R. J. Jackson, C. U. Hellen, and T. V. Pestova, The mechanism of eukaryotic translation initiation and principles of its regulation, Nature Reviews Molecular Cell Biology, vol.4, issue.2, pp.113-127, 2009.
DOI : 10.1038/nrm2838

S. K. Jang, H. G. Krausslich, M. J. Nicklin, G. M. Duke, A. C. Palmenberg et al., A segment of the 5' nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation, J. Virol, vol.62, pp.2636-2643, 1988.

J. Pelletier and N. Sonenberg, Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA, Nature, vol.334, issue.6180, pp.320-325, 1988.
DOI : 10.1038/334320a0

V. G. Kolupaeva, I. B. Lomakin, T. V. Pestova, and C. U. Hellen, Eukaryotic Initiation Factors 4G and 4A Mediate Conformational Changes Downstream of the Initiation Codon of the Encephalomyocarditis Virus Internal Ribosomal Entry Site, Molecular and Cellular Biology, vol.23, issue.2, pp.687-698, 2003.
DOI : 10.1128/MCB.23.2.687-698.2003

I. B. Lomakin, C. U. Hellen, and T. V. Pestova, Physical Association of Eukaryotic Initiation Factor 4G (eIF4G) with eIF4A Strongly Enhances Binding of eIF4G to the Internal Ribosomal Entry Site of Encephalomyocarditis Virus and Is Required for Internal Initiation of Translation, Molecular and Cellular Biology, vol.20, issue.16, pp.6019-6029, 2000.
DOI : 10.1128/MCB.20.16.6019-6029.2000

T. V. Pestova, I. N. Shatsky, and C. U. Hellen, Functional dissection of eukaryotic initiation factor 4F: the 4A subunit and the central domain of the 4G subunit are sufficient to mediate internal entry of 43S preinitiation complexes., Molecular and Cellular Biology, vol.16, issue.12, pp.6870-6878, 1996.
DOI : 10.1128/MCB.16.12.6870

T. R. Sweeney, I. S. Abaeva, T. V. Pestova, and C. U. Hellen, The mechanism of translation initiation on Type 1 picornavirus IRESs, The EMBO Journal, vol.80, issue.1, pp.76-92, 2014.
DOI : 10.1002/embj.201386124

S. De-breyne, Y. Yu, A. Unbehaun, T. V. Pestova, and C. U. Hellen, Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites, Proceedings of the National Academy of Sciences, vol.168, issue.2, pp.9197-9202, 2009.
DOI : 10.1128/JVI.01327-06

J. Angulo, N. Ulryck, J. Deforges, N. Chamond, M. Lopez-lastra et al., LOOP IIId of the HCV IRES is essential for the structural rearrangement of the 40S-HCV IRES complex, Nucleic Acids Research, vol.44, issue.3, pp.1309-1325, 2016.
DOI : 10.1093/nar/gkv1325

T. V. Pestova, I. N. Shatsky, S. P. Fletcher, R. J. Jackson, and C. U. Hellen, A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initation of hepatitis C and classical swine fever virus??RNAs, Genes & Development, vol.12, issue.1, pp.67-83, 1998.
DOI : 10.1101/gad.12.1.67

N. Quade, D. Boehringer, M. Leibundgut, J. Van-den-heuvel, and N. Ban, Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-?? resolution, Nature Communications, vol.515, p.7646, 2015.
DOI : 10.1038/nmeth.2727

H. Yamamoto, A. Unbehaun, J. Loerke, E. Behrmann, M. Collier et al., Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV-IRES RNA, Nature Structural & Molecular Biology, vol.483, issue.8, pp.721-727, 2014.
DOI : 10.1093/bioinformatics/bti770

Y. Hashem, A. Des-georges, V. Dhote, R. Langlois, H. Y. Liao et al., Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit, Nature, vol.1, issue.7477, pp.539-543, 2013.
DOI : 10.1038/nature12658

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4106463

D. A. Costantino, J. S. Pfingsten, R. P. Rambo, and J. S. Kieft, tRNA???mRNA mimicry drives translation initiation from a viral IRES, Nature Structural & Molecular Biology, vol.276, issue.1, pp.57-64, 2008.
DOI : 10.1261/rna.7214405

