M. Bachman, S. Uribe-lewis, Y. X. Williams, M. Murrell, A. Balasubramanian et al., 5-Hydroxymethylcytosine is a predominantly stable DNA modification, Nat Chem, vol.6, pp.1049-1055, 2014.

S. C. Biddie, S. John, P. J. Sabo, R. E. Thurman, T. A. Johnson et al., Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding, Mol Cell, vol.43, pp.145-155, 2011.

A. Bird, The dinucleotide CG as a genomic signaling module, J Mol Biol, vol.409, pp.47-53, 2011.

E. Calo and J. Wysocka, Modification of enhancer chromatin: what, how, and why, Mol Cell, vol.49, pp.825-837, 2013.

C. P. Chang, Y. Jacobs, T. Nakamura, N. A. Jenkins, N. G. Copeland et al., Meis proteins are major in vivo DNA binding partners for wild-type but not chimeric Pbx proteins, Mol Cell Biol, vol.17, pp.5679-5687, 1997.

R. L. De-la, J. Rodríguez-ubreva, M. García, A. B. Islam, J. M. Urquiza et al., PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation, Genome Biol, vol.14, p.99, 2013.

D. Dong, L. Meng, Q. Yu, G. Tan, M. Ding et al., Stable expression of FoxA1 promotes pluripotent P19 embryonal carcinoma cells to be neural stem-like cells, Gene Expr, vol.15, pp.153-162, 2012.

J. Eeckhoute, M. Lupien, C. A. Meyer, M. P. Verzi, R. A. Shivdasani et al., Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00369667

, Genome Res, vol.19, pp.372-380

S. Ghisletti, I. Barozzi, F. Mietton, S. Polletti, D. Santa et al., Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages, Immunity, vol.32, pp.317-328, 2010.

P. G. Giresi, J. Kim, R. M. Mcdaniell, V. R. Iyer, and J. D. Lieb, FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin, Genome Res, vol.17, pp.877-885, 2007.

. Resultats-partie-i,

H. Mohammed, C. Santos, A. A. Serandour, H. R. Ali, G. D. Brown et al., Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor, Cell Rep, vol.21, pp.342-349, 2013.

D. Szklarczyk, A. Franceschini, S. Wyder, K. Forslund, D. Heller et al., STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Res, vol.43, pp.447-452, 2015.

A. Untergasser, I. Cutcutache, T. Koressaar, J. Ye, B. C. Faircloth et al., , 2012.

, Primer3--new capabilities and interfaces, Nucleic Acids Res, vol.40, p.115

. Bailey, Practical guidelines for the comprehensive analysis of ChIP-seq data, PLOS Comput. Biol, vol.9, p.11, 2013.

. Angelini, Is this the right normalization? A diagnostic tool for ChIP-seq normalization, BMC Bioinformatics, vol.16, p.150, 2015.

. Orlando, Quantitative ChIP-seq normalization reveals global modulation of the epigenome, Cell Reports, vol.9, p.1163, 2014.

. Xu, A signal noise model for significance analysis of ChIP-seq with négative control, Nat. Biotechnol, vol.26, p.1199, 2008.

J. , An integrated software system foa analysing ChIP-chip and ChIP-seq data, Nat. Biotechnol, vol.26, p.1293, 2008.

&. Liang and . Keles, Normalization on ChIP-seq data with control, BMC Bioinformatics, vol.13, p.199, 2012.

. Diaz, Normalization, bias correction, and peak calling for ChIP-seq, Stat. Appl. Gen. Mol. Biol, p.11, 2012.

. Mahé, Cytosine modifications modulate the chromatin architecture of transcriptional enhancers

. Nicol, The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets, Bioinformatics, vol.25, p.2730, 2009.

. Rudin, Non-linear total variation based noise removal algorithms, Physica D, vol.60, p.259, 1992.

. Serandour, Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-asociated enhancers, Nucleic Acid Res, vol.40, p.8255, 2012.

. Saeed, TM4: a free, open-source system for microarray data management and analysis, Biotechniques, vol.34, p.374, 2003.

. Liu, Cistrome: an integrative platform for transcriptional regulation studies, Genome Biology, p.12, 2011.

. Lickwar, Genome-wide protein DNA binding dynamics suggest a molecular clutch for transcription factor function, Nature, vol.484, p.251, 2012.

. Siersbaek, Extensive chromatin remodelling and establishment of transcription factor hotspots during early adipogenesis, The EMBO Journal, vol.30, p.1459, 2011.

C. C. Adams and J. L. Workman, Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative, Mol Cell Biol, vol.15, issue.3, pp.1405-1421, 1995.

K. Adelman and J. T. Lis, Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans, Nat Rev Genet, vol.13, issue.10, pp.720-731, 2012.

S. Aerts, Computational strategies for the genome-wide identification of cis-regulatory elements and transcriptional targets, Curr Top Dev Biol, vol.98, pp.121-145, 2012.

A. Akalin, D. Fredman, E. Arner, X. Dong, J. C. Bryne et al., Transcriptional features of genomic regulatory blocks, Genome Biol, vol.10, issue.4, p.38, 2009.

B. L. Allen and D. J. Taatjes, The Mediator complex: a central integrator of transcription, Nat Rev Mol Cell Biol, vol.16, issue.3, pp.155-166, 2015.

R. Andersson, C. Gebhard, I. Miguel-escalada, I. Hoof, J. Bornholdt et al.,

. Fantom-consortium, A. R. Forrest, P. Carninci, M. Rehli, and A. Sandelin, An atlas of active enhancers across human cell types and tissues, Nature, vol.507, issue.7493, pp.455-461, 2014.

R. Andersson, A. Sandelin, and C. G. Danko, A unified architecture of transcriptional regulatory elements, Trends Genet, vol.31, issue.8, pp.426-433, 2015.

F. Antequera and A. Bird, Number of CpG islands and genes in human and mouse, Proc Natl Acad Sci U S A, vol.90, issue.24, pp.11995-11999, 1993.

G. Arents and E. N. Moudrianakis, The histone fold: a ubiquitous architectural motif utilized in DNA compaction and protein dimerization, Proc Natl Acad Sci U S A, vol.92, issue.24, pp.11170-11174, 1995.

C. D. Arnold, D. Gerlach, C. Stelzer, ?. M. Bory?, M. Rath et al., Genome-wide quantitative enhancer activity maps identified by STARR-seq, Science, vol.339, issue.6123, pp.1074-1077

C. Attanasio, A. S. Nord, Y. Zhu, M. J. Blow, Z. Li et al., Fine tuning of craniofacial morphology by distant-acting enhancers, Science, vol.342, p.1241006, 2013.

G. Auclair, J. Borgel, L. A. Sanz, J. Vallet, S. Guibert et al., EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos, Genome Res, 2015.

M. Bachman, S. Uribe-lewis, Y. X. Burgess, H. E. Iurlaro, M. Reik et al., 5-Formylcytosine can be a stable DNA modification in mammals, Nat Chem Biol, vol.11, issue.8, pp.555-557, 2015.

M. Bachman, S. Uribe-lewis, Y. X. Williams, M. Murrell, A. Balasubramanian et al., 5-Hydroxymethylcytosine is a predominantly stable DNA modification, Nat Chem, vol.6, issue.12, pp.1049-55, 2014.

T. L. Bailey, M. Boden, F. A. Buske, M. Frith, C. E. Grant et al., MEME SUITE: tools for motif discovery and searching, Nucleic Acids Res, vol.37, pp.202-208, 2009.

T. L. Bailey and W. S. Noble, Searching for statistically significant regulatory modules, Bioinformatics, vol.19, pp.16-25, 2003.

A. J. Bannister and T. Kouzarides, Regulation of chromatin by histone modifications, Cell Res, vol.21, issue.3, pp.381-395, 2011.

A. Barski, S. Cuddapah, K. Cui, T. Y. Roh, D. E. Schones et al., Highresolution profiling of histone methylations in the human genome, Cell, vol.129, issue.4, pp.823-837, 2007.

T. Baubec, R. Ivánek, F. Lienert, and D. Schübeler, Methylation-dependent and -independent genomic targeting principles of the MBD protein family, Cell, vol.153, issue.2, pp.480-492, 2013.

C. Bauer, K. Göbel, N. Nagaraj, C. Colantuoni, M. Wang et al., Phosphorylation of TET proteins is regulated via O-GlcNAcylation by the O-linked N-acetylglucosamine transferase (OGT), J Biol Chem, vol.290, issue.8, pp.4801-4812, 2015.

R. Belotserkovskaya, S. Oh, V. A. Bondarenko, G. Orphanides, V. M. Studitsky et al., FACT facilitates transcription-dependent nucleosome alteration, Science, vol.301, issue.5636, pp.1090-1093, 2003.

M. Bergsland, D. Ramsköld, C. Zaouter, S. Klum, R. Sandberg et al., Sequentially acting Sox transcription factors in neural lineage development, Genes Dev, vol.25, issue.23, pp.2453-2464, 2011.

B. E. Bernstein, T. S. Mikkelsen, X. Xie, M. Kamal, D. J. Huebert et al., A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell, vol.125, issue.2, pp.315-326, 2006.

S. C. Biddie, S. John, P. J. Sabo, R. E. Thurman, T. A. Johnson et al., Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding, Mol Cell, vol.43, issue.1, pp.145-155, 2011.

E. M. Blackwood and J. T. Kadonaga, Going the distance: a current view of enhancer action, Science, vol.281, issue.5373, pp.60-63, 1998.

M. J. Blow, D. J. Mcculley, Z. Li, T. Zhang, J. A. Akiyama et al., ChIP-Seq identification of weakly conserved heart enhancers, Nat Genet, vol.42, issue.9, pp.806-810, 2010.

J. Boeke, O. Ammerpohl, S. Kegel, U. Moehren, and R. Renkawitz, The minimal repression domain of MBD2b overlaps with the methyl-CpG-binding domain and binds directly to Sin3A, J Biol Chem, vol.275, issue.45, pp.34963-34967, 2000.

A. Bolzer, G. Kreth, I. Solovei, D. Koehler, K. Saracoglu et al., Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes, PLoS Biol, vol.3, issue.5, p.157, 2005.

S. Bonn, R. P. Zinzen, C. Girardot, E. H. Gustafson, A. Perez-gonzalez et al., Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development, Nat Genet, vol.44, issue.2, pp.148-156, 2012.

M. J. Booth, M. R. Branco, G. Ficz, D. Oxley, F. Krueger et al., Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution, Science, vol.336, issue.6083, pp.934-937, 2012.

M. J. Booth, G. Marsico, M. Bachman, D. Beraldi, and S. Balasubramanian, Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution, Nat Chem, vol.6, issue.5, pp.435-440, 2014.

J. Borgel, S. Guibert, Y. Li, H. Chiba, D. Schübeler et al., Targets and dynamics of promoter DNA methylation during early mouse development, Nat Genet, vol.42, issue.12, pp.1093-1100, 2010.

M. Bostick, J. K. Kim, P. O. Estève, A. Clark, S. Pradhan et al., UHRF1 plays a role in maintaining DNA methylation in mammalian cells, Science, vol.317, issue.5845, pp.1760-1764, 2007.

D. Bourc'his, G. L. Xu, C. S. Lin, B. Bollman, and T. H. Bestor, Dnmt3L and the establishment of maternal genomic imprints, Science, vol.294, issue.5551, pp.2536-2539, 2001.

T. Boveri, Die Blastomerenkerne von Ascaris megalocephala und die Theorie der Chromosomenindividualität, Arch Zellforsch, vol.3, pp.181-268, 1909.

J. Boyes and A. Bird, DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein, Cell, vol.64, issue.6, pp.1123-1134, 1991.

J. Boyes and A. Bird, Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein, EMBO J, vol.11, issue.1, pp.327-333, 1992.

J. Boyes and G. Felsenfeld, Tissue-specific factors additively increase the probability of the all-or-none formation of a hypersensitive site, EMBO J, vol.15, issue.10, pp.2496-2507, 1996.

S. Boyle, S. Gilchrist, J. M. Bridger, N. L. Mahy, J. A. Ellis et al., The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells, Hum Mol Genet, vol.10, issue.3, pp.211-219, 2001.

M. Brandeis, D. Frank, I. Keshet, Z. Siegfried, M. Mendelsohn et al., Sp1 elements protect a CpG island from de novo methylation, Nature, vol.371, issue.6496, pp.435-438, 1994.

A. Breiling and F. Lyko, Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond, Epigenetics Chromatin, vol.8, p.24, 2015.

C. Brenner, R. Deplus, C. Didelot, A. Loriot, E. Viré et al., Myc represses transcription through recruitment of DNA methyltransferase corepressor, EMBO J, vol.24, issue.2, pp.336-346, 2005.

M. Brunelle, N. Markovits, A. Rodrigue, S. Lupien, M. Jacques et al., The histone variant H2A.Z is an important regulator of enhancer activity, Nucleic Acids Res, vol.43, issue.20, pp.9742-9756, 2015.

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, pp.1213-1218, 2013.

A. Bulut-karslioglu, V. Perrera, M. Scaranaro, I. A. De-la-rosa-velazquez, S. Van-de-nobelen et al., A transcription factor-based mechanism for mouse heterochromatin formation, Nat Struct Mol Biol, vol.19, issue.10, pp.1023-1030, 2012.

