D. Matsuda and T. W. Dreher, Close spacing of AUG initiation codons confers dicistronic character on a eukaryotic mRNA, RNA, vol.12, pp.1338-1349, 2006.

M. Kozak, The scanning model for translation: an update, J. Cell Biol, vol.108, pp.229-241, 1989.

A. G. Hinnebusch, The scanning mechanism of eukaryotic translation initiation, Annu. Rev. Biochem, vol.83, pp.779-812, 2014.

M. Kozak, How do eucaryotic ribosomes select initiation regions in messenger RNA?, Cell, vol.15, pp.1109-1123, 1978.

M. Kozak, Initiation of translation in prokaryotes and eukaryotes, Gene, vol.234, pp.187-208, 1999.

E. S. Lander, L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody et al., Initial sequencing and analysis of the human genome, Nature, vol.409, pp.860-921, 2001.

M. D. Adams, S. E. Celniker, R. A. Holt, C. A. Evans, J. D. Gocayne et al., The genome sequence of Drosophila melanogaster, Science, vol.287, pp.2185-2195, 2000.

R. A. Gibbs, G. M. Weinstock, M. L. Metzker, D. M. Muzny, E. J. Sodergren et al., Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, vol.428, pp.493-521, 2004.

V. Curwen, E. Eyras, T. D. Andrews, L. Clarke, E. Mongin et al., The Ensembl automatic gene annotation system, Genome Res, vol.14, pp.942-950, 2004.

B. J. Haas, S. L. Salzberg, W. Zhu, M. Pertea, J. E. Allen et al., Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments, Genome Biol, vol.9, pp.7-2008, 2008.

R. Madupu, L. M. Brinkac, J. Harrow, L. G. Wilming, U. Bohme et al., ) Meeting report: a workshop on Best Practices in Genome Annotation. Database (Oxford)., baq001, 2010.

Y. Okazaki, M. Furuno, T. Kasukawa, J. Adachi, H. Bono et al., Analysis of the mouse transcriptome based on functional annotation of 60, 770 full-length cDNAs, Nature, vol.420, pp.563-573, 2002.

E. Birney, M. Clamp, and T. Hubbard, Databases and tools for browsing genomes, Annu. Rev. Genomics Hum. Genet, vol.3, pp.293-310, 2002.

T. Imanishi, T. Itoh, Y. Y. Suzuki, C. O'donovan, S. Fukuchi et al., Integrative annotation of 21, 037 human genes validated by full-length cDNA clones, PLoS Biol, vol.2, p.162, 2004.
URL : https://hal.archives-ouvertes.fr/inria-00099938

M. R. Brent, Genome annotation past, present, and future: how to define an ORF at each locus, Genome Res, vol.15, pp.1777-1786, 2005.

M. Q. Zhang, Computational prediction of eukaryotic protein-coding genes, Nat. Rev, vol.3, pp.698-709, 2002.

C. Mathe, M. F. Sagot, T. Schiex, and P. Rouze, Current methods of gene prediction, their strengths and weaknesses, Nucleic Acids Res, vol.30, pp.4103-4117, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00427288

S. Rogic, A. K. Mackworth, and F. B. Ouellette, Evaluation of gene-finding programs on mammalian sequences, Genome Res, vol.11, pp.817-832, 2001.

M. C. Frith, T. L. Bailey, T. Kasukawa, F. Mignone, S. K. Kummerfeld et al., Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA RIB, RNA Biol, vol.3, pp.40-48, 2006.

M. Yandell and D. Ence, A beginner's guide to eukaryotic genome annotation, Nat. Rev, vol.13, pp.329-342, 2012.

M. R. Brent, How does eukaryotic gene prediction work?, Nat. Biotechnol, vol.25, pp.883-885, 2007.

I. Dunham, N. Shimizu, B. A. Roe, S. Chissoe, A. R. Hunt et al., The DNA sequence of human chromosome 22, Nature, vol.402, pp.489-495, 1999.

A. A. Salamov and V. V. Solovyev, Ab initio gene finding in Drosophila genomic DNA, Genome Res, vol.10, pp.516-522, 2000.