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748805

I. S. Fernandez, X. C. Bai, G. Murshudov, S. H. Scheres, and V. Ramakrishnan, Initiation of Translation by Cricket Paralysis Virus IRES Requires Its Translocation in the Ribosome, Cell, vol.157, issue.4, pp.823-831, 2014.
DOI : 10.1016/j.cell.2014.04.015

C. S. Koh, A. F. Brilot, N. Grigorieff, and A. A. Korostelev, Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center, Proceedings of the National Academy of Sciences, vol.336, issue.6089, pp.9139-9144, 2014.
DOI : 10.1126/science.1220270

J. E. Wilson, T. V. Pestova, C. U. Hellen, and P. Sarnow, Initiation of Protein Synthesis from the A Site of the Ribosome, Cell, vol.102, issue.4, pp.511-520, 2000.
DOI : 10.1016/S0092-8674(00)00055-6

I. S. Abaeva, T. V. Pestova, and C. U. Hellen, Attachment of ribosomal complexes and retrograde scanning during initiation on the Halastavi ??rva virus IRES, Nucleic Acids Research, vol.44, issue.5, pp.2362-2377, 2016.
DOI : 10.1093/nar/gkw016

I. K. Ali, L. Mckendrick, S. J. Morley, and R. J. Jackson, Activity of the Hepatitis A Virus IRES Requires Association between the Cap-Binding Translation Initiation Factor (eIF4E) and eIF4G, Journal of Virology, vol.75, issue.17, pp.7854-7863, 2001.
DOI : 10.1128/JVI.75.17.7854-7863.2001

A. M. Borman, Y. M. Michel, and K. M. Kean, Detailed Analysis of the Requirements of Hepatitis A Virus Internal Ribosome Entry Segment for the Eukaryotic Initiation Factor Complex eIF4F, Journal of Virology, vol.75, issue.17, pp.7864-7871, 2001.
DOI : 10.1128/JVI.75.17.7864-7871.2001

C. J. Caceres, N. Contreras, J. Angulo, J. Vera-otarola, C. Pino-ajenjo et al., Polypyrimidine tract-binding protein binds to the 5??? untranslated region of the mouse mammary tumor virus mRNA and stimulates cap-independent translation initiation, The FEBS Journal, vol.15, issue.10, pp.1880-1901, 2016.
DOI : 10.1111/febs.13708

E. Olivares, D. M. Landry, C. J. Caceres, K. Pino, F. Rossi et al., The 5' Untranslated Region of the Human T-Cell Lymphotropic Virus Type 1 mRNA Enables Cap-Independent Translation Initiation, Journal of Virology, vol.88, issue.11, pp.5936-5955, 2014.
DOI : 10.1128/JVI.00279-14

Z. Othman, M. K. Sulaiman, M. M. Willcocks, N. Ulryck, D. J. Blackbourn et al., Functional analysis of Kaposi's sarcoma???associated herpesvirus vFLIP expression reveals a new mode of IRES-mediated translation, RNA, vol.20, issue.11, pp.1803-1814, 2014.
DOI : 10.1261/rna.045328.114

I. M. Terenin, S. E. Dmitriev, D. E. Andreev, E. Royall, G. J. Belsham et al., A Cross-Kingdom Internal Ribosome Entry Site Reveals a Simplified Mode of Internal Ribosome Entry, Molecular and Cellular Biology, vol.25, issue.17, pp.7879-7888, 2005.
DOI : 10.1128/MCB.25.17.7879-7888.2005

M. Vallejos, P. Ramdohr, F. Valiente-echeverria, K. Tapia, F. E. Rodriguez et al., The 5'-untranslated region of the mouse mammary tumor virus mRNA exhibits cap-independent translation initiation, Nucleic Acids Research, vol.38, issue.2, pp.618-632, 2010.
DOI : 10.1093/nar/gkp890

N. Chamond, J. Deforges, N. Ulryck, and B. Sargueil, 40S recruitment in the absence of eIF4G/4A by EMCV IRES refines the model for translation initiation on the archetype of Type II IRESs, Nucleic Acids Research, vol.42, issue.16, pp.10373-10384, 2014.
DOI : 10.1093/nar/gku720

URL : https://hal.archives-ouvertes.fr/hal-01075147

N. Locker, N. Chamond, and B. Sargueil, A conserved structure within the HIV gag open reading frame that controls translation initiation directly recruits the 40S subunit and eIF3, Nucleic Acids Research, vol.39, issue.6, pp.2367-2377, 2011.
DOI : 10.1093/nar/gkq1118