T. W. Burke and J. T. Kadonaga, The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila, Genes Dev, vol.11, issue.22, pp.3020-3031, 1997.

A. K. Byrd and K. D. Raney, Superfamily 2 helicases. Front Biosci (Landmark Ed, vol.17, pp.2070-2088, 2012.

B. R. Cairns, Y. J. Kim, M. H. Sayre, B. C. Laurent, and R. D. Kornberg, A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast, Proc Natl Acad Sci U S A, vol.91, issue.5, pp.1950-1954, 1994.

B. R. Cairns, Y. Lorch, Y. Li, M. Zhang, L. Lacomis et al., RSC, an essential, abundant chromatin-remodeling complex, Cell, vol.87, issue.7, pp.1249-1260, 1996.

E. Calo and J. Wysocka, Modification of enhancer chromatin: what, how, and why?, Mol Cell, vol.49, issue.5, pp.825-837, 2013.

E. Cannavò, P. Khoueiry, D. A. Garfield, P. Geeleher, T. Zichner et al., Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks, Curr Biol, vol.26, issue.1, pp.38-51, 2016.

P. Carninci, A. Sandelin, B. Lenhard, S. Katayama, K. Shimokawa et al., Genome-wide analysis of mammalian promoter architecture and evolution, Nat Genet, vol.38, issue.6, pp.626-635, 2006.

G. Caron, M. Hussein, M. Kulis, C. Delaloy, F. Chatonnet et al., Cell-Cycle-Dependent Reconfiguration of the DNA Methylome during Terminal Differentiation of Human B Cells into Plasma Cells, Cell Rep, vol.13, issue.5, pp.1059-1071, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01219671

J. S. Carroll, X. S. Liu, A. S. Brodsky, W. Li, C. A. Meyer et al., Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1, Cell, vol.122, issue.1, pp.33-43, 2005.

P. F. Cartron, A. Nadaradjane, F. Lepape, L. Lalier, B. Gardie et al., Identification of TET1 Partners That Control Its DNA-Demethylating Function, Genes Cancer, vol.4, issue.5-6, pp.235-241, 2013.

G. E. Chalkley and C. P. Verrijzer, DNA binding site selection by RNA polymerase II TAFs: a TAF(II)250-TAF(II)150 complex recognizes the initiator, EMBO J, vol.18, issue.17, pp.4835-4845, 1999.

C. C. Chen, K. Y. Wang, and C. K. Shen, The mammalian de novo DNA methyltransferases DNMT3A and DNMT3B are also DNA 5-hydroxymethylcytosine dehydroxymethylases, J Biol Chem, vol.287, issue.40, pp.33116-33121, 2012.

Q. Chen, Y. Chen, C. Bian, R. Fujiki, and X. Yu, TET2 promotes histone O-GlcNAcylation during gene transcription, Nature, vol.493, issue.7433, pp.561-564, 2013.

I. Chepelev, G. Wei, D. Wangsa, Q. Tang, and K. Zhao, Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization, Cell Res, vol.22, issue.3, pp.490-503, 2012.

L. A. Cirillo, F. R. Lin, I. Cuesta, D. Friedman, M. Jarnik et al., Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4, Mol Cell, vol.9, issue.2, pp.279-289, 2002.

L. A. Cirillo and K. S. Zaret, An early developmental transcription factor complex that is more stable on nucleosome core particles than on free DNA, Mol Cell, vol.4, issue.6, pp.961-969, 1999.

M. L. Conerly, S. S. Teves, D. Diolaiti, M. Ulrich, R. N. Eisenman et al., Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis, Genome Res, vol.20, issue.10, pp.1383-1390, 2010.

D. N. Cooper and M. Krawczak, Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes, Hum Genet, vol.83, issue.2, pp.181-188, 1989.

L. J. Core, A. L. Martins, C. G. Danko, C. T. Waters, A. Siepel et al., Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers, Nat Genet, vol.46, issue.12, pp.1311-1320, 2014.

L. J. Core, J. J. Waterfall, and J. T. Lis, Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters, Science, vol.322, issue.5909, pp.1845-1848, 2008.

D. Cortázar, C. Kunz, J. Selfridge, T. Lettieri, Y. Saito et al., Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability, Nature Feb, vol.470, issue.7334, pp.419-423, 2011.

S. Cortellino, J. Xu, M. Sannai, R. Moore, E. Caretti et al., Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair, Cell, vol.146, issue.1, pp.67-79, 2011.

Y. Costa, J. Ding, T. W. Theunissen, F. Faiola, T. A. Hore et al., NANOG-dependent function of TET1 and TET2 in establishment of pluripotency, Nature, vol.495, issue.7441, pp.370-374, 2013.

J. Côté, J. Quinn, J. L. Workman, and C. L. Peterson, Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF protein complex, Science, vol.265, issue.5168, pp.53-60, 1994.

M. P. Creyghton, A. W. Cheng, G. G. Welstead, T. Kooistra, B. W. Carey et al., Histone H3K27ac separates active from poised enhancers and predicts developmental state, Proc Natl Acad Sci U S A, vol.107, issue.50, pp.21931-21936, 2010.

M. P. Creyghton, S. Markoulaki, S. S. Levine, J. Hanna, M. A. Lodato et al., H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment, Cell, vol.135, issue.4, pp.649-661, 2008.

J. A. Croft, J. M. Bridger, S. Boyle, P. Perry, P. Teague et al., Differences in the localization and morphology of chromosomes in the human nucleus, J Cell Biol, vol.145, issue.6, pp.1119-1131, 1999.

K. Cui, C. Zang, T. Y. Roh, D. E. Schones, R. W. Childs et al., Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation, Cell Stem Cell, vol.4, issue.1, pp.80-93, 2009.

M. Curradi, A. Izzo, G. Badaracco, and N. Landsberger, Molecular mechanisms of gene silencing mediated by DNA methylation, Mol Cell Biol, vol.22, issue.9, pp.3157-3173, 2002.

R. L. De-la, J. Rodríguez-ubreva, M. García, A. B. Islam, J. M. Urquiza et al., PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation, Genome Biol, vol.14, issue.9, p.99, 2013.

D. Santa, F. Barozzi, I. Mietton, F. Ghisletti, S. Polletti et al., A large fraction of extragenic RNA pol II transcription sites overlap enhancers, PLoS Biol, vol.8, issue.5, p.1000384, 2010.

E. De-wit, E. S. Vos, S. J. Holwerda, C. Valdes-quezada, M. J. Verstegen et al., CTCF Binding Polarity Determines Chromatin Looping. Mol Cell, vol.60, issue.4, pp.676-684, 2015.

S. C. Degner, J. Verma-gaur, T. P. Wong, C. Bossen, G. M. Iverson et al., CCCTCbinding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells, Proc Natl Acad Sci U S A, vol.108, issue.23, pp.9566-9571, 2011.

R. Deplus, B. Delatte, M. K. Schwinn, M. Defrance, J. Méndez et al., TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS, EMBO J, vol.32, issue.5, pp.645-55, 2013.

A. Dhayalan, A. Rajavelu, P. Rathert, R. Tamas, R. Z. Jurkowska et al., The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation, J Biol Chem, vol.285, issue.34, pp.26114-26120, 2010.

P. Dimitri, R. Caizzi, G. E. , C. Accardo, M. Lattanzi et al., Constitutive heterochromatin: a surprising variety of expressed sequences, Chromosoma, vol.118, issue.4, pp.419-435, 2009.

C. Dinant, G. Ampatziadis-michailidis, H. Lans, M. Tresini, A. Lagarou et al., Enhanced chromatin dynamics by FACT promotes transcriptional restart after UV-induced DNA damage, Mol Cell, vol.51, issue.4, pp.469-479, 2013.

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, pp.376-380, 2012.

C. M. Doyen, F. Montel, T. Gautier, H. Menoni, C. Claudet et al., Dissection of the unusual structural and functional properties of the variant H2A.Bbd nucleosome, EMBO J, vol.25, issue.18, pp.4234-4244, 2006.
URL : https://hal.archives-ouvertes.fr/inserm-00335077

C. M. Doyen, W. An, D. Angelov, V. Bondarenko, F. Mietton et al., Mechanism of polymerase II transcription repression by the histone variant macroH2A, Mol Cell Biol, vol.26, issue.3, pp.1156-1164, 2006.
URL : https://hal.archives-ouvertes.fr/inserm-00091626

P. Drané, K. Ouararhni, A. Depaux, M. Shuaib, and A. Hamiche, The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3, Genes Dev, vol.24, issue.12, pp.1253-1265, 2010.

R. Drissen, R. J. Palstra, N. Gillemans, E. Splinter, F. Grosveld et al., The active spatial organization of the beta-globin locus requires the transcription factor EKLF, Genes Dev, vol.18, issue.20, pp.2485-2490, 2004.

A. Dvir, Promoter escape by RNA polymerase II, Biochim Biophys Acta, vol.1577, issue.2, pp.208-223, 2002.

S. R. Eberhardy and P. J. Farnham, Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter, J Biol Chem, vol.277, issue.42, pp.40156-40162, 2002.

D. H. Ebert, H. W. Gabel, N. D. Robinson, N. R. Kastan, L. S. Hu et al., Activity-dependent phosphorylation of MeCP2 threonine 308 regulates interaction with NCoR, Nature, vol.499, issue.7458, pp.341-345, 2013.

J. Eeckhoute, E. K. Keeton, M. Lupien, S. A. Krum, J. S. Carroll et al., Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer, Cancer Res, vol.67, issue.13, pp.6477-6483, 2007.

J. Eeckhoute, M. Lupien, C. A. Meyer, M. P. Verzi, R. A. Shivdasani et al., Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers, Genome Res, vol.19, issue.3, pp.372-380, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00369667

. Encode-project-consortium and E. Birney, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, vol.447, issue.7146, pp.799-816, 2007.

. Encode-project-consortium, An integrated encyclopedia of DNA elements in the human genome, Nature, vol.489, issue.7414, pp.57-74, 2012.

J. Ernst and M. Kellis, Discovery and characterization of chromatin states for systematic annotation of the human genome, Nat Biotechnol, vol.28, issue.8, pp.817-825, 2010.

J. Ernst, P. Kheradpour, T. S. Mikkelsen, N. Shoresh, L. D. Ward et al., Mapping and analysis of chromatin state dynamics in nine human cell types, Nature, vol.473, issue.7345, pp.43-49, 2011.

C. Esnault, Y. Ghavi-helm, S. Brun, J. Soutourina, N. Van-berkum et al., Mediator-dependent recruitment of TFIIH modules in preinitiation complex, Mol Cell, vol.31, issue.3, pp.337-346, 2008.

N. Feldman, A. Gerson, J. Fang, E. Li, Y. Zhang et al., G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis, Nat Cell Biol, vol.8, issue.2, pp.188-194, 2006.

S. Feng, S. J. Cokus, X. Zhang, P. Y. Chen, M. Bostick et al., Conservation and divergence of methylation patterning in plants and animals, Proc Natl Acad Sci U S A, vol.107, pp.8689-8694, 2010.

Y. Q. Feng, R. Desprat, H. Fu, E. Olivier, C. M. Lin et al., DNA methylation supports intrinsic epigenetic memory in mammalian cells, PLoS Genet, vol.2, issue.4, p.65, 2006.

H. Ferreira, A. Flaus, and T. Owen-hughes, Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms, J. Mol. Biol, vol.374, issue.3, pp.563-579, 2007.

G. Ficz, M. R. Branco, S. Seisenberger, F. Santos, F. Krueger et al., Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation, Nature, vol.473, issue.7347, pp.398-402, 2011.

G. J. Filion, J. G. Van-bemmel, U. Braunschweig, W. Talhout, J. Kind et al., Systematic protein location mapping reveals five principal chromatin types in Drosophila cells, Cell, vol.143, issue.2, pp.212-224, 2010.

L. E. Finlan, D. Sproul, I. Thomson, S. Boyle, E. Kerr et al., Recruitment to the nuclear periphery can alter expression of genes in human cells, PLoS Genet, vol.4, issue.3, p.1000039, 2008.

A. B. Fleming, C. F. Kao, C. Hillyer, M. Pikaart, and M. A. Osley, H2B ubiquitylation plays a role in nucleosome dynamics during transcription elongation, Mol Cell, vol.31, issue.1, pp.57-66, 2008.

S. D. Fouse, Y. Shen, M. Pellegrini, S. Cole, A. Meissner et al., Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation, Cell Stem Cell, vol.2, issue.2, pp.160-169, 2008.

C. Frauer, T. Hoffmann, S. Bultmann, V. Casa, M. C. Cardoso et al., Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain, PLoS One, vol.6, issue.6, p.21306, 2011.

E. L. Fritz and F. N. Papavasiliou, Cytidine deaminases: AIDing DNA demethylation?, Genes Dev, vol.24, pp.2107-2114, 2010.

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.

R. Fujiki, W. Hashiba, H. Sekine, A. Yokoyama, T. Chikanishi et al., GlcNAcylation of histone H2B facilitates its monoubiquitination, Nature, vol.480, issue.7378, pp.557-560, 2011.

