Rev. Mol. Cell Biol, vol.4, p.605, 2003.

K. Lee, Z. Ambrose, T. D. Martin, I. Oztop, A. Mulky et al., Flexible use of nuclear import pathways by HIV-1, Cell Host Microbe, vol.7, pp.221-233, 2010.

M. Lelek, N. Casartelli, D. Pellin, E. Rizzi, P. Souque et al., Chromatin organization at the nuclear pore favours HIV replication, Nat. Commun, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01536149

A. G. Matera, Nuclear bodies: multifaceted subdomains of the interchromatin space, 1999.

S. V. Costes, D. Daelemans, E. H. Cho, Z. Dobbin, G. Pavlakis et al., Automatic and Quantitative Measurement of Protein-Protein Colocalization in Live Cells, Biophys. J, vol.86, pp.3993-4003, 2004.

S. Durand, X. Nguyen, J. Turpin, S. Cordeil, N. Nazaret et al., Tailored HIV-1 Vectors for Genetic Modification of Primary Human Dendritic Cells and Monocytes, J. Virol, vol.87, pp.234-242, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02322702

M. Lelek, N. Casartelli, D. Pellin, E. Rizzi, P. Souque et al., Chromatin organization at the nuclear pore favours HIV replication, Nat. Commun, vol.6, p.6483, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01536149

W. Ouyang, F. Mueller, M. Hjelmare, E. Lundberg, and C. Zimmer, ImJoy: an open-source computational platform for the deep learning era, Nat. Methods, vol.16, pp.1199-1200, 2019.
URL : https://hal.archives-ouvertes.fr/pasteur-02401584

C. Petit, O. Schwartz, and F. Mammano, Oligomerization within Virions and Subcellular Localization of Human Immunodeficiency Virus Type 1 Integrase, J. Virol, vol.73, pp.5079-5088, 1999.
URL : https://hal.archives-ouvertes.fr/pasteur-01372744

J. Schindelin, I. Arganda-carreras, E. Frise, V. Kaynig, M. Longair et al.,