L. Weill, L. James, N. Ulryck, N. Chamond, C. H. Herbreteau et al., A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA, Nucleic Acids Research, vol.38, issue.4, pp.1367-1381, 2010.
DOI : 10.1093/nar/gkp1109

F. Baudin, R. Marquet, C. Isel, J. L. Darlix, B. Ehresmann et al., Functional Sites in the 5??? Region of Human Immunodeficiency Virus Type 1 RNA Form Defined Structural Domains, Journal of Molecular Biology, vol.229, issue.2, pp.382-397, 1993.
DOI : 10.1006/jmbi.1993.1041

B. Berkhout, Structure and Function of the Human Immunodeficiency Virus Leader RNA, Prog. Nucleic Acid Res. Mol. Biol, vol.54, pp.1-34, 1996.
DOI : 10.1016/S0079-6603(08)60359-1

A. M. Dirac, H. Huthoff, J. Kjems, and B. Berkhout, Regulated HIV-2 RNA dimerization by means of alternative RNA conformations, Nucleic Acids Research, vol.30, issue.12, pp.2647-2655, 2002.
DOI : 10.1093/nar/gkf381

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC117293/pdf

L. James and B. Sargueil, RNA secondary structure of the feline immunodeficiency virus 5???UTR and Gag coding region, Nucleic Acids Research, vol.36, issue.14, pp.4653-4666, 2008.
DOI : 10.1093/nar/gkn447

J. C. Kenyon, A. Ghazawi, W. K. Cheung, P. S. Phillip, T. A. Rizvi et al., The secondary structure of the 5' end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem-loop, RNA, vol.14, issue.12, pp.2597-2608, 2008.
DOI : 10.1261/rna.1284908

S. Guerrero, J. Batisse, C. Libre, S. Bernacchi, R. Marquet et al., HIV-1 Replication and the Cellular Eukaryotic Translation Apparatus, Viruses, vol.267, issue.1, pp.199-218, 2015.
DOI : 10.1038/nsmb.1838

URL : http://doi.org/10.3390/v7010199

N. T. Parkin, E. A. Cohen, A. Darveau, C. Rosen, W. Haseltine et al., Mutational analysis of the 5' non-coding region of human immunodeficiency virus type 1: effects of secondary structure on translation, EMBO J, vol.7, pp.2831-2837, 1988.

R. Soto-rifo, P. S. Rubilar, T. Limousin, S. De-breyne, D. Decimo et al., DEAD-box protein DDX3 associates with eIF4F to promote translation of selected mRNAs, The EMBO Journal, vol.119, issue.18, pp.3745-3756, 2012.
DOI : 10.1038/emboj.2012.220

Y. V. Svitkin, A. Pause, and N. Sonenberg, La autoantigen alleviates translational repression by the 5' leader sequence of the human immunodeficiency virus type 1 mRNA, J. Virol, vol.68, pp.7001-7007, 1994.

S. Pyronnet and N. Sonenberg, Cell-cycle-dependent translational control, Current Opinion in Genetics & Development, vol.11, issue.1, pp.13-18, 2001.
DOI : 10.1016/S0959-437X(00)00150-7

C. Bolinger, A. Sharma, D. Singh, L. Yu, and K. Boris-lawrie, RNA helicase A modulates translation of HIV-1 and infectivity of progeny virions, Nucleic Acids Research, vol.38, issue.5, pp.1686-1696, 2010.
DOI : 10.1093/nar/gkp1075

A. Sharma, A. Yilmaz, K. Marsh, A. Cochrane, and K. Boris-lawrie, Thriving under Stress: Selective Translation of HIV-1 Structural Protein mRNA during Vpr-Mediated Impairment of eIF4E Translation Activity, PLoS Pathogens, vol.7, issue.3, p.1002612, 2012.
DOI : 10.1371/journal.ppat.1002612.s003

R. Amorim, S. M. Costa, N. P. Cavaleiro, E. E. Da-silva, and L. J. Da-costa, HIV-1 Transcripts Use IRES-Initiation under Conditions Where Cap-Dependent Translation Is Restricted by Poliovirus 2A Protease, PLoS ONE, vol.8, issue.2, p.88619, 2014.
DOI : 10.1371/journal.pone.0088619.g008

