S. Heinz, C. E. Romanoski, C. Benner, K. A. Allison, M. U. Kaikkonen et al., Effect of natural genetic variation on enhancer selection and function, Nature, vol.503, pp.487-492, 2013.

A. A. Sérandour, S. Avner, F. Percevault, F. Demay, M. Bizot et al., Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers, Genome Res, vol.21, pp.555-565, 2011.

A. G. Cristancho and M. A. Lazar, Forming functional fat: a growing understanding of adipocyte differentiation, Nat. Rev. Mol. Cell Biol, vol.12, pp.722-734, 2011.

Q. Q. Tang and M. D. Lane, Adipogenesis: from stem cell to adipocyte, Annu. Rev. Biochem, vol.81, pp.715-736, 2012.

F. Wang, S. E. Mullican, J. R. Dispirito, L. C. Peed, and M. A. Lazar, Lipoatrophy and severe metabolic disturbance in mice with fat-specific deletion of PPAR?, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.18656-18661, 2013.

A. K. Haakonsson, M. Stahl-madsen, R. Nielsen, A. Sandelin, and S. Mandrup, Acute genome-wide effects of rosiglitazone on PPAR? transcriptional networks in adipocytes, Mol. Endocrinol, vol.27, pp.1536-1549, 2013.

B. Lefebvre, Y. Benomar, A. Guédin, A. Langlois, N. Hennuyer et al., Proteasomal degradation of retinoid X receptor alpha reprograms transcriptional activity of PPARgamma in obese mice and humans, J. Clin. Invest, vol.120, pp.1454-1468, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00472906

M. I. Lefterova, A. K. Haakonsson, M. A. Lazar, and S. Mandrup, PPAR? and the global map of adipogenesis and beyond, Trends Endocrinol. Metab, vol.25, pp.293-302, 2014.

E. Mueller, Understanding the variegation of fat: novel regulators of adipocyte differentiation and fat tissue biology, Biochim. Biophys. Acta, vol.1842, pp.352-357, 2013.

J. Eeckhoute, F. Oger, B. Staels, and P. Lefebvre, Coordinated regulation of PPAR? expression and activity through control of chromatin structure in adipogenesis and obesity, PPAR Res, p.164140, 2012.

R. Siersbaek, R. Nielsen, S. John, M. Sung, S. Baek et al., Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis, EMBO J, vol.30, pp.1459-1472, 2011.

T. S. Mikkelsen, Z. Xu, X. Zhang, L. Wang, J. M. Gimble et al., Comparative epigenomic analysis of murine and human adipogenesis, Cell, vol.143, pp.156-169, 2010.

H. Waki, M. Nakamura, T. Yamauchi, K. Wakabayashi, J. Yu et al., Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation, PLoS Genet, vol.7, p.1002311, 2011.

K. Fujiki, A. Shinoda, F. Kano, R. Sato, K. Shirahige et al., PPAR? -induced PARylation promotes local DNA demethylation by production of 5-hydroxymethylcytosine, Nat. Commun, vol.4, p.2262, 2013.

A. A. Sérandour, S. Avner, F. Oger, M. Bizot, F. Percevault et al., Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers, Nucleic Acids Res, vol.40, pp.8255-8265, 2012.

B. Lee and V. R. Iyer, Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation, J. Biol. Chem, vol.287, pp.30906-30913, 2012.

