K. Adelman and J. T. Lis, Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans, Nat Rev Genet, vol.13, pp.720-731, 2012.

U. Alon, Network motifs: theory and experimental approaches, Nat Rev Genet, vol.8, pp.450-461, 2007.

A. A. Avilion, S. K. Nicolis, L. H. Pevny, L. Perez, N. Vivian et al., Multipotent cell lineages in early mouse development depend on SOX2 function, Genes Dev, vol.17, pp.126-140, 2003.

Z. Bar-joseph, G. K. Gerber, T. I. Lee, N. J. Rinaldi, J. Y. Yoo et al., Computational discovery of gene modules and regulatory networks, Nat Biotechnol, vol.21, pp.1337-1342, 2003.

E. Barnea and Y. Bergman, Synergy of SF1 and RAR in activation of Oct-3/4 promoter, J Biol Chem, vol.275, pp.6608-6619, 2000.

D. E. Bauer, S. C. Kamran, S. Lessard, J. Xu, Y. Fujiwara et al., An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level, Science, vol.342, pp.253-257, 2013.

M. F. Berger, G. Badis, A. R. Gehrke, S. Talukder, A. A. Philippakis et al., Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences, Cell, vol.133, pp.1266-1276, 2008.

B. E. Bernstein, J. A. Stamatoyannopoulos, J. F. Costello, B. Ren, A. Milosavljevic et al., The NIH Roadmap Epigenomics Mapping Consortium, vol.28, pp.1045-1048, 2010.

R. Bonasio, S. Tu, and D. Reinberg, Molecular signals of epigenetic states, Science, vol.330, pp.612-616, 2010.

L. A. Boyer, T. I. Lee, M. F. Cole, S. E. Johnstone, S. S. Levine et al., Core transcriptional regulatory circuitry in human embryonic stem cells, Cell, vol.122, pp.947-956, 2005.

Y. Buganim, D. A. Faddah, and R. Jaenisch, Mechanisms and models of somatic cell reprogramming, Nat Rev Genet, vol.14, pp.427-439, 2013.

R. Catena, C. Tiveron, A. Ronchi, S. Porta, A. Ferri et al., Conserved POU binding DNA sites in the Sox2 upstream enhancer regulate gene expression in embryonic and neural stem cells, J Biol Chem, vol.279, pp.41846-41857, 2004.

I. Chambers, D. Colby, M. Robertson, J. Nichols, S. Lee et al., Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells, Cell, vol.113, pp.643-655, 2003.

B. Chapuy, M. R. Mckeown, C. Y. Lin, S. Monti, M. Roemer et al., Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma, Cancer Cell, vol.24, pp.777-790, 2013.

D. Cheasley, L. Pereira, S. Lightowler, E. Vincan, J. Malaterre et al., Myb controls intestinal stem cell genes and self-renewal, Stem Cells, vol.29, pp.2042-2050, 2011.

X. Chen, V. B. Vega, and H. Ng, Transcriptional regulatory networks in embryonic stem cells, Cold Spring Harb Symp Quant Biol, vol.73, pp.203-209, 2008.

J. Chew, Y. Loh, W. Zhang, X. Chen, W. Tam et al., Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells, Mol Cell Biol, vol.25, pp.6031-6046, 2005.

N. Chia, Y. Chan, B. Feng, X. Lu, Y. L. Orlov et al., A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity, Nature, vol.468, pp.316-320, 2010.

R. C. Conaway and J. W. Conaway, Origins and activity of the Mediator complex, Semin Cell Dev Biol, vol.22, pp.729-734, 2011.

O. Corradin, A. Saiakhova, B. Akhtar-zaidi, L. Myeroff, J. Willis et al., Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits, Genome Res, vol.24, pp.1-13, 2014.

R. Cowper-sal-lari, X. Zhang, J. B. Wright, S. D. Bailey, M. D. Cole et al., Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression, Nat Genet, vol.44, pp.1191-1198, 2012.

E. H. Davidson, Emerging properties of animal gene regulatory networks, Nature, vol.468, pp.911-920, 2010.

E. De-wit, B. Bouwman, Y. Zhu, P. Klous, E. Splinter et al., The pluripotent genome in three dimensions is shaped around pluripotency factors, Nature, vol.501, pp.227-231, 2013.

J. Declercq, P. Sheshadri, C. M. Verfaillie, and A. Kumar, Zic3 enhances the generation of mouse induced pluripotent stem cells, Stem Cells Dev, vol.22, pp.2017-2025, 2013.