URL : http://doi.org/10.1371/journal.pone.0088619

A. Brasey, M. Lopez-lastra, T. Ohlmann, N. Beerens, B. Berkhout et al., The Leader of Human Immunodeficiency Virus Type 1 Genomic RNA Harbors an Internal Ribosome Entry Segment That Is Active during the G2/M Phase of the Cell Cycle, Journal of Virology, vol.77, issue.7, pp.3939-3949, 2003.
DOI : 10.1128/JVI.77.7.3939-3949.2003

C. B. Buck, X. Shen, M. A. Egan, T. C. Pierson, C. M. Walker et al., The Human Immunodeficiency Virus Type 1 gag Gene Encodes an Internal Ribosome Entry Site, Journal of Virology, vol.75, issue.1, pp.181-191, 2001.
DOI : 10.1128/JVI.75.1.181-191.2001

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC113911

F. Carvajal, M. Vallejos, B. Walters, N. Contreras, M. I. Hertz et al., Structural domains within the HIV-1 mRNA and the ribosomal protein S25 influence cap-independent translation initiation, The FEBS Journal, vol.50, issue.Suppl 5, pp.2508-2527, 2016.
DOI : 10.1111/febs.13756

A. Monette, F. Valiente-echeverria, M. Rivero, E. A. Cohen, M. Lopez-lastra et al., Dual Mechanisms of Translation Initiation of the Full-Length HIV-1 mRNA Contribute to Gag Synthesis, PLoS ONE, vol.20, issue.7, p.68108, 2013.
DOI : 10.1371/journal.pone.0068108.s001

K. Gendron, G. Ferbeyre, N. Heveker, and L. Brakier-gingras, The activity of the HIV-1 IRES is stimulated by oxidative stress and controlled by a negative regulatory element, Nucleic Acids Research, vol.39, issue.3, pp.902-912, 2011.
DOI : 10.1093/nar/gkq885

T. D. Plank, J. T. Whitehurst, and J. S. Kieft, Cell type specificity and structural determinants of IRES activity from the 5??? leaders of different HIV-1 transcripts, Nucleic Acids Research, vol.41, issue.13, pp.6698-6714, 2013.
DOI : 10.1093/nar/gkt358

M. Vallejos, J. Deforges, T. D. Plank, A. Letelier, P. Ramdohr et al., Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors, Nucleic Acids Research, vol.39, issue.14, pp.6186-6200, 2011.
DOI : 10.1093/nar/gkr189

C. H. Herbreteau, L. Weill, D. Decimo, D. Prevot, J. L. Darlix et al., HIV-2 genomic RNA contains a novel type of IRES located downstream of its initiation codon, Nature Structural & Molecular Biology, vol.6, issue.11, pp.1001-1007, 2005.
DOI : 10.1093/nar/gkh835

N. Chamond, N. Locker, and B. Sargueil, The different pathways of HIV genomic RNA translation, Biochemical Society Transactions, vol.38, issue.6, pp.1548-1552, 2010.
DOI : 10.1042/BST0381548

M. G. Nicholson, S. M. Rue, J. E. Clements, and S. A. Barber, An internal ribosome entry site promotes translation of a novel SIV Pr55Gag isoform, Virology, vol.349, issue.2, pp.325-334, 2006.
DOI : 10.1016/j.virol.2006.01.034

S. De-breyne, N. Chamond, D. Decimo, M. A. Trabaud, P. Andre et al., studies reveal that different modes of initiation on HIV-1 mRNA have different levels of requirement for eukaryotic initiation factor???4F, FEBS Journal, vol.460, issue.17, pp.3098-3111, 2012.
DOI : 10.1111/j.1742-4658.2012.08689.x

URL : https://hal.archives-ouvertes.fr/hal-00965629

C. Daude, D. Decimo, M. A. Trabaud, P. Andre, T. Ohlmann et al., HIV-1 sequences isolated from patients promote expression of shorter isoforms of the Gag polyprotein, Archives of Virology, vol.31, issue.12, pp.3495-3507, 2016.
DOI : 10.1126/science.aad4939

S. De-breyne, R. Soto-rifo, M. Lopez-lastra, and T. Ohlmann, Translation initiation is driven by different mechanisms on the HIV-1 and HIV-2 genomic RNAs, Virus Research, vol.171, issue.2, pp.366-381, 2013.
DOI : 10.1016/j.virusres.2012.10.006

URL : https://hal.archives-ouvertes.fr/hal-00965625

B. Rojas-araya, T. Ohlmann, and R. Soto-rifo, Translational Control of the HIV Unspliced Genomic RNA, Viruses, vol.68, issue.8, pp.4326-4351, 2015.
DOI : 10.1128/JVI.02596-05

G. Miele, A. Mouland, G. P. Harrison, E. Cohen, and A. M. Lever, The human immunodeficiency virus type 1 5' packaging signal structure affects translation but does not function as an internal ribosome entry site structure, J. Virol, vol.70, pp.944-951, 1996.

