L. Klein, B. Kyewski, P. Allen, and K. Hogquist, Positive and negative selection of the T cell repertoire: what thymocytes see (and don't see), Nature Reviews Immunology, vol.12, issue.6, pp.377-91, 2014.
DOI : 10.1002/eji.200737982

J. Derbinski, A. Schulte, B. Kyewski, and L. Klein, Promiscuous gene expression in medullary thymic epithelial cells mirrors the peripheral self, Nature Immunology, vol.25, issue.11, pp.1032-1041, 2001.
DOI : 10.1038/ni723

M. Anderson, E. Venanzi, L. Klein, Z. Chen, S. Berzins et al., Projection of an Immunological Self Shadow Within the Thymus by the Aire Protein, Science, vol.298, issue.5597, pp.1395-401, 2002.
DOI : 10.1126/science.1075958

P. Peterson, T. Org, and A. Rebane, Transcriptional regulation by AIRE: molecular mechanisms of central tolerance, Nature Reviews Immunology, vol.8, issue.12, pp.948-57, 2008.
DOI : 10.1038/nri2450

K. Nagamine, P. Peterson, H. Scott, J. Kudoh, S. Minoshima et al., Positional cloning of the APECED gene, Nature Genetics, vol.7, issue.4, pp.393-401, 1997.
DOI : 10.1016/0092-8674(94)90331-X

B. Graveley, Alternative splicing: increasing diversity in the proteomic world, Trends in Genetics, vol.17, issue.2, pp.100-107, 2001.
DOI : 10.1016/S0168-9525(00)02176-4

J. Rosenthal, The emerging role of RNA editing in plasticity, Journal of Experimental Biology, vol.218, issue.12, pp.1812-1833, 2015.
DOI : 10.1242/jeb.119065

Q. Pan, O. Shai, L. Lee, B. Frey, and B. Blencowe, Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing, Nature Genetics, vol.76, issue.12, pp.1413-1418, 2008.
DOI : 10.1016/j.molcel.2004.12.004

E. Wang, R. Sandberg, S. Luo, I. Khrebtukova, L. Zhang et al., Alternative isoform regulation in human tissue transcriptomes, Nature, vol.15, issue.7221, pp.470-476, 2008.
DOI : 10.1038/nature07509

T. Nilsen and B. Graveley, Expansion of the eukaryotic proteome by alternative splicing, Nature, vol.114, issue.7280, pp.457-63, 2010.
DOI : 10.1038/nature08909

S. Stamm, S. Ben-ari, I. Rafalska, Y. Tang, Z. Zhang et al., Function of alternative splicing, Gene, vol.344, pp.1-20, 2005.
DOI : 10.1016/j.gene.2004.10.022

O. Kelemen, P. Convertini, Z. Zhang, Y. Wen, M. Shen et al., Function of alternative splicing, Gene, vol.514, issue.1, pp.1-30, 2013.
DOI : 10.1016/j.gene.2012.07.083

E. Kim, A. Goren, and G. Ast, Alternative splicing: current perspectives, BioEssays, vol.33, issue.1, pp.38-47, 2008.
DOI : 10.1002/bies.20692

K. Nishikura, Functions and Regulation of RNA Editing by ADAR Deaminases, Annual Review of Biochemistry, vol.79, issue.1, pp.321-370, 2010.
DOI : 10.1146/annurev-biochem-060208-105251

Y. Savva, L. Rieder, and R. Reenan, The ADAR protein family, Genome Biology, vol.13, issue.12, p.252, 2012.
DOI : 10.1126/science.1169957

H. Porath, S. Carmi, and E. Levanon, A genome-wide map of hyper-edited RNA reveals numerous new sites, Nature Communications, vol.132, p.4726, 2014.
DOI : 10.1093/nar/gkg595

C. Burns, H. Chu, S. Rueter, L. Hutchinson, H. Canton et al., Regulation of serotonin-2C receptor G-protein coupling by RNA editing, Nature, vol.387, issue.6630, pp.303-311, 1997.
DOI : 10.1038/387303a0

G. Ramaswami and J. Li, RADAR: a rigorously annotated database of A-to-I RNA editing, Nucleic Acids Research, vol.42, issue.D1, pp.109-122, 2014.
DOI : 10.1093/nar/gkt996

P. Danecek, C. Nellåker, R. Mcintyre, J. Buendia-buendia, S. Bumpstead et al., High levels of RNA-editing site conservation amongst 15 laboratory mouse strains, Genome Biology, vol.13, issue.4, p.26, 2012.
DOI : 10.1186/gb-2012-13-4-r26

L. Bazak, A. Haviv, M. Barak, J. Jacob-hirsch, P. Deng et al., A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes, Genome Research, vol.24, issue.3, pp.365-76, 2014.
DOI : 10.1101/gr.164749.113

O. Connell, M. Keller, and W. , Purification and properties of double-stranded RNAspecific adenosine deaminase from calf thymus, Cell Biol, vol.91, pp.105-10600, 1994.

