V. The-pmx-inv, P. Cj, . Or-pmx-del, and . Sjbredemeyer, For V(D)J recombination assay, v-abl-transformed , Bcl2/pMX-INV-infected pro-B cells (10 6 /ml) were treated with 3 mM of the v-abl kinase inhibitor STI571 (referred to as ABLki in this study, Novartis) and assayed for rearrangement by FACS analysis of GFP expression or Southern blotting at 0, 72, and/or 96 hr In some experiments, the ATM kinase inhibitor KU55933 was added at 15 mM together with STI571. For FACS analysis, V(D)J recombination efficiency was scored as the percentage of GFP-positive cells among hCD4-positive cells (human CD4-PE, Miltenyi Biotec, 1:20 dilution) The pMX-INV-mCherry substrate was built by replacing the inverted GFP cDNA from pMX-RSS-GFP/IRES-hCD4 (pMX-INV) by an inverted mCherry cDNA. Southern Blot Southern blots were performed as previously described 50 mg of gDNA from untreated, ABLki-treated and ABLki/ATMki-treated pro-B cell lines were digested overnight with EcoRV for both pMX-DEL CJ and pMX- DEL SJ and with EcoRV or EcoRV/NcoI for pMX-INV. Digested gDNA samples were run overnight on an agarose gel, denatured by incubating the gel with 0.5 M NaOH Blots were incubated at 42 C in pre-hybridization buffer for at least 1 hr and then, 6M NaCl for 1 hr, and then transferred overnight on a Zeta- Probe GT nylon membrane (BioRad). DNA was cross-linked on the membrane using a UV Cross-linker CL-508 Blots were washed in 2XSSC/0.1% SDS at 65 C and exposed to a Storage Phosphor Screen (GE Healthcare) for 2 to 5 days. The screen was then scanned using a Storm 860 PhosphoImager (Molecular Dynamics), 2002.

P. Analysis, V. Cjs, and P. Sjsbredemeyer, and pMX-INV HJs were amplified using pC (GCACGAAGTCTTGAGACCT) and IRES-REV5 (CTCGACTAAACACATG TAAAGC) oligonucleotides. pMX-INV CJs were amplified using pA (CACAA CATCGAGGACGG) and IRES-REV5 primers as previously described Il-2 gene was amplified using IMR42 (CTAGGCCACAGAATTGAAAGATCT) and IMR43 (GTAGGTG GAAATTCTAGCATGATGC) primers and was used as loading control. pMX- DEL SJ SJ PCR products were incubated with the restriction enzyme, RAG1 and RAG2 form a stable postcleavage synaptic complex with DNA containing signal ends in V(D)J recombination, pp.43-53, 1997.

S. N. Andres, M. Modesti, C. J. Tsai, G. Chu, and M. S. Junop, Crystal Structure of Human XLF: A Twist in Nonhomologous DNA End-Joining, Molecular Cell, vol.28, issue.6, pp.1093-1101, 2007.
DOI : 10.1016/j.molcel.2007.10.024

C. H. Bassing, W. Swat, A. , and F. W. , The Mechanism and Regulation of Chromosomal V(D)J Recombination, Cell, vol.109, issue.2, pp.45-55, 2002.
DOI : 10.1016/S0092-8674(02)00675-X

A. N. Blackford, J. Nieminuszczy, R. A. Schwab, Y. Galanty, S. P. Jackson et al., TopBP1 Interacts with BLM to Maintain Genome Stability but Is Dispensable for Preventing BLM Degradation, Molecular Cell, vol.57, issue.6, pp.1133-1141, 2015.
DOI : 10.1016/j.molcel.2015.02.012

T. Blunt, N. J. Finnie, G. E. Taccioli, G. C. Smith, J. Demengeot et al., Defective DNA-dependent protein kinase activity is linked to V(D)J recombination and DNA repair defects associated with the murine scid mutation, Cell, vol.80, issue.5, pp.813-823, 1995.
DOI : 10.1016/0092-8674(95)90360-7

M. A. Bogue, C. Jhappan, R. , and D. B. , Analysis of variable (diversity) joining recombination in DNAdependent protein kinase (DNA-PK)-deficient mice reveals DNA-PK-independent pathways for both signal and coding joint formation, Proc. Natl. Acad. Sci. USA 95, pp.15559-15564, 1998.
DOI : 10.1073/pnas.95.26.15559

A. L. Bredemeyer, G. G. Sharma, C. Huang, B. A. Helmink, L. M. Walker et al., ATM stabilizes DNA double-strand-break complexes during V(D)J recombination, Nature, vol.194, issue.7101, pp.466-470, 2006.
DOI : 10.1038/nature04866

I. Callebaut, L. Malivert, A. Fischer, J. P. Mornon, P. Revy et al., Cernunnos Interacts with the XRCC4{middle dot}DNA-ligase IV Complex and Is Homologous to the Yeast Nonhomologous End-joining Factor Nej1, Journal of Biological Chemistry, vol.281, issue.20, pp.13857-13860, 2006.
DOI : 10.1074/jbc.C500473200

