A. C. Hayday and D. J. Pennington, Key factors in the organized chaos of early T cell development, Nat Immunol, vol.8, pp.137-181, 2007.

S. Spicuglia, J. Zacarias-cabeza, A. Pekowska, and P. Ferrier, Epigenetic regulation of antigen receptor gene rearrangement, F1000 Biology Reports, vol.2, p.23, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00601949

T. Taghon and E. V. Rothenberg, Molecular mechanisms that control mouse and human TCR-alphabeta and TCR-gammadelta T cell development, Semin Immunopathol, vol.30, pp.383-98, 2008.

A. C. Carpenter and R. Bosselut, Decision checkpoints in the thymus, Nat Immunol, vol.11, pp.666-73, 2010.

A. Pekowska, H3K4 tri-methylation provides an epigenetic signature of active enhancers, EMBO J, vol.30, pp.4198-210, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01614961

J. A. Zhang, A. Mortazavi, B. A. Williams, B. J. Wold, and E. V. Rothenberg, Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity, Cell, vol.149, pp.467-82, 2012.

I. Aifantis, E. Raetz, and S. Buonamici, Molecular pathogenesis of T-cell leukaemia and lymphoma, Nat Rev Immunol, vol.8, pp.380-90, 2008.

P. Ntziachristos, O. Abdel-wahab, and I. Aifantis, Emerging concepts of epigenetic dysregulation in hematological malignancies, Nature Immunology, 2016.

L. D. Notarangelo, Immunodeficiency and immune dysregulation associated with proximal defects of T cell receptor signaling, Curr Opin Immunol, vol.31, pp.97-101, 2014.

S. Spicuglia, M. A. Maqbool, D. Puthier, and J. C. Andrau, An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function, Methods, vol.63, pp.3-17, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01595815

S. Geisler and J. Coller, RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts, Nat Rev Mol Cell Biol, vol.14, pp.699-712, 2013.

M. Guttman and J. L. Rinn, Modular regulatory principles of large non-coding RNAs, Nature, vol.482, pp.339-385, 2012.

F. Morceau, S. Chateauvieux, A. Gaigneaux, M. Dicato, and M. Diederich, Long and short non-coding RNAs as regulators of hematopoietic differentiation, Int J Mol Sci, vol.14, pp.14744-70, 2013.

R. Bonasio and R. Shiekhattar, Regulation of transcription by long noncoding RNAs, Annu Rev Genet, vol.48, pp.433-55, 2014.

J. R. Alvarez-dominguez, Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation, vol.123, pp.570-581, 2014.

M. K. Atianand and K. A. Fitzgerald, Long non-coding RNAs and control of gene expression in the immune system, Trends Mol Med, vol.20, pp.623-654, 2014.

K. A. Fitzgerald and D. R. Caffrey, Long noncoding RNAs in innate and adaptive immunity, Curr Opin Immunol, vol.26, pp.140-146, 2014.
DOI : 10.1016/j.coi.2013.12.001

URL : http://europepmc.org/articles/pmc3932021?pdf=render

L. Zhu and P. C. Xu, Downregulated LncRNA-ANCR promotes osteoblast differentiation by targeting EZH2 and regulating Runx2 expression, Biochem Biophys Res Commun, vol.432, pp.612-619, 2013.
DOI : 10.1016/j.bbrc.2013.02.036

F. Xia, Dynamic Transcription of Long Non-Coding RNA Genes during CD4+ T Cell Development and Activation, PLoS ONE, vol.9, 2014.

T. Isoda, Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate, Cell, vol.171, pp.103-119, 2017.
DOI : 10.1016/j.cell.2017.09.001

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5621651

M. Pagani, Role of microRNAs and long-non-coding RNAs in CD4+ T-cell differentiation, Immunological Reviews, vol.253, pp.82-96, 2013.

D. Casero, Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages, Nature Immunology, vol.16, pp.1282-1291, 2015.

J. A. Gomez, The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus, Cell, vol.152, pp.743-54, 2013.

A. T. Willingham, A strategy for probing the function of noncoding RNAs finds a repressor of NFAT, Science, vol.309, pp.1570-1573, 2005.

Y. Wang, Long noncoding RNA derived from CD244 signaling epigenetically controls CD8+ T-cell immune responses in tuberculosis infection, Proc Natl Acad Sci, vol.112, pp.3883-92, 2015.

R. Garzon, Expression and prognostic impact of lncRNAs in acute myeloid leukemia, Proc Natl Acad Sci, vol.111, pp.18679-84, 2014.