V. V. Smirnova, I. M. Terenin, A. A. Khutornenko, D. E. Andreev, S. E. Dmitriev et al., Does HIV-1 mRNA 5'-untranslated region bear an internal ribosome entry site?, Biochimie, vol.121, pp.228-237, 2016.
DOI : 10.1016/j.biochi.2015.12.004

A. Yilmaz, C. Bolinger, and K. Boris-lawrie, Retrovirus Translation Initiation: Issues and Hypotheses Derived from Study of HIV-1, Current HIV Research, vol.4, issue.2, pp.131-139, 2006.
DOI : 10.2174/157016206776055039

R. Soto-rifo, E. P. Ricci, D. Decimo, O. Moncorge, and T. Ohlmann, Back to basics: the untreated rabbit reticulocyte lysate as a competitive system to recapitulate cap/poly(A) synergy and the selective advantage of IRES-driven translation, Nucleic Acids Research, vol.35, issue.18, p.121, 2007.
DOI : 10.1093/nar/gkm682

R. Lorenz, S. H. Bernhart, C. Honer-zu-siederdissen, H. Tafer, C. Flamm et al., ViennaRNA Package 2.0, Algorithms for Molecular Biology, vol.6, issue.1, p.26, 2011.
DOI : 10.1016/0005-2795(75)90109-9

URL : http://doi.org/10.1186/1748-7188-6-26

S. Wuchty, W. Fontana, I. L. Hofacker, and P. Schuster, Complete suboptimal folding of RNA and the stability of secondary structures, Biopolymers, vol.4, issue.2, pp.145-165, 1999.
DOI : 10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G

E. J. Merino, K. A. Wilkinson, J. L. Coughlan, and K. M. Weeks, RNA Structure Analysis at Single Nucleotide Resolution by Selective 2???-Hydroxyl Acylation and Primer Extension (SHAPE), Journal of the American Chemical Society, vol.127, issue.12, pp.4223-4231, 2005.
DOI : 10.1021/ja043822v

D. H. Mathews, M. D. Disney, J. L. Childs, S. J. Schroeder, M. Zuker et al., Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proceedings of the National Academy of Sciences, vol.4, issue.9, pp.7287-7292, 2004.
DOI : 10.1017/S1355838298980670

Y. Ding, C. Y. Chan, and C. E. Lawrence, RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble, RNA, vol.11, issue.8, pp.1157-1166, 2005.
DOI : 10.1261/rna.2500605

K. E. Deigan, T. W. Li, D. H. Mathews, and K. M. Weeks, Accurate SHAPE-directed RNA structure determination, Proceedings of the National Academy of Sciences, vol.3, issue.37, pp.97-102, 2009.
DOI : 10.1186/1471-2105-3-2

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629221

K. Wang, J. Zhang, D. Li, X. Zhang, and T. Guo, L??? Optimal control of SISO continuous-time systems, Automatica, vol.33, issue.1, pp.85-115, 2007.
DOI : 10.1016/S0005-1098(96)00126-4

D. Sculley, Web-scale k-means clustering, Proceedings of the 19th international conference on World wide web, WWW '10, p.1177, 2010.
DOI : 10.1145/1772690.1772862

F. Pedregosa, G. Varoquaux, A. Gramfort, V. Michel, B. Thirion et al., Scikit-learn: machine learning in python, JMLR, vol.12, pp.2825-2830, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00650905

Z. J. Lu, J. W. Gloor, and D. H. Mathews, Improved RNA secondary structure prediction by maximizing expected pair accuracy, RNA, vol.15, issue.10, pp.1805-1813, 2009.
DOI : 10.1261/rna.1643609

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743040

M. Mattson and A. Messac, Pareto Frontier Based Concept Selection Under Uncertainty, with Visualization, Optimization and Engineering, vol.6, issue.1, pp.85-115, 2005.
DOI : 10.1023/B:OPTE.0000048538.35456.45