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

A. Craxton, J. Somers, D. Munnur, R. Jukes-jones, K. Cain et al., XLS (c9orf142) is a new component of mammalian DNA double-stranded break repair, Cell Death and Differentiation, vol.27, issue.6, pp.890-897, 2015.
DOI : 10.1371/journal.pone.0007016

L. Deriano, R. , and D. B. , Modernizing the Nonhomologous End-Joining Repertoire: Alternative and Classical NHEJ Share the Stage, Annual Review of Genetics, vol.47, issue.1, pp.433-455, 2013.
DOI : 10.1146/annurev-genet-110711-155540

URL : https://hal.archives-ouvertes.fr/pasteur-01471700

Y. Gao, Y. Sun, K. M. Frank, P. Dikkes, Y. Fujiwara et al., A Critical Role for DNA End-Joining Proteins in Both Lymphogenesis and Neurogenesis, Cell, vol.95, issue.7, pp.891-902, 1998.
DOI : 10.1016/S0092-8674(00)81714-6

T. M. Gottlieb, J. , and S. P. , The DNA-dependent protein kinase: Requirement for DNA ends and association with Ku antigen, Cell, vol.72, issue.1, pp.131-142, 1993.
DOI : 10.1016/0092-8674(93)90057-W

M. Hammel, M. Rey, Y. Yu, R. S. Mani, S. Classen et al., XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair, Journal of Biological Chemistry, vol.286, issue.37, pp.32638-32650, 2011.
DOI : 10.1074/jbc.M111.272641

J. A. Harrigan, R. Belotserkovskaya, J. Coates, D. S. Dimitrova, S. E. Polo et al., Replication stress induces 53BP1-containing OPT domains in G1 cells, The Journal of Cell Biology, vol.521, issue.1, pp.97-108, 2011.
DOI : 10.1093/nar/22.9.1655

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

B. A. Helmink, A. T. Tubbs, Y. Dorsett, J. J. Bednarski, L. M. Walker et al., H2AX prevents CtIP-mediated DNA end resection and aberrant repair in G1-phase lymphocytes, Nature, vol.37, issue.7329, pp.245-249, 2011.
DOI : 10.1038/nature09585

I. Hickson, Y. Zhao, C. J. Richardson, S. J. Green, N. M. Martin et al., Identification and Characterization of a Novel and Specific Inhibitor of the Ataxia-Telangiectasia Mutated Kinase ATM, Cancer Research, vol.64, issue.24, pp.9152-9159, 2004.
DOI : 10.1158/0008-5472.CAN-04-2727

K. Hiom and M. Gellert, Assembly of a 12/23 Paired Signal Complex: A Critical Control Point in V(D)J Recombination, Molecular Cell, vol.1, issue.7, pp.1011-1019, 1998.
DOI : 10.1016/S1097-2765(00)80101-X

V. Kumar, F. W. Alt, and V. Oksenych, Functional overlaps between XLF and the ATM-dependent DNA double strand break response, DNA Repair, vol.16, pp.11-22, 2014.
DOI : 10.1016/j.dnarep.2014.01.010

C. Lescale and L. Deriano, V(D)J Recombination: Orchestrating Diversity without Damage, Encyclopedia of Cell Biology, vol.3, pp.550-566, 2016.
DOI : 10.1016/B978-0-12-394447-4.30073-6

C. Lescale, V. Abramowski, M. Bedora-faure, V. Murigneux, G. Vera et al., RAG2 and XLF/Cernunnos interplay reveals a novel role for the RAG complex in DNA repair, Nature Communications, vol.3, 2016.
DOI : 10.1093/bioinformatics/btr670

URL : https://hal.archives-ouvertes.fr/pasteur-01295756

Z. Li, T. Otevrel, Y. Gao, H. Cheng, B. Seed et al., The XRCC4 gene encodes a novel protein involved in DNA double-strand break repair and V(D)J recombination, Cell, vol.83, issue.7, pp.1079-1089, 1995.
DOI : 10.1016/0092-8674(95)90135-3

G. Li, F. W. Alt, H. L. Cheng, J. W. Brush, P. H. Goff et al., Lymphocyte-Specific Compensation for XLF/Cernunnos End-Joining Functions in V(D)J Recombination, Molecular Cell, vol.31, issue.5, pp.631-640, 2008.
DOI : 10.1016/j.molcel.2008.07.017

Y. Li, D. Y. Chirgadze, V. M. Bolanos-garcia, B. L. Sibanda, O. R. Davies et al., Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ, The EMBO Journal, vol.40, issue.1, pp.290-300, 2008.
DOI : 10.1038/sj.emboj.7601942

H. E. Liang, L. Y. Hsu, D. Cado, L. G. Cowell, G. Kelsoe et al., The ???Dispensable??? Portion of RAG2 Is Necessary for Efficient V-to-DJ Rearrangement during B and T Cell Development, Immunity, vol.17, issue.5, pp.639-651, 2002.
DOI : 10.1016/S1074-7613(02)00448-X

M. R. Lieber, The Mechanism of Double-Strand DNA Break Repair by the Nonhomologous DNA End-Joining Pathway, Annual Review of Biochemistry, vol.79, issue.1, pp.181-211, 2010.
DOI : 10.1146/annurev.biochem.052308.093131