W. H. Majoros, M. Pertea, and S. L. Salzberg, TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders, 2004.

, Bioinformatics, vol.20, pp.2878-2879

T. Yada, T. Takagi, Y. Totoki, Y. Sakaki, and Y. Takaeda, Digit: a Novel Gene Finding Program By Combining Gene-Finders, 2003.

. Biocomput, -Proc. Pacific Symp, vol.8, pp.375-387, 2003.

X. J. Min, G. Butler, R. Storms, and A. Tsang, OrfPredictor: predicting protein-coding regions in EST-derived sequences, Nucleic Acids Res, vol.33, pp.677-680, 2005.

A. G. Hatzigeorgiou, P. Fiziev, and M. Reczko, DIANA-EST: a statistical analysis, Bioinformatics, vol.17, pp.913-919, 2001.

M. Furuno, T. Kasukawa, R. Saito, J. Adachi, H. Suzuki et al., CDS annotation in full-length cDNA sequence, Genome Res, vol.13, pp.1478-1487, 2003.

C. Iseli, C. V. Jongeneel, P. Bucher, and V. Jongeneel, ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences, Proc Int Conf Intell Syst Mol Biol, vol.1999, pp.138-148, 1999.

Y. Fukunishi and Y. Hayashizaki, Amino acid translation program for full-length cDNA sequences with frameshift errors, Physiol. Genomics, vol.5, pp.81-87, 2001.

T. Ota, Y. Suzuki, T. Nishikawa, T. Otsuki, T. Sugiyama et al., Complete sequencing and characterization of 21, 243 full-length human cDNAs, Nat. Genet, vol.36, pp.40-45, 2004.

M. F. Lin, I. Jungreis, and M. Kellis, PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions, Bioinformatics, vol.27, pp.275-282, 2011.

S. J. Andrews and J. Rothnagel, Emerging evidence for functional peptides encoded by short open reading frames, Nat. Rev. Genet, vol.15, pp.193-204, 2014.

K. S. Ramamurthi and G. Storz, The small protein floodgates are opening; now the functional analysis begins, BMC Biol, vol.12, p.96, 2014.

S. C. Chng, L. Ho, J. Tian, and B. Reversade, ELABELA: a hormone essential for heart development signals via the apelin receptor, Dev. Cell, vol.27, pp.672-680, 2013.

D. Thierry-mieg and J. Thierry-mieg, AceView: a comprehensive cDNA-supported gene and transcripts annotation, 2006.

, Genome Biol, vol.7, pp.12-14

J. Harrow, A. Frankish, J. M. Gonzalez, E. Tapanari, M. Diekhans et al., GENCODE: the reference human genome annotation for the ENCODE project, Genome Res, vol.22, pp.1760-1774, 2012.

K. D. Pruitt, G. R. Brown, S. M. Hiatt, F. Thibaud-nissen, A. Astashyn et al., RefSeq: an update on mammalian reference sequences, Nucleic Acids Res, vol.42, pp.756-763, 2014.

F. Cunningham, M. R. Amode, D. Barrell, K. Beal, K. Billis et al., Nucleic Acids Res, vol.43, pp.662-669, 2014.

J. L. Harrow, C. A. Steward, A. Frankish, J. G. Gilbert, J. M. Gonzalez et al., The vertebrate genome annotation browser 10 years on, Nucleic Acids Res, vol.42, pp.771-779, 2014.

C. M. Farrell, N. A. O'leary, R. Harte, J. E. Loveland, L. G. Wilming et al., , 2020.

, Nucleic Acids Research, vol.44, issue.1, p.21, 2016.

B. Aken, Current status and new features of the Consensus Coding Sequence database, Nucleic Acids Res, vol.42, pp.865-872, 2014.

K. Wethmar, A. Barbosa-silva, M. A. Andrade-navarro, and A. Leutz, uORFdb-a comprehensive literature database on eukaryotic uORF biology, Nucleic Acids Res, vol.42, pp.60-67, 2014.

S. E. Calvo, D. J. Pagliarini, and V. K. Mootha, Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans, Proc. Natl. Acad. Sci. U.S.A, vol.106, pp.7507-7512, 2009.

