M. A. Havens, D. M. Duelli, and M. L. Hastings, Targeting RNA splicing for disease therapy, Wiley Interdisciplinary Reviews: RNA, vol.120, issue.3, pp.247-266, 2013.
DOI : 10.1182/blood-2012-05-430876
URL : http://onlinelibrary.wiley.com/doi/10.1002/wrna.1158/pdf

Z. Dominski and R. Kole, Restoration of correct splicing in thalassemic premRNA by antisense oligonucleotides, Proc. Natl. Acad. Sci. USA 90, pp.8673-8677, 1993.

A. J. Ward, C. , and T. A. , The pathobiology of splicing, The Journal of Pathology, vol.325, pp.152-163, 2010.
DOI : 10.1016/S1525-1578(10)60533-8

J. H. Chan, S. Lim, and W. S. Wong, ANTISENSE OLIGONUCLEOTIDES: FROM DESIGN TO THERAPEUTIC APPLICATION, Clinical and Experimental Pharmacology and Physiology, vol.97, issue.5-6, pp.533-540, 2006.
DOI : 10.1158/1078-0432.CCR-04-2091
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1440-1681.2006.04403.x/pdf

A. F. Saleh, A. A. Arzumanov, and M. J. Gait, Overview of Alternative Oligonucleotide Chemistries for Exon Skipping, Methods Mol. Biol, vol.867, pp.365-378, 2012.
DOI : 10.1007/978-1-61779-767-5_23

T. Voit, H. Topaloglu, V. Straub, F. Muntoni, N. Deconinck et al., Safety and efficacy of drisapersen for the treatment of Duchenne muscular dystrophy (DEMAND II): an exploratory, randomised, placebo-controlled phase 2 study, The Lancet Neurology, vol.13, issue.10, pp.987-996, 2014.
DOI : 10.1016/S1474-4422(14)70195-4

E. H. Niks and A. Aartsma-rus, Exon skipping: a first in class strategy for Duchenne muscular dystrophy, Expert Opinion on Biological Therapy, vol.21, issue.2, pp.225-236, 2017.
DOI : 10.1097/WCO.0000000000000235

L. Gorman, D. Suter, V. Emerick, D. Schümperli, and R. Kole, Stable alteration of pre-mRNA splicing patterns by modified U7 small nuclear RNAs, Proc. Natl, 1998.
DOI : 10.1007/BF00210743

A. Goyenvalle, A. Vulin, F. Fougerousse, F. Leturcq, J. C. Kaplan et al., Rescue of Dystrophic Muscle Through U7 snRNA-Mediated Exon Skipping, Science, vol.306, issue.5702, pp.1796-1799, 2004.
DOI : 10.1126/science.1104297

M. A. Denti, A. Rosa, G. D-'antona, O. Sthandier, F. G. De-angelis et al., Body-wide gene therapy of Duchenne muscular dystrophy in the mdx mouse model, Proc. Natl, 2006.
DOI : 10.1113/jphysiol.2003.046276

M. B. Asparuhova, G. Marti, S. Liu, F. Serhan, D. Trono et al., Inhibition of HIV-1 multiplication by a modified U7 snRNA inducing Tat and Rev exon skipping, The Journal of Gene Medicine, vol.12, issue.5, pp.323-334, 2007.
DOI : 10.1002/jgm.1027

T. Geib and K. J. Hertel, Restoration of Full-Length SMN Promoted by Adenoviral Vectors Expressing RNA Antisense Oligonucleotides Embedded in U7 snRNAs, PLoS ONE, vol.4, issue.12, p.8204, 2009.
DOI : 10.1371/journal.pone.0008204.g004

C. Gedicke-hornung, V. Behrens-gawlik, S. Reischmann, B. Geertz, D. Stimpel et al., -targeted knock-in mice, EMBO Molecular Medicine, vol.12, issue.7, pp.1128-1145, 2013.
DOI : 10.1002/jgm.1446

T. Kiss, Biogenesis of small nuclear RNPs, Journal of Cell Science, vol.117, issue.25, pp.5949-5951, 2004.
DOI : 10.1242/jcs.01487
URL : https://hal.archives-ouvertes.fr/hal-00022395

K. L. Mowry and J. A. Steitz, Identification of the human U7 snRNP as one of several factors involved in the 3' end maturation of histone premessenger RNA's, Science, vol.238, issue.4834, pp.1682-1687, 1987.
DOI : 10.1126/science.2825355

C. Grimm, B. Stefanovic, and D. Schümperli, The low abundance of U7 snRNA is partly determined by its Sm binding site, EMBO J, vol.12, pp.1229-1238, 1993.