J. R. Dixon, I. Jung, S. Selvaraj, Y. Shen, J. E. Antosiewicz-bourget et al., Chromatin architecture reorganization during stem cell differentiation, Nature, vol.518, pp.331-336, 2015.

S. Doulatov, L. T. Vo, S. S. Chou, P. G. Kim, N. Arora et al., Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors, Cell Stem Cell, vol.13, pp.459-470, 2013.

J. M. Dowen, Z. P. Fan, D. Hnisz, G. Ren, B. J. Abraham et al., Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes, Cell, vol.159, pp.374-387, 2014.

J. Dutkowski, M. Kramer, M. A. Surma, R. Balakrishnan, J. M. Cherry et al., A gene ontology inferred from molecular networks, Nat Biotechnol, vol.31, pp.38-45, 2013.

K. Farh, A. Marson, J. Zhu, M. Kleinewietfeld, W. J. Housley et al., Genetic and epigenetic fine mapping of causal autoimmune disease variants, Nature, vol.518, pp.337-343, 2015.

A. Ferri, Sox2 deficiency causes neurodegeneration and impaired neurogenesis in the adult mouse brain, Development, vol.131, pp.3805-3819, 2004.

J. D. French, M. Ghoussaini, S. L. Edwards, K. B. Meyer, K. Michailidou et al., Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers, Am J Hum Genet, vol.92, pp.489-503, 2013.

M. B. Gerstein, A. Kundaje, M. Hariharan, S. G. Landt, K. Yan et al., Architecture of the human regulatory network derived from ENCODE data, Nature, vol.489, pp.91-100, 2012.

J. Gertz, D. Savic, K. E. Varley, E. C. Partridge, A. Safi et al., Distinct properties of cell-type-specific and shared transcription factor binding sites, Mol Cell, vol.52, pp.25-36, 2013.

C. A. Gifford, M. J. Ziller, H. Gu, C. Trapnell, J. Donaghey et al., Transcriptional and epigenetic dynamics during specification of human embryonic stem cells, Cell, vol.153, pp.1149-1163, 2013.

T. Graf and T. Enver, Forcing cells to change lineages, Nature, vol.462, pp.587-594, 2009.

V. Graham, J. Khudyakov, P. Ellis, and L. Pevny, SOX2 functions to maintain neural progenitor identity, Neuron, vol.39, pp.749-765, 2003.

C. E. Grant, T. L. Bailey, and W. S. Noble, FIMO: scanning for occurrences of a given motif, Bioinformatics, vol.27, pp.1017-1018, 2011.

G. Guo and A. Smith, A genome-wide screen in EpiSCs identifies Nr5a nuclear receptors as potent inducers of ground state pluripotency, Development, vol.137, pp.3185-3192, 2010.

R. D. Hawkins, G. C. Hon, C. Yang, J. E. Antosiewicz-bourget, L. K. Lee et al., Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency, Cell Res, vol.21, pp.1393-1409, 2011.

D. Hnisz, B. J. Abraham, T. I. Lee, A. Lau, V. Saint-andré et al., Super-enhancers in the control of cell identity and disease, Cell, vol.155, pp.934-947, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-02871951

D. Hnisz, J. Schuijers, C. Y. Lin, A. S. Weintraub, B. J. Abraham et al., Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers, Mol Cell, vol.58, pp.362-370, 2015.

F. Holst, P. R. Stahl, C. Ruiz, O. Hellwinkel, Z. Jehan et al., Estrogen receptor ? (ESR1) gene amplification is frequent in breast cancer, Nat Genet, vol.39, pp.655-660, 2007.

M. E. Horb, C. N. Shen, D. Tosh, and J. Slack, Experimental conversion of liver to pancreas, Curr Biol, vol.13, pp.105-115, 2003.

M. A. Hume, L. A. Barrera, S. S. Gisselbrecht, and M. L. Bulyk, UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions, Nucleic Acids Res, vol.43, pp.117-122, 2015.

M. Ieda, J. Fu, P. Delgado-olguin, V. Vedantham, Y. Hayashi et al., Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors, Cell, vol.142, pp.375-386, 2010.

R. Jaenisch and R. Young, Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming, Cell, vol.132, pp.567-582, 2008.

A. Jolma, J. Yan, T. Whitington, J. Toivonen, K. R. Nitta et al., DNA-binding specificities of human transcription factors, Cell, vol.152, pp.327-339, 2013.