X. Yang, A Network Based Method for Analysis of lncRNA-Disease Associations and Prediction of lncRNAs Implicated in Diseases, PLOS ONE, vol.9, 2014.

T. Trimarchi, Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia, Cell, vol.158, pp.593-606, 2014.

A. Wallaert, Long noncoding RNA signatures define oncogenic subtypes in T-cell acute lymphoblastic leukemia, Leukemia, 2016.

P. C. Ngoc, Identification of novel lncRNAs regulated by the TAL1 complex in T-cell acute lymphoblastic leukemia, Leukemia, 2018.

R. Gioia, LncRNAs downregulated in childhood acute lymphoblastic leukemia modulate apoptosis, cell migration, and DNA damage response, Oncotarget, vol.8, pp.80645-80650, 2017.

J. R. Alvarez-dominguez and H. F. Lodish, Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis, Blood, vol.130, pp.1965-1975, 2017.

A. Salviano-silva, S. C. Lobo-alves, R. C. Almeida, D. Malheiros, and M. L. Petzl-erler, Besides Pathology: Long Non-Coding RNA in Cell and Tissue Homeostasis, Noncoding RNA, vol.4, 2018.

P. Mombaerts, C. Terhorst, T. Jacks, S. Tonegawa, and J. Sancho, Characterization of immature thymocyte lines derived from T-cell receptor or recombination activating gene 1 and p53 double mutant mice, Immunology, vol.92, pp.7420-7424, 1995.

L. Vanhille, High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq, Nat Commun, vol.6, p.6905, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01614948

T. Chatila, L. Silverman, R. Millerand, and R. Geha, Mechanisms of T cell activation by the calcium ionophore ionomycin, J Immunol, vol.143, pp.1283-1289, 1989.

D. Blanco, B. Garcia-mariscal, A. Wiest, D. L. Hernandez-munain, and C. , Tcra enhancer activation by inducible transcription factors downstream of pre-TCR signaling, J Immunol, vol.188, pp.3278-93, 2012.

M. Oh-hora, Calcium signaling in the development and function of T-lineage cells, Immunological Reviews, vol.231, pp.210-224, 2009.

R. Brignall, Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells, J Immunol, vol.199, pp.2652-2667, 2017.

R. C. Su, R. Sridharan, and S. T. Smale, Assembly of silent chromatin during thymocyte development, Semin Immunol, vol.17, pp.129-169, 2005.

N. S. Holden, Phorbol ester-stimulated NF-kappaB-dependent transcription: roles for isoforms of novel protein kinase C, Cell Signal, vol.20, pp.1338-1386, 2008.

B. Reizis and P. Leder, The Upstream Enhancer Is Necessary and Sufficient for the Expression of the Pre-T Cell Receptor ? Gene in Immature T Lymphocytes, J. Exp. Med, vol.194, pp.979-990, 2001.

D. Silva, T. A. Oliveira-brito, P. K. Goncalves, T. E. Vendruscolo, P. E. Roque-barreira et al., ArtinM Mediates Murine T Cell Activation and Induces Cell Death in Jurkat Human Leukemic T Cells. Int J Mol Sci, vol.18, 2017.

R. N. Germain, T-cell development and the CD4-CD8 lineage decision, Nat Rev Immunol, vol.2, pp.309-331, 2002.

M. Mingueneau, The transcriptional landscape of alphabeta T cell differentiation, Nat Immunol, vol.14, pp.619-651, 2013.

C. Y. Mclean, GREAT improves functional interpretation of cis-regulatory regions, Nat Biotechnol, vol.28, pp.495-501, 2010.

M. Vanden-bempt, Cooperative Enhancer Activation by TLX1 and STAT5 Drives Development of NUP214-ABL1/TLX1-Positive T Cell Acute Lymphoblastic Leukemia, Cancer Cell, vol.34, pp.271-285, 2018.

B. Burlacu, Regulation of apoptosis by Bcl-2 family proteins, J. Cell. Mol. Med, vol.7, pp.249-257, 2003.

V. Kirkin, S. Joos, and M. Zornig, The role of Bcl-2 family members in tumorigenesis, Biochim Biophys Acta, vol.1644, pp.229-278, 2004.

A. Dunkle and Y. W. He, Apoptosis and autophagy in the regulation of T lymphocyte function, Immunol Res, vol.49, pp.70-86, 2011.

A. N. Hata, J. A. Engelman, and A. C. Faber, The BCL2 Family: Key Mediators of the Apoptotic Response to Targeted Anticancer Therapeutics, Cancer Discov, vol.5, pp.475-87, 2015.