E. Basner-tschakarjan, E. Bijjiga, and A. T. Martino, Pre-Clinical Assessment of Immune Responses to Adeno-Associated Virus (AAV) Vectors, Frontiers in Immunology, vol.5, p.28, 2014.
DOI : 10.3389/fimmu.2014.00028

V. M. Rivera, G. P. Gao, R. L. Grant, M. A. Schnell, P. W. Zoltick et al., Long-term pharmacologically regulated expression of erythropoietin in primates following AAV-mediated gene transfer, Blood, vol.105, issue.4, pp.1424-1430, 2005.
DOI : 10.1182/blood-2004-06-2501

A. C. Nathwani, U. M. Reiss, E. G. Tuddenham, C. Rosales, P. Chowdary et al., Longterm safety and efficacy of factor IX gene therapy in hemophilia B, N. Engl. J. Med, vol.371, 1994.

L. T. Bish, M. M. Sleeper, S. C. Forbes, B. Wang, C. Reynolds et al., Long-term Restoration of Cardiac Dystrophin Expression in Golden Retriever Muscular Dystrophy Following rAAV6-mediated Exon Skipping, Molecular Therapy, vol.20, issue.3, pp.580-589, 2012.
DOI : 10.1038/mt.2011.264

A. Vulin, I. Barthélémy, A. Goyenvalle, J. Thibaud, C. Beley et al., Muscle Function Recovery in Golden Retriever Muscular Dystrophy After AAV1-U7 Exon Skipping, Molecular Therapy, vol.20, issue.11, pp.2120-2133, 2012.
DOI : 10.1038/mt.2012.181

L. Guiner, C. Montus, M. Servais, L. Cherel, Y. Francois et al., Forelimb Treatment in a Large Cohort of Dystrophic Dogs Supports Delivery of a Recombinant AAV for Exon Skipping in Duchenne Patients, Molecular Therapy, vol.22, issue.11, pp.1923-1935, 2014.
DOI : 10.1038/mt.2014.151

J. R. Mendell, C. Shilling, N. D. Leslie, K. M. Flanigan, R. Dahhak et al., Evidence-based path to newborn screening for duchenne muscular dystrophy, Annals of Neurology, vol.10, issue.1, pp.304-313, 2012.
DOI : 10.1093/hmg/10.25.2851

K. Bushby, R. Finkel, D. J. Birnkrant, L. E. Case, P. R. Clemens et al., Diagnosis and management of Duchenne muscular dystrophy, part 1: diagnosis, and pharmacological and psychosocial management, The Lancet Neurology, vol.9, issue.1, pp.77-93, 2010.
DOI : 10.1016/S1474-4422(09)70271-6

E. P. Hoffman, R. H. Brown, . Jr, and L. M. Kunkel, Dystrophin: The protein product of the duchenne muscular dystrophy locus, Cell, vol.51, issue.6, pp.919-928, 1987.
DOI : 10.1016/0092-8674(87)90579-4

L. J. Popplewell, C. Adkin, V. Arechavala-gomeza, A. Aartsma-rus, C. L. De-winter et al., Comparative analysis of antisense oligonucleotide sequences targeting exon 53 of the human DMD gene: Implications for future clinical trials, Neuromuscular Disorders, vol.20, issue.2, pp.102-110, 2010.
DOI : 10.1016/j.nmd.2009.10.013

A. L. Jackson, S. R. Bartz, J. Schelter, S. V. Kobayashi, J. Burchard et al., Expression profiling reveals off-target gene regulation by RNAi, Nature Biotechnology, vol.19, issue.6, pp.635-637, 2003.
DOI : 10.1038/86730

A. Gupta, X. Meng, L. J. Zhu, N. D. Lawson, and S. A. Wolfe, Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases, Nucleic Acids Research, vol.14, issue.1, pp.381-392, 2011.
DOI : 10.1101/gr.849004

Y. Fu, J. A. Foden, C. Khayter, M. L. Maeder, D. Reyon et al., High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells, Nature Biotechnology, vol.31, issue.9, pp.822-826, 2013.
DOI : 10.1021/bi00035a029

C. Mussolino, R. Morbitzer, F. Lütge, N. Dannemann, T. Lahaye et al., A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity, Nucleic Acids Research, vol.150, issue.21, pp.9283-9293, 2011.
DOI : 10.1093/nar/gkr151

