A. Engelman and P. Cherepanov, Retroviral Integrase Structure and DNA Recombination Mechanism, Microbiology Spectrum, vol.2, issue.6, pp.1-22, 2014.
DOI : 10.1128/microbiolspec.MDNA3-0024-2014

D. Santo and R. , Inhibiting the HIV Integration Process: Past, Present, and the Future, Journal of Medicinal Chemistry, vol.57, issue.3, pp.539-566, 2014.
DOI : 10.1021/jm400674a

URL : https://hal.archives-ouvertes.fr/pasteur-00968857

J. Demeulemeester, J. De-rijck, R. Gijsbers, and Z. Debyser, Retroviral integration: Site matters, BioEssays, vol.49, issue.11, pp.1202-1214, 2015.
DOI : 10.1002/bies.201500051

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5053271

E. Serrao and A. N. 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, 2015.
DOI : 10.1016/0378-1119(94)90091-4

M. Lelek, N. Casartelli, D. Pellin, E. Rizzi, P. Souque et al., Chromatin organization at the nuclear pore favours HIV replication, Nature Communications, vol.5, p.6483, 2015.
DOI : 10.1038/ncomms7483

B. Marini, A. Kertesz-farkas, H. Ali, B. Lucic, K. Lisek et al., Nuclear architecture dictates HIV-1 integration site selection, Nature, vol.138, issue.7551, pp.227-231, 2015.
DOI : 10.1038/nature14226

C. Cattoglio, D. Pellin, E. Rizzi, G. Maruggi, G. Corti et al., High-definition mapping of retroviral integration sites identifies active regulatory elements in human multipotent hematopoietic progenitors, Blood, vol.116, issue.25, pp.5507-5517, 2010.
DOI : 10.1182/blood-2010-05-283523

A. R. Schroder, P. Shinn, H. Chen, C. Berry, J. R. 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

G. P. Wang, A. Ciuffi, J. Leipzig, C. C. Berry, and F. D. Bushman, HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications, Genome Research, vol.17, issue.8, 2007.
DOI : 10.1101/gr.6286907

P. K. Singh, M. R. Plumb, A. L. Ferris, J. R. 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647561

A. Ciuffi, M. Llano, E. Poeschla, C. Hoffmann, J. Leipzig et al., A role for LEDGF/p75 in targeting HIV DNA integration, Nature Medicine, vol.17, issue.12, pp.1287-1289, 2005.
DOI : 10.1038/nm1329

H. M. Marshall, K. Ronen, C. Berry, M. Llano, H. Sutherland et al., Role of PSIP1/LEDGF/p75 in Lentiviral Infectivity and Integration Targeting, lentiviral infectivity and integration targeting, p.1340, 2007.
DOI : 10.1371/journal.pone.0001340.s003

M. Shun, N. K. Ragahvendra, N. Vandergraaf, J. E. Daigle, S. Hughes et al., LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration, Genes & Development, vol.21, issue.14, pp.1767-1778, 2007.
DOI : 10.1101/gad.1565107

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920171

S. Rasheedi, M. C. Shun, E. Serrao, G. A. Sowd, J. Qian et al., ) Complex Mediates HIV-1 Integration into Genes, Journal of Biological Chemistry, vol.291, issue.22, pp.11809-11819, 2016.
DOI : 10.1074/jbc.M116.721647

G. A. Sowd, E. Serrao, H. Wang, W. Wang, H. J. Fadel et al., A critical role for alternative polyadenylation factor CPSF6 in targeting HIV-1 integration to transcriptionally active chromatin, Proceedings of the National Academy of Sciences, vol.113, issue.8, pp.1054-1063, 2016.
DOI : 10.1073/pnas.1524213113

M. Daugaard, A. Baude, K. Fugger, L. K. Povlsen, H. Beck et al., LEDGF (p75) promotes DNA-end resection and homologous recombination, Nature Structural & Molecular Biology, vol.4, issue.8, pp.803-810, 2012.
DOI : 10.1038/nsmb.2314

J. O. Eidahl, B. L. Crowe, J. A. North, C. J. 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

M. M. Pradeepa, H. G. Sutherland, J. Ule, G. R. Grimes, and W. A. Bickmore, Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing, PLoS Genetics, vol.122, issue.5, p.1002717, 2012.
DOI : 10.1371/journal.pgen.1002717.s004