J. Gratiot-deans, R. Merino, G. Nunez, and L. A. Turka, Bcl-2 expression during T-cell development: Early loss and late return occur at specific stages of commitment to differentiation and survival, Proc. Nati. Acad. Sci. USA, vol.91, pp.10685-10689, 1994.

M. Tanahashi, Effect of phorbol ester and calcium ionophore on human thymocytes, Human Immunology, vol.62, pp.771-781, 2001.

H. Feng, T-lymphoblastic lymphoma cells express high levels of BCL2, S1P1, and ICAM1, leading to a blockade of tumor cell intravasation, Cancer Cell, vol.18, pp.353-66, 2010.

E. Coustan-smith, Clinical Relevance of BCL-2 Overexpression in Childhood Acute Lymphoblastic Leukemia, Blood, vol.87, 1996.

A. W. Roberts and D. Huang, Targeting BCL2 With BH3 Mimetics: Basic Science and Clinical Application of Venetoclax in Chronic Lymphocytic Leukemia and Related B Cell Malignancies, Clin Pharmacol Ther, vol.101, pp.89-98, 2017.

S. Bornschein, Defining the molecular basis of oncogenic cooperation between TAL1 expression and Pten deletion in T-ALL using a novel pro-T-cell model system, Leukemia, vol.32, pp.941-951, 2018.

E. S. Hoffman, Productive T-cell receptor beta-chain gene rearrangement: coincident regulation of cell cycle and clonality during development in vivo, Genes & Development, vol.10, pp.948-962, 1996.

L. M. Kingeter, S. Paul, S. K. Maynard, N. G. Cartwright, and B. C. Schaefer, Cutting edge: TCR ligation triggers digital activation of NF-kappaB, J Immunol, vol.185, pp.4520-4524, 2010.

I. Aifantis, F. Gounari, L. Scorrano, C. Borowski, and H. Von-boehmer, Constitutive pre-TCR signaling promotes differentiation through Ca2+ mobilization and activation of NF-?B and NFAT, Nature Immunology, vol.2, p.403, 2001.

R. E. Voll, NF-?B Activation by the Pre-T Cell Receptor Serves as a Selective Survival Signal in T Lymphocyte Development, Immunity, vol.13, pp.677-689, 2000.

A. Wallaert, K. Durinck, T. Taghon, P. Van-vlierberghe, and F. Speleman, T-ALL and thymocytes: a message of noncoding RNAs, J Hematol Oncol, vol.10, p.66, 2017.

U. A. Orom and R. Shiekhattar, Long noncoding RNAs usher in a new era in the biology of enhancers, Cell, vol.154, pp.1190-1193, 2013.

S. J. Liu, CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells, Science, vol.355, 2017.

M. Guttman, lincRNAs act in the circuitry controlling pluripotency and differentiation, Nature, vol.477, pp.295-300, 2011.

M. S. Ivaldi, Fetal gamma-globin genes are regulated by the BGLT3 long non-coding RNA locus, Blood, 2018.

S. W. Cho, Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element, Cell, vol.173, p.22, 2018.

G. Natoli and J. C. Andrau, Noncoding transcription at enhancers: general principles and functional models, Annu Rev Genet, vol.46, pp.1-19, 2012.
DOI : 10.1146/annurev-genet-110711-155459

V. R. Paralkar, Unlinking an lncRNA from Its Associated cis Element, Mol Cell, vol.62, pp.104-114, 2016.

J. M. Engreitz, Local regulation of gene expression by lncRNA promoters, transcription and splicing, Nature, vol.539, pp.452-455, 2016.

C. L. Sentman, J. R. Shutter, D. Hockenbery, O. Kanagawa, and S. J. Korsmeyer, bcl-2 Inhibits Multiple Forms of Apoptosis but Not Negative Selection in Thymocytes, cell, vol.67, pp.879-888, 1991.

K. Akashi, M. Kondo, U. Von-freeden-jeffry, R. Murray, and I. L. Weissman, Bcl-2 Rescues T Lymphopoiesis in Interleukin-7 Receptor-Deficient Mice, cell, vol.89, pp.1033-1041, 1997.

E. Maraskovsky, Bcl-2 Can Rescue T Lymphocyte Development in Interleukin-7 Receptor-Deficient Mice but Not in Mutant rag-1?/?Mice, cell, vol.89, pp.1011-1019, 1997.