R. Mizuta, H. L. Cheng, Y. Gao, A. , and F. W. , Molecular genetic characterization of XRCC4 function, International Immunology, vol.9, issue.10, pp.1607-1613, 1997.
DOI : 10.1093/intimm/9.10.1607

S. A. Muljo and M. S. Schlissel, A small molecule Abl kinase inhibitor induces differentiation of Abelson virus???transformed pre-B cell lines, Nature Immunology, vol.4, issue.1, pp.31-37, 2003.
DOI : 10.1038/ni870

T. Ochi, Q. Wu, and T. L. Blundell, The spatial organization of non-homologous end joining: From bridging to end joining, DNA Repair, vol.17, pp.98-109, 2014.
DOI : 10.1016/j.dnarep.2014.02.010

T. Ochi, A. N. Blackford, J. Coates, S. Jhujh, S. Mehmood et al., PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair, Science, vol.347, issue.6218, pp.185-188, 2015.
DOI : 10.1126/science.1261971

D. A. Ramsden, T. T. Paull, and M. Gellert, Cell-free V(D)J recombination, Nature, vol.388, pp.488-491, 1997.

D. A. Reid, S. Keegan, A. Leo-macias, G. Watanabe, N. T. Strande et al., Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair, Proc. Natl. Acad. Sci. USA, pp.2575-2584, 2015.
DOI : 10.1073/pnas.1420115112

P. Revy, D. Buck, F. Le-deist, and J. P. De-villartay, The Repair of DNA Damages/Modifications During the Maturation of the Immune System: Lessons from Human Primary Immunodeficiency Disorders and Animal Models, Adv. Immunol, vol.87, pp.237-295, 2005.
DOI : 10.1016/S0065-2776(05)87007-5

E. Riballo, L. Woodbine, T. Stiff, S. A. Walker, A. A. Goodarzi et al., XLF-Cernunnos promotes DNA ligase IV-XRCC4 re-adenylation following ligation, Nucleic Acids Research, vol.37, issue.2, pp.482-492, 2009.
DOI : 10.1093/nar/gkn957

S. Rooney, J. Chaudhuri, A. , and F. W. , The role of the non-homologous end-joining pathway in lymphocyte development, Immunological Reviews, vol.14, issue.1, pp.115-131, 2004.
DOI : 10.1016/S0960-9822(01)00048-3

V. Ropars, P. Drevet, P. Legrand, S. Baconnais, J. Amram et al., Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining, Proc. Natl. Acad. Sci. USA, pp.12663-12668, 2011.
DOI : 10.1073/pnas.1100758108

URL : https://hal.archives-ouvertes.fr/hal-00613194

S. Roy, A. J. De-melo, Y. Xu, S. K. Tadi, A. Negrel et al., XRCC4/XLF Interaction Is Variably Required for DNA Repair and Is Not Required for Ligase IV Stimulation, Molecular and Cellular Biology, vol.35, issue.17, 2015.
DOI : 10.1128/MCB.01503-14

URL : https://hal.archives-ouvertes.fr/hal-01456279

D. G. Schatz and P. C. Swanson, V(D)J Recombination: Mechanisms of Initiation, Annual Review of Genetics, vol.45, issue.1, pp.167-202, 2011.
DOI : 10.1146/annurev-genet-110410-132552

M. Schwartz, Y. S. Oren, A. C. Bester, A. Rahat, R. Sfez et al., Impaired Replication Stress Response in Cells from Immunodeficiency Patients Carrying Cernunnos/XLF Mutations, PLoS ONE, vol.277, issue.2, p.4516, 2009.
DOI : 10.1371/journal.pone.0004516.g006

Y. Shinkai, G. Rathbun, K. Lam, E. M. Oltz, V. Stewart et al., RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement, Cell, vol.68, issue.5, pp.855-867, 1992.
DOI : 10.1016/0092-8674(92)90029-C

C. J. Tsai, S. A. Kim, C. , and G. , Cernunnos/XLF promotes the ligation of mismatched and noncohesive DNA ends, Proc. Natl. Acad. Sci. USA, pp.7851-7856, 2007.
DOI : 10.1073/pnas.0702620104

G. Vera, P. Rivera-munoz, V. Abramowski, L. Malivert, A. Lim et al., Cernunnos Deficiency Reduces Thymocyte Life Span and Alters the T Cell Repertoire in Mice and Humans, Molecular and Cellular Biology, vol.33, issue.4, pp.701-711, 2013.
DOI : 10.1128/MCB.01057-12

M. Xing, M. Yang, W. Huo, F. Feng, L. Wei et al., Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway, Nature Communications, vol.6, p.6233, 2015.
DOI : 10.1038/emboj.2012.304

S. Zha, C. Guo, C. Boboila, V. Oksenych, H. L. Cheng et al., ATM damage response and XLF repair factor are functionally redundant in joining DNA breaks, Nature, vol.296, issue.7329, pp.250-254, 2011.
DOI : 10.1038/nature09604