S. Augui, G. J. Filion, S. Huart, E. Nora, M. Guggiari et al., Sensing X Chromosome Pairs Before X Inactivation via a Novel X-Pairing Region of the Xic, Science, vol.318, issue.5856, pp.1632-1636, 2007.
DOI : 10.1126/science.1149420

C. P. Bacher, M. Guggiari, B. Brors, S. Augui, P. Clerc et al., Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation, Nature Cell Biology, vol.379, issue.3, pp.293-299, 2006.
DOI : 10.1038/ncb1365

S. Boyle, M. J. Rodesch, H. A. Halvensleben, J. A. Jeddeloh, and W. A. Bickmore, Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis, Chromosome Research, vol.132, issue.7, pp.901-909, 2011.
DOI : 10.1007/s10577-011-9245-0

S. Chambeyron and W. A. Bickmore, Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription, Genes & Development, vol.18, issue.10, 2004.
DOI : 10.1101/gad.292104

J. Chaumeil and J. A. Skok, The role of CTCF in regulating V(D)J recombination, Current Opinion in Immunology, vol.24, issue.2, pp.153-159, 2012.
DOI : 10.1016/j.coi.2012.01.003

J. Chaumeil, P. Le-baccon, A. Wutz, and E. Heard, A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced, Genes & Development, vol.20, issue.16, pp.2223-2237, 2006.
DOI : 10.1101/gad.380906

J. Chaumeil, S. Augui, J. C. Chow, and E. Heard, Combined Immunofluorescence, RNA Fluorescent In Situ Hybridization, and DNA Fluorescent In Situ Hybridization to Study Chromatin Changes, Transcriptional Activity, Nuclear Organization, and X-Chromosome Inactivation, Methods Mol. Biol, vol.463, pp.297-308, 2008.
DOI : 10.1007/978-1-59745-406-3_18

J. Chaumeil, M. Micsinai, and J. A. Skok, Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization, Journal of Visualized Experiments, vol.72, issue.72, p.50087, 2013.
DOI : 10.3791/50087

H. T. Chen, A. Bhandoola, M. J. Difilippantonio, J. Zhu, M. J. Brown et al., Response to RAG-Mediated V(D)J Cleavage by NBS1 and gamma-H2AX, Science, vol.290, issue.5498, pp.1962-1965, 2000.
DOI : 10.1126/science.290.5498.1962

T. Cheutin, C. , and G. , Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion, PLoS Genetics, vol.15, issue.1, 2012.
DOI : 10.1371/journal.pgen.1002465.s018
URL : http://doi.org/10.1371/journal.pgen.1002465

M. Ciofani, Z. , ?. Iga-pflü-cker, and J. C. , Determining gd versus aß T cell development, Nat. Rev. Immunol, vol.10, pp.657-663, 2010.

L. Deriano, J. Chaumeil, M. Coussens, A. Multani, Y. Chou et al., The RAG2 C terminus suppresses genomic instability and lymphomagenesis, Nature, vol.101, issue.7336, pp.119-123, 2011.
DOI : 10.1038/nature09755
URL : https://hal.archives-ouvertes.fr/pasteur-01471708

M. Farago, C. Rosenbluh, M. Tevlin, S. Fraenkel, S. Schlesinger et al., Clonal allelic predetermination of immunoglobulin-?? rearrangement, Nature, vol.179, issue.7421, pp.561-565, 2012.
DOI : 10.1073/pnas.0608130103

P. Fraser and W. Bickmore, Nuclear organization of the genome and the potential for gene regulation, Nature, vol.428, issue.7143, pp.413-417, 2007.
DOI : 10.1038/nature05916

S. D. Fugmann, I. J. Villey, L. M. Ptaszek, and D. G. Schatz, Identification of Two Catalytic Residues in RAG1 that Define a Single Active Site within the RAG1/RAG2 Protein Complex, Molecular Cell, vol.5, issue.1, pp.97-107, 2000.
DOI : 10.1016/S1097-2765(00)80406-2