K. Wethmar, The regulatory potential of upstream open reading frames in eukaryotic gene expression, Wiley Interdiscip. Rev. RNA, vol.5, pp.765-778

M. Klemke, R. H. Kehlenbach, and W. B. Huttner, Two overlapping reading frames in a single exon encode interacting proteins -A novel way of gene usage, EMBO J, vol.20, pp.3849-3860, 2001.

K. J. Autio, A. J. Kastaniotis, H. Pospiech, I. J. Miinalainen, M. S. Schonauer et al., An ancient genetic link between vertebrate mitochondrial fatty acid synthesis and RNA processing, FASEB J, vol.22, pp.569-578, 2008.

N. T. Ingolia, G. A. Brar, N. Stern-ginossar, M. S. Harris, G. J. Talhouarne et al., Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes, Cell Rep, vol.8, pp.1365-1379, 2014.

N. T. Ingolia, L. F. Lareau, and J. S. Weissman, Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes, Cell, vol.147, pp.789-802, 2011.

J. Ruiz-orera and X. Messeguer, Long non-coding RNAs as a source of new peptides, p.3523, 2014.

D. M. Anderson, K. M. Anderson, C. Chang, C. A. Makarewich, B. R. Nelson et al., A micropeptide encoded by a putative long noncoding RNA regulates muscle performance, Cell, vol.160, pp.595-606, 2015.

A. Bazzini, T. G. Johnstone, R. Christiano, S. D. Mackowiak, B. Obermayer et al., Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation, EMBO J, vol.33, pp.981-993, 2014.

S. D. Mackowiak, H. Zauber, C. Bielow, D. Thiel, K. Kutz et al., Extensive identification and analysis of conserved small ORFs in animals, Genome Biol, vol.16, p.179, 2015.

A. Pauli, M. L. Norris, E. Valen, G. Chew, J. A. Gagnon et al., Toddler: an embryonic signal that promotes cell movement via apelin receptors, Science, p.1248636, 2014.

H. Yoshida, T. Matsui, A. Yamamoto, T. Okada, and K. Mori, XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor, Cell, vol.107, pp.881-891, 2001.

D. E. Quelle, F. Zindy, R. A. Ashmun, and C. J. Sherr, Alternative reading frames of the INK4a tumor suppressor gene encode two unrelated proteins capable of inducing cell cycle arrest, Cell, vol.83, pp.993-1000, 1995.

W. Chung, S. Wadhawan, R. Szklarczyk, S. K. Pond, and A. Nekrutenko, A first look at ARFome: dual-coding genes in mammalian genomes, PLoS Comput. Biol, vol.3, p.91, 2007.

S. Ribrioux, A. Brüngger, B. Baumgarten, K. Seuwen, and M. R. John, Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts, BMC Genomics, vol.9, p.122, 2008.

H. Xu, P. Wang, Y. Fu, Y. Zheng, Q. Tang et al., Length of the ORF, position of the first AUG and the Kozak motif are important factors in potential dual-coding transcripts, Cell Res, vol.20, pp.445-457, 2010.

B. Vanderperre, J. Lucier, and X. Roucou, HAltORF: a database of predicted out-of-frame alternative open reading frames in human, Database (Oxford), p.25, 2012.

B. Vanderperre, J. Lucier, C. Bissonnette, J. Motard, G. Tremblay et al., Direct detection of alternative open reading frames translation products in human significantly expands the proteome, PLoS One, vol.8, p.70698, 2013.

A. Skarshewski, M. Stanton-cook, T. Huber, S. Al-mansoori, R. Smith et al., uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation, BMC Bioinformatics, p.36, 2014.

S. Lee, B. Liu, S. Lee, S. Huang, B. Shen et al., Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution, Proc. Natl. Acad. Sci. U.S.A, vol.109, pp.2424-2432, 2012.

C. Fritsch, A. Herrmann, M. Nothnagel, K. Szafranski, K. Huse et al., Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting, 2012.

, Genome Res, vol.22, pp.2208-2218

I. P. Ivanov, A. E. Firth, A. M. Michel, J. F. Atkins, and P. V. Baranov, Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences, Nucleic Acids Res, vol.39, pp.4220-4234, 2011.