Y. Botbol, N. K. Raghavendra, S. Rahman, A. Engelman, and M. Lavigne, Chromatinized templates reveal the requirement for the LEDGF/p75 PWWP domain during HIV-1 integration in vitro, Nucleic Acids Research, vol.36, issue.4, pp.1237-1246, 2008.
DOI : 10.1093/nar/gkm1127

M. C. Shun, Y. Botbol, X. Li, D. Nunzio, F. Daigle et al., Identification and Characterization of PWWP Domain Residues Critical for LEDGF/p75 Chromatin Binding and Human Immunodeficiency Virus Type 1 Infectivity, Journal of Virology, vol.82, issue.23, pp.11555-11567, 2008.
DOI : 10.1128/JVI.01561-08

F. Michel, C. Crucifix, F. Granger, S. Eiler, J. F. 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

M. S. Benleulmi, J. Matysiak, D. R. 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

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

D. P. Maskell, L. Renault, E. Serrao, P. Lesbats, R. Matadeen et al., Structural basis for retroviral integration into nucleosomes, Nature, vol.14, issue.7560, pp.366-369, 2015.
DOI : 10.1038/nature14495

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530500

M. Naughtin, Z. Haftek-terreau, J. Xavier, S. Meyer, M. Silvain et al., DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity, PLOS ONE, vol.36, issue.11, p.129427, 2015.
DOI : 10.1371/journal.pone.0129427.s007

URL : https://hal.archives-ouvertes.fr/pasteur-01416841

D. Pruss, F. D. Bushman, and A. P. Wolffe, Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core., Proceedings of the National Academy of Sciences, vol.91, issue.13, pp.5913-5917, 1994.
DOI : 10.1073/pnas.91.13.5913

P. M. Pryciak and H. E. Varmus, 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

K. D. Taganov, I. Cuesta, R. Daniel, L. A. Cirillo, R. A. Katz et al., Integrase-Specific Enhancement and Suppression of Retroviral DNA Integration by Compacted Chromatin Structure In Vitro, Journal of Virology, vol.78, issue.11, pp.5848-5855, 2004.
DOI : 10.1128/JVI.78.11.5848-5855.2004

X. Wu, Y. Li, B. Crise, S. M. Burgess, and D. J. Munroe, Weak Palindromic Consensus Sequences Are a Common Feature Found at the Integration Target Sites of Many Retroviruses, Journal of Virology, vol.79, issue.8, pp.5211-5214, 2005.
DOI : 10.1128/JVI.79.8.5211-5214.2005

E. Serrao, L. Krishnan, M. C. Shun, X. Li, P. Cherepanov et al., Integrase residues that determine nucleotide preferences at sites of HIV-1 integration: implications for the mechanism of target DNA binding, Nucleic Acids Research, vol.42, issue.8, pp.5164-5176, 2014.
DOI : 10.1093/nar/gku136

E. Serrao, A. Ballandras-colas, P. Cherepanov, G. N. Maertens, and A. N. Engelman, Key determinants of target DNA recognition by retroviral intasomes, Retrovirology, vol.10, issue.1, p.39, 2015.
DOI : 10.1186/s12977-015-0167-3

G. N. 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

Z. Yin, K. Shi, S. Banerjee, K. K. Pandey, S. Bera et al., Crystal structure of the Rous sarcoma virus intasome, Nature, vol.289, issue.7590, pp.362-366, 2016.
DOI : 10.1038/nature16950

S. L. Roth, N. Malani, and F. D. Bushman, Gammaretroviral Integration into Nucleosomal Target DNA In Vivo, Journal of Virology, vol.85, issue.14, pp.7393-7401, 2011.
DOI : 10.1128/JVI.00635-11

A. D. Bates, A. Noy, M. M. Piperakis, S. A. Harris, and A. Maxwell, Small DNA circles as probes of DNA topology, Biochemical Society Transactions, vol.8, issue.2, pp.565-570, 2013.
DOI : 10.1021/bi952433y

Q. Du, A. Kotlyar, and A. Vologodskii, Kinking the double helix by bending deformation, Nucleic Acids Research, vol.36, issue.4, pp.1120-1128, 2008.
DOI : 10.1093/nar/gkm1125

URL : http://doi.org/10.1093/nar/gkm1125

T. A. Lionberger, E. D. Meyhofer, A. Amzallag, E. J. Rawdon, J. H. Maddocks et al., Bending the rules of transcriptional repression: tightly looped DNA directly represses T7 RNA polymerase Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles, Biophys. J. Nucleic Acids Res, vol.99, issue.37, pp.1139-1148, 2009.

