J. Banerji, S. Rusconi, and W. Schaffner, Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences, Cell, vol.27, issue.2, pp.299-308, 1981.

T. Maniatis, S. Goodbourn, and J. Fischer, Regulation of inducible and tissue-specific gene expression. Science, vol.236, p.3296191, 1987.

H. K. Long, S. L. Prescott, and J. Wysocka, Review Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution, Cell, vol.167, issue.5, p.27863239, 2016.

E. Z. Kvon, Using transgenic reporter assays to functionally characterize enhancers in animals. Genomics, vol.106, p.26072435, 2015.
DOI : 10.1016/j.ygeno.2015.06.007

URL : https://manuscript.elsevier.com/S0888754315300124/pdf/S0888754315300124.pdf

S. Ruf, O. Symmons, V. V. Uslu, D. Dolle, C. Hot et al., Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor, Nat Genet, vol.43, issue.4, p.21423180, 2011.

O. Symmons, V. V. Uslu, T. Tsujimura, S. Ruf, S. Nassari et al., Functional and topological characteristics of mammalian regulatory domains, Genome Res, vol.24, issue.3, p.24398455, 2014.

L. Dunipace, A. Saunders, H. Ashe, and A. Stathopoulos, Autoregulatory feedback controls sequential action of cis-regulatory modules at the brinker locus, Dev Cell, vol.26, issue.5, p.24044892, 2013.

K. S. Zaret and J. S. Carroll, Pioneer transcription factors: Establishing competence for gene expression, Genes Dev, vol.25, issue.21, p.22056668, 2011.
DOI : 10.1101/gad.176826.111

URL : http://genesdev.cshlp.org/content/25/21/2227.full.pdf

J. H. Gibcus and J. Dekker, The hierarchy of the 3D genome, Mol Cell, vol.49, issue.5, p.23473598, 2013.

E. P. Nora, B. R. Lajoie, E. G. Schulz, L. Giorgetti, I. Okamoto et al., Spatial partitioning of the regulatory landscape of the X-inactivation centre, Nature, vol.485, issue.7398, p.22495304, 2012.

J. R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li et al., Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, vol.485, issue.7398, p.22495300, 2012.

P. Chavrier, M. Zerial, P. Lemaire, J. Almendral, R. Bravo et al., A gene encoding a protein with zinc fingers is activated during G0/G1 transition in cultured cells, EMBO J, vol.7, issue.1, p.3129290, 1988.

D. Chomette, M. Frain, S. Cereghini, P. Charnay, and J. Ghislain, Krox20 hindbrain cis-regulatory landscape: interplay between multiple long-range initiation and autoregulatory elements, Development, vol.133, issue.7, p.16495311, 2006.
DOI : 10.1242/dev.02289

URL : http://dev.biologists.org/content/133/7/1253.full.pdf

A. Lumsden and R. Krumlauf, Patterning the vertebrate neuraxis, Science, vol.274, issue.5290, p.8895453, 1996.

S. Schneider-maunoury, P. Topilko, T. Seitandou, G. Levi, M. Cohen-tannoudji et al., Disruption of Krox-20 results in alteration of rhombomeres 3 and 5 in the developing hindbrain, Cell, vol.75, issue.6, p.7903221, 1993.

S. Schneider-maunoury, T. Seitanidou, P. Charnay, and . Lumsden-a, Segmental and neuronal architecture of the hindbrain of Krox-20 mouse mutants, Development, vol.124, issue.6, p.9102308, 1997.

O. Voiculescu, E. Taillebourg, C. Pujades, C. Kress, S. Buart et al., Hindbrain patterning: Krox20 couples segmentation and specification of regional identity, Development, vol.128, issue.24, p.11748134, 2001.

Y. X. Bouchoucha, J. Reingruber, C. Labalette, E. Wassef-m-a,-thierion, and C. Desmarquet-trin-dinh, Dissection of a Krox20 positive feedback loop driving cell fate choices in hindbrain patterning, Mol Syst Biol, vol.9, issue.690, 2013.

C. Labalette, Y. X. Bouchoucha, M. A. Wassef, P. A. Gongal, L. Men et al., Hindbrain patterning requires fine-tuning of early krox20 transcription by Sprouty 4. Development, vol.138, p.21177344, 2011.

C. Labalette, M. A. Wassef, C. Desmarquet-trin-dinh, Y. X. Bouchoucha, L. Men et al., Molecular dissection of segment formation in the developing hindbrain, Development, vol.142, issue.1, p.25516974, 2015.

D. Wassef-m-a,-chomette, M. Pouilhe, A. Stedman, E. Havis, and C. Desmarquet-trin-dinh, Rostral hindbrain patterning involves the direct activation of a Krox20 transcriptional enhancer by Hox/Pbx and Meis factors, Development, vol.135, p.18787068, 1920.