I. Bab, E. Smith, H. Gavish, M. Attar-namdar, M. Chorev et al., Biosynthesis of osteogenic growth peptide via alternative translational initiation at AUG85 of histone H4 mRNA, J. Biol. Chem, vol.274, pp.14474-14481, 1999.

J. Abramowitz, D. Grenet, M. Birnbaumer, H. N. Torres, and L. Birnbaumer, XLalphas, the extra-long form of the alpha-subunit of the Gs G protein, is significantly longer than suspected, and so is its companion Alex, Proc. Natl. Acad. Sci. U.S.A, vol.101, pp.8366-8371, 2004.

B. Vanderperre, A. B. Staskevicius, G. Tremblay, M. Mccoy, M. A. O'neill et al., An overlapping reading frame in the PRNP gene encodes a novel polypeptide distinct from the prion protein, FASEB J, vol.25, pp.2373-2386, 2011.

D. Bergeron, C. Lapointe, C. Bissonnette, G. Tremblay, J. Motard et al., An out-of-frame overlapping reading frame in the ataxin-1 coding sequence encodes a novel ataxin-1 interacting protein, J. Biol. Chem, vol.288, pp.21824-21835, 2013.

C. Lee, H. Lai, Y. Lee, C. Chien, and Y. Chern, The A2A Adenosine Receptor Is a Dual Coding Gene: A novel mechanism of gene usage and signal transduction, J. Biol. Chem, vol.289, pp.1257-1270, 2014.

C. Akimoto, E. Sakashita, K. Kasashima, K. Kuroiwa, K. Tominaga et al., Translational repression of the McKusick-Kaufman syndrome transcript by unique upstream open reading frames encoding mitochondrial proteins with alternative polyadenylation sites, Biochim. Biophys. Acta -Gen. Subj, vol.1830, pp.2728-2738, 2013.

G. Yosten, J. Liu, H. Ji, K. Sandberg, R. Speth et al., A 5 -Upstream short open reading frame encoded peptide regulates angiotensin type 1a receptor production and signaling via the beta-arrestin pathway, J. Physiol, 2015.

K. Freson, J. Jaeken, M. Van-helvoirt, F. De-zegher, C. Wittevrongel et al., Functional polymorphisms in the paternally expressed XLalphas and its cofactor ALEX decrease their mutual interaction and enhance receptor-mediated cAMP formation, Hum. Mol. Genet, vol.12, pp.1121-1130, 2003.

R. F. Wang, S. L. Johnston, G. Zeng, S. L. Topalian, D. J. Schwartzentruber et al., A breast and melanoma-shared tumor antigen: T cell responses to antigenic peptides translated from different open reading frames, J. Immunol, vol.161, pp.3598-3606, 1998.

R. F. Wang, M. R. Parkhurst, Y. Kawakami, P. F. Robbins, and S. A. Rosenberg, Utilization of an alternative open reading frame of a normal gene in generating a novel human cancer antigen, J. Exp. Med, vol.183, pp.1131-1140, 1996.

C. Ronsin, V. Chung-scott, I. Poullion, N. Aknouche, C. Gaudin et al., A non-AUG-defined alternative open reading frame of the intestinal carboxyl esterase mRNA generates an epitope recognized by renal cell carcinoma-reactive tumor-infiltrating lymphocytes in situ, J. Immunol, vol.163, pp.483-490, 1999.

S. A. Rosenberg, P. Tong-on, Y. Li, J. P. Riley, M. El-gamil et al., Identification of BING-4 cancer antigen translated from an alternative open reading frame of a gene in the extended MHC class II region using lymphocytes from a patient with a durable complete regression following immunotherapy, J. Immunol, vol.168, pp.2402-2407, 2002.

S. Oh, M. Terabe, C. D. Pendleton, A. Bhattacharyya, T. K. Bera et al., Human CTLs to wild-type and enhanced epitopes of a novel prostate and breast tumor-associated protein, TARP, lyse human breast cancer cells, Cancer Res, vol.64, pp.2610-2618, 2004.