S. Obad, C. O. Dos-santos, A. Petri, M. Heidenblad, O. Broom et al., Silencing of microRNA families by seed-targeting tiny LNAs, Nature Genetics, vol.442, issue.4, pp.371-378, 2011.
DOI : 10.1074/mcp.M800029-MCP200

F. Schmid, T. Hiller, G. Korner, E. Glaus, W. Berger et al., A Gene Therapeutic Approach to Correct Splice Defects with Modified U1 and U6 snRNPs, Human Gene Therapy, vol.24, issue.1, pp.97-104, 2013.
DOI : 10.1089/hum.2012.110
URL : http://www.zora.uzh.ch/id/eprint/77022/1/A_gene_therapeutic_approach_to_correct_splice_defects_with_modified_U1_and_U6_snRNPs..pdf

J. C. Chen, O. D. King, Y. Zhang, N. P. Clayton, C. Spencer et al., Morpholino-mediated Knockdown of DUX4 Toward Facioscapulohumeral Muscular Dystrophy Therapeutics, Molecular Therapy, vol.24, issue.8, pp.1405-1411, 2016.
DOI : 10.1038/mt.2016.111

A. Guillouzo, A. Corlu, C. Aninat, D. Glaise, F. Morel et al., The human hepatoma HepaRG cells: A highly differentiated model for studies of liver metabolism and toxicity of xenobiotics, Chemico-Biological Interactions, vol.168, issue.1, pp.66-73, 2007.
DOI : 10.1016/j.cbi.2006.12.003

L. G. Glushakova, M. J. Lisankie, E. B. Eruslanov, C. Ojano-dirain, I. Zolotukhin et al., AAV3-mediated transfer and expression of the pyruvate dehydrogenase E1 alpha subunit gene causes metabolic remodeling and apoptosis of human liver cancer cells, Molecular Genetics and Metabolism, vol.98, issue.3, pp.289-299, 2009.
DOI : 10.1016/j.ymgme.2009.05.010

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.28, issue.1, pp.15-21, 2013.
DOI : 10.1093/bioinformatics/btr712
URL : https://academic.oup.com/bioinformatics/article-pdf/29/1/15/17101697/bts635.pdf

M. I. Love, W. Huber, A. , and S. , Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biology, vol.14, issue.12, p.550, 2014.
DOI : 10.1186/gb-2013-14-4-r36

S. Anders, A. Reyes, and W. Huber, Detecting differential usage of exons from RNA-seq data, Genome Res, vol.22, 2008.

Y. Li, X. Rao, W. W. Mattox, C. I. Amos, and B. Liu, RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq, PLOS ONE, vol.102, issue.45, 2015.
DOI : 10.1371/journal.pone.0136653.s004

A. J. Enright, B. John, U. Gaul, T. Tuschl, C. Sander et al., MicroRNA targets in Drosophila, Genome Biology, vol.5, issue.1, p.1, 2003.
DOI : 10.1186/gb-2003-5-1-r1

Y. Katz, E. T. Wang, J. Silterra, S. Schwartz, B. Wong et al., Sashimi plots: quantitative visualization of RNA sequencing read alignments, 2013.

S. Bar, E. Barnea, Z. Levy, S. Neuman, D. Yaffe et al., A novel product of the Duchenne muscular dystrophy gene which greatly differs from the known isoforms in its structure and tissue distribution, Biochemical Journal, vol.272, issue.2, pp.557-560, 1990.
DOI : 10.1042/bj2720557

X. H. Zhang, C. S. Leslie, C. , and L. A. , Dichotomous splicing signals in exon flanks, Genome Research, vol.15, issue.6, pp.768-779, 2005.
DOI : 10.1101/gr.3217705
URL : http://genome.cshlp.org/content/15/6/768.full.pdf

X. Meng, M. B. Noyes, L. J. Zhu, N. D. Lawson, and S. A. Wolfe, Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases, Nature Biotechnology, vol.14, issue.6, pp.695-701, 2008.
DOI : 10.1038/nbt1398
URL : http://europepmc.org/articles/pmc2502069?pdf=render

J. E. Summerton, Morpholino, siRNA, and S-DNA Compared: Impact of Structure and Mechanism of Action on Off-Target Effects and Sequence Specificity, Current Topics in Medicinal Chemistry, vol.7, issue.7, pp.651-660, 2007.
DOI : 10.2174/156802607780487740