H. Smith, R. Bennett, A. Kizilyer, W. Mcdougall, and K. Prohaska, Functions and regulation of the APOBEC family of proteins, Seminars in Cell & Developmental Biology, vol.23, issue.3, pp.258-68, 2012.
DOI : 10.1016/j.semcdb.2011.10.004

V. Blanc and N. Davidson, APOBEC-1-mediated RNA editing, Wiley Interdisciplinary Reviews: Systems Biology and Medicine, vol.282, issue.Pt 5, pp.594-602, 2010.
DOI : 10.1002/wsbm.82

L. Powell, S. Wallis, R. Pease, Y. Edwards, T. Knott et al., A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine, Cell, vol.50, issue.6, pp.831-871, 1987.
DOI : 10.1016/0092-8674(87)90510-1

S. Chen, G. Habib, C. Yang, Z. Gu, B. Lee et al., Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon, Science, vol.238, issue.4825, pp.363-369, 1987.
DOI : 10.1126/science.3659919

S. Sharma, S. Patnaik, R. Taggart, E. Kannisto, S. Enriquez et al., APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages, Nature Communications, vol.45, p.6881, 2015.
DOI : 10.1038/ncomms7881

V. Blanc, E. Park, S. Schaefer, M. Miller, Y. Lin et al., Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver, Genome Biology, vol.15, issue.6, p.79, 2014.
DOI : 10.1186/gb-2014-15-6-r79

B. Rosenberg, C. Hamilton, M. Mwangi, S. Dewell, and F. Papavasiliou, Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3??? UTRs, Nature Structural & Molecular Biology, vol.2, issue.2, pp.230-236, 2011.
DOI : 10.1038/nsmb.1975

B. Kyewski and J. Derbinski, Self-representation in the thymus: an extended view, Nature Reviews Immunology, vol.6, issue.9, pp.688-98, 2004.
DOI : 10.1046/j.1523-1747.2003.12413.x

A. Anderson, L. Nicholson, K. Legge, V. Turchin, H. Zaghouani et al., High Frequency of Autoreactive Myelin Proteolipid Protein???Specific T Cells in the Periphery of Naive Mice, The Journal of Experimental Medicine, vol.147, issue.5, pp.761-70, 2000.
DOI : 10.1084/jem.179.3.973

B. Kyewski and L. Klein, A CENTRAL ROLE FOR CENTRAL TOLERANCE, Annual Review of Immunology, vol.24, issue.1, pp.571-606, 2006.
DOI : 10.1146/annurev.immunol.23.021704.115601

J. Merkin, C. Russell, P. Chen, and C. Burge, Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues, Science, vol.338, issue.6114, pp.1593-1602, 2012.
DOI : 10.1126/science.1228186

C. St-pierre, S. Brochu, J. Vanegas, M. Dumont-lagacé, S. Lemieux et al., Transcriptome sequencing of neonatal thymic epithelial cells, Scientific Reports, vol.411, p.1860, 2013.
DOI : 10.1038/srep01860

M. Soumillon, A. Necsulea, M. Weier, D. Brawand, X. Zhang et al., Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis, Cell Reports, vol.3, issue.6, pp.2179-90, 2013.
DOI : 10.1016/j.celrep.2013.05.031

URL : https://hal.archives-ouvertes.fr/hal-00852777

D. Ramsköld, E. Wang, C. Burge, and R. Sandberg, An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data, PLoS Computational Biology, vol.10, issue.12, p.1000598, 2009.
DOI : 10.1371/journal.pcbi.1000598.s011

M. Johnson, Y. Kawasawa, C. Mason, Z. Krsnik, G. Coppola et al., Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis, Neuron, vol.62, issue.4, pp.494-509, 2009.
DOI : 10.1016/j.neuron.2009.03.027