M. Goldmit, Y. Ji, J. Skok, E. Roldan, S. Jung et al., Epigenetic ontogeny of the Igk locus during B cell development, Nature Immunology, vol.13, issue.2, pp.198-203, 2005.
DOI : 10.1016/0092-8674(94)90365-4

E. Heard and W. Bickmore, The ins and outs of gene regulation and chromosome territory organisation, Current Opinion in Cell Biology, vol.19, issue.3, pp.311-316, 2007.
DOI : 10.1016/j.ceb.2007.04.016

B. A. Helmink and B. P. Sleckman, The Response to and Repair of RAG-Mediated DNA Double-Strand Breaks, Annual Review of Immunology, vol.30, issue.1, pp.175-202, 2012.
DOI : 10.1146/annurev-immunol-030409-101320

S. L. Hewitt, B. Yin, Y. Ji, J. Chaumeil, K. Marszalek et al., RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci, Nature Immunology, vol.17, issue.6, pp.655-664, 2009.
DOI : 10.1038/ni.1735

S. L. Hewitt, J. Chaumeil, and J. A. Skok, Chromosome dynamics and the regulation of V(D)J recombination, Immunological Reviews, vol.89, issue.1, pp.43-54, 2010.
DOI : 10.1111/j.1600-065X.2010.00931.x

Y. Ji, W. Resch, E. Corbett, A. Yamane, R. Casellas et al., The In Vivo Pattern of Binding of RAG1 and RAG2 to Antigen Receptor Loci, Cell, vol.141, issue.3, pp.419-431, 2010.
DOI : 10.1016/j.cell.2010.03.010

R. Kalhor, H. Tjong, N. Jayathilaka, F. Alber, C. et al., Genome architectures revealed by tethered chromosome conformation capture and population-based modeling, Nature Biotechnology, vol.67, issue.1, pp.90-98, 2012.
DOI : 10.1146/annurev.biochem.77.060407.135530
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3782096

D. R. Kim, Y. Dai, C. L. Mundy, W. Yang, and M. A. Oettinger, Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase, Genes & Development, vol.13, issue.23, pp.3070-3080, 1999.
DOI : 10.1101/gad.13.23.3070

Y. Kobayashi, B. Tycko, A. L. Soreng, and J. Sklar, Transrearrangements between antigen receptor genes in normal human lymphoid tissues and in ataxia telangiectasia, J. Immunol, vol.147, pp.3201-3209, 1991.

M. S. Krangel, Mechanics of T cell receptor gene rearrangement, Current Opinion in Immunology, vol.21, issue.2, pp.133-139, 2009.
DOI : 10.1016/j.coi.2009.03.009

M. A. Landree, J. A. Wibbenmeyer, R. , and D. B. , Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination, Genes & Development, vol.13, issue.23, pp.3059-3069, 1999.
DOI : 10.1101/gad.13.23.3059

Y. Liu, R. Subrahmanyam, T. Chakraborty, R. Sen, and S. Desiderio, A Plant Homeodomain in Rag-2 that Binds Hypermethylated Lysine 4 of Histone H3 Is Necessary for Efficient Antigen-Receptor-Gene Rearrangement, Immunity, vol.27, issue.4, pp.561-571, 2007.
DOI : 10.1016/j.immuni.2007.09.005

F. Livá-k, M. Tourigny, D. G. Schatz, and H. T. Petrie, Characterization of TCR gene rearrangements during adult murine T cell development, J. Immunol, vol.162, pp.2575-2580, 1999.

M. Liyanage, Z. Weaver, C. Barlow, A. Coleman, D. G. Pankratz et al., Abnormal rearrangement within the alpha/delta T-cell receptor locus in lymphomas from Atm-deficient mice, Blood, vol.96, pp.1940-1946, 2000.