D. Lai, J. R. Proctor, J. Y. Zhu, and I. M. Meyer, R-CHIE: a web server and R package for visualizing RNA secondary structures, Nucleic Acids Research, vol.40, issue.12, p.95, 2012.
DOI : 10.1093/nar/gks241

URL : http://doi.org/10.1093/nar/gks241

L. M. Hellman and M. G. Fried, Electrophoretic mobility shift assay (EMSA) for detecting protein???nucleic acid interactions, Nature Protocols, vol.82, issue.8, pp.1849-1861, 2007.
DOI : 10.1074/jbc.M000266200

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2757439

B. Chesebro, K. Wehrly, J. Nishio, and S. Perryman, Macrophage-tropic human immunodeficiency virus isolates from different patients exhibit unusual V3 envelope sequence homogeneity in comparison with T-cell-tropic isolates: definition of critical amino acids involved in cell tropism, J. Virol, vol.66, pp.6547-6554, 1992.

K. Toohey, K. Wehrly, J. Nishio, S. Perryman, and B. Chesebro, Human Immunodeficiency Virus Envelope V1 and V2 Regions Influence Replication Efficiency in Macrophages by Affecting Virus Spread, Virology, vol.213, issue.1, pp.70-79, 1995.
DOI : 10.1006/viro.1995.1547

URL : http://doi.org/10.1006/viro.1995.1547

K. Wehrly and B. Chesebro, p24 Antigen Capture Assay for Quantification of Human Immunodeficiency Virus Using Readily Available Inexpensive Reagents, Methods, vol.12, issue.4, pp.288-293, 1997.
DOI : 10.1006/meth.1997.0481

H. B. Lowman and D. E. Draper, On the recognition of helical RNA by cobra venom V1 nuclease, J. Biol. Chem, vol.261, pp.5396-5403, 1986.

K. Sobczak, G. Michlewski, M. De-mezer, J. Krol, and W. J. Krzyzosiak, Trinucleotide repeat system for sequence specificity analysis of RNA structure probing reagents, Analytical Biochemistry, vol.402, issue.1, pp.40-46, 2010.
DOI : 10.1016/j.ab.2010.03.021

S. A. Mortimer and K. M. Weeks, A Fast-Acting Reagent for Accurate Analysis of RNA Secondary and Tertiary Structure by SHAPE Chemistry, Journal of the American Chemical Society, vol.129, issue.14, pp.4144-4145, 2007.
DOI : 10.1021/ja0704028

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 Biology, vol.45, issue.4, p.96, 2008.
DOI : 10.1371/journal.pbio.0060096.sg001

URL : http://doi.org/10.1371/journal.pbio.0060096

K. A. Steen, G. M. Rice, and K. M. Weeks, Fingerprinting Noncanonical and Tertiary RNA Structures by Differential SHAPE Reactivity, Journal of the American Chemical Society, vol.134, issue.32, pp.13160-13163, 2012.
DOI : 10.1021/ja304027m

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3425954

B. Foley, T. Leitner, C. Apetrei, B. Hahn, I. Mizrachi et al., Los Alamos National Laboratory, theoretical biology and biophysics, 2016.

S. E. Dmitriev, A. V. Pisarev, M. P. Rubtsova, Y. E. Dunaevsky, and I. N. Shatsky, Conversion of 48S translation preinitiation complexes into 80S initiation complexes as revealed by toeprinting, FEBS Letters, vol.11, issue.1, pp.99-104, 2003.
DOI : 10.1016/S0014-5793(02)03776-6

M. Kozak, Primer extension analysis of eukaryotic ribosome-mRNA complexes, Nucleic Acids Research, vol.26, issue.21, pp.4853-4859, 1998.
DOI : 10.1093/nar/26.21.4853

S. P. Ryder, M. I. Recht, and J. R. Williamson, Quantitative Analysis of Protein-RNA Interactions by Gel Mobility Shift, Methods Mol. Biol, vol.488, pp.99-115, 2008.
DOI : 10.1007/978-1-60327-475-3_7

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928675

M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research, vol.31, issue.13, pp.3406-3415, 2003.
DOI : 10.1093/nar/gkg595

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169194/pdf

Z. Z. Xu and D. H. Mathews, Secondary Structure Prediction of Single Sequences Using RNAstructure, Methods Mol. Biol, vol.12, pp.15-34, 1490.
DOI : 10.1007/978-1-4939-6433-8_2