N. Fujita, S. Takebayashi, K. Okumura, S. Kudo, T. Chiba et al., Methylation-mediated transcriptional silencing in euchromatin by methyl-CpG binding protein MBD1 isoforms, Mol Cell Biol, vol.19, issue.9, pp.6415-6426, 1999.

F. Fuks, W. A. Burgers, A. Brehm, L. Hughes-davies, and T. Kouzarides, DNA methyltransferase Dnmt1 associates with histone deacetylase activity, Nat Genet, vol.24, issue.1, pp.88-91, 2000.

F. Fuks, P. J. Hurd, R. Deplus, and T. Kouzarides, The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase, Nucleic Acids Res, vol.31, issue.9, pp.2305-2312, 2003.

M. J. Fullwood, M. H. Liu, Y. F. Pan, J. Liu, H. Xu et al., An oestrogen-receptor-alpha-bound human chromatin interactome, Nature, vol.462, issue.7269, pp.58-64, 2009.

B. W. Futscher, M. M. Oshiro, R. J. Wozniak, N. Holtan, C. L. Hanigan et al., Role for DNA methylation in the control of cell type specific maspin expression, Nat Genet, vol.31, issue.2, pp.175-179, 2002.

D. Gackowski, E. Zarakowska, M. Starczak, M. Modrzejewska, and R. Olinski, Tissue-Specific Differences in DNA Modifications (5-Hydroxymethylcytosine, 5-Formylcytosine, 5-Carboxylcytosine and 5-Hydroxymethyluracil) and Their Interrelationships, PLoS One, vol.10, issue.12, p.144859, 2015.

M. J. Gamble, K. M. Frizzell, C. Yang, R. Krishnakumar, and W. L. Kraus, The histone variant macroH2A1 marks repressed autosomal chromatin, but protects a subset of its target genes from silencing, Genes Dev, vol.24, issue.1, pp.21-32, 2010.

N. Gao, J. Zhang, M. A. Rao, T. C. Case, J. Mirosevich et al., The role of hepatocyte nuclear factor-3 alpha (Forkhead Box A1) and androgen receptor in transcriptional regulation of prostatic genes, Mol Endocrinol, vol.17, issue.8, pp.1484-1507, 2003.

M. Gaszner and G. Felsenfeld, Insulators: exploiting transcriptional and epigenetic mechanisms, Nat Rev Genet, issue.9, pp.703-713, 2006.

Y. Z. Ge, M. T. Pu, H. Gowher, H. P. Wu, J. P. Ding et al., Chromatin targeting of de novo DNA methyltransferases by the PWWP domain, J Biol Chem, vol.279, issue.24, pp.25447-25454, 2004.

T. M. Geiman, U. T. Sankpal, A. K. Robertson, Y. Zhao, Y. Zhao et al., DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system, Biochem Biophys Res Commun, vol.318, issue.2, pp.544-555, 2004.

S. Ghisletti, I. Barozzi, F. Mietton, S. Polletti, D. Santa et al., Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages, Immunity, vol.32, issue.3, pp.317-328, 2010.

H. J. Gierman, M. H. Indemans, J. Koster, S. Goetze, J. Seppen et al., Domainwide regulation of gene expression in the human genome, Genome Res, vol.17, issue.9, pp.1286-1295, 2007.

D. Globisch, M. Münzel, M. Müller, S. Michalakis, M. Wagner et al., Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates, PLoS One, vol.5, issue.12, p.15367, 2010.

S. Goetze, J. Mateos-langerak, H. J. Gierman, W. De-leeuw, O. Giromus et al., The three-dimensional structure of human interphase chromosomes is related to the transcriptome map, Mol Cell Biol, vol.27, issue.12, pp.4475-4487, 2007.

A. D. Goldberg, L. A. Banaszynski, K. M. Noh, P. W. Lewis, S. J. Elsaesser et al., Distinct factors control histone variant H3.3 localization at specific genomic regions, Cell, vol.140, issue.5, pp.678-691, 2010.

J. A. Goldman, J. D. Garlick, and R. E. Kingston, Chromatin remodeling by imitation switch (ISWI) class ATPdependent remodelers is stimulated by histone variant H2A, Z. J Biol Chem, vol.285, issue.7, pp.4645-4651, 2010.

J. P. Golla, J. Zhao, I. K. Mann, S. K. Sayeed, A. Mandal et al., Carboxylation of cytosine (5caC) in the CG dinucleotide in the E-box motif (CGCAG|GTG) increases binding of the Tcf3|Ascl1 helix-loophelix heterodimer 10-fold, Biochem Biophys Res Commun, vol.449, issue.2, pp.248-255, 2014.

J. A. Goodrich and R. Tjian, Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation, Nat Rev Genet, vol.11, issue.8, pp.549-558, 2010.

D. Gosselin, V. M. Link, C. E. Romanoski, G. J. Fonseca, D. Z. Eichenfield et al., Environment drives selection and function of enhancers controlling tissuespecific macrophage identities, Cell, vol.159, issue.6, pp.1327-1340, 2014.

Y. Guo, Q. Xu, D. Canzio, J. Shou, J. Li et al., CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function, Cell, vol.162, issue.4, pp.900-910, 2015.

N. Hah, S. Murakami, A. Nagari, C. G. Danko, and W. L. Kraus, Enhancer transcripts mark active estrogen receptor binding sites, Genome Res, vol.23, issue.8, pp.1210-1223, 2013.

L. Handoko, H. Xu, G. Li, C. Y. Ngan, E. Chew et al., CTCF-mediated functional chromatin interactome in pluripotent cells, Nat Genet, vol.43, issue.7, pp.630-638, 2011.

H. Hashimoto, Y. O. Olanrewaju, Y. Zheng, G. G. Wilson, X. Zhang et al., Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence, Genes Dev, vol.28, issue.20, pp.2304-2313, 2014.

K. Havas, I. Whitehouse, and T. Owen-hughes, ATP-dependent chromatin remodeling activities, Cell Mol Life Sci, vol.58, issue.5-6, pp.673-682, 2001.

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, issue.10, pp.1393-1409, 2011.

H. H. He, C. A. Meyer, H. Shin, S. T. Bailey, G. Wei et al., Nucleosome dynamics define transcriptional enhancers, Nat Genet, vol.42, issue.4, pp.343-347, 2010.

Y. F. He, B. Z. Li, Z. Li, P. Liu, Y. Wang et al., Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA, Science, vol.333, issue.6047, pp.1303-1307, 2011.

A. B. Heidt, A. Rojas, I. S. Harris, and B. L. Black, Determinants of myogenic specificity within MyoD are required for noncanonical E box binding, Mol Cell Biol, vol.27, issue.16, pp.5910-520, 2007.

N. D. Heintzman, G. C. Hon, R. D. Hawkins, P. Kheradpour, A. Stark et al., Histone modifications at human enhancers reflect global cell-typespecific gene expression, Nature, vol.459, issue.7243, pp.108-120, 2009.

N. D. Heintzman and B. Ren, The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome, Cell Mol Life Sci, vol.64, issue.4, pp.386-400, 2007.

N. D. Heintzman, R. K. Stuart, G. Hon, Y. Fu, C. W. Ching et al., Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome, Nat Genet, vol.39, issue.3, pp.311-318, 2007.

S. Heinz, C. Benner, N. Spann, E. Bertolino, Y. C. Lin et al., Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol Cell, vol.38, issue.4, pp.576-589, 2010.

S. Heinz, C. E. Romanoski, C. Benner, and C. K. Glass, The selection and function of cell type-specific enhancers, Nat Rev Mol Cell Biol, vol.16, issue.3, pp.144-154, 2015.

B. Hendrich and A. Bird, Identification and characterization of a family of mammalian methyl-CpG binding proteins, Mol Cell Biol, vol.18, issue.11, pp.6538-6547, 1998.

B. Hendrich, U. Hardeland, H. H. Ng, J. Jiricny, and A. Bird, The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites, Nature, vol.401, issue.6750, pp.301-304, 1999.

C. Hepperger, A. Mannes, J. Merz, J. Peters, and S. Dietzel, Three-dimensional positioning of genes in mouse cell nuclei, Chromosoma, vol.117, issue.6, pp.535-551, 2008.

A. Hermann, R. Goyal, and A. Jeltsch, The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites, J Biol Chem, vol.279, pp.48350-48359, 2004.

E. Hervouet, F. M. Vallette, and P. F. Cartron, Dnmt3/transcription factor interactions as crucial players in targeted DNA methylation, Epigenetics, vol.4, issue.7, pp.487-499, 2009.

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, issue.4, pp.934-947, 2013.

F. C. Holstege, P. C. Van-der-vliet, and H. T. Timmers, Opening of an RNA polymerase II promoter occurs in two distinct steps and requires the basal transcription factors IIE and IIH, EMBO J, vol.15, issue.7, pp.1666-1677, 1996.

G. Hon, W. Wang, and B. Ren, Discovery and annotation of functional chromatin signatures in the human genome, PLoS Comput Biol, vol.5, issue.11, p.1000566, 2009.

G. C. Hon, C. X. Song, T. Du, J. F. Selvaraj, S. Lee et al., 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation, Mol Cell, vol.56, issue.2, pp.286-297, 2014.

J. W. Hong, D. A. Hendrix, and M. S. Levine, Shadow enhancers as a source of evolutionary novelty, Science, vol.321, issue.5894, p.1314, 2008.

G. Hu, K. Cui, D. Northrup, C. Liu, C. Wang et al., H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation, Cell Stem, vol.12, issue.2, pp.180-192, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01290624

L. Hu, J. Lu, J. Cheng, Q. Rao, Z. Li et al., Structural insight into substrate preference for TET-mediated oxidation, Nature, vol.527, issue.7576, pp.118-122, 2015.

A. Hurtado, K. A. Holmes, C. S. Ross-innes, D. Schmidt, and J. S. Carroll, FOXA1 is a key determinant of estrogen receptor function and endocrine response, Nat Genet, vol.43, issue.1, pp.27-33, 2011.

S. M. Iguchi-ariga and W. Schaffner, CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation, Genes Dev, vol.3, issue.5, pp.612-619, 1989.

S. Ito, D. 'alessio, A. C. Taranova, O. V. Hong, K. Sowers et al., Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification, Nature, vol.466, issue.7310, pp.1129-1133, 2010.

S. Ito, L. Shen, Q. Dai, S. C. Wu, L. B. Collins et al., Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine, Science, vol.333, issue.6047, pp.1300-1303, 2011.

T. Ito, M. Bulger, M. J. Pazin, R. Kobayashi, and J. T. Kadonaga, ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor, Cell, vol.90, issue.1, pp.145-155, 1997.

M. Iurlaro, G. Ficz, D. Oxley, E. A. Raiber, M. Bachman et al., A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation, Genome Biol, vol.14, issue.10, p.119, 2013.

L. M. Iyer, M. Tahiliani, A. Rao, and L. Aravind, Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids, Cell Cycle, vol.8, issue.11, pp.1698-1710, 2009.

R. H. Jacobson, A. G. Ladurner, D. S. King, and R. Tjian, Structure and function of a human TAFII250 double bromodomain module, Science, vol.288, issue.5470, pp.1422-1425, 2000.

C. Jin and G. Felsenfeld, Nucleosome stability mediated by histone variants H3.3 and H2A, Z. Genes Dev, vol.21, issue.12, pp.1519-1529, 2007.

C. Jin, C. Zang, G. Wei, K. Cui, W. Peng et al., H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions, Nat Genet, vol.41, issue.8, pp.941-945, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01292426

F. Jin, Y. Li, J. R. Dixon, S. Selvaraj, Z. Ye et al., A highresolution map of the three-dimensional chromatin interactome in human cells, Nature, vol.503, issue.7475, pp.290-294, 2013.

O. Johansson, W. Alkema, W. W. Wasserman, and J. Lagergren, Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm, Bioinformatics, vol.19, pp.169-176, 2003.

P. A. Jones and G. Liang, Rethinking how DNA methylation patterns are maintained, Nat Rev Genet, vol.10, issue.11, pp.805-811, 2009.

P. L. Jones, G. J. Veenstra, P. A. Wade, D. Vermaak, S. U. Kass et al., Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription, Nat Genet, vol.19, issue.2, pp.187-191, 1998.

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, issue.7314, pp.430-435, 2010.

M. U. Kaikkonen, N. J. Spann, S. Heinz, C. E. Romanoski, K. A. Allison et al., Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription, Mol Cell, vol.51, issue.3, pp.310-325, 2013.

H. Kamiya, H. Tsuchiya, N. Karino, Y. Ueno, A. Matsuda et al., Mutagenicity of 5-formylcytosine, an oxidation product of 5-methylcytosine, in DNA in mammalian cells, J Biochem, vol.132, issue.4, pp.551-555, 2002.

M. Kanemaki, Y. Kurokawa, T. Matsu-ura, Y. Makino, A. Masani et al., TIP49b, a new RuvB-like DNA helicase, is included in a complex together with another RuvB-like DNA helicase, TIP49a, J Biol Chem, vol.274, issue.32, pp.22437-22444, 1999.