O. Weth and R. Renkawitz, CTCF function is modulated by neighboring DNA binding factors, Biochem. Cell Biol, vol.89, pp.459-468, 2011.
DOI : 10.1139/o11-033

J. Zlatanova and P. Caiafa, CTCF and its protein partners: divide and rule, J. Cell Sci, vol.122, pp.1275-1284, 2009.
DOI : 10.1242/jcs.039990

URL : http://jcs.biologists.org/content/122/9/1275.full.pdf

V. C. Seitan, A. J. Faure, Y. Zhan, R. P. Mccord, B. R. Lajoie et al., Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments, 2013.
DOI : 10.1101/gr.161620.113

URL : http://genome.cshlp.org/content/23/12/2066.full.pdf

, Genome Res, vol.23, pp.2066-2077

S. Sofueva, E. Yaffe, W. Chan, D. Georgopoulou, M. Rudan et al., Cohesin-mediated interactions organize chromosomal domain architecture, EMBO J, vol.32, pp.3119-3129, 2013.
DOI : 10.1038/emboj.2013.237

URL : http://emboj.embopress.org/content/32/24/3119.full.pdf

J. Zuin, J. R. Dixon, M. I. Van-der-reijden, Z. Ye, P. Kolovos et al., Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells, Proc. Natl. Acad. Sci. U.S.A, vol.111, pp.996-1001, 2013.

M. Herold, M. Bartkuhn, and R. Renkawitz, CTCF: insights into insulator function during development, Development, vol.139, pp.1045-1057, 2012.
DOI : 10.1242/dev.065268

URL : http://dev.biologists.org/content/139/6/1045.full.pdf

F. J. Calero-nieto, F. S. Ng, N. K. Wilson, R. Hannah, V. Moignard et al., Key regulators control distinct transcriptional programmes in blood progenitor and mast cells, EMBO J, vol.33, pp.1212-1226, 2014.

B. Lee, A. A. Bhinge, A. Battenhouse, R. M. Mcdaniell, Z. Liu et al., Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells, 2012.

, Genome Res, vol.22, pp.9-24

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, pp.116-120, 2012.

D. Martin, C. Pantoja, A. Fernández-miñán, C. Valdes-quezada, E. Moltó et al., Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the at Institut Pasteur on October, vol.3, 2011.

, Downloaded from identification of disease-associated genes, Nat. Struct. Mol. Biol, vol.18, pp.708-714

P. C. Schwalie, M. C. Ward, C. E. Cain, A. J. Faure, Y. Gilad et al., Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes, Genome Biol, vol.14, p.148, 2013.

N. C. Sheffield, R. E. Thurman, L. Song, A. Safi, J. A. Stamatoyannopoulos et al., Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions, Genome Res, vol.23, pp.777-788, 2013.

H. Wang, M. T. Maurano, H. Qu, K. E. Varley, J. Gertz et al., Widespread plasticity in CTCF occupancy linked to DNA methylation, Genome Res, vol.22, pp.1680-1688, 2012.

K. Essien, S. Vigneau, S. Apreleva, L. N. Singh, M. S. Bartolomei et al., CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features, 2009.
DOI : 10.1186/gb-2009-10-11-r131

URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2009-10-11-r131

, Genome Biol, vol.10, p.131

F. Oger, C. Gheeraert, D. Mogilenko, Y. Benomar, O. Molendi-coste et al., Cell-specific dysregulation of microRNA expression in obese white adipose tissue, J. Clin. Endocrinol. Metab, vol.99, pp.2821-2833, 2014.

T. N. Nguyen and J. A. Goodrich, Protein-protein interaction assays: eliminating false positive interactions, Nat. Methods, vol.3, pp.135-139, 2006.

S. Caron, C. Huaman-samanez, H. Dehondt, M. Ploton, O. Briand et al., , 2013.

, Farnesoid X receptor inhibits the transcriptional activity of carbohydrate response element binding protein in human hepatocytes, Mol. Cell. Biol, vol.33, pp.2202-2211

F. Oger, J. Dubois-chevalier, C. Gheeraert, S. Avner, E. Durand et al., Peroxisome proliferator-activated receptor ? (PPAR? ) regulates genes involved in insulin/IGF signalling and lipid metabolism during adipogenesis through functionally distinct enhancer classes, J. Biol. Chem, vol.289, pp.708-722, 2014.