E. H. Slager, M. Borghi, C. E. Van-der-minne, C. A. Aarnoudse, M. J. Havenga et al., CD4+ Th2 cell recognition of HLA-DR-restricted epitopes derived from CAMEL: a tumor antigen translated in an alternative open reading frame, J. Immunol, vol.170, pp.1490-1497, 2003.

M. Magrane and U. Consortium, UniProt Knowledgebase: a hub of integrated protein data, Database, p.9, 2011.

M. Oyama, C. Itagaki, H. Hata, Y. Suzuki, T. Izumi et al., Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs, 2004.

, Genome Res, vol.14, pp.2048-2052

S. A. Slavoff, A. J. Mitchell, A. G. Schwaid, M. N. Cabili, J. Ma et al., Peptidomic discovery of short open reading frame-encoded peptides in human cells, Nat. Chem. Biol, vol.9, pp.59-64, 2013.

J. Ma, C. C. Ward, I. Jungreis, S. A. Slavoff, A. G. Schwaid et al., Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue, J. Proteome Res, vol.13, pp.1757-1765, 2014.

N. T. Ingolia, S. Ghaemmaghami, J. R. Newman, and J. S. Weissman, Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling, Science, vol.324, pp.218-223, 2009.

N. T. Ingolia, Ribosome profiling: new views of translation, from single codons to genome scale, Nat. Rev. Genet, vol.15, pp.205-213, 2014.

G. A. Brar and J. S. Weissman, Ribosome profiling reveals the what, when, where and how of protein synthesis, Nat. Rev. Mol. Cell Biol, vol.16, pp.651-664, 2015.

A. M. Michel and P. V. Baranov, Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale, Wiley Interdiscip. Rev. RNA, vol.4, pp.473-490, 2013.

E. De-klerk, I. F. Fokkema, K. A. Thiadens, J. J. Goeman, M. Palmblad et al., Assessing the translational landscape of myogenic differentiation by ribosome profiling, Nucleic Acids Res, vol.43, pp.4408-4428, 2015.

G. A. Brar, M. Yassour, N. Friedman, A. Regev, N. T. Ingolia et al., High-resolution view of the yeast meiotic program revealed by ribosome profiling, Science, vol.335, pp.552-557, 2012.

D. E. Andreev, P. B. O'connor, A. V. Zhdanov, R. I. Dmitriev, I. N. Shatsky et al., Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes, Genome Biol, vol.16, p.90, 2015.

X. Gao, J. Wan, B. Liu, M. Ma, B. Shen et al., Quantitative profiling of initiating ribosomes in vivo, Nat. Methods, vol.12, pp.147-153, 2015.

J. L. Aspden, Y. C. Eyre-walker, R. J. Philips, U. Amin, M. A. Mumtaz et al., Extensive translation of small ORFs revealed by Poly-Ribo-Seq, 2014.

A. M. Michel, K. R. Choudhury, A. E. Firth, N. T. Ingolia, J. F. Atkins et al., Observation of dually decoded regions of the human genome using ribosome profiling data, 2012.

, Genome Res, vol.22, pp.2219-2229

A. M. Michel, G. Fox, A. Kiran, C. De-bo, P. B. O'connor et al., GWIPS-viz: development of a ribo-seq genome browser, Nucleic Acids Res, vol.42, pp.859-864, 2014.

J. Wan and S. B. Qian, TISdb: A database for alternative translation initiation in mammalian cells, Nucleic Acids Res, vol.42, pp.845-850, 2014.

J. Crappé, E. Ndah, A. Koch, S. Steyaert, D. Gawron et al., PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration, Nucleic Acids Res, vol.43, p.29, 2014.

S. Xie, P. Nie, Y. Wang, H. Wang, H. Li et al., RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling, Nucleic Acids Res, 2015.

T. P. Miettinen and M. Björklund, Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3 untranslated regions, Nucleic Acids Res, vol.43, pp.1019-1034, 2015.

D. J. Young, N. R. Guydosh, F. Zhang, A. G. Hinnebusch, and R. Green, Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3 UTRs In Vivo, vol.162, pp.872-884, 2015.