A. Strasser, A. W. Harris, L. M. Corcoran, and S. Cory, Bcl-2 expression promotes B-but not T-lymphoid development in scid mice, nature, vol.368, pp.457-60, 1994.
DOI : 10.1038/368457a0

D. J. Veis, C. M. Sorenson, J. R. Shutter, and S. J. Korsmeyer, Bcl-2-deficient mice demonstrate fulminant lymphoid apoptosis, polycystic kidneys, and hypopigmented hair, cell, vol.75, pp.229-240, 1993.

M. Mandal, The BCL2A1 gene as a pre-T cell receptor-induced regulator of thymocyte survival, J Exp Med, vol.201, pp.603-617, 2005.

C. Murga and D. F. Barber, Molecular Mechanisms of Pre-T Cell Receptor-induced Survival, Journal of Biological Chemistry, vol.277, pp.39156-39162, 2002.

C. J. Guidos, V(D)J recombination activates a p53-dependent DNA damage checkpoint in scid lymphocyte precursors, Genes & Development, vol.10, pp.2038-2054, 1996.

R. Fotedar, Effect ofp21(waf1/cip1) transgene on radiation induced apoptosis in T cells, Oncogene, vol.18, pp.3652-3660, 1999.

M. C. Haks, P. Krimpenfort, J. H. Van-den-brakel, and A. M. Kruisbeek, Pre-TCR Signaling and Inactivation of p53 Induces Crucial Cell Survival Pathways in Pre-T Cells, Immunity, vol.11, pp.91-101, 1999.

R. Berga-bolanos, M. Alberdi, M. Buxade, J. Aramburu, and C. Lopez-rodriguez, NFAT5 induction by the pre-T-cell receptor serves as a selective survival signal in T-lymphocyte development, Proceedings of the National Academy of Sciences, vol.110, pp.16091-16096, 2013.

D. Hanahan and R. A. Weinberg, Hallmarks of cancer: the next generation, Cell, vol.144, pp.646-74, 2011.

A. Strasser, The role of BH3-only proteins in the immune system, Nat Rev Immunol, vol.5, pp.189-200, 2005.

J. M. Adams and S. Cory, The Bcl-2 apoptotic switch in cancer development and therapy, Oncogene, vol.26, pp.1324-1361, 2007.

S. Peirs, ABT-199 mediated inhibition of BCL-2 as a novel therapeutic strategy in T-cell acute lymphoblastic leukemia, vol.124, pp.3738-3785, 2014.

T. Sanda, TYK2-STAT1-BCL2 pathway dependence in T-cell acute lymphoblastic leukemia, Cancer Discov, vol.3, pp.564-77, 2013.

B. Knoechel, An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia, Nat Genet, vol.46, pp.364-70, 2014.

G. Hu, Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation, Nat Immunol, vol.14, pp.1190-1198, 2013.

H. Thorvaldsdottir, J. T. Robinson, and J. P. Mesirov, Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration, Brief Bioinform, vol.14, pp.178-92, 2013.

S. Lin, Comparison of the transcriptional landscapes between human and mouse tissues, Proceedings of the National Academy of Sciences, vol.111, pp.17224-17229, 2014.

C. Trapnell, Differential analysis of gene regulation at transcript resolution with RNA-seq, Nat Biotechnol, vol.31, pp.46-53, 2013.

N. Kryuchkova-mostacci and M. Robinson-rechavi, A benchmark of gene expression tissue-specificity metrics, Brief Bioinform, vol.18, pp.205-214, 2017.

K. Ito and D. Murphy, Application of ggplot2 to Pharmacometric Graphics, CPT Pharmacometrics Syst Pharmacol, vol.2, p.79, 2013.

, Scientific RepoRts |, vol.9, p.4707, 2019.

J. Reimand, T. Arak, and J. Vilo, Profiler-a web server for functional interpretation of gene lists, Nucleic Acids Res, vol.39, pp.307-322, 2011.

A. Subramanian, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc Natl Acad Sci, vol.102, pp.15545-50, 2005.
DOI : 10.1073/pnas.0506580102

URL : http://www.pnas.org/content/102/43/15545.full.pdf

A. Subramanian, H. Kuehn, J. Gould, P. Tamayo, and J. P. Mesirov, GSEA-P: a desktop application for Gene Set Enrichment Analysis, Bioinformatics, vol.23, pp.3251-3254, 2007.

Y. Naito, K. Hino, H. Bono, and K. Ui-tei, CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites, Bioinformatics, vol.31, pp.1120-1123, 2015.
DOI : 10.1093/bioinformatics/btu743

URL : https://academic.oup.com/bioinformatics/article-pdf/31/7/1120/17124046/btu743.pdf