J. Jonsson, L. Carlsson, T. Edlund, and H. Edlund, Insulin-promoter-factor 1 is required for pancreas development in mice, Nature, vol.371, pp.606-609, 1994.

M. H. Kagey, J. J. Newman, S. Bilodeau, Y. Zhan, D. A. Orlando et al., Mediator and cohesin connect gene expression and chromatin architecture, Nature, vol.467, pp.430-435, 2010.

M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, and M. Tanabe, KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Res, vol.40, pp.109-114, 2012.

P. Kemmeren, K. Sameith, L. Van-de-pasch, J. J. Benschop, T. L. Lenstra et al., Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors, Cell, vol.157, pp.740-752, 2014.

M. Kertesz, N. Iovino, U. Unnerstall, U. Gaul, and E. Segal, The role of site accessibility in microRNA target recognition, Nat Genet, vol.39, pp.1278-1284, 2007.

H. A. Krebs, The citric acid cycle and the Szent-Györgyi cycle in pigeon breast muscle, Biochem J, vol.34, pp.775-779, 1940.

R. M. Kumar, P. Cahan, A. K. Shalek, R. Satija, J. Daleykeyser et al., Deconstructing transcriptional heterogeneity in pluripotent stem cells, Nature, vol.516, pp.56-61, 2014.

G. Kunarso, N. Chia, J. Jeyakani, C. Hwang, X. Lu et al., Transposable elements have rewired the core regulatory network of human embryonic stem cells, Nat Genet, vol.42, pp.631-634, 2010.

T. Kuroda, M. Tada, H. Kubota, H. Kimura, S. Hatano et al., Octamer and Sox elements are required for transcriptional cis regulation of Nanog gene expression, Mol Cell Biol, vol.25, pp.2475-2485, 2005.

A. N. Kuzmichev, S. Kim, D. 'alessio, A. C. Chenoweth, J. G. Wittko et al., Sox2 acts through Sox21 to regulate transcription in pluripotent and differentiated cells, Curr Biol, vol.22, pp.1705-1710, 2012.

N. Kwiatkowski, T. Zhang, P. B. Rahl, B. J. Abraham, J. Reddy et al., Targeting transcription regulation in cancer with a covalent CDK7 inhibitor, Nature, vol.511, pp.616-620, 2014.

T. I. Lee and R. A. Young, Transcriptional regulation and its misregulation in disease, Cell, vol.152, pp.1237-1251, 2013.

T. I. Lee, N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-joseph et al., Transcriptional regulatory networks in Saccharomyces cerevisiae, Science, vol.298, pp.799-804, 2002.

C. Lefebvre, P. Rajbhandari, M. J. Alvarez, P. Bandaru, W. K. Lim et al., A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers, Mol Syst Biol, vol.6, p.377, 2010.

M. Levine, C. Cattoglio, and R. Tjian, Looping back to leap forward: transcription enters a new era, Cell, vol.157, pp.13-25, 2014.

B. P. Lewis, C. B. Burge, and D. P. Bartel, Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, vol.120, pp.15-20, 2005.

Y. Li, Z. Lv, G. He, J. Wang, X. Zhang et al., The SOX17/miR-371-5p/SOX2 axis inhibits EMT, stem cell properties and metastasis in colorectal cancer, Oncotarget, vol.6, pp.9099-9112, 2015.

Y. K. Lieu and E. P. Reddy, Conditional c-myb knockout in adult hematopoietic stem cells leads to loss of self-renewal due to impaired proliferation and accelerated differentiation, Proc Natl Acad Sci, vol.106, pp.21689-21694, 2009.

L. S. Lim, Y. Loh, W. Zhang, Y. Li, X. Chen et al., Zic3 is required for maintenance of pluripotency in embryonic stem cells, Mol Biol Cell, vol.18, pp.1348-1358, 2007.

A. Loft, I. Forss, M. S. Siersbaek, S. F. Schmidt, A. Larsen et al., Browning of human adipocytes requires KLF11 and reprogramming of PPAR? superenhancers, Genes Dev, vol.29, pp.7-22, 2015.

Y. Loh, Q. Wu, J. Chew, V. B. Vega, W. Zhang et al., The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells, Nat Genet, vol.38, pp.431-440, 2006.

J. Lovén, H. A. Hoke, C. Y. Lin, A. Lau, D. A. Orlando et al., Selective inhibition of tumor oncogenes by disruption of super-enhancers, Cell, vol.153, pp.320-334, 2013.