M. Kozak, An analysis of vertebrate mRNA sequences: intimations of translational control, J. Cell Biol, vol.115, pp.887-903, 1991.

M. Kozak, Pushing the limits of the scanning mechanism for initiation of translation, Gene, vol.299, pp.1-34, 2002.

T. A. Pöyry, A. Kaminski, E. J. Connell, C. S. Fraser, and R. J. Jackson, The mechanism of an exceptional case of reinitiation after translation of a long ORF reveals why such events do not generally occur in mammalian mRNA translation, Genes Dev, vol.21, pp.3149-3162, 2007.

M. A. Skabkin, O. V. Skabkina, C. T. Hellen, and T. V. Pestova, Reinitiation and other unconventional posttermination events during eukaryotic translation, Mol. Cell, vol.51, pp.249-264, 2013.

T. A. Pöyry, A. Kaminski, and R. J. Jackson, What determines whether mammalian ribosomes resume scanning after translation of a short upstream open reading frame?, Genes Dev, vol.18, pp.62-75, 2004.

M. Kozak, Constraints on reinitiation of translation in mammals, Nucleic Acids Res, vol.29, pp.5226-5232, 2001.

B. G. Luukkonen, W. Tan, and S. Schwartz, Efficiency of reinitiation of translation on human immunodeficiency virus type 1 mRNAs is determined by the length of the upstream open reading frame and by intercistronic distance, J. Virol, vol.69, pp.4086-4094, 1995.

S. Schleich, K. Strassburger, P. C. Janiesch, T. Koledachkina, K. K. Miller et al., DENR-MCT-1 promotes translation re-initiation downstream of uORFs to control tissue growth, Nature, vol.512, pp.208-212, 2014.

M. Kim, S. M. Pinto, D. Getnet, R. S. Nirujogi, S. S. Manda et al., A draft map of the human proteome, Nature, vol.509, pp.575-581, 2014.

D. E. Andreev, P. B. O'connor, C. Fahey, E. M. Kenny, I. M. Terenin et al., Translation of 5 leaders is pervasive in genes resistant to eIF2 repression, p.3971, 2015.

E. Smith, T. E. Meyerrose, T. Kohler, M. Namdar-attar, N. Bab et al., Leaky ribosomal scanning in mammalian genomes: significance of histone H4 alternative translation in vivo, Nucleic Acids Res, vol.33, pp.1298-1308, 2005.

A. E. Firth and I. Brierley, Non-canonical translation in RNA viruses, J. Gen. Virol, vol.93, pp.1385-1409, 2012.

T. Racine and R. Duncan, Facilitated leaky scanning and atypical ribosome shunting direct downstream translation initiation on the tricistronic S1 mRNA of avian reovirus, Nucleic Acids Res, vol.38, pp.7260-7272, 2010.

S. Guerrero, J. Batisse, C. Libre, S. Bernacchi, R. Marquet et al., HIV-1 replication and the cellular eukaryotic translation apparatus, Viruses, vol.7, pp.199-218, 2015.

K. D. Fitzgerald and B. L. Semler, Bridging IRES elements in mRNAs to the eukaryotic translation apparatus, Biochim. Biophys. Acta, vol.1789, pp.518-528, 2009.

M. Kozak, A second look at cellular mRNA sequences said to function as internal ribosome entry sites, Nucleic Acids Res, vol.33, pp.6593-6602, 2005.

R. J. Jackson, The Current Status of Vertebrate Cellular mRNA IRESs, Cold Spring Harb. Perspect. Biol, vol.5, p.11569, 2013.

W. V. Gilbert, Alternative ways to think about cellular internal ribosome entry, J. Biol. Chem, vol.285, pp.29033-29038, 2010.

A. Yueh and R. J. Schneider, Translation by ribosome shunting on adenovirus and hsp70 mRNAs facilitated by complementarity to 18S rRNA, Genes Dev, vol.14, pp.414-421, 2000.

, Nucleic Acids Research, vol.44, issue.1, p.23, 2016.

K. W. Sherrill and R. E. Lloyd, Translation of cIAP2 mRNA is mediated exclusively by a stress-modulated ribosome shunt, Mol. Cell. Biol, vol.28, pp.2011-2022, 2008.