A. Aartsma-rus, D. Winter, C. L. Janson, A. A. Kaman, W. E. Van-ommen et al., Functional Analysis of 114 Exon-Internal AONs for Targeted DMD Exon Skipping: Indication for Steric Hindrance of SR Protein Binding Sites, Oligonucleotides, vol.15, issue.4, pp.284-297, 2005.
DOI : 10.1089/oli.2005.15.284

R. Gabriel, A. Lombardo, A. Arens, J. C. Miller, P. Genovese et al., An unbiased genome-wide analysis of zinc-finger nuclease specificity, Nature Biotechnology, vol.649, issue.9, pp.816-823, 2011.
DOI : 10.1006/jmbi.1990.9999

J. Burchard, A. L. Jackson, V. Malkov, R. H. Needham, Y. Tan et al., MicroRNA-like off-target transcript regulation by siRNAs is species specific, RNA, vol.15, issue.2, pp.308-315, 2009.
DOI : 10.1261/rna.1326809
URL : http://rnajournal.cshlp.org/content/15/2/308.full.pdf

C. Webster and H. M. Blau, Accelerated age-related decline in replicative life-span of Duchenne muscular dystrophy myoblasts: Implications for cell and gene therapy, Somatic Cell and Molecular Genetics, vol.337, issue.6, pp.557-565, 1990.
DOI : 10.1007/BF01233096

A. Aartsma-rus, A. A. Janson, W. E. Kaman, M. Bremmer-bout, J. T. Den-dunnen et al., Therapeutic antisense-induced exon skipping in cultured muscle cells from six different DMD patients, Human Molecular Genetics, vol.12, issue.8, pp.907-914, 2003.
DOI : 10.1093/hmg/ddg100

J. L. Stilwell and R. J. Samulski, Role of Viral Vectors and Virion Shells in Cellular Gene Expression, Molecular Therapy, vol.9, issue.3, pp.337-346, 2004.
DOI : 10.1016/j.ymthe.2003.11.007

A. P. Mccaffrey, P. Fawcett, H. Nakai, R. L. Mccaffrey, A. Ehrhardt et al., The Host Response to Adenovirus, Helper-dependent Adenovirus, and Adeno-associated Virus in Mouse Liver, Molecular Therapy, vol.16, issue.5, pp.931-941, 2008.
DOI : 10.1038/mt.2008.37

O. Snøve, . Jr, and T. Holen, Many commonly used siRNAs risk off-target activity, Biochemical and Biophysical Research Communications, vol.319, issue.1, pp.256-263, 2004.
DOI : 10.1016/j.bbrc.2004.04.175

R. Chandramohan, P. Wu, J. H. Phan, and M. D. Wang, Benchmarking RNA-Seq quantification tools, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp.647-650, 2013.
DOI : 10.1109/EMBC.2013.6609583
URL : http://europepmc.org/articles/pmc5003039?pdf=render

M. Dapas, M. Kandpal, Y. Bi, and R. V. Davuluri, Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms, Briefings in Bioinformatics, vol.142, issue.1, pp.260-269, 2017.
DOI : 10.1093/bioinformatics/btp120

T. Maier, M. Güell, and L. Serrano, Correlation of mRNA and protein in complex biological samples, FEBS Letters, vol.583, issue.24, pp.3966-3973, 2009.
DOI : 10.1016/j.febslet.2009.03.035

T. C. Roberts, H. J. Johansson, G. Mcclorey, C. Godfrey, K. E. Blomberg et al., Multi-level omics analysis in a murine model of dystrophin loss and therapeutic restoration, Human Molecular Genetics, vol.2, issue.23, pp.6756-6768, 2015.
DOI : 10.1093/nar/gkp427

C. Vandamme, O. Adjali, and F. Mingozzi, Unraveling the Complex Story of Immune Responses to AAV Vectors Trial After Trial, Human Gene Therapy, vol.28, issue.11, pp.1061-1074, 2017.
DOI : 10.1089/hum.2017.150

S. Anders, P. T. Pyl, and W. Huber, HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.13, issue.1, pp.166-169, 2015.
DOI : 10.1093/bioinformatics/btp616

M. Noiret, A. Méreau, G. Angrand, M. Bervas, C. Gautier-courteille et al., Robust identification of Ptbp1-dependent splicing events by a junction-centric approach in Xenopus laevis, Developmental Biology, vol.426, issue.2, pp.449-459, 2017.
DOI : 10.1016/j.ydbio.2016.08.021
URL : https://hal.archives-ouvertes.fr/hal-01533247