E. Lujan, S. Chanda, H. Ahlenius, T. C. Südhof, and M. Wernig, Direct conversion of mouse fibroblasts to self-renewing, tripotent neural precursor cells, Proc Natl Acad Sci, vol.109, pp.2527-2532, 2012.

M. R. Mansour, B. J. Abraham, L. Anders, A. Berezovskaya, A. Gutierrez et al., An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element, Science, vol.346, pp.1373-1377, 2014.

S. Masui, Y. Nakatake, Y. Toyooka, D. Shimosato, R. Yagi et al., Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells, Nat Cell Biol, vol.9, pp.625-635, 2007.

A. Mathelier, X. Zhao, A. W. Zhang, F. Parcy, R. Worsley-hunt et al., JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles, Nucleic Acids Res, vol.42, pp.142-147, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00943558

V. Matys, O. V. Kel-margoulis, E. Fricke, I. Liebich, S. Land et al., TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes, Nucleic Acids Res, vol.34, pp.108-110, 2006.

M. T. Maurano, R. Humbert, E. Rynes, R. E. Thurman, E. Haugen et al., Systematic localization of common disease-associated variation in regulatory DNA, Science, vol.337, pp.1190-1195, 2012.

L. A. Medeiros, L. M. Dennis, M. E. Gill, H. Houbaviy, S. Markoulaki et al., Mir-290-295 deficiency in mice results in partially penetrant embryonic lethality and germ cell defects, Proc Natl Acad Sci, vol.108, pp.14163-14168, 2011.

K. Mitsui, Y. Tokuzawa, H. Itoh, K. Segawa, M. Murakami et al., The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells, Cell, vol.113, pp.631-642, 2003.

S. A. Morris and G. Q. Daley, A blueprint for engineering cell fate: current technologies to reprogram cell identity, Cell Res, vol.23, pp.33-48, 2013.

Y. Nam, C. Lubczyk, M. Bhakta, T. Zang, A. Fernandez-perez et al., Induction of diverse cardiac cell types by reprogramming fibroblasts with cardiac transcription factors, Development, vol.141, pp.4267-4278, 2014.

P. Navarro, N. Festuccia, D. Colby, A. Gagliardi, N. P. Mullin et al., OCT4/SOX2-independent Nanog autorepression modulates heterogeneous Nanog gene expression in mouse ES cells, EMBO J, vol.31, pp.4547-4562, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-02025074

S. Neph, A. B. Stergachis, A. Reynolds, R. Sandstrom, E. Borenstein et al., Circuitry and dynamics of human transcription factor regulatory networks, Cell, vol.150, pp.1274-1286, 2012.

J. Nichols, B. Zevnik, K. Anastassiadis, H. Niwa, D. Klewe-nebenius et al., Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4, Cell, vol.95, pp.379-391, 1998.

H. Niwa, J. Miyazaki, and A. G. Smith, Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells, Nat Genet, vol.24, pp.372-376, 2000.

N. Novershtern, A. Subramanian, L. N. Lawton, R. H. Mak, W. N. Haining et al., Densely interconnected transcriptional circuits control cell states in human hematopoiesis, Cell, vol.144, pp.296-309, 2011.

D. T. Odom, N. Zizlsperger, D. B. Gordon, G. W. Bell, N. J. Rinaldi et al., Control of pancreas and liver gene expression by HNF transcription factors, Science, vol.303, pp.1378-1381, 2004.

D. T. Odom, R. D. Dowell, E. S. Jacobsen, L. Nekludova, P. A. Rolfe et al., Core transcriptional regulatory circuitry in human hepatocytes, Mol Syst Biol, vol.2, p.17, 2006.

S. Okumura-nakanishi, M. Saito, H. Niwa, and F. Ishikawa, Oct-3/4 and Sox2 regulate Oct-3/4 gene in embryonic stem cells, J Biol Chem, vol.280, pp.5307-5317, 2005.

C. G. Palii, C. Perez-iratxeta, Z. Yao, Y. Cao, F. Dai et al., Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages, EMBO J, vol.30, pp.494-509, 2011.

S. Parker, M. L. Stitzel, D. L. Taylor, J. M. Orozco, M. R. Erdos et al., Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants, Proc Natl Acad Sci, vol.110, pp.17921-17926, 2013.

I. S. Peter, E. Faure, and E. H. Davidson, Predictive computation of genomic logic processing functions in embryonic development, Proc Natl Acad Sci, vol.109, pp.16434-16442, 2012.

R. Pique-regi, J. F. Degner, A. A. Pai, D. J. Gaffney, Y. Gilad et al., Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data, Genome Res, vol.21, pp.447-455, 2011.