R. Nielsen, T. A. Pedersen, D. Hagenbeek, P. Moulos, R. Siersbaek et al., Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis, Genes Dev, vol.22, pp.2953-2967, 2008.

B. M. Colquitt, W. E. Allen, G. Barnea, and S. Lomvardas, Alteration of genic 5-hydroxymethylcytosine patterning in olfactory neurons correlates with changes in gene expression and cell identity, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.14682-14687, 2013.

M. Mellén, P. Ayata, S. Dewell, S. Kriaucionis, and N. Heintz, MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system, Cell, vol.151, pp.1417-1430, 2012.

F. Neri, D. Incarnato, A. Krepelova, S. Rapelli, A. Pagnani et al., Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells, Genome Biol, vol.14, p.91, 2013.

S. K. Raghav, S. M. Waszak, I. Krier, C. Gubelmann, A. Isakova et al., Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBP? and KAISO, Mol. Cell, vol.46, pp.335-350, 2012.

M. S. Siersbaek, A. Loft, M. M. Aagaard, R. Nielsen, S. F. Schmidt et al., Genome-wide profiling of peroxisome proliferator-activated receptor ? in primary epididymal, inguinal, and brown adipocytes reveals depot-selective binding correlated with gene expression, Mol. Cell. Biol, vol.32, pp.3452-3463, 2012.

Y. Xu, F. Wu, L. Tan, L. Kong, L. Xiong et al., Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells, Mol. Cell, vol.42, pp.451-464, 2011.

H. Wu, A. C. D'alessio, S. Ito, K. Xia, Z. Wang et al., Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells, Nature, vol.473, pp.389-393, 2011.

B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, p.25, 2009.

J. W. Nicol, G. A. Helt, S. G. Blanchard, A. Raja, and A. E. Loraine, The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets, Bioinformatics, vol.25, pp.2730-2731, 2009.

B. J. Raney, M. S. Cline, K. R. Rosenbloom, T. R. Dreszer, K. Learned et al., ENCODE whole-genome data in the UCSC genome browser, Nucleic Acids Res, vol.39, pp.871-875, 2011.

J. D. Ziebarth, A. Bhattacharya, and Y. Cui, CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization, Nucleic Acids Res, vol.41, pp.188-194, 2013.
DOI : 10.1093/nar/gks1165

URL : https://academic.oup.com/nar/article-pdf/41/D1/D188/3665130/gks1165.pdf

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.

J. Feng, T. Liu, and Y. Zhang, Using MACS to identify peaks from ChIP-Seq data, Curr. Protoc. Bioinformatics, issue.2, 2011.

J. K. Pickrell, D. J. Gaffney, Y. Gilad, and J. K. Pritchard, False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions, Bioinformatics, vol.27, pp.2144-2146, 2011.

T. Liu, J. A. Ortiz, L. Taing, C. A. Meyer, B. Lee et al., Cistrome: an integrative platform for transcriptional regulation studies, Genome Biol, vol.12, p.83, 2011.

M. Mendoza-parra, W. Van-gool, M. A. Mohamed-saleem, D. G. Ceschin, and H. Gronemeyer, A quality control system for profiles obtained by ChIP sequencing, Nucleic Acids Res, vol.41, p.196, 2013.

Z. Shao, Y. Zhang, G. Yuan, S. H. Orkin, and D. J. Waxman, MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets, Genome Biol, vol.13, p.16, 2012.

E. Forgy, Cluster analysis of multivariate data: efficiency versus interpretability of classifications, Biometrics, vol.21, pp.768-769, 1965.

Z. Zhang, C. W. Chang, W. L. Goh, W. Sung, and E. Cheung, CENTDIST: discovery of co-associated factors by motif distribution, Nucleic Acids Res, vol.39, pp.391-399, 2011.