S. Kangaspeska, B. Stride, R. Métivier, M. Polycarpou-schwarz, D. Ibberson et al., Transient cyclical methylation of promoter DNA, Nature, vol.452, issue.7183, pp.112-115, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00266286

M. W. Kellinger, C. X. Song, J. Chong, X. Y. Lu, C. He et al., 5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription, Nat Struct Mol Biol, vol.19, issue.8, pp.831-833, 2012.

K. R. Kieffer-kwon, Z. Tang, E. Mathe, J. Qian, M. H. Sung et al., Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation, Cell, vol.155, issue.7, pp.1507-1520, 2013.

T. H. Kim, Z. K. Abdullaev, A. D. Smith, K. A. Ching, D. I. Loukinov et al., Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome, Cell, vol.128, issue.6, pp.1231-1245, 2007.

T. K. Kim, M. Hemberg, J. M. Gray, A. M. Costa, D. M. Bear et al., Widespread transcription at neuronal activity-regulated enhancers, Nature, vol.465, issue.7295, pp.182-187, 2010.

T. K. Kim and R. Shiekhattar, Architectural and Functional Commonalities between Enhancers and Promoters, Cell, vol.162, issue.5, pp.948-959, 2015.

Y. W. Kim, S. Lee, J. Yun, and A. Kim, Chromatin looping and eRNA transcription precede the transcriptional activation of gene in the -globin locus, Biosci Rep, vol.35, issue.2, p.179, 2015.

Y. J. Kim, S. Bjorklund, Y. Li, M. H. Sayre, and R. D. Kornberg, A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II, Cell, vol.77, issue.4, pp.599-608, 1994.

H. Kimura and P. R. Cook, Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B, J Cell Biol, vol.153, issue.7, pp.1341-1353, 2001.

R. J. Klose and A. P. Bird, MeCP2 behaves as an elongated monomer that does not stably associate with the Sin3a chromatin remodeling complex, J Biol Chem, vol.279, issue.45, pp.46490-46496, 2004.

M. Ko, J. An, H. S. Bandukwala, L. Chavez, T. Aijö et al., Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX, Nature, vol.497, issue.7447, pp.122-126, 2013.

M. S. Kobor, S. Venkatasubrahmanyam, M. D. Meneghini, J. W. Gin, J. L. Jennings et al., A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin, PLoS Biol, vol.2, issue.5, p.131, 2004.

C. M. Koch, R. M. Andrews, P. Flicek, S. C. Dillon, U. Karaöz et al., The landscape of histone modifications across 1% of the human genome in five human cell lines, Genome Res, vol.17, issue.6, pp.691-707, 2007.

F. Koch, R. Fenouil, M. Gut, P. Cauchy, T. K. Albert et al., Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters, Nat Struct Mol Biol, vol.18, issue.8, pp.956-963, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00609674

R. Kodzius, M. Kojima, H. Nishiyori, M. Nakamura, S. Fukuda et al., CAGE: cap analysis of gene expression, Nat Methods, vol.3, issue.3, pp.211-222, 2006.

A. J. Koleske and R. A. Young, An RNA polymerase II holoenzyme responsive to activators, Nature, vol.368, issue.6470, pp.466-469, 1994.

S. T. Kosak, J. A. Skok, K. L. Medina, R. Riblet, L. Beau et al., Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development, Science, vol.296, issue.5565, pp.158-62, 2002.

S. Kriaucionis and N. Heintz, The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain, Science, vol.324, issue.5929, pp.929-930, 2009.

M. Ku, J. D. Jaffe, R. P. Koche, E. Rheinbay, M. Endoh et al., H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions, Genome Biol, vol.13, issue.10, p.85, 2012.

O. I. Kulaeva, D. A. Gaykalova, and V. M. Studitsky, Transcription through chromatin by RNA polymerase II: histone displacement and exchange, Mutat Res, vol.618, issue.1-2, pp.116-129, 2007.

R. I. Kumaran and D. L. Spector, A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence, J Cell Biol, vol.180, issue.1, pp.51-65, 2008.

H. Kwon, A. N. Imbalzano, P. A. Khavari, R. E. Kingston, and M. R. Green, Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex, Nature, vol.370, issue.6489, pp.477-481, 1994.

M. Lachner, D. O'carroll, S. Rea, K. Mechtler, and T. Jenuwein, Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins, Nature, vol.410, issue.6824, pp.116-120, 2001.

D. S. Latchman, Eukaryotic transcription factors, Biochem J, vol.270, issue.2, pp.281-2819, 1990.

Y. Lavin, D. Winter, R. Blecher-gonen, D. E. Keren-shaul, H. Merad et al., Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment, Cell, vol.159, issue.6, pp.1312-1326, 2014.

D. H. Lee, N. Gershenzon, M. Gupta, I. P. Ioshikhes, D. Reinberg et al., Functional characterization of core promoter elements: the downstream core element is recognized by TAF1, Mol Cell Biol, vol.25, issue.21, pp.9674-9686, 2005.

M. P. Lee, K. Howcroft, A. Kotekar, H. H. Yang, K. H. Buetow et al., ATG deserts define a novel core promoter subclass, Genome Res, vol.15, issue.9, pp.1189-1197, 2005.

B. Lehnertz, Y. Ueda, A. A. Derijck, U. Braunschweig, L. Perez-burgos et al., Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin, Curr Biol, vol.13, issue.14, pp.1192-1200, 2003.

B. Lenhard, A. Sandelin, and P. Carninci, Metazoan promoters: emerging characteristics and insights into transcriptional regulation, Nat Rev Genet, vol.13, issue.4, pp.233-245, 2012.

H. Leonhardt, A. W. Page, H. U. Weier, and T. H. Bestor, A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei, Cell, vol.71, issue.5, pp.865-873, 1992.

G. Leroy, G. Orphanides, W. S. Lane, and D. Reinberg, Requirement of RSF and FACT for transcription of chromatin templates in vitro, Science, vol.282, issue.5395, pp.1900-1904, 1998.

J. D. Lewis, R. R. Meehan, W. J. Henzel, I. Maurer-fogy, P. Jeppesen et al., Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA, Cell, vol.69, issue.6, pp.905-914, 1992.

E. Li, C. Beard, and R. Jaenisch, Role for DNA methylation in genomic imprinting, Nature, vol.366, issue.6453, pp.362-365, 1993.

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, issue.1-2, pp.84-98, 2012.

W. Li, D. Notani, Q. Ma, B. Tanasa, E. Nunez et al., Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation, Nature, vol.498, issue.7455, pp.516-520, 2013.

Z. Li, H. Dai, S. N. Martos, B. Xu, Y. Gao et al., Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells, 2015.

, Genome Biol, vol.16, p.115

Z. Li, P. Gadue, K. Chen, Y. Jiao, G. Tuteja et al., Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation, Cell, vol.151, issue.7, pp.1608-1616, 2012.

D. Liber, R. Domaschenz, P. H. Holmqvist, L. Mazzarella, A. Georgiou et al., Epigenetic priming of a pre-B cell-specific enhancer through binding of Sox2 and Foxd3 at the ESC stage, Cell Stem Cell, vol.7, issue.1, pp.114-126, 2010.

E. Lieberman-aiden, N. L. Van-berkum, L. Williams, M. Imakaev, T. Ragoczy et al., Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, vol.326, issue.5950, pp.289-293, 2009.

Y. C. Lin, C. Benner, R. Mansson, S. Heinz, K. Miyazaki et al., Global changes in the nuclear positioning of genes and intra-and interdomain genomic interactions that orchestrate B cell fate, Nat Immunol, vol.13, issue.12, pp.1196-1204, 2012.

R. Lister, M. Pelizzola, R. H. Dowen, R. D. Hawkins, G. Hon et al., Human DNA methylomes at base resolution show widespread epigenomic differences, Nature, vol.462, issue.7271, pp.315-322, 2009.

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, issue.8, p.83, 2011.

Y. Liu, Y. O. Olanrewaju, X. Zhang, and X. Cheng, DNA recognition of 5-carboxylcytosine by a Zfp57 mutant at an atomic resolution of 0.97 Å, Biochemistry, vol.52, issue.51, pp.9310-9317, 2013.

H. K. Long, N. P. Blackledge, and R. J. Klose, ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection, Biochem Soc Trans, vol.41, issue.3, pp.727-740, 2013.

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, issue.2, pp.320-334, 2013.

F. Lu, Y. Liu, L. Jiang, S. Yamaguchi, and Y. Zhang, Role of Tet proteins in enhancer activity and telomere elongation, Genes Dev, vol.28, pp.2103-2119, 2014.

J. Lu, L. Hu, J. Cheng, D. Fang, C. Wang et al., A computational investigation on the substrate preference of ten-eleven-translocation 2 (TET2), Phys Chem Chem PhysJan, vol.22, 2016.

K. Luger, A. W. Mäder, R. K. Richmond, D. F. Sargent, and T. J. Richmond, Crystal structure of the nucleosome core particle at 2.8 A resolution, Nature, vol.389, issue.6648, pp.251-260, 1997.

E. Luk, N. D. Vu, K. Patteson, G. Mizuguchi, W. H. Wu et al., Chz1, a nuclear chaperone for histone H2AZ, Mol Cell, vol.25, issue.3, pp.357-368, 2007.

M. Lundgren, C. M. Chow, P. Sabbattini, A. Georgiou, S. Minaee et al., Transcription factor dosage affects changes in higher order chromatin structure associated with activation of a heterochromatic gene, Cell, vol.103, issue.5, pp.733-743, 2000.

D. G. Lupiáñez, K. Kraft, V. Heinrich, P. Krawitz, F. Brancati et al., Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions, Cell, vol.161, issue.5, pp.1012-1025, 2015.

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, issue.6, pp.958-970, 2008.

M. J. Lyst, R. Ekiert, D. H. Ebert, C. Merusi, J. Nowak et al., Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor, Nat Neurosci, vol.16, issue.7, pp.898-902, 2013.

D. Macleod, J. Charlton, J. Mullins, and A. P. Bird, Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island, Genes Dev, vol.8, pp.2282-2292, 1994.

L. Magnani, E. B. Ballantyne, X. Zhang, and M. Lupien, PBX1 genomic pioneer function drives ER? signaling underlying progression in breast cancer, PLoS Genet, vol.7, issue.11, p.1002368, 2011.

E. A. Mahé and G. Salbert, DNA demethylation by TET proteins: a potential therapeutic target in cancer, Epigenetic Diagnosis & Therapy, vol.1, pp.49-59, 2015.

A. Maiti and A. C. Drohat, Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites, J Biol Chem, vol.286, issue.41, pp.35334-35338, 2011.

V. Matys, E. Fricke, R. Geffers, E. Gössling, M. Haubrock et al., TRANSFAC: transcriptional regulation, from patterns to profiles, Nucleic Acids Res, vol.31, issue.1, pp.374-378, 2003.

A. K. Maunakea, R. P. Nagarajan, M. Bilenky, T. J. Ballinger, D. Souza et al., Conserved role of intragenic DNA methylation in regulating alternative promoters, Nature, vol.466, issue.7303, pp.253-257, 2010.

R. Mayer, A. Brero, J. Von-hase, T. Schroeder, T. Cremer et al., Common themes and cell type specific variations of higher order chromatin arrangements in the mouse, BMC Cell Biol, vol.6, p.44, 2005.

E. Mckittrick, P. R. Gafken, K. Ahmad, and S. Henikoff, Histone H3.3 is enriched in covalent modifications associated with active chromatin, Proc Natl Acad Sci U S A, vol.101, issue.6, pp.1525-1530, 2004.

S. Mcmanus, A. Ebert, G. Salvagiotto, J. Medvedovic, Q. Sun et al., The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in committed B cells, EMBO J, vol.30, issue.12, pp.2388-2404, 2011.

R. R. Meehan, J. D. Lewis, S. Mckay, E. L. Kleiner, and A. P. Bird, Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs, Cell, vol.58, issue.3, pp.499-507, 1989.

A. Meissner, T. S. Mikkelsen, H. Gu, M. Wernig, J. Hanna et al., Genome-scale DNA methylation maps of pluripotent and differentiated cells, Nature, vol.454, issue.7205, pp.766-770, 2008.

M. F. Melgar, F. S. Collins, and P. Sethupathy, Discovery of active enhancers through bidirectional expression of short transcripts, Genome Biol, vol.12, issue.11, p.113, 2011.

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, issue.7, pp.1417-1430, 2012.

A. Mendonca, E. H. Chang, W. Liu, and C. Yuan, Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro, Biochim Biophys Acta, vol.1839, issue.11, pp.1323-1329, 2014.

E. Meshorer, D. Yellajoshula, E. George, P. J. Scambler, D. T. Brown et al., Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells, Dev Cell, vol.10, issue.1, pp.105-116, 2006.

R. Métivier, R. Gallais, C. Tiffoche, L. Péron, C. Jurkowska et al., Cyclical DNA methylation of a transcriptionally active promoter, Nature, vol.452, issue.7183, pp.45-50, 2008.

A. Miele and J. Dekker, Mapping cis-and trans-chromatin interaction networks using chromosome conformation capture (3C), Methods Mol Biol, vol.464, pp.105-126, 2009.

T. Mishiro, K. Ishihara, S. Hino, S. Tsutsumi, H. Aburatani et al., Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster, EMBO J, vol.28, issue.9, pp.1234-1245, 2009.