A. M. Quintana, Y. E. Zhou, J. J. Pena, J. P. O'rourke, and S. A. Ness, Dramatic repositioning of c-Myb to different promoters during the cell cycle observed by combining cell sorting with chromatin immunoprecipitation, PLoS One, vol.6, p.17362, 2011.

I. Rajapakse, M. D. Perlman, D. Scalzo, C. Kooperberg, M. Groudine et al., The emergence of lineage-specific chromosomal topologies from coordinate gene regulation, Proc Natl Acad Sci, vol.106, pp.6679-6684, 2009.

K. Robasky and M. L. Bulyk, UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions, Nucleic Acids Res, vol.39, pp.124-128, 2011.

D. J. Rodda, J. Chew, L. Lim, Y. Loh, B. Wang et al., Transcriptional regulation of Nanog by OCT4 and SOX2, J Biol Chem, vol.280, pp.24731-24737, 2005.

R. G. Roeder, Transcriptional regulation and the role of diverse coactivators in animal cells, FEBS Lett, vol.579, pp.909-915, 2005.

T. Rolland, M. Ta?-an, B. Charloteaux, S. J. Pevzner, Q. Zhong et al., A proteome-scale map of the human interactome network, Cell, vol.159, pp.1212-1226, 2014.

T. Sanda, L. N. Lawton, M. I. Barrasa, Z. P. Fan, H. Kohlhammer et al., Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia, Cancer Cell, vol.22, pp.209-221, 2012.

S. F. Schmidt, B. D. Larsen, A. Loft, R. Nielsen, J. Madsen et al., Acute TNF-induced repression of cell identity genes is mediated by NF?B-directed redistribution of cofactors from super-enhancers, 2015.

, Genome Res, vol.25, pp.1281-1294

R. Siersbaek, S. Baek, A. Rabiee, R. Nielsen, S. Traynor et al., Molecular architecture of transcription factor hotspots in early adipogenesis, Cell Rep, vol.7, pp.1434-1442, 2014.

R. Siersbaek, A. Rabiee, R. Nielsen, S. Sidoli, S. Traynor et al., Transcription factor cooperativity in early adipogenic hotspots and super-enhancers, Cell Rep, vol.7, pp.1443-1455, 2014.

J. Silva, J. Nichols, T. W. Theunissen, G. Guo, A. L. Van-oosten et al., Nanog is the gateway to the pluripotent ground state, Cell, vol.138, pp.722-737, 2009.

S. M. Sisodiya, N. K. Ragge, G. L. Cavalleri, A. Hever, B. Lorenz et al., Role of SOX2 mutations in human hippocampal malformations and epilepsy, Epilepsia, vol.47, pp.534-542, 2006.

K. Song, Y. Nam, X. Luo, X. Qi, W. Tan et al., Heart repair by reprogramming non-myocytes with cardiac transcription factors, Nature, vol.485, pp.599-604, 2012.

F. Spitz and E. Furlong, Transcription factors: from enhancer binding to developmental control, Nat Rev Genet, vol.13, pp.613-626, 2012.

A. B. Stergachis, S. Neph, R. Sandstrom, E. Haugen, A. P. Reynolds et al., Conservation of trans-acting circuitry during mammalian regulatory evolution, Nature, vol.515, pp.365-370, 2014.

I. K. Sur, O. Hallikas, A. Vähärautio, J. Yan, M. Turunen et al., Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors, Science, vol.338, pp.1360-1363, 2012.

K. Takahashi and S. Yamanaka, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, vol.126, pp.663-676, 2006.

T. W. Theunissen, A. L. Van-oosten, G. Castelo-branco, J. Hall, A. Smith et al., Nanog overcomes reprogramming barriers and induces pluripotency in minimal conditions, Curr Biol, vol.21, pp.65-71, 2011.

M. Tomioka, M. Nishimoto, S. Miyagi, T. Katayanagi, N. Fukui et al., Identification of Sox-2 regulatory region which is under the control of Oct-3/4-Sox-2 complex, Nucleic Acids Res, vol.30, pp.3202-3213, 2002.

A. M. Tsankov, H. Gu, V. Akopian, M. J. Ziller, J. Donaghey et al., Transcription factor binding dynamics during human ES cell differentiation, Nature, vol.518, pp.344-349, 2015.

S. Tuupanen, M. Turunen, R. Lehtonen, O. Hallikas, S. Vanharanta et al., The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling, Nat Genet, vol.41, pp.885-890, 2009.