M. I. Hertz, D. M. Landry, A. E. Willis, G. Luo, and S. R. Thompson, Ribosomal protein S25 dependency reveals a common mechanism for diverse internal ribosome entry sites and ribosome shunting, Mol. Cell. Biol, vol.33, pp.1016-1026, 2013.

X. Wang and J. A. Rothnagel, 5 -untranslated regions with multiple upstream AUG codons can support low-level translation via leaky scanning and reinitiation, Nucleic Acids Res, vol.32, pp.1382-1391, 2004.

S. Lee, Expression of growth/differentiation factor 1 in the nervous system: conservation of a bicistronic structure, Proc. Natl. Acad. Sci. U.S.A, vol.88, pp.4250-4254, 1991.

T. Gray, S. Saitoh, and R. D. Nicholls, An imprinted, mammalian bicistronic transcript encodes two independent proteins, Proc. Natl. Acad. Sci. U.S.A, vol.96, pp.5616-5621, 1999.

Y. Kanamori, Y. Hayakawa, H. Matsumoto, Y. Yasukochi, S. Shimura et al., A eukaryotic (insect) tricistronic mRNA encodes three proteins selected by context-dependent scanning, J. Biol. Chem, vol.285, pp.36933-36944, 2010.

T. Kondo, Y. Hashimoto, K. Kato, S. Inagaki, S. Hayashi et al., Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA, Nat. Cell Biol, vol.9, pp.660-665, 2007.

J. Savard, H. Marques-souza, M. Aranda, and D. Tautz, A segmentation gene in tribolium produces a polycistronic mRNA that codes for multiple conserved peptides, Cell, vol.126, pp.559-569, 2006.

M. I. Galindo, J. I. Pueyo, S. Fouix, S. A. Bishop, and J. P. Couso, Peptides encoded by short ORFs control development and define a new eukaryotic gene family, PLoS Biol, vol.5, p.106, 2007.

S. A. Chappell, G. M. Edelman, and V. P. Mauro, Ribosomal tethering and clustering as mechanisms for translation initiation, Proc. Natl. Acad. Sci. U.S.A, vol.103, pp.18077-18082, 2006.

F. Martin, S. Barends, S. Jaeger, L. Schaeffer, L. Prongidi-fix et al., Cap-Assisted Internal Initiation of Translation of Histone H4, Mol. Cell, vol.41, pp.197-209, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00561405

K. Y. Paek, K. Y. Hong, I. Ryu, S. M. Park, S. J. Keum et al., Translation initiation mediated by RNA looping, Proc. Natl. Acad. Sci. U.S.A, vol.112, pp.1041-1046, 2015.

C. Li, K. Goudy, M. Hirsch, A. Asokan, Y. Fan et al., Cellular immune response to cryptic epitopes during therapeutic gene transfer, Proc. Natl. Acad. Sci. U.S.A, vol.106, pp.10770-10774, 2009.

R. C. Hunt, V. L. Simhadri, M. Iandoli, Z. E. Sauna, and C. Kimchi-sarfaty, Exposing synonymous mutations, Trends Genet, vol.30, pp.308-321, 2014.

A. V. Kochetov, Alternative translation start sites and hidden coding potential of eukaryotic mRNAs, BioEssays, vol.30, pp.683-691, 2008.

C. R. Landry, X. Zhong, L. Nielly-thibault, and X. Roucou, Found in translation: functions and evolution of a recently discovered alternative proteome, Curr. Opin. Struct. Biol, vol.32, pp.74-80, 2015.

A. Koch, D. Gawron, S. Steyaert, E. Ndah, J. Crappé et al., A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites, Proteomics, vol.14, pp.2688-2698, 2014.

T. Gaj, C. A. Gersbach, and C. F. Barbas, ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering, Trends Biotechnol, vol.31, pp.397-405, 2013.

N. Stern-ginossar, B. Weisburd, A. Michalski, V. T. Le, M. Y. Hein et al., Decoding human cytomegalovirus, Science, vol.338, pp.1088-1093, 2012.