Y. Mito, J. G. Henikoff, and S. Henikoff, Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet, vol.37, issue.10, pp.1090-1097, 2005.

G. Mizuguchi, X. Shen, J. Landry, W. H. Wu, S. Sen et al., ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex, Science, vol.303, issue.5656, pp.343-348, 2004.

T. Mohandas, R. S. Sparkes, and L. J. Shapiro, Reactivation of an inactive human X chromosome: evidence for X inactivation by DNA methylation, Science, vol.211, issue.4480, pp.393-396, 1981.

F. Mohn, M. Weber, M. Rebhan, T. C. Roloff, J. Richter et al., Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors, Mol Cell, vol.30, issue.6, pp.755-66, 2008.

T. Montavon, N. Soshnikova, B. Mascrez, J. E. Thevenet, L. Splinter et al., A regulatory archipelago controls Hox genes transcription in digits, Cell, vol.147, issue.5, pp.1132-1145, 2011.

A. C. Mullen, D. A. Orlando, J. J. Newman, J. Lovén, R. M. Kumar et al., Master transcription factors determine cell-type-specific responses to TGF-signaling, Cell, vol.147, issue.3, pp.565-576, 2011.

U. Müller, C. Bauer, M. Siegl, A. Rottach, and H. Leonhardt, TET-mediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent gene reactivation, Nucleic Acids Res, vol.42, issue.13, pp.8592-8604, 2014.

M. Münzel, U. Lischke, D. Stathis, T. Pfaffeneder, F. A. Gnerlich et al., Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, Chemistry, vol.17, issue.49, pp.13782-13788, 2011.

X. Nan, H. H. Ng, C. A. Johnson, C. D. Laherty, B. M. Turner et al., Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex, Nature, vol.393, issue.6683, pp.386-389, 1998.

G. Natoli and J. C. Andrau, Noncoding transcription at enhancers: general principles and functional models, Annu Rev Genet, vol.46, pp.1-19, 2012.

S. Neph, J. Vierstra, A. B. Stergachis, A. P. Reynolds, E. Haugen et al., An expansive human regulatory lexicon encoded in transcription factor footprints, Nature, vol.489, issue.7414, pp.83-90, 2012.

F. Neri, D. Incarnato, A. Krepelova, S. Rapelli, F. Anselmi et al., Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics, Cell Rep, vol.pii, issue.15, pp.9-10, 2015.

H. H. Ng, Y. Zhang, B. Hendrich, C. A. Johnson, B. M. Turner et al., MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex, Nat Genet, vol.23, issue.1, pp.58-61, 1999.

Z. Ni, A. Saunders, N. J. Fuda, J. Yao, J. R. Suarez et al., P-TEFb is critical for the maturation of RNA polymerase II into productive elongation in vivo, Mol Cell Biol, vol.28, issue.3, pp.1161-1170, 2008.

M. A. Nobrega, I. Ovcharenko, V. Afzal, and E. M. Rubin, Scanning human gene deserts for long-range enhancers, Science, vol.302, issue.5644, p.413, 2003.

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, pp.381-385, 2012.

A. Obri, K. Ouararhni, C. Papin, M. L. Diebold, K. Padmanabhan et al., ANP32E is a histone chaperone that removes H2A.Z from chromatin, Nature, vol.505, issue.7485, pp.648-653, 2014.

K. Okamura, K. A. Matsumoto, and K. Nakai, Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution, BMC Bioinformatics, vol.11, 2010.

M. Okano, S. Xie, and L. E. , Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases, Nat Genet, vol.19, issue.3, pp.219-220, 1998.

M. Okano, D. W. Bell, D. A. Haber, and E. Li, DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development, Cell, vol.99, issue.3, pp.247-257, 1999.

N. Okashita, Y. Kumaki, K. Ebi, M. Nishi, Y. Okamoto et al., PRDM14 promotes active DNA demethylation through the ten-eleven translocation (TET)-mediated base excision repair pathway in embryonic stem cells, Development, vol.141, issue.2, pp.269-280, 2014.

M. Okuwaki, K. Kato, H. Shimahara, S. Tate, and K. Nagata, Assembly and disassembly of nucleosome core particles containing histone variants by human nucleosome assembly protein I, Mol Cell Biol, vol.25, issue.23, pp.10639-10651, 2005.

C. T. Ong and V. G. Corces, Enhancer function: new insights into the regulation of tissue-specific gene expression, Nat Rev Genet, vol.12, issue.4, pp.283-93, 2011.

S. K. Ooi, C. Qiu, E. Bernstein, K. Li, D. Jia et al., DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA, Nature, vol.448, issue.7154, pp.714-717, 2007.

G. Orphanides, W. H. Wu, W. S. Lane, M. Hampsey, and D. Reinberg, The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins, Nature, vol.400, issue.6741, pp.284-288, 1999.

R. Ostuni, V. Piccolo, I. Barozzi, S. Polletti, A. Termanini et al., Latent enhancers activated by stimulation in differentiated cells, Cell, vol.152, issue.1-2, pp.157-171, 2013.

J. Otani, T. Nankumo, K. Arita, S. Inamoto, M. Ariyoshi et al., Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain, EMBO Rep, vol.10, issue.11, pp.1235-1241, 2009.

M. Papamichos-chronakis, S. Watanabe, O. J. Rando, and C. L. Peterson, Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity, Cell, vol.144, issue.2, pp.200-213, 2011.

L. A. Parada, P. G. Mcqueen, and T. Misteli, Tissue-specific spatial organization of genomes, Genome Biol, vol.5, issue.7, p.44, 2004.

V. Parelho, S. Hadjur, M. Spivakov, M. Leleu, S. Sauer et al., Cohesins functionally associate with CTCF on mammalian chromosome arms, Cell, vol.132, issue.3, pp.422-433, 2008.

Y. J. Park, J. V. Chodaparambil, Y. Bao, S. J. Mcbryant, and K. Luger, Nucleosome assembly protein 1 exchanges histone H2A-H2B dimers and assists nucleosome sliding, J Biol Chem, vol.280, issue.3, pp.1817-1825, 2005.

W. A. Pastor, U. J. Pape, Y. Huang, H. R. Henderson, R. Lister et al., Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells, Nature, vol.473, issue.7347, pp.394-397, 2011.

G. A. Patikoglou, J. L. Kim, L. Sun, S. H. Yang, T. Kodadek et al., TATA element recognition by the TATA box-binding protein has been conserved throughout evolution, Genes Dev, vol.13, issue.24, pp.3217-3230, 1999.

J. R. Pehrson and V. A. Fried, MacroH2A, a core histone containing a large nonhistone region, Science, vol.257, issue.5075, pp.1398-1400, 1992.

A. Pekowska, T. Benoukraf, J. Zacarias-cabeza, M. Belhocine, F. Koch et al., H3K4 tri-methylation provides an epigenetic signature of active enhancers, EMBO J, vol.30, issue.20, pp.4198-4210, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01614961

L. A. Pennacchio, N. Ahituv, A. M. Moses, S. Prabhakar, M. A. Nobrega et al., In vivo enhancer analysis of human conserved non-coding sequences, Nature, vol.444, issue.7118, pp.499-502, 2006.

D. Peric-hupkes, W. Meuleman, L. Pagie, S. W. Bruggeman, I. Solovei et al., Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation, Mol Cell, vol.38, issue.4, pp.603-613, 2010.

E. Portales-casamar, S. Thongjuea, A. T. Kwon, D. Arenillas, X. Zhao et al., JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles, Nucleic Acids Res, vol.38, pp.105-110, 2010.

S. Pott and J. D. Lieb, What are super-enhancers?, Nat Genet, vol.47, issue.1, pp.8-12, 2015.

M. Pradhan, P. O. Estève, H. G. Chin, M. Samaranayke, G. D. Kim et al., CXXC domain of human DNMT1 is essential for enzymatic activity, Biochemistry, vol.47, issue.38, pp.10000-10009, 2008.

E. L. Putiri, R. L. Tiedemann, J. J. Thompson, C. Liu, T. Ho et al., Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells, 2014.

, Genome Biol, vol.15, issue.6, p.81

P. Qin, J. M. Haberbusch, Z. Zhang, K. J. Soprano, and D. R. Soprano, Pre-B cell leukemia transcription factor (PBX) proteins are important mediators for retinoic acid-dependent endodermal and neuronal differentiation of mouse embryonal carcinoma P19 cells, J Biol Chem, vol.279, issue.16, pp.16263-16271, 2004.

J. Quintin, L. Péron, C. Palierne, G. Bizot, M. Cunha et al., Dynamic estrogen receptor interactomes control estrogen-responsive trefoil Factor (TFF) locus cell-specific activities, Mol Cell Biol, vol.34, issue.13, pp.2418-2436, 2014.

C. Rabl, 1885. Über Zelltheilung. Morph Jb, vol.10, pp.214-330

E. A. Rach, D. R. Winter, A. M. Benjamin, D. L. Corcoran, T. Ni et al., Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level, PLoS Genet, vol.7, issue.1, p.1001274, 2011.

A. Rada-iglesias, R. Bajpai, T. Swigut, S. A. Brugmann, R. A. Flynn et al., A unique chromatin signature uncovers early developmental enhancers in humans, Nature, vol.470, issue.7333, pp.279-283, 2011.

G. Raddatz, P. M. Guzzardo, N. Olova, M. R. Fantappié, M. Rampp et al., Dnmt2-dependent methylomes lack defined DNA methylation patterns, Proc Natl Acad Sci U S A, vol.110, issue.21, pp.8627-8631, 2013.

E. A. Raiber, D. Beraldi, G. Ficz, H. E. Burgess, M. R. Branco et al., Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase, Genome Biol, vol.13, issue.8, p.69, 2012.

S. S. Rao, M. H. Huntley, N. C. Durand, E. K. Stamenova, I. D. Bochkov et al., A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping, Cell, vol.159, issue.7, pp.1665-1680, 2014.

K. L. Reddy, J. M. Zullo, E. Bertolino, and H. Singh, Transcriptional repression mediated by repositioning of genes to the nuclear lamina, Nature, vol.452, issue.7184, pp.243-247, 2008.

, Integrative analysis of 111 reference human epigenomes, Roadmap Epigenomics Consortium, vol.518, pp.317-330, 2015.

K. D. Robertson, DNA methylation and human disease, Nat Rev Genet, vol.6, issue.8, pp.597-610, 2005.

R. G. Roeder, The role of general initiation factors in transcription by RNA polymerase II, Trends Biochem Sci, vol.21, issue.9, pp.327-335, 1996.

T. Y. Roh, S. Cuddapah, and K. Zhao, Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping, Genes Dev, vol.19, issue.5, pp.542-552, 2005.

A. L. Roy and D. S. Singer, Core promoters in transcription: old problem, new insights, Trends Biochem Sci, vol.40, issue.3, pp.165-171, 2015.

E. D. Rubio, D. J. Reiss, P. L. Welcsh, C. M. Disteche, G. N. Filippova et al., CTCF physically links cohesin to chromatin, Proc Natl Acad Sci U S A, vol.105, issue.24, pp.8309-8314, 2008.

M. Saitou, S. Kagiwada, and K. Kurimoto, Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells, Development, vol.139, issue.1, pp.15-31, 2012.

R. M. Samstein, A. Arvey, S. Z. Josefowicz, X. Peng, A. Reynolds et al., Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification, Cell, vol.151, issue.1, pp.153-166, 2012.

A. Sanyal, B. R. Lajoie, G. Jain, J. Dekker, and . 2012, The long-range interaction landscape of gene promoters, Nature, vol.489, issue.7414, pp.109-113

E. Sarcinella, P. C. Zuzarte, P. N. Lau, R. Draker, and P. Cheung, Monoubiquitylation of H2A.Z distinguishes its association with euchromatin or facultative heterochromatin, Mol Cell Biol, vol.27, issue.18, pp.6457-6468, 2007.

S. A. Sarraf and I. Stancheva, Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly, Mol Cell, vol.15, issue.4, pp.595-605, 2004.

S. K. Sayeed, J. Zhao, B. K. Sathyanarayana, J. P. Golla, and C. Vinson, C/EBP (CEBPB) protein binding to the C/EBP|CRE DNA 8-mer TTGC|GTCA is inhibited by 5hmC and enhanced by 5mC, 5fC, and 5caC in the CG dinucleotide, Biochim Biophys Acta, vol.1849, issue.6, pp.583-589, 2015.

C. A. Schaaf, H. Kwak, A. Koenig, Z. Misulovin, D. W. Gohara et al., Genome-wide control of RNA polymerase II activity by cohesin, PLoS Genet, vol.9, issue.3, p.1003382, 2013.

C. Schmidl, M. Klug, T. J. Boeld, R. Andreesen, P. Hoffmann et al., Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity, Genome Res, vol.19, issue.7, pp.1165-1174, 2009.

D. Schmidt, M. D. Wilson, C. Spyrou, G. D. Brown, J. Hadfield et al., ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions, Methods, vol.48, issue.3, pp.240-248, 2009.

D. Schübeler, ESCI award lecture: regulation, function and biomarker potential of DNA methylation, Eur J Clin Invest, vol.45, issue.3, pp.288-293, 2015.