Z. Zhang, C. W. Chang, W. Hugo, E. Cheung, and W. Sung, Simultaneously learning DNA motif along with its position and sequence rank preferences through expectation maximization algorithm, J. Comput. Biol, vol.20, pp.237-248, 2013.
DOI : 10.1089/cmb.2012.0233

C. T. Workman, Y. Yin, D. L. Corcoran, T. Ideker, G. D. Stormo et al., enoLOGOS: a versatile web tool for energy normalized sequence logos, Nucleic Acids Res, vol.33, pp.389-392, 2005.

D. W. Huang, B. T. Sherman, and R. A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc, vol.4, pp.44-57, 2009.

F. Murtagh and A. Heck, Multivariate Data Analysis, 1986.

D. J. Steger, G. R. Grant, M. Schupp, T. Tomaru, M. I. Lefterova et al., Propagation of adipogenic signals through an epigenomic transition state, Genes Dev, vol.24, pp.1035-1044, 2010.

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.

T. Pham, J. Minderjahn, C. Schmidl, H. Hoffmeister, S. Schmidhofer et al., Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1, Nucleic Acids Res, vol.41, pp.6391-6402, 2013.

J. R. Hughes, N. Roberts, S. Mcgowan, D. Hay, E. Giannoulatou et al., Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment, Nat Genet, vol.46, pp.205-212, 2014.

M. Lupien, J. Eeckhoute, C. A. Meyer, Q. Wang, Y. Zhang et al., FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription, Cell, vol.132, pp.958-970, 2008.
DOI : 10.1016/j.cell.2008.01.018

URL : https://doi.org/10.1016/j.cell.2008.01.018

K. D. Macisaac, K. A. Lo, W. Gordon, S. Motola, T. Mazor et al., A quantitative model of transcriptional regulation, Nucleic Acids Research, vol.42, issue.17, p.10959, 2010.

, reveals the influence of binding location on expression, PLoS Comput. Biol, vol.6, p.1000773

R. Mcbeath, D. M. Pirone, C. M. Nelson, K. Bhadriraju, and C. S. Chen, Cell shape, cytoskeletal tension, and RhoA regulate stem cell lineage commitment, Dev. Cell, vol.6, pp.483-495, 2004.

E. M. Klenova, R. H. Nicolas, H. F. Paterson, A. F. Carne, C. M. Heath et al., CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms, Mol. Cell. Biol, vol.13, pp.7612-7624, 1993.

E. M. Klenova, R. H. Nicolas, A. F. Carne, R. E. Lee, V. V. Lobanenkov et al., Molecular weight abnormalities of the CTCF transcription factor: CTCF migrates aberrantly in SDS-PAGE and the size of the expressed protein is affected by the UTRs and sequences within the coding region of the CTCF gene, Nucleic Acids Res, vol.25, pp.466-474, 1997.

J. Lee and K. Ge, Transcriptional and epigenetic regulation of PPAR? expression during adipogenesis, Cell Biosci, vol.4, p.29, 2014.

R. Siersbaek, R. Nielsen, and S. Mandrup, Transcriptional networks and chromatin remodeling controlling adipogenesis, Trends Endocrinol. Metab, vol.23, pp.56-64, 2011.

K. Wakabayashi, M. Okamura, S. Tsutsumi, N. S. Nishikawa, T. Tanaka et al., The peroxisome proliferator-activated receptor gamma/retinoid X receptor alpha heterodimer targets the histone modification enzyme PR-Set7/Setd8 gene and regulates adipogenesis through a positive feedback loop, Mol. Cell. Biol, vol.29, pp.3544-3555, 2009.

T. Nikolic, D. Movita, M. E. Lambers, C. Ribeiro-de-almeida, P. Biesta et al., The DNA-binding factor Ctcf critically controls gene expression in macrophages, Cell. Mol. Immunol, vol.11, pp.58-70, 2014.

