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
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. ,
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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. ,
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
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. ,
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
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
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
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
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
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
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
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
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
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
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
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
The different pathways of HIV genomic RNA translation, Biochemical Society Transactions, vol.38, issue.6, pp.1548-1552, 2010. ,
DOI : 10.1042/BST0381548
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
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
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
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
Translational Control of the HIV Unspliced Genomic RNA, Viruses, vol.68, issue.8, pp.4326-4351, 2015. ,
DOI : 10.1128/JVI.02596-05
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. ,
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
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
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
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
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
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
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
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
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
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
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
Scikit-learn: machine learning in python, JMLR, vol.12, pp.2825-2830, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00650905
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
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
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
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
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. ,
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
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
On the recognition of helical RNA by cobra venom V1 nuclease, J. Biol. Chem, vol.261, pp.5396-5403, 1986. ,
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
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
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
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
Los Alamos National Laboratory, theoretical biology and biophysics, 2016. ,
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
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
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
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
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
RNA secondary structure analysis using the Vienna RNA package, Curr. Protoc. Bioinformatics, 2009. ,
DOI : 10.1002/0471250953.bi1202s04
Architecture and secondary structure of an entire HIV-1 RNA genome, Nature, vol.14, issue.7256, pp.711-716, 2009. ,
DOI : 10.1038/nature08237
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
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
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
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
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
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
Lentiviral RNAs can use different mechanisms for translation initiation, Biochemical Society Transactions, vol.36, issue.4, pp.690-693, 2008. ,
DOI : 10.1042/BST0360690
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
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
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
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