T. A. Lionberger, D. Demurtas, G. Witz, J. Dorier, T. Lillian et al., Cooperative kinking at distant sites in mechanically stressed DNA, Nucleic Acids Research, vol.39, issue.22, pp.9820-9832, 2011.
DOI : 10.1093/nar/gkr666

URL : http://doi.org/10.1093/nar/gkr666

S. A. Harris, C. A. Laughton, and T. B. Liverpool, Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations, Nucleic Acids Research, vol.36, issue.1, pp.21-29, 2008.
DOI : 10.1093/nar/gkm891

F. Lankas, R. Lavery, and J. H. Maddocks, Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles, Structure, vol.14, issue.10, pp.1527-1534, 2006.
DOI : 10.1016/j.str.2006.08.004

URL : https://hal.archives-ouvertes.fr/hal-00314897

J. S. Mitchell, C. A. Laughton, and S. A. Harris, Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA, Nucleic Acids Research, vol.39, issue.9, pp.3928-3938, 2011.
DOI : 10.1093/nar/gkq1312

URL : http://doi.org/10.1093/nar/gkq1312

S. R. Sanghani, K. Zakrzewska, S. C. Harvey, and R. Lavery, Molecular Modelling of (A4T4NN)n and (T4A4NN)n: Sequence Elements Responsible for Curvature, Nucleic Acids Research, vol.24, issue.9, pp.1632-1637, 1996.
DOI : 10.1093/nar/24.9.1632

URL : https://hal.archives-ouvertes.fr/hal-00313424

P. N. Dyer, R. S. Edayathumangalam, C. L. White, Y. Bao, S. Chakravarthy et al., Reconstitution of Nucleosome Core Particles from Recombinant Histones and DNA, Methods Enzymol, vol.375, pp.23-44, 2004.
DOI : 10.1016/S0076-6879(03)75002-2

E. Valkov, S. S. Gupta, S. Hare, A. Helander, P. Roversi et al., Functional and structural characterization of the integrase from the prototype foamy virus, Nucleic Acids Research, vol.37, issue.1, pp.243-255, 2009.
DOI : 10.1093/nar/gkn938

R. Lavery, K. Zakrzewska, and H. Sklenar, JUMNA (junction minimisation of nucleic acids), Computer Physics Communications, vol.91, issue.1-3, pp.135-158, 1995.
DOI : 10.1016/0010-4655(95)00046-I

T. E. Cheatham, P. Cieplak, and P. A. Kollman, Force Field with Improved Sugar Pucker Phases and Helical Repeat, Journal of Biomolecular Structure and Dynamics, vol.16, issue.4, pp.845-862, 1999.
DOI : 10.1021/jp953080f

A. Pérez, I. Marchand, D. Svozil, J. Sponer, T. E. Cheatham et al., Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of ??/?? Conformers, Biophysical Journal, vol.92, issue.11, pp.3817-3829, 2007.
DOI : 10.1529/biophysj.106.097782

H. J. Berendsen, J. R. Grigera, and T. P. Stratsma, The missing term in effective pair potentials, The Journal of Physical Chemistry, vol.91, issue.24, pp.6269-6271, 1987.
DOI : 10.1021/j100308a038

L. X. Dang, Mechanism and Thermodynamics of Ion Selectivity in Aqueous Solutions of 18-Crown-6 Ether: A Molecular Dynamics Study, Journal of the American Chemical Society, vol.117, issue.26, pp.6954-6960, 1995.
DOI : 10.1021/ja00131a018

H. J. Berendsen, D. Van-der-spoel, and R. Van-druner, GROMACS: A message-passing parallel molecular dynamics implementation, Computer Physics Communications, vol.91, issue.1-3, pp.43-56, 1995.
DOI : 10.1016/0010-4655(95)00042-E

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.123.3928

E. Lindahl, B. Hess, and D. Van-der-spoel, GROMACS 3.0: a package for molecular simulation and trajectory analysis, Journal of Molecular Modeling, vol.7, issue.8, pp.306-317, 2001.
DOI : 10.1007/s008940100045

D. Van-der-spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark et al., GROMACS: Fast, flexible, and free, Journal of Computational Chemistry, vol.26, issue.16, pp.1701-1718, 2005.
DOI : 10.1002/jcc.20291