N. D. Heintzman, G. C. Hon, R. D. Hawkins, P. Kheradpour, A. Stark et al., Histone modifications at human enhancers reflect global cell-type-specific gene expression, Nature, vol.459, pp.108-112, 2009.
DOI : 10.1038/nature07829

URL : http://europepmc.org/articles/pmc2910248?pdf=render

V. B. Teif, D. A. Beshnova, Y. Vainshtein, C. Marth, J. Mallm et al., Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development, Genome Res, vol.24, pp.1285-1295, 2014.
DOI : 10.1101/gr.164418.113

URL : http://europepmc.org/articles/pmc4120082?pdf=render

R. D. Hawkins, G. C. Hon, L. K. Lee, Q. Ngo, R. Lister et al., Distinct epigenomic landscapes of pluripotent and lineage-committed human cells, Cell Stem Cell, vol.6, pp.479-491, 2010.

A. S. Nord, M. J. Blow, C. Attanasio, J. A. Akiyama, A. Holt et al., Rapid and pervasive changes in genome-wide enhancer usage during mammalian development, Cell, vol.155, pp.1521-1531, 2013.
DOI : 10.1016/j.cell.2013.11.033

URL : https://doi.org/10.1016/j.cell.2013.11.033

T. Inoue, T. Kohro, T. Tanaka, Y. Kanki, G. Li et al., Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements, Genome Biol, vol.15, p.63, 2014.

F. Jin, Y. Li, J. R. Dixon, S. Selvaraj, Z. Ye et al., A high-resolution map of the three-dimensional chromatin interactome in human cells, Nature, vol.503, pp.290-294, 2013.

G. Li, X. Ruan, R. K. Auerbach, K. S. Sandhu, M. Zheng et al., Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation, Cell, vol.148, pp.84-98, 2012.
DOI : 10.1016/j.cell.2011.12.014

URL : https://doi.org/10.1016/j.cell.2011.12.014

A. Feldmann, R. Ivanek, R. Murr, D. Gaidatzis, L. Burger et al., Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions, PLoS Genet, vol.9, p.1003994, 2013.

S. Guibert and M. Weber, Functions of DNA methylation and hydroxymethylation in mammalian development, Curr. Top. Dev. Biol, vol.104, pp.47-83, 2013.

W. A. Pastor, L. Aravind, and A. Rao, TETonic shift: biological roles of TET proteins in DNA demethylation and transcription, Nat. Rev. Mol. Cell Biol, vol.14, pp.341-356, 2013.

C. J. Kemp, J. M. Moore, R. Moser, B. Bernard, M. Teater et al., CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer, Cell Rep, vol.7, pp.1020-1029, 2014.
DOI : 10.1016/j.celrep.2014.04.004

URL : https://doi.org/10.1016/j.celrep.2014.04.004

B. Delatte, R. Deplus, and F. Fuks, Playing TETris with DNA modifications, EMBO J, vol.33, pp.1198-1211, 2014.
DOI : 10.15252/embj.201488290

URL : http://emboj.embopress.org/content/33/11/1198.full.pdf

C. G. Spruijt, F. Gnerlich, A. H. Smits, T. Pfaffeneder, P. W. Jansen et al., Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives, Cell, vol.152, pp.1146-1159, 2013.

O. Yildirim, R. Li, J. Hung, P. B. Chen, X. Dong et al., Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells, Cell, vol.147, pp.1498-1510, 2011.

Y. Fu, M. Sinha, C. L. Peterson, and Z. Weng, The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome, PLoS Genet, vol.4, p.1000138, 2008.

Z. Liu, D. R. Scannell, M. B. Eisen, and R. Tjian, Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell, vol.146, pp.720-731, 2011.

H. Chen, Y. Tian, W. Shu, X. Bo, and S. Wang, Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome, PLoS One, vol.7, p.41374, 2012.

S. Cuddapah, R. Jothi, D. E. Schones, T. Roh, K. Cui et al., Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains, at Institut Pasteur on October, vol.19, pp.24-32, 2009.