J. Schug, W. P. Schuller, C. Kappen, J. M. Salbaum, M. Bucan et al., Promoter features related to tissue specificity as measured by Shannon entropy, Genome Biol, vol.6, issue.4, p.33, 2005.

E. W. Scott, M. C. Simon, J. Anastasi, and H. Singh, Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages, Science, vol.265, issue.5178, pp.1573-1577, 1994.

B. S. Scruggs, D. A. Gilchrist, S. Nechaev, G. W. Muse, A. Burkholder et al., Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin, Mol Cell, vol.58, issue.6, pp.1101-1112, 2015.

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, issue.17, pp.8255-8265, 2012.

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, issue.4, pp.555-565, 2011.

T. Sexton, E. Yaffe, E. Kenigsberg, F. Bantignies, B. Leblanc et al., Three-dimensional folding and functional organization principles of the Drosophila genome, Cell, vol.148, issue.3, pp.458-472, 2012.

A. Shakya, C. Callister, A. Goren, N. Yosef, N. Garg et al., Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion, Mol Cell Biol, vol.35, issue.6, pp.1014-1039, 2015.

J. Sharif, M. Muto, S. Takebayashi, I. Suetake, A. Iwamatsu et al., The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA, Nature, vol.450, issue.7171, pp.908-912, 2007.

L. Shen, Y. Kondo, Y. Guo, J. Zhang, L. Zhang et al., Genomewide profiling of DNA methylation reveals a class of normally methylated CpG island promoters, PLoS Genet, vol.3, issue.10, pp.2023-2036, 2007.

L. Shen, H. Wu, D. Diep, S. Yamaguchi, D. 'alessio et al., Genome-wide analysis reveals TET-and TDG-dependent 5-methylcytosine oxidation dynamics, Cell, vol.153, issue.3, pp.692-706, 2013.

X. Shen, G. Mizuguchi, A. Hamiche, and C. Wu, A chromatin remodelling complex involved in transcription and DNA processing, Nature, vol.406, issue.6795, pp.541-544, 2000.

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.116-120, 2012.

F. T. Shi, H. Kim, W. Lu, Q. He, D. Liu et al., Ten-eleven translocation 1 (Tet1) is regulated by O-linked N-acetylglucosamine transferase (Ogt) for target gene repression in mouse embryonic stem cells, J Biol Chem, vol.288, issue.29, pp.20776-20784, 2013.

J. Shi, M. Zheng, Y. Ye, M. Li, X. Chen et al., Drosophila Brahma complex remodels nucleosome organizations in multiple aspects, Nucleic Acids Res, vol.42, issue.15, pp.9730-9739, 2014.

T. Shibutani, S. Ito, M. Toda, R. Kanao, L. B. Collins et al., Guanine-5-carboxylcytosine base pairs mimic mismatches during, DNA replication. Sci Rep, vol.4, p.5220, 2014.

A. Siepel, G. Bejerano, J. S. Pedersen, A. S. Hinrichs, M. Hou et al., Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes, Genome Res, vol.15, issue.8, pp.1034-1050, 2005.

R. Siersbaek, R. Nielsen, S. John, M. H. Sung, S. Baek et al., Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis, EMBO J, vol.30, issue.8, pp.1459-1472, 2011.

M. Simonis, P. Klous, E. Splinter, Y. Moshkin, R. Willemsen et al., Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-onchip (4C), Nat Genet, vol.38, issue.11, pp.1348-1354, 2006.

Z. D. Smith and A. Meissner, DNA methylation: roles in mammalian development, Nat Rev Genet, vol.14, issue.3, pp.204-220, 2013.

C. X. Song, K. E. Szulwach, Q. Dai, Y. Fu, S. Q. Mao et al., Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming, Cell, vol.153, issue.3, pp.678-691, 2013.

C. X. Song, K. E. Szulwach, Y. Fu, Q. Dai, C. Yi et al., Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine, Nat Biotechnol, vol.29, issue.1, pp.68-72, 2011.

F. Song, S. Mahmood, S. Ghosh, P. Liang, D. J. Smiraglia et al., Tissue specific differentially methylated regions (TDMR): Changes in DNA methylation during development, Genomics, vol.93, issue.2, pp.130-139, 2009.

D. L. Spector, The dynamics of chromosome organization and gene regulation, Annu Rev Biochem, vol.72, pp.573-608, 2003.

P. T. Spellman and G. M. Rubin, Evidence for large domains of similarly expressed genes in the Drosophila genome, J Biol, vol.1, issue.1, p.5, 2002.

C. G. Spilianakis and R. A. Flavell, Long-range intrachromosomal interactions in the T helper type 2 cytokine locus, Nat Immunol, vol.5, issue.10, pp.1017-1027, 2004.

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, issue.5, pp.1146-1159, 2013.

S. M. Stack, D. B. Brown, and W. C. Dewey, Visualization of interphase chromosomes, J Cell Sci, vol.26, pp.281-299, 1977.

M. B. Stadler, R. Murr, L. Burger, R. Ivanek, F. Lienert et al., DNA-binding factors shape the mouse methylome at distal regulatory regions, Nature, vol.480, issue.7378, pp.490-495, 2011.

H. Stroud, S. Feng, M. Kinney, S. Pradhan, S. Jacobsen et al., 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells, Genome Biol, vol.12, issue.6, p.54, 2011.

I. Suetake, F. Shinozaki, J. Miyagawa, H. Takeshima, and S. Tajima, DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction, J Biol Chem, vol.279, issue.26, pp.27816-2723, 2004.

E. Szenker, D. Ray-gallet, and G. Almouzni, The double face of the histone variant H3.3, Cell Res, vol.21, issue.3, pp.421-434, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00742959

K. E. Szulwach, X. Li, Y. Li, C. X. Song, J. W. Han et al., Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells, PLoS Genet, vol.7, issue.6, p.1002154, 2011.

A. Szwagierczak, S. Bultmann, C. S. Schmidt, F. Spada, and H. Leonhardt, Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA, Nucleic Acids Res, vol.38, p.181, 2010.

H. Tagami, D. Ray-gallet, G. Almouzni, and Y. Nakatani, Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis, Cell, vol.116, issue.1, pp.51-61, 2004.

M. Tahiliani, K. P. Koh, Y. Shen, W. A. Pastor, H. Bandukwala et al., Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1, Science, vol.324, issue.5929, pp.930-935, 2009.

K. Takayama, A. Misawa, T. Suzuki, K. Takagi, Y. Hayashizaki et al., TET2 repression by androgen hormone regulates global hydroxymethylation status and prostate cancer progression, Nat Commun, vol.6, p.8219, 2015.

H. Tanabe, S. Müller, M. Neusser, J. Von-hase, E. Calcagno et al., Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates, Proc Natl Acad Sci U S A, vol.99, issue.7, pp.4424-4429, 2002.

V. B. Teif, D. A. Beshnova, Y. Vainshtein, C. Marth, J. P. Mallm et al., Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development, Genome Res, vol.24, issue.8, pp.1285-1295, 2014.

M. Y. Tolstorukov, J. A. Goldman, C. Gilbert, V. Ogryzko, R. E. Kingston et al., Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells, Mol Cell, vol.47, issue.4, pp.596-5607, 2012.

J. K. Tong, C. A. Hassig, G. R. Schnitzler, R. E. Kingston, and S. L. Schreiber, Chromatin deacetylation by an ATPdependent nucleosome remodelling complex, Nature, vol.395, issue.6705, pp.917-921, 1998.

T. Tsukiyama, C. Daniel, J. Tamkun, and C. Wu, ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor, Cell, vol.83, issue.6, pp.1021-1026, 1995.

T. Tsukiyama, J. Palmer, C. C. Landel, J. Shiloach, and C. Wu, Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae, Genes Dev, vol.13, issue.6, pp.686-697, 1999.

T. Tsukiyama and C. Wu, Purification and properties of an ATP-dependent nucleosome remodeling factor, Cell, vol.83, issue.6, pp.1011-1020, 1995.

C. R. Vakoc, D. L. Letting, N. Gheldof, T. Sawado, M. A. Bender et al., Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1, Mol Cell, vol.17, issue.3, pp.453-462, 2005.

C. Van-oevelen, S. Collombet, G. Vicent, M. Hoogenkamp, C. Lepoivre et al., 2015. C/EBP? Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis, Stem Cell Reports, vol.5, issue.2, pp.232-247

L. Vanhille, A. Griffon, M. A. Maqbool, J. Zacarias-cabeza, L. T. Dao et al., 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

P. D. Varga-weisz, M. Wilm, E. Bonte, K. Dumas, M. Mann et al., Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II, Nature, vol.388, issue.6642, pp.598-602, 1997.

G. Velasco, F. Hubé, J. Rollin, D. Neuillet, C. Philippe et al., Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues, Proc Natl Acad Sci U S A, vol.107, issue.20, pp.9281-9286, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02127331

P. Vella, A. Scelfo, S. Jammula, F. Chiacchiera, K. Williams et al., Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells, Mol Cell, vol.49, issue.4, pp.645-656, 2013.

S. Venkatesh and J. L. Workman, Histone exchange, chromatin structure and the regulation of transcription, Nat Rev Mol Cell Biol, vol.16, issue.3, pp.178-189, 2015.

M. Vermeulen, K. W. Mulder, S. Denissov, W. W. Pijnappel, F. M. Van-schaik et al., Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4, Cell, vol.131, issue.1, pp.58-69, 2007.

A. Visel, M. J. Blow, Z. Li, T. Zhang, J. A. Akiyama et al., ChIP-seq accurately predicts tissue-specific activity of enhancers, Nature, vol.457, issue.7231, pp.854-858, 2009.

A. Visel, S. Minovitsky, I. Dubchak, and L. A. Pennacchio, VISTA Enhancer Browser--a database of tissuespecific human enhancers, Nucleic Acids Res, vol.35, pp.88-92, 2007.

K. S. Voo, D. L. Carlone, B. M. Jacobsen, A. Flodin, and D. G. Skalnik, Cloning of a mammalian transcriptional activator that binds unmethylated CpG motifs and shares a CXXC domain with DNA methyltransferase, human trithorax, and methyl-CpG binding domain protein 1, Mol Cell Biol, vol.20, issue.6, pp.2108-2121, 2000.

C. P. Walsh, J. R. Chaillet, and T. H. Bestor, Transcription of IAP endogenous retroviruses is constrained by cytosine methylation, Nat Genet, vol.20, issue.2, pp.116-117, 1998.

C. Wang, M. Q. Zhang, and Z. Zhang, Computational identification of active enhancers in model organisms, Genomics Proteomics Bioinformatics, vol.11, issue.3, pp.142-150, 2013.

Q. Wang, W. Li, X. S. Liu, J. S. Carroll, O. A. Jänne et al., A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth, Mol Cell, vol.27, issue.3, pp.380-392, 2007.

Z. Wang, C. Zang, J. A. Rosenfeld, D. E. Schones, A. Barski et al., Combinatorial patterns of histone acetylations and methylations in the human genome, Nat Genet, vol.40, issue.7, pp.897-903, 2008.

D. Watanabe, I. Suetake, T. Tada, and S. Tajima, Stage-and cell-specific expression of Dnmt3a and Dnmt3b during embryogenesis, Mech Dev, vol.118, issue.1-2, pp.187-190, 2002.

F. Watt and P. L. Molloy, Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter, Genes Dev, vol.2, issue.9, pp.1136-1143

M. Weber, I. Hellmann, M. B. Stadler, L. Ramos, S. Pääbo et al., Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome, Nat Genet, vol.39, issue.4, pp.457-466, 2007.

K. S. Wendt, K. Yoshida, T. Itoh, M. Bando, B. Koch et al., Cohesin mediates transcriptional insulation by CCCTC-binding factor, Nature, vol.451, issue.7180, pp.796-801, 2008.

J. A. West, A. Cook, B. H. Alver, M. Stadtfeld, A. M. Deaton et al., Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming, Nat Commun, vol.5, p.4719, 2014.

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, issue.2, pp.307-319, 2013.

B. L. Wienholz, M. S. Kareta, A. H. Moarefi, C. A. Gordon, P. A. Ginno et al., DNMT3L modulates significant and distinct flanking sequence preference for DNA methylation by DNMT3A and DNMT3B in vivo, PLoS Genet, vol.6, issue.9, p.1001106, 2010.

K. Williams, J. Christensen, M. T. Pedersen, J. V. Johansen, P. A. Cloos et al., TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity, Nature, vol.473, issue.7347, pp.343-348, 2011.

R. R. Williams, V. Azuara, P. Perry, S. Sauer, M. Dvorkina et al., Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus, J Cell Sci, vol.119, pp.132-140, 2006.

H. Wu, D. 'alessio, A. C. Ito, S. Wang, Z. Cui et al., Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells, Genes Dev, vol.25, issue.7, pp.679-684

H. Wu, D. 'alessio, A. C. Ito, S. Xia, K. Wang et al., Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells, Nature, vol.473, issue.7347, pp.389-393, 2011.

S. Xie, Z. Wang, M. Okano, M. Nogami, Y. Li et al., Cloning, expression and chromosome locations of the human DNMT3 gene family, Gene, vol.236, issue.1, pp.87-95, 1999.