E. Schmidt, Transcriptional promiscuity in testes, Current Biology, vol.6, issue.7, pp.768-777, 1996.
DOI : 10.1016/S0960-9822(02)00589-4

S. Sansom, N. Shikama-dorn, S. Zhanybekova, G. Nusspaumer, I. Macaulay et al., dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia, Genome Research, vol.3, issue.12, pp.1918-1949, 2014.
DOI : 10.4049/jimmunol.1203210

M. Meredith, D. Zemmour, D. Mathis, and C. Benoist, Aire controls gene expression in the thymic epithelium with ordered stochasticity, Nature Immunology, vol.9, issue.9, pp.942-951, 2015.
DOI : 10.1093/bioinformatics/btr167

P. Brennecke, A. Reyes, S. Pinto, K. Rattay, M. Nguyen et al., Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells, Nature Immunology, vol.16, issue.9, pp.933-974, 2015.
DOI : 10.1186/gb-2010-11-10-r106

B. Kyewski, J. Derbinski, J. Gotter, and L. Klein, Promiscuous gene expression and central T-cell tolerance: more than meets the eye, Trends in Immunology, vol.23, issue.7, pp.364-71, 2002.
DOI : 10.1016/S1471-4906(02)02248-2

P. Keane, R. Ceredig, and C. Seoighe, Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells, Bioinformatics, vol.31, issue.7, pp.986-90, 2015.
DOI : 10.1093/bioinformatics/btu785

P. Grabowski and D. Black, Alternative RNA splicing in the nervous system, Progress in Neurobiology, vol.65, issue.3, pp.289-308, 2001.
DOI : 10.1016/S0301-0082(01)00007-7

S. Shen, J. Park, Z. Lu, L. Lin, M. Henry et al., rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data, Proceedings of the National Academy of Sciences, vol.111, issue.51, pp.5593-601, 2014.
DOI : 10.1073/pnas.1419161111

M. Cooke and R. Perlmutter, Expression of a novel form of the fyn protooncogene in hematopoietic cells, New Biol, vol.1, pp.66-74, 1989.

D. Karolchik, R. Baertsch, M. Diekhans, T. Furey, A. Hinrichs et al., The UCSC Genome Browser Database, Nucleic Acids Research, vol.31, issue.1, pp.51-55, 2003.
DOI : 10.1093/nar/gkg129

S. Farajollahi and S. Maas, Molecular diversity through RNA editing: a balancing act, Trends in Genetics, vol.26, issue.5, pp.221-251, 2010.
DOI : 10.1016/j.tig.2010.02.001

S. Conticello, The AID/APOBEC family of nucleic acid mutators, Genome Biology, vol.9, issue.6, p.229, 2008.
DOI : 10.1186/gb-2008-9-6-229

M. Paul and B. Bass, Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA, The EMBO Journal, vol.17, issue.4, pp.1120-1127, 1998.
DOI : 10.1093/emboj/17.4.1120

S. Young, Recent progress in understanding apolipoprotein B, Circulation, vol.82, issue.5, pp.1574-94, 1990.
DOI : 10.1161/01.CIR.82.5.1574

K. Higuchi, K. Kitagawa, K. Kogishi, and T. Takeda, Developmental and age-related changes in apolipoprotein B mRNA editing in mice, J Lipid Res, vol.33, pp.1753-64, 1992.

G. Anderson and Y. Takahama, Thymic epithelial cells: working class heroes for T cell development and repertoire selection, Trends in Immunology, vol.33, issue.6, pp.256-63, 2012.
DOI : 10.1016/j.it.2012.03.005

G. Stritesky, S. Jameson, and K. Hogquist, Selection of Self-Reactive T Cells in the Thymus, Annual Review of Immunology, vol.30, issue.1, pp.95-114, 2012.
DOI : 10.1146/annurev-immunol-020711-075035

K. Aschenbrenner, D. Cruz, L. Vollmann, E. Hinterberger, M. Emmerich et al., Selection of Foxp3+ regulatory T cells specific for self antigen expressed and presented by Aire+ medullary thymic epithelial cells, Nature Immunology, vol.173, issue.4, pp.351-359, 2007.
DOI : 10.1186/1471-2172-7-6