G. Bussi, D. Donaldio, and M. Parinello, Canonical sampling through velocity rescaling, The Journal of Chemical Physics, vol.126, issue.1, p.14101, 2007.
DOI : 10.1063/1.2408420

URL : http://arxiv.org/abs/0803.4060

H. J. Berendsen, J. P. Postma, W. F. Van-gunsteren, A. Dinola, and J. R. Haak, Molecular dynamics with coupling to an external bath, The Journal of Chemical Physics, vol.81, issue.8, pp.3684-3690, 1984.
DOI : 10.1063/1.448118

U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee et al., A smooth particle mesh Ewald method, The Journal of Chemical Physics, vol.103, issue.19, pp.8577-8593, 1995.
DOI : 10.1063/1.470117

B. Hess, H. Bekker, H. J. Berendsen, and J. G. Fraaije, LINCS: A linear constraint solver for molecular simulations, Journal of Computational Chemistry, vol.19, issue.12, pp.1463-1472, 1997.
DOI : 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H

B. Hess, C. Kutzner, D. Van-der-spoel, and E. Lindahl, GROMACS 4:?? Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, Journal of Chemical Theory and Computation, vol.4, issue.3, pp.435-447, 2008.
DOI : 10.1021/ct700301q

URL : http://hdl.handle.net/11858/00-001M-0000-000F-7903-4

M. Pasi, J. H. Maddocks, D. Beveridge, T. C. Bishop, D. A. Case et al., muABC: a systematic microsecond molecular dynamics Nucleic Acids Research, p.7847, 2014.

E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt et al., UCSF Chimera?A visualization system for exploratory research and analysis, Journal of Computational Chemistry, vol.373, issue.13, pp.1605-1612, 2004.
DOI : 10.1002/jcc.20084

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.456.9442

R. Lavery, M. Moakher, J. H. Maddocks, D. Petkeviciute, and K. Zakrzewska, Conformational analysis of nucleic acids revisited: Curves+, Nucleic Acids Research, vol.37, issue.17, pp.5917-5929, 2009.
DOI : 10.1093/nar/gkp608

C. Blanchet, M. Pasi, K. Zakrzewska, and R. Lavery, CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures, Nucleic Acids Research, vol.39, issue.suppl, pp.68-73, 2011.
DOI : 10.1093/nar/gkr316

R. Lavery, J. H. Maddocks, M. Pasi, and K. Zakrzewska, Analyzing ion distributions around DNA, Nucleic Acids Research, vol.42, issue.12, pp.8138-8149, 2014.
DOI : 10.1093/nar/gku504

J. D. Hunter, Matplotlib: A 2D Graphics Environment, Computing in Science & Engineering, vol.9, issue.3, pp.90-95, 2007.
DOI : 10.1109/MCSE.2007.55

K. Luger, A. W. Mader, R. K. Richmond, D. F. Sargent, R. et al., Crystal structure of the nucleosome core particle at 2.8 A resolution, Nature, vol.389, pp.251-260, 1997.

G. Schnitzler, S. Sif, and R. E. Kingston, Human SWI/SNF Interconverts a Nucleosome between Its Base State and a Stable Remodeled State, Cell, vol.94, issue.1, pp.17-27, 1998.
DOI : 10.1016/S0092-8674(00)81217-9

URL : http://doi.org/10.1016/s0092-8674(00)81217-9

J. Curuksu, M. Zacharias, R. Lavery, and K. Zakrzewska, Local and global effects of strong DNA bending induced during molecular dynamics simulations, Nucleic Acids Research, vol.37, issue.11, pp.3766-3773, 2009.
DOI : 10.1093/nar/gkp234

A. Faure, C. Calmels, C. Desjobert, M. Castroviejo, A. Caumont-sarcos et al., HIV-1 integrase crosslinked oligomers are active in vitro, Nucleic Acids Research, vol.33, issue.3, pp.977-986, 2005.
DOI : 10.1093/nar/gki241

H. P. Muller and H. E. Varmus, DNA bending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes, EMBO J, vol.13, pp.4704-4714, 1994.

D. Pruss, R. Reeves, F. D. Bushman, A. P. Wolffe, S. Carteau et al., The influence of DNA and nucleosome structure on integration events directed by HIV integrase, J. Biol. Chem, vol.269, pp.25031-25041, 1994.