J. Xu, S. D. Pope, A. R. Jazirehi, J. L. Attema, P. Papathanasiou et al., Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells, Proc Natl Acad Sci U S A, vol.104, issue.30, pp.12377-12382, 2007.

J. Xu, J. A. Watts, S. D. Pope, P. Gadue, M. Kamps et al., Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells, Genes Dev, vol.23, issue.24, pp.2824-2838, 2009.

S. Xu, W. Li, J. Zhu, R. Wang, Z. Li et al., Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase, Cell Res, vol.23, issue.11, pp.1296-1309, 2013.

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, issue.4, pp.451-464, 2011.

Y. Xu, C. Xu, A. Kato, W. Tempel, J. G. Abreu et al., Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development, Cell, vol.151, issue.6, pp.1200-1213, 2012.

Y. Xue, J. Wong, G. T. Moreno, M. K. Young, J. Côté et al., NURD, a novel complex with both ATPdependent chromatin-remodeling and histone deacetylase activities, Mol Cell, vol.2, issue.6, pp.851-861, 1998.

E. Yaffe and A. Tanay, Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture, Nat Genet, vol.43, issue.11, pp.1059-1065, 2011.

T. Yamada, Y. Urano-tashiro, S. Tanaka, H. Akiyama, and F. Tashiro, Involvement of crosstalk between Oct4 and Meis1a in neural cell fate decision, PLoS One, vol.8, issue.2, p.56997, 2013.

Y. Yamaguchi, T. Takagi, T. Wada, K. Yano, A. Furuya et al., NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation, Cell, vol.97, issue.1, pp.41-51, 1999.

R. Yamashita, Y. Suzuki, S. Sugano, and K. Nakai, Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity, Gene, vol.350, issue.2, pp.129-136, 2005.

Z. Yang, J. H. Yik, R. Chen, N. He, M. K. Jang et al., Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4, Mol Cell, vol.19, issue.4, pp.535-545, 2005.

T. P. Yao, S. P. Oh, M. Fuchs, N. D. Zhou, L. E. Ch'ng et al., Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300, Cell, vol.93, issue.3, pp.361-372, 1998.

O. Yildirim, R. Li, J. H. 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, issue.7, pp.1498-1510, 2011.

H. G. Yoon, D. W. Chan, A. B. Reynolds, J. Qin, and J. Wong, N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso, Mol Cell, vol.12, issue.3, pp.723-734, 2003.

M. Yu, G. C. Hon, K. E. Szulwach, C. X. Song, L. Zhang et al., Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome, Cell, vol.149, issue.6, pp.1368-1380, 2012.

J. Zeitlinger, A. Stark, M. Kellis, J. W. Hong, and S. Nechaev, RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo, Nat Genet, vol.39, issue.12, pp.1512-1516, 2007.

A. Zemach, I. E. Mcdaniel, P. Silva, and D. Zilberman, Genome-wide evolutionary analysis of eukaryotic DNA methylation, Science, vol.328, issue.5980, pp.916-919, 2010.

G. E. Zentner, P. J. Tesar, and P. C. Scacheri, Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions, Genome Res, vol.21, issue.8, pp.1273-1283, 2011.

H. Zhang, X. Zhang, E. Clark, M. Mulcahey, S. Huang et al., TET1 is a DNA-binding protein that modulates DNA methylation and gene transcription via hydroxylation of 5-methylcytosine, Cell Res, vol.20, issue.12, pp.1390-1393, 2010.

Q. Zhang, X. Liu, W. Gao, P. Li, J. Hou et al., Differential regulation of the ten-eleven translocation (TET) family of dioxygenases by O-linked -N-acetylglucosamine transferase (OGT), J Biol Chem, vol.289, issue.9, pp.5986-5996, 2014.

Q. Zhang, K. Zhao, Q. Shen, Y. Han, Y. Gu et al., Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6, Nature, vol.525, issue.7569, pp.389-393, 2015.

Y. Zhang, R. Jurkowska, S. Soeroes, A. Rajavelu, A. Dhayalan et al., Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail, Nucleic Acids Res, vol.38, issue.13, pp.4246-4253, 2010.

Y. Zhang, G. Leroy, H. P. Seelig, W. S. Lane, and D. Reinberg, The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities, Cell, vol.95, issue.2, pp.279-289, 1998.

Y. Zhang, H. H. Ng, H. Erdjument-bromage, P. Tempst, A. Bird et al., Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation, Genes Dev, vol.13, issue.15, pp.1924-1935, 1999.

Y. Zhang, C. H. Wong, R. Y. Birnbaum, G. Li, R. Favaro et al., Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations, Nature, vol.504, issue.7479, pp.306-310, 2013.

J. Zhu, M. Adli, J. Y. Zou, G. Verstappen, M. Coyne et al., Genome-wide chromatin state transitions associated with developmental and environmental cues, Cell, vol.152, issue.3, pp.642-654, 2013.

D. Zilberman, D. Coleman-derr, T. Ballinger, and S. Henikoff, Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks, Nature, vol.456, issue.7218, pp.125-129, 2008.

M. J. Ziller, H. Gu, F. Müller, J. Donaghey, L. T. Tsai et al., Charting a dynamic DNA methylation landscape of the human genome, 2013.

S. Kriaucionis and N. Heintz, The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain, Science, vol.324, pp.929-959, 2009.

M. Tahiliani, K. P. Koh, and Y. Shen, Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1, Science, vol.324, pp.930-935, 2009.

L. M. Iyer, M. Tahiliani, A. Rao, and L. Aravind, Prediction of novel enzymes involved in oxidative and other complex modifications of bases in nucleic acids, Cell cycle, vol.8, pp.1698-710, 2009.

H. Zhang, X. Zhang, and E. Clark, TET1 is a DNA-binding protein that modulates DNA methylation and gene transcription via hydroxylation of 5-methylcytosine, Cell Res, vol.20, pp.1390-1393, 2010.

Y. Xu, F. Wu, and L. Tan, Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells, Mol Cell, vol.42, pp.451-64, 2011.

L. Hu, Z. Li, and J. Cheng, Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation, Cell, vol.19, pp.1545-55, 2013.

H. Hashimoto, J. E. Pais, and X. Zhang, Structure of a Naegleria Tetlike dioxygenase in complex with 5-methylcytosine DNA, Nature, vol.506, pp.391-396, 2014.

S. Ito, D. 'alessio, A. C. Taranova, and O. V. , Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification, Nature, vol.466, pp.1129-1162, 2010.

S. Ito, L. Shen, and Q. Dai, Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine, Science, vol.333, pp.1300-1303, 2011.

Y. F. He, B. Z. Li, and Z. Li, Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA, Science, vol.333, pp.1303-1310, 2011.

D. Globisch, M. Münzel, and M. Müller, Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates, PLoS One, vol.5, p.15367, 2010.

M. Münzel, D. Globisch, and T. Brückl, Quantification of the sixth DNA base hydroxymethylcytosine in the brain, Angew Chem Int Ed Engl, vol.49, pp.5375-5382, 2010.

A. Szwagierczak, S. Bultmann, C. S. Schmidt, F. Spada, and H. Leonhardt, Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA, Nucleic Acids Res, vol.38, p.181, 2010.

C. X. Song, K. E. Szulwach, and Y. Fu, Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

, Nat Biotechnol, vol.29, pp.68-72, 2011.

H. Yang, Y. Liu, and F. Bai, Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation, Oncogene, vol.32, pp.663-672, 2013.

C. X. Song, K. E. Szulwach, and Q. Dai, Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming, Cell, vol.153, pp.678-91, 2013.

L. Shen, H. Wu, and D. Diep, Genome-wide analysis reveals TETand TDG-dependent 5-methylcytosine oxidation dynamics, Cell, vol.153, pp.692-706, 2013.

M. J. Booth, G. Marsico, M. Bachman, D. Beraldi, and S. Balasubramanian, Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution, Nat Chem, vol.6, pp.435-475, 2014.

A. Inoue, L. Shen, Q. Dai, C. He, and Y. Zhang, Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development, Cell Res, vol.21, pp.1670-1676, 2011.

R. J. Klose and A. P. Bird, Genomic DNA methylation: the mark and its mediators, Trends Biochem Sci, vol.31, pp.89-97, 2006.

M. Okano, D. W. Bell, D. A. Haber, and E. Li, DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development, Cell, vol.99, pp.247-57, 1999.

A. Inoue and Y. Zhang, Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos, Science, vol.334, p.194, 2011.

J. A. Hackett, R. Sengupta, and J. J. Zylicz, Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine, Science, vol.339, pp.448-52, 2013.

V. Valinluck and L. C. Sowers, Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1, Cancer Res, vol.67, pp.946-50, 2007.

H. Hashimoto, Y. Liu, and A. K. Upadhyay, Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation, Nucleic Acids Res, vol.40, pp.4841-4850, 2012.

J. Otani, H. Kimura, and J. Sharif, Cell cycle-dependent turnover of 5-hydroxymethyl cytosine in mouse embryonic stem cells, PLoS One, vol.8, p.82961, 2013.

C. Frauer, T. Hoffmann, and S. Bultmann, Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain, PLoS One, vol.6, p.21306, 2011.

A. Maiti and A. C. Drohat, Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for TET Pathway in Cancer Epigenetic Diagnosis & Therapy, J Biol Chem, vol.1, issue.1, pp.35334-35342, 2011.

U. Müller, C. Bauer, M. Siegl, A. Rottach, and H. Leonhardt, TETmediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent gene reactivation, Nucleic Acids Res, vol.4, pp.8592-604, 2014.

S. Schiesser, B. Hackner, and T. Pfaffeneder, Mechanism and stemcell activity of 5-carboxycytosine decarboxylation determined by isotope tracing, Angew Chem Int Ed Engl, vol.51, pp.6516-6536, 2012.

S. Xu, W. Li, and J. Zhu, Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyluracil decarboxylation and shed light on the search for DNA decarboxylase, Cell Res, vol.23, pp.1296-309, 2013.

J. U. Guo, Y. Su, C. Zhong, G. L. Ming, and H. Song, Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain, Cell, vol.145, pp.423-457, 2011.

S. Cortellino, J. Xu, and M. Sannai, Thymine DNA glycosylase is essential for active DNA demethylation by linked deaminationbase excision repair, Cell, vol.146, pp.67-79, 2011.

H. Hashimoto, X. Zhang, and X. Cheng, Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation, Nucleic Acids Res, vol.40, pp.8276-84, 2012.

C. S. Nabel, H. Jia, and Y. Ye, AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation, Nat Chem Biol, vol.8, pp.751-759, 2012.

T. Pfaffeneder, F. Spada, and M. Wagner, Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA, Nat Chem Biol, vol.10, pp.574-81, 2014.

M. Weber, J. J. Davies, and D. Wittig, Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells, Nat Genet, vol.37, pp.853-62, 2005.

H. Wu, D. 'alessio, A. C. Ito, and S. , Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells, Genes Dev, vol.25, pp.679-84, 2011.

G. Ficz, M. R. Branco, and S. Seisenberger, Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation, Nature, vol.473, pp.398-402, 2011.

K. Williams, J. Christensen, and M. T. Pedersen, TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity, Nature, vol.473, pp.343-351, 2011.

H. Stroud, S. Feng, M. Kinney, S. Pradhan, S. Jacobsen et al., 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells, Genome Biol, vol.12, p.54, 2011.

S. G. Jin, X. Wu, A. X. Li, and G. P. Pfeifer, Genomic mapping of 5-hydroxymethylcytosine in the human brain, Nucleic Acids Res, vol.39, pp.5015-5039, 2011.

A. A. Sérandour, S. Avner, and F. Oger, Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers, Nucleic Acids Res, vol.40, pp.8255-65, 2012.

W. A. Pastor, U. J. Pape, and Y. Huang, Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells, Nature, vol.473, pp.394-401, 2011.

W. A. Pastor, Y. Huang, H. R. Henderson, S. Agarwal, and A. Rao, The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine, Nat Protoc, vol.7, pp.1909-1926, 2012.

B. A. Flusberg, D. R. Webster, and J. H. Lee, Direct detection of DNA methylation during single-molecule, real-time sequencing, Nat Methods, vol.7, pp.461-466, 2010.

Z. Sun, J. Terragni, and J. G. Borgaro, High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells, Cell Rep, vol.3, pp.567-76, 2013.

A. Petterson, T. Chung, D. Tan, X. Sun, and X. Y. Jia, RRHP: a tag-based approach for 5-hydroxymethylcytosine mapping at single-site resolution, Genome Biol, vol.15, p.456, 2014.

Y. Huang, W. A. Pastor, and Y. Shen, The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing, PLoS One, vol.5, p.8888, 2010.

M. J. Booth, M. R. Branco, and G. Ficz, Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution, Science, vol.336, pp.934-941, 2012.

M. J. Booth, T. W. Ost, and D. Beraldi, Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine, Nat Protoc, vol.8, pp.1841-51, 2013.

M. Yu, G. C. Hon, and K. E. Szulwach, Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome, Cell, vol.149, pp.1368-80, 2012.