I. R. Matei, R. A. Gladdy, L. M. Nutter, A. Canty, C. J. Guidos et al., ATM deficiency disrupts Tcra locus integrity and the maturation of CD4+CD8+ thymocytes, Blood, vol.109, issue.5, pp.1887-1896, 2007.
DOI : 10.1182/blood-2006-05-020917

C. Morey, C. Kress, and W. A. Bickmore, Lack of bystander activation shows that localization exterior to chromosome territories is not sufficient to up-regulate gene expression, Genome Research, vol.19, issue.7, pp.1184-1194, 2009.
DOI : 10.1101/gr.089045.108

R. Mostoslavsky, N. Singh, T. Tenzen, M. Goldmit, C. Gabay et al., Asynchronous replication and allelic exclusion in the immune system, Nature, vol.69, issue.6860, pp.221-225, 2001.
DOI : 10.1038/35102606

N. Puebla-osorio and C. Zhu, DNA damage and repair during lymphoid development: antigen receptor diversity, genomic integrity and lymphomagenesis, Immunologic Research, vol.440, issue.2, pp.103-122, 2008.
DOI : 10.1007/s12026-008-8015-3

D. G. Schatz, J. , and Y. , Recombination centres and the orchestration of V(D)J recombination, Nature Reviews Immunology, vol.8, issue.4, pp.251-263, 2011.
DOI : 10.1038/nri2941

S. Schoenfelder, T. Sexton, L. Chakalova, N. F. Cope, A. Horton et al., Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells, Nature Genetics, vol.13, issue.1, pp.53-61, 2010.
DOI : 10.1093/bioinformatics/18.8.1135

N. M. Shanbhag, I. U. Rafalska-metcalf, C. Balane-bolivar, S. M. Janicki, and R. A. Greenberg, ATM-Dependent Chromatin Changes Silence Transcription In cis to DNA Double-Strand Breaks, Cell, vol.141, issue.6, pp.970-981, 2010.
DOI : 10.1016/j.cell.2010.04.038

N. Shimazaki, A. G. Tsai, and M. R. Lieber, H3K4me3 Stimulates the V(D)J RAG Complex for Both Nicking and Hairpinning in trans in Addition to Tethering in cis: Implications for Translocations, Molecular Cell, vol.34, issue.5, pp.535-544, 2009.
DOI : 10.1016/j.molcel.2009.05.011

M. Simonis, P. Klous, E. Splinter, Y. Moshkin, R. Willemsen et al., Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture???on-chip (4C), Nature Genetics, vol.7, issue.11, pp.1348-1354, 2006.
DOI : 10.1038/ng1896

J. A. Skok, R. Gisler, M. Novatchkova, D. Farmer, W. De-laat et al., Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes, Nature Immunology, vol.171, issue.4, pp.378-387, 2007.
DOI : 10.1084/jem.188.1.5

E. Splinter, E. De-wit, E. P. Nora, P. Klous, H. J. Van-de-werken et al., The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA, Genes & Development, vol.25, issue.13, pp.1371-1383, 2011.
DOI : 10.1101/gad.633311

R. C. Su, K. E. Brown, S. Saaber, A. G. Fisher, M. Merkenschlager et al., Dynamic assembly of silent chromatin during thymocyte maturation, Nature Genetics, vol.10, issue.5, pp.502-506, 2004.
DOI : 10.1084/jem.186.7.1149

I. M. Ward, K. Minn, J. Van-deursen, C. , and J. , p53 Binding Protein 53BP1 Is Required for DNA Damage Responses and Tumor Suppression in Mice, Molecular and Cellular Biology, vol.23, issue.7, pp.2556-2563, 2003.
DOI : 10.1128/MCB.23.7.2556-2563.2003

S. Zha, C. H. Bassing, T. Sanda, J. W. Brush, H. Patel et al., rearrangement and gene amplification, The Journal of Experimental Medicine, vol.96, issue.7, pp.1369-1380, 2010.
DOI : 10.1073/pnas.79.9.3015