T. Seitanidou, S. Schneider-maunoury, C. Desmarquet, D. G. Wilkinson, and P. Charnay, Krox-20 is a key regulator of rhombomere-specific gene expression in the developing hindbrain, Mech Dev, vol.65, issue.1-2, p.9256343, 1997.

O. Voiculescu, P. Charnay, and S. Schneider-maunoury, Expression pattern of a Krox-20/Cre knock-in allele in the developing hindbrain, bones, and peripheral nervous system, Genesis, vol.26, issue.2, p.10686605, 2000.

H. Van-de-werken, G. Landan, S. Holwerda, M. Hoichman, P. Klous et al., Robust 4C-seq data analysis to screen for regulatory DNA interactions, Nat Methods, vol.9, issue.10, p.22961246, 2012.

C. Irving, . Nieto-m-a, R. Dasgupta, P. Charnay, and D. G. Wilkinson, Progressive spatial restriction of Sek-1 and Krox-20 gene expression during hindbrain segmentation, Dev Biol, vol.173, issue.1, p.8575627, 1996.
DOI : 10.1006/dbio.1996.0004

URL : https://doi.org/10.1006/dbio.1996.0004

A. Barski, S. Cuddapah, K. Cui, T. Y. Roh, D. E. Schones et al., High-Resolution Profiling of Histone Methylations in the Human Genome, Cell, vol.129, issue.4, p.17512414, 2007.

V. W. Zhou, A. Goren, and B. E. Bernstein, Charting histone modifications and the functional organization of mammalian genomes, Nat Rev Genet, vol.12, issue.1, p.21116306, 2011.

J. Ghislain, C. Desmarquet-trin-dinh, P. Gilardi-hebenstreit, P. Charnay, and M. Frain, Neural crest patterning: autoregulatory and crest-specific elements co-operate for Krox20 transcriptional control, Development, vol.130, issue.5, p.12538520, 2003.

T. Theil, M. Frain, P. Gilardi-hebenstreit, A. Flenniken, P. Charnay et al., Segmental expression of the EphA4 (Sek-1) receptor tyrosine kinase in the hindbrain is under direct transcriptional control of Krox-20, Development, vol.125, issue.3, p.9425139, 1998.

H. B. Wood and V. Episkopou, Comparative expression of the mouse Sox1, Sox2 and Sox3 genes from pregastrulation to early somite stages, Mech Dev, vol.86, issue.1-2, p.10446282, 1999.

J. D. Buenrostro, P. G. Giresi, L. C. Zaba, H. Y. Chang, and W. J. Greenleaf, Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position, Nat Methods, vol.10, issue.12, p.24097267, 2013.

C. Labalette, M. A. Wassef, C. Desmarquet-trin-dinh, Y. X. Bouchoucha, L. Men et al., Molecular dissection of segment formation in the developing hindbrain, Development, vol.142, issue.1, p.25516974, 2015.

E. L. Wiellette and H. Sive, vhnf1 and Fgf signals synergize to specify rhombomere identity in the zebrafish hindbrain, Development, vol.130, issue.16, p.12835397, 2003.

S. P. Cordes and G. S. Barsh, The mouse segmentation gene kr encodes a novel basic domain-leucine zipper transcription factor, Cell, vol.79, issue.6, p.8001130, 1994.

A. J. Waskiewicz, H. Rikhof, and C. B. Moens, Reveals a Hindbrain Ground State, Dev Cell, vol.3, p.12431378, 2002.

S. Choe, N. Vlachakis, and C. G. Sagerström, Meis family proteins are required for hindbrain development in the zebrafish, Development, vol.129, issue.3, p.11830560, 2002.

C. L. Mcnulty, J. N. Peres, N. Bardine, W. Van-den-akker, and A. J. Durston, Knockdown of the complete Hox paralogous group 1 leads to dramatic hindbrain and neural crest defects, Development, vol.132, issue.12, p.15930115, 2005.

J. Walshe, H. Maroon, I. M. Mcgonnell, C. Dickson, and I. Mason, Establishment of hindbrain segmental identity requires signaling by FGF3 and FGF8, Curr Biol, vol.12, issue.13, p.12121619, 2002.

F. Aragon and C. Pujades, FGF signaling controls caudal hindbrain specification through Ras-ERK1/2 pathway, BMC Dev Biol, vol.9, p.61, 2009.
DOI : 10.1186/1471-213x-9-61

URL : https://bmcdevbiol.biomedcentral.com/track/pdf/10.1186/1471-213X-9-61

J. Hong, . Hendrix-d-a, and M. S. Levine, Shadow enhancers as a source of evolutionary novelty, Science, vol.321, issue.5894, p.18772429, 2008.