I. L. Hofacker, RNA secondary structure analysis using the Vienna RNA package, Curr. Protoc. Bioinformatics, 2009.
DOI : 10.1002/0471250953.bi1202s04

J. M. Watts, K. K. Dang, R. J. Gorelick, C. W. Leonard, J. W. Bess et al., Architecture and secondary structure of an entire HIV-1 RNA genome, Nature, vol.14, issue.7256, pp.711-716, 2009.
DOI : 10.1038/nature08237

N. A. Siegfried, S. Busan, G. M. Rice, J. A. Nelson, and K. M. Weeks, RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP), Nature Methods, vol.63, issue.9, pp.959-965, 2014.
DOI : 10.1093/bioinformatics/btr507

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259394

Y. L. Dorokhov, M. V. Skulachev, P. A. Ivanov, S. D. Zvereva, L. G. Tjulkina et al., Polypurine (A)-rich sequences promote cross-kingdom conservation of internal ribosome entry, Proceedings of the National Academy of Sciences, vol.9, issue.5, pp.5301-5306, 2002.
DOI : 10.1105/tpc.9.5.809

W. V. Gilbert, K. Zhou, T. K. Butler, and J. A. Doudna, Cap-Independent Translation Is Required for Starvation-Induced Differentiation in Yeast, Science, vol.144, issue.3, pp.317-1224, 2007.
DOI : 10.1038/sj.onc.1207551

N. E. Shirokikh and A. S. Spirin, Poly(A) leader of eukaryotic mRNA bypasses the dependence of translation on initiation factors, Proceedings of the National Academy of Sciences, vol.430, issue.19, pp.10738-10743, 2008.
DOI : 10.1016/S0076-6879(07)30007-4

B. Berkhout and F. J. Van-hemert, The unusual nucleotide content of the HIV RNA genome results in a biased amino acid composition of HIV proteins, Nucleic Acids Research, vol.22, issue.9, pp.1705-1711, 1994.
DOI : 10.1093/nar/22.9.1705

L. Balvay, M. L. Lastra, B. Sargueil, J. L. Darlix, and T. Ohlmann, Translational control of retroviruses, Nature Reviews Microbiology, vol.15, issue.2, pp.128-140, 2007.
DOI : 10.1083/jcb.108.2.229

URL : https://hal.archives-ouvertes.fr/hal-00136396

E. P. Ricci, R. Soto-rifo, C. H. Herbreteau, D. Decimo, and T. Ohlmann, Lentiviral RNAs can use different mechanisms for translation initiation, Biochemical Society Transactions, vol.36, issue.4, pp.690-693, 2008.
DOI : 10.1042/BST0360690

E. P. Ricci, C. H. Herbreteau, D. Decimo, A. Schaupp, S. A. Datta et al., In vitro expression of the HIV-2 genomic RNA is controlled by three distinct internal ribosome entry segments that are regulated by the HIV protease and the Gag polyprotein, RNA, vol.14, issue.7, pp.1443-1455, 2008.
DOI : 10.1261/rna.813608

R. Soto-rifo, P. S. Rubilar, and T. Ohlmann, The DEAD-box helicase DDX3 substitutes for the cap-binding protein eIF4E to promote compartmentalized translation initiation of the HIV-1 genomic RNA, Nucleic Acids Research, vol.41, issue.12, pp.6286-6299, 2013.
DOI : 10.1093/nar/gkt306

URL : https://hal.archives-ouvertes.fr/hal-00972286

S. Cardinaud, G. Consiglieri, R. Bouziat, A. Urrutia, S. Graff-dubois et al., CTL Escape Mediated by Proteasomal Destruction of an HIV-1 Cryptic Epitope, PLoS Pathogens, vol.108, issue.12, p.1002049, 2011.
DOI : 10.1371/journal.ppat.1002049.s003

URL : https://hal.archives-ouvertes.fr/pasteur-01372493

S. Cardinaud, A. Moris, M. Fevrier, P. S. Rohrlich, L. Weiss et al., Identification of Cryptic MHC I???restricted Epitopes Encoded by HIV-1 Alternative Reading Frames, The Journal of Experimental Medicine, vol.157, issue.8, pp.1053-1063, 2004.
DOI : 10.1126/science.1089553

URL : https://hal.archives-ouvertes.fr/pasteur-01372661