J. Cowan, S. Parnell, K. Nakamura, J. Caamano, P. Lane et al., thymocyte development, The Journal of Experimental Medicine, vol.210, issue.4, pp.675-81, 2013.
DOI : 10.1038/23287

E. Wang, N. Cody, S. Jog, M. Biancolella, T. Wang et al., Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins, Cell, vol.150, issue.4, pp.710-734, 2012.
DOI : 10.1016/j.cell.2012.06.041

T. Metzger, I. Khan, J. Gardner, M. Mouchess, K. Johannes et al., Lineage Tracing and Cell Ablation Identify a Post-Aire-Expressing Thymic Epithelial Cell Population, Cell Reports, vol.5, issue.1, pp.166-79, 2013.
DOI : 10.1016/j.celrep.2013.08.038

E. Lkhagvasuren, M. Sakata, I. Ohigashi, and Y. Takahama, Lymphotoxin ?? Receptor Regulates the Development of CCL21-Expressing Subset of Postnatal Medullary Thymic Epithelial Cells, The Journal of Immunology, vol.190, issue.10, pp.5110-5117, 2013.
DOI : 10.4049/jimmunol.1203203

J. Derbinski, J. Gäbler, B. Brors, S. Tierling, S. Jonnakuty et al., Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels, The Journal of Experimental Medicine, vol.57, issue.1, pp.33-45, 2005.
DOI : 10.1073/pnas.95.25.14863

S. Amor, N. Groome, C. Linington, M. Morris, K. Dornmair et al., Identification of epitopes of myelin oligodendrocyte glycoprotein for the induction of experimental allergic encephalomyelitis in SJL and Biozzi AB/H mice, J Immunol, vol.153, pp.4349-56, 1994.

Y. Sakamoto, T. Matsumoto, Y. Mizunoe, M. Haraoka, M. Sakumoto et al., Testicular Injury Induces Cell-Mediated Autoimmune Response to Testis, The Journal of Urology, vol.153, issue.4, pp.1316-1336, 1995.
DOI : 10.1016/S0022-5347(01)67593-1

W. Ritchie, S. Granjeaud, D. Puthier, and D. Gautheret, Entropy Measures Quantify Global Splicing Disorders in Cancer, PLoS Computational Biology, vol.5, issue.3, p.1000011, 2008.
DOI : 10.1371/journal.pcbi.1000011.s004

URL : https://hal.archives-ouvertes.fr/hal-00286322

J. Pickrell, A. Pai, Y. Gilad, and J. Pritchard, Noisy Splicing Drives mRNA Isoform Diversity in Human Cells, PLoS Genetics, vol.25, issue.12, p.1001236, 2010.
DOI : 10.1371/journal.pgen.1001236.s009

E. Melamud and J. Moult, Stochastic noise in splicing machinery, Nucleic Acids Research, vol.37, issue.14, pp.4873-86, 2009.
DOI : 10.1093/nar/gkp471

A. Chuprin, A. Avin, Y. Goldfarb, Y. Herzig, B. Levi et al., The deacetylase Sirt1 is an essential regulator of Aire-mediated induction of central immunological tolerance, Nature Immunology, vol.16, issue.7, pp.737-782, 2015.
DOI : 10.1073/pnas.0906801106

A. Dobin, C. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, issue.1, pp.15-21, 2013.
DOI : 10.1093/bioinformatics/bts635

Y. Liao, G. Smyth, and W. Shi, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, vol.30, issue.7, pp.923-953, 2013.
DOI : 10.1093/bioinformatics/btt656

B. Li and C. Dewey, RSEM, BMC Bioinformatics, vol.12, p.323, 2011.
DOI : 10.1201/b16589-5

E. Picardi and G. Pesole, REDItools: high-throughput RNA editing detection made easy, Bioinformatics, vol.29, issue.14, pp.1813-1817, 2013.
DOI : 10.1093/bioinformatics/btt287

K. Wang, M. Li, and H. Hakonarson, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data, Nucleic Acids Research, vol.38, issue.16, p.164, 2010.
DOI : 10.1093/nar/gkq603

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biology, vol.11, issue.10, p.106, 2010.
DOI : 10.1186/gb-2010-11-10-r106

M. Fiume, V. Williams, A. Brook, and M. Brudno, Savant: genome browser for high-throughput sequencing data, Bioinformatics, vol.26, issue.16, pp.1938-1982, 2010.
DOI : 10.1093/bioinformatics/btq332