X. Lu, C. X. Song, and K. Szulwach, Chemical modification-assisted bisulfite sequencing (CAB-Seq) for 5-carboxylcytosine detection in DNA, J Am Chem Soc, vol.135, pp.9315-9322, 2013.

H. Wu, X. Wu, L. Shen, and Y. Zhang, Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing, Nat Biotechnol, 2014.

H. Wu, D. 'alessio, A. C. Ito, and S. , Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells, Nature, vol.473, pp.389-93, 2011.

K. E. Szulwach, X. Li, and Y. Li, Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells, PLoS Genet, vol.7, p.1002154, 2011.

E. L. Putiri, R. L. Tiedemann, and J. J. Thompson, Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells

, Genome Biol, vol.15, p.81, 2014.

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.1417-1447, 2012.

Y. Huang, L. Chavez, and X. Chang, Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells, Proc Natl Acad Sci U S A, vol.111, pp.1361-1367, 2014.

R. Deplus, B. Delatte, and M. K. Schwinn, TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS, EMBO J, vol.32, pp.645-55, 2013.

P. F. Cartron, A. Nadaradjane, F. Lepape, L. Lalier, B. Gardie et al., Identification of TET1 Partners That Control Its DNADemethylating Function, Genes Cancer, vol.4, pp.235-276, 2013.

F. T. Shi, H. Kim, and W. Lu, Ten-eleven translocation 1 (Tet1) is regulated by O-linked N-acetylglucosamine transferase (Ogt) for target gene repression in mouse embryonic stem cells, J Biol Chem, vol.288, pp.20776-84, 2013.

O. Yildirim, R. Li, and J. H. Hung, Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells, Cell, vol.147, pp.1498-510, 2011.

P. Vella, A. Scelfo, and S. Jammula, Tet proteins connect the Olinked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells, Mol Cell, vol.49, pp.645-56, 2013.

Q. Chen, Y. Chen, C. Bian, R. Fujiki, and X. Yu, TET2 promotes histone O-GlcNAcylation during gene transcription, Nature, vol.493, pp.561-565, 2013.

R. Ito, S. Katsura, and H. Shimada, TET3-OGT interaction increases the stability and the presence of OGT in chromatin, Genes Cells, vol.19, pp.52-65, 2014.

Q. Zhang, X. Liu, and W. Gao, Differential regulation of the teneleven translocation (TET) family of dioxygenases by O-linked ?-N-acetylglucosamine transferase (OGT), J Biol Chem, vol.289, pp.5986-96, 2014.

G. W. Hart, M. P. Housley, and C. Slawson, Cycling of O-linked beta-Nacetylglucosamine on nucleocytoplasmic proteins, Nature, vol.446, pp.1017-1039, 2007.

M. M. Dawlaty, A. Breiling, and T. Le, Loss of Tet enzymes compromises proper differentiation of embryonic stem cells, Dev Cell, vol.29, pp.102-113, 2014.

M. M. Dawlaty, K. Ganz, and B. E. Powell, Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development, Cell Stem Cell, vol.9, pp.166-75, 2011.

K. P. Koh, A. Yabuuchi, and S. Rao, Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells, Cell Stem Cell, vol.8, pp.200-213, 2011.

Y. Wu, Z. Guo, and Y. Liu, Oct4 and the small molecule inhibitor, SC1, regulates Tet2 expression in mouse embryonic stem cells

, Mol Biol Rep, vol.40, pp.2897-906, 2013.

N. Okashita, Y. Kumaki, and K. Ebi, PRDM14 promotes active DNA demethylation through the ten-eleven translocation (TET)-mediated base excision repair pathway in embryonic stem cells, Development, vol.141, pp.269-80, 2014.

Y. Xu, C. Xu, and A. Kato, Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development, Cell, vol.151, pp.1200-1213, 2012.

S. Mahé,

M. A. Hahn, R. Qiu, and X. Wu, Dynamics of 5-hydroxymethylcytosine and chromatin marks in Mammalian neurogenesis, Cell Rep, vol.3, pp.291-300, 2013.

R. R. Zhang, Q. Y. Cui, and K. Murai, Tet1 regulates adult hippocampal neurogenesis and cognition, Cell Stem Cell, vol.13, pp.237-282, 2013.

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.14682-14689, 2013.

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.

R. L. De-la, J. Rodríguez-ubreva, and M. García, 1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation

, Genome Biol, vol.14, p.99, 2013.

J. Madzo, H. Liu, and A. Rodriguez, Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis, Cell Rep, vol.6, pp.231-275, 2014.

L. Ge, R. P. Zhang, and F. Wan, TET2 plays an essential role in erythropoiesis by regulating lineage-specific genes via DNA oxidative demethylation in a zebrafish model

X. Zhao, J. Dai, Y. Ma, Y. Mi, D. Cui et al., Dynamics of ten-eleven translocation hydroxylase family proteins and 5-hydroxymethylcytosine in oligodendrocyte differentiation, Glia, vol.62, pp.914-940, 2014.

P. W. Hill, R. Amouroux, and P. Hajkova, DNA demethylation, Tet proteins and 5-hydroxymethylcytosine in epigenetic reprogramming: An emerging complex story, Genomics, issue.14, pp.154-156, 2014.

K. Iqbal, S. G. Jin, G. P. Pfeifer, and P. E. Szabó, Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine, Proc Natl Acad Sci U S A, vol.108, pp.3642-3649, 2011.

T. P. Gu, F. Guo, H. Yang, H. P. Wu, G. F. Xu et al., The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes, Nature, vol.477, pp.606-616, 2011.

M. Wossidlo, T. Nakamura, and K. Lepikhov, 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming, Nat Commun, vol.2, p.241, 2011.

C. Bian and X. Yu, PGC7 suppresses TET3 for protecting DNA methylation, Nucleic Acids Res, vol.42, pp.2893-905, 2014.

T. Nakamura, Y. J. Liu, and H. Nakashima, PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos, Nature, vol.486, pp.415-424, 2012.

S. Yamaguchi, L. Shen, Y. Liu, D. Sendler, and Y. Zhang, Role of Tet1 in erasure of genomic imprinting, Nature, vol.504, pp.460-464, 2013.

Y. Costa, J. Ding, and T. W. Theunissen, NANOG-dependent function of TET1 and TET2 in establishment of pluripotency, Nature, vol.495, pp.370-374, 2013.

C. A. Doege, K. Inoue, T. Yamashita, D. B. Rhee, S. Travis et al., Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2, Nature, vol.488, pp.652-657, 2012.

Y. Gao, J. Chen, and K. Li, Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming, Cell Stem Cell, vol.12, pp.453-69, 2013.

R. Ono, T. Taki, T. Taketani, M. Taniwaki, H. Kobayashi et al., LCX, leukemia-associated protein with a CXXC domain is fused to MLL in myeloid leukemia with trilineage dysplasia having t(10;11)(q22;q23), Cancer Res, vol.62, pp.4075-80, 2002.

R. B. Lorsbach, J. Moore, S. Mathew, S. C. Raimondi, S. T. Mukatira et al., TET1, a member of a novel protein family, is fused to MLL in acute myeloid leukemia containing the t(10;11)(q22;q23), Leukemia, vol.17, pp.637-678, 2003.

F. Delhommeau, S. Dupont, D. Valle, and V. , Mutations in TET2 in meyloid cancers, N Engl J Med, vol.360, pp.2289-301, 2009.

A. Mullally, A. Hedvat, and C. , Genetic characterization of TET1, TET2, and TET3 mutations in myeloid malignancies, Blood, vol.114, pp.144-151, 2009.

M. Ko, Y. Huang, and A. M. Jankowska, Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2, Nature, vol.468, pp.839-882, 2010.

K. Moran-crusio, L. Reavie, and A. Shih, Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation, Cancer Cell, vol.20, pp.11-24, 2011.

C. Quivoron, L. Couronné, D. Valle, and V. , TET2 inactivation results in pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during human lymphomagenesis, Cancer Cell, vol.20, pp.25-38, 2011.

E. Papaemmanuil, M. Gerstung, and L. Malcovati, Clinical and biological implications of driver mutations in myelodisplastic syndromes, Blood, vol.122, pp.3616-3643, 2013.

W. C. Chou, S. C. Chou, and C. Y. Liu, TET2 mutation is an unfavorable prognostic factor in acute myeloid leukemia patients with intermediate-risk cytogenetics, Blood, vol.118, pp.3803-3813, 2011.

T. Haferlach, Y. Nagata, and V. Grossmann, Landscape of genetic lesions in 944 patients with myelodysplastic syndromes, Leukemia, vol.28, pp.241-248, 2014.

T. Muto, G. Sashida, and M. Oshima, Concurrent loss of Ezh2 and Tet2 cooperates in the pathogenesis of myelodisplastic disorders, J Exp Med, vol.210, pp.2627-2666, 2013.

F. Song, C. I. Amos, and J. E. Lee, Indentification of a melanoma susceptibility locus and somatic mutation in TET2, Carcinogenesis, vol.35, pp.2097-101, 2014.

S. Seshagiri, E. W. Stawiski, and S. Durinck, Recurrent R-spondin fusions in colon cancer, Nature, vol.488, pp.660-664, 2012.

Y. Sato, T. Yoshizato, and Y. Shiraishi, Integrated molecular analysis of clear-cell renal cell carcinoma, Nat Genet, vol.45, pp.860-867, 2013.

S. Bamford, E. Dawson, and S. Forbes, The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website, Br J Cancer, vol.91, pp.355-363, 2004.

S. G. Jin, Y. Jiang, and R. Qiu, 5-hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations, Cancer Res, vol.71, pp.7360-7365, 2011.

C. G. Lian, Y. Xu, and C. Ceol, Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma, Cell, vol.150, pp.1135-1181, 2012.

Y. H. Kim, D. Pierscianek, and M. Mittelbronn, TET2 promoter methylation in low-grade diffuse gliomas lacking IDH1/2 mutations, J Clin Pathol, vol.64, pp.850-852, 2011.

E. Musialik, M. Bujko, A. Wypych, M. Matysiak, and J. A. Siedlecki, TET2 promoter DNA methylation and expression analysis in pediatric Bcell acute lymphoblastic leukemia, Hematol Rep, vol.6, p.5333, 2014.

M. B. Stadler, R. Murr, and L. Burger, DNA-binding factors shape the mouse methylome at distal regulatory regions, Nature, vol.480, pp.490-495, 2011.

M. Sun, C. X. Song, and H. Huang, HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis, Proc Natl Acad Sci, vol.110, pp.9920-9925, 2013.

A. Loriot, A. Van-tongelen, and J. Blanco, A novel cancergermline transcript carrying pro-metastatic miR-105 and TETtargeting miR-767 induced by DNA hypomethylation in tumors, Epigenetics, vol.9, pp.1163-71, 2014.

S. Morita, T. Horii, M. Kimura, T. Ochiya, S. Tajima et al., miR-29 represses the activities of DNA methyltransferases and DNA demethylases, Int J Mol Sci, vol.14, pp.14647-58, 2013.

P. Zhang, B. Huang, X. Xu, and W. C. Sessa, Ten-eleven translocation (Tet) and thymidine DNA glycosylase (TDG), components of the demethylation pathway, are direct targets of miRNA-29a, Biochem Biophys Res Commun, vol.437, pp.368-73, 2013.

S. J. Song, L. Poliseno, and M. S. Song, MicroRNA-antagonism regulates breast cancer stemness and metastasis vie TET-familydependent chromatin remodeling, Cell, vol.154, pp.311-335, 2013.

J. Cheng, S. Guo, and S. Chen, An extensive network of TET2-targeting MicroRNAs regulates malignant hematopoiesis, Cell Rep, vol.5, pp.471-81, 2013.

M. Ko, J. An, and H. S. Bandukwala, Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX, Nature, vol.497, pp.122-128, 2013.

A. V. Nguyen, C. G. Albers, and R. F. Holcombe, Differentiation of tubular and villous adenomas based on Wnt pathway-related gene expression profiles, Int J Mol Med, vol.26, pp.121-126, 2010.

G. Shin, T. Kang, and S. Yang, GENT: gene expression database of normal and tumor tissue, Cancer Inform, vol.10, pp.149-57, 2011.

, TET Pathway in Cancer Epigenetic Diagnosis & Therapy, vol.1, issue.1, p.59, 2015.

Y. Wang and Y. Zhang, Regulation of TET protein stability by calpains, Cell Rep, vol.6, pp.278-284, 2013.

F. E. Bleeker, S. Lamba, and S. Leenstra, IDH1 mutations at residue p.R132 (IDH1(R132)) occur frequently in high-grade glioma but not in other solid tumors, Hum Mutat, vol.30, pp.7-11, 2009.

H. Yan, D. W. Parsons, and G. Jin, IDH1 and IDH2 mutations in gliomas, N Engl J Med, vol.360, pp.765-73, 2009.

E. R. Mardis, L. Ding, and D. J. Dooling, Recurring mutations found by sequencing an acute myeloid leukemia genome, N Engl J Med, vol.361, pp.1058-66, 2009.

P. Paschka, R. F. Schlenk, and V. I. Gaidzik, IDH1 and IDH2 mutations are frequent genetic alterations in acute myeloid leukemia and confer adverse prognosis in cytogenetically normal acute myeloid leukemia with NPM1 