J. Usary, V. Llaca, G. Karaca, S. Presswala, M. Karaca et al., Mutation of GATA3 in human breast tumors, Oncogene, vol.23, pp.7669-7678, 2004.

M. Van-den-boogaard, L. Wong, F. Tessadori, M. L. Bakker, L. K. Dreizehnter et al., Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer, J Clin Invest, vol.122, pp.2519-2530, 2012.

J. M. Vaquerizas, S. K. Kummerfeld, S. A. Teichmann, and N. M. Luscombe, A census of human transcription factors: function, expression and evolution, Nat Rev Genet, vol.10, pp.252-263, 2009.

W. Wang, J. Yang, H. Liu, D. Lu, X. Chen et al., Rapid and efficient reprogramming of somatic cells to induced pluripotent stem cells by retinoic acid receptor ? and liver receptor homolog 1, Proc Natl Acad Sci, vol.108, pp.18283-18288, 2011.

G. Wei, G. Badis, M. F. Berger, T. Kivioja, K. Palin et al., Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo, EMBO J, vol.29, pp.2147-2160, 2010.

J. R. White and K. Weston, Myb is required for self-renewal in a model system of early hematopoiesis, Oncogene, vol.19, pp.1196-1205, 2000.

W. A. Whyte, D. A. Orlando, D. Hnisz, B. J. Abraham, C. Y. Lin et al., Master transcription factors and mediator establish super-enhancers at key cell identity genes, Cell, vol.153, pp.307-319, 2013.

N. Wong and X. Wang, miRDB: an online resource for microRNA target prediction and functional annotations, Nucleic Acids Res, vol.43, pp.146-152, 2015.

J. Yan, M. Enge, T. Whitington, D. K. Liu, J. Sur et al., Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites, Cell, vol.154, pp.801-813, 2013.

H. Yang, H. Do, D. Kim, J. Park, C. Chung et al., Transcriptional regulation of human Oct4 by steroidogenic factor-1, J Cell Biochem, vol.101, pp.1198-1209, 2007.

N. Yosef, A. K. Shalek, J. T. Gaublomme, J. H. Lee, Y. Awasthi et al., Dynamic regulatory network controlling T H 17 cell differentiation, Nature, vol.496, pp.461-468, 2013.

R. A. Young, Control of the embryonic stem cell state, Cell, vol.144, pp.940-954, 2011.

J. Yu, M. A. Vodyanik, K. Smuga-otto, A. Bourget, J. Frane et al., Induced pluripotent stem cell lines derived from human somatic cells, Science, vol.318, pp.1917-1920, 2007.

Y. Zhang, T. Liu, C. A. Meyer, J. Eeckhoute, D. S. Johnson et al., Model-based analysis of ChIP-Seq (MACS), Genome Biol, vol.9, p.137, 2008.

X. Zhang, S. Yalcin, D. Lee, T. Yeh, S. Lee et al., FOXO1 is an essential regulator of pluripotency in human embryonic stem cells, Nat Cell Biol, vol.13, pp.1092-1099, 2011.

S. Zhong, X. He, and Z. Bar-joseph, Predicting tissue specific transcription factor binding sites, BMC Genomics, vol.14, p.796, 2013.

Q. Zhou, J. Brown, A. Kanarek, J. Rajagopal, and D. A. Melton, In vivo reprogramming of adult pancreatic exocrine cells to ?-cells, Nature, vol.455, pp.627-632, 2008.

Q. Zhou, T. Li, and D. H. Price, RNA polymerase II elongation control, Annu Rev Biochem, vol.81, pp.119-143, 2012.

Y. Zhu, J. A. Richardson, L. F. Parada, and J. M. Graff, Smad3 mutant mice develop metastatic colorectal cancer, Cell, vol.94, pp.703-714, 1998.

M. J. Ziller, R. Edri, Y. Yaffe, J. Donaghey, R. Pop et al., Dissecting neural differentiation regulatory networks through epigenetic footprinting, Nature, vol.518, pp.355-359, 2014.

J. Zuber, A. R. Rappaport, W. Luo, E. Wang, C. Chen et al., An integrated approach to dissecting oncogene addiction implicates a Myb-coordinated self-renewal program as essential for leukemia maintenance, Genes Dev, vol.25, pp.1628-1640, 2011.

,

, Access the most recent version at doi, vol.26, pp.385-396, 2016.

, Genome Res

V. Saint-andré, A. J. Federation, and C. Y. Lin, Models of human core transcriptional regulatory circuitries Material Supplemental