D. Kurokawa, H. Kiyonari, R. Nakayama, C. Kimura-yoshida, I. Matsuo et al., Regulation of Otx2 expression and its functions in mouse forebrain and midbrain, Development, vol.131, issue.14, p.15201224, 2004.

D. D. Lam, F. De-souza, S. Nasif, M. Yamashita, R. López-leal et al., Partially Redundant Enhancers Cooperatively Maintain Mammalian Pomc Expression Above a Critical Functional Threshold, PLOS Genet, vol.11, issue.2, p.25671638, 2015.
DOI : 10.1371/journal.pgen.1004935

URL : https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1004935&type=printable

M. Lagha, J. P. Bothma, and M. Levine, Mechanisms of transcriptional precision in animal development, Trends Genet, vol.28, issue.8, p.22513408, 2012.

M. Z. Ludwig, . Manu, R. Kittler, K. P. White, and M. Kreitman, Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness, PLoS Genet, vol.7, issue.11, 2011.

M. Leddin, C. Perrod, M. Hoogenkamp, S. Ghani, S. Assi et al., Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells, Blood, vol.117, issue.10, p.21239694, 2011.
DOI : 10.1182/blood-2010-08-302976

URL : http://www.bloodjournal.org/content/bloodjournal/117/10/2827.full.pdf

W. Li, D. Notani, and M. G. Rosenfeld, Enhancers as non-coding RNA transcription units: recent insights and future perspectives, Nat Rev Genet, vol.17, issue.4, p.26948815, 2016.
DOI : 10.1038/nrg.2016.4

Y. Lallemand, V. Luria, R. Haffner-krausz, and P. Lonai, Maternally expressed PGK-Cre transgene as a tool for early and uniform activation of the Cre site-specific recombinase, Transgenic Res, vol.7, issue.2, p.9608738, 1998.

F. Giudicelli, E. Taillebourg, P. Charnay, and P. Gilardi-hebenstreit, Krox-20 patterns the hindbrain through both cell-autonomous and non cell-autonomous mechanisms, Genes Dev, vol.15, issue.5, p.11238377, 2001.

D. G. Wilkinson, S. Bhatt, P. Chavrier, R. Bravo, and P. Charnay, Segment-specific expression of a zinc-finger gene in the developing nervous system of the mouse, Nature, vol.337, issue.6206, p.2915691, 1989.

P. Gilardi-hebenstreit, M. A. Nieto, M. Frain, M. G. Mattéi, A. Chestier et al., An Eph-related receptor protein tyrosine kinase gene segmentally expressed in the developing mouse hindbrain. Oncogene, vol.7, p.1281307, 1992.

A. Vitobello, E. Ferretti, X. Lampe, N. Vilain, S. Ducret et al., Hox and Pbx Factors Control Retinoic Acid Synthesis during Hindbrain Segmentation, Dev Cell, vol.20, issue.4, p.21497760, 2011.
DOI : 10.1016/j.devcel.2011.03.011

URL : https://doi.org/10.1016/j.devcel.2011.03.011

L. Jourdren, M. Bernard, M. A. Dillies, L. Crom, and S. Eoulsan, A cloud computing-based framework facilitating high throughput sequencing analyses, Bioinformatics, vol.28, issue.11, p.22492314, 2012.

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., Ultrafast universal RNAseq aligner, Bioinformatics, vol.29, issue.1, p.23104886, 2013.
DOI : 10.1093/bioinformatics/bts635

URL : https://academic.oup.com/bioinformatics/article-pdf/29/1/15/17101697/bts635.pdf

F. Ramírez, F. Dündar, S. Diehl, B. A. Grüning, and T. Manke, DeepTools: A flexible platform for exploring deepsequencing data, Nucleic Acids Res, vol.42, issue.W1, pp.187-91, 2014.

M. Matelot and D. Noordermeer, Determination of High-Resolution 3D Chromatin Organization Using Circular Chromosome Conformation Capture (4C-seq), pp.223-264, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01412298

F. David, J. Delafontaine, S. Carat, F. J. Ross, G. Lefebvre et al., HTSstation: A web application and open-access libraries for high-throughput sequencing data analysis, PLoS One, vol.9, issue.1, 2014.

S. Picelli, A. K. Björklund, B. Reinius, S. Sagasser, G. Winberg et al., Tn5 transposase and tagmentation procedures for massively scaled sequencing projects, Genome Res, vol.24, issue.12, p.25079858, 2014.
DOI : 10.1101/gr.177881.114

URL : http://genome.cshlp.org/content/24/12/2033.full.pdf

Y. Shen, F. Yue, D. F. Mccleary, Z. Ye, L. Edsall et al., A map of the cis-regulatory sequences in the mouse genome, Nature, vol.488, issue.7409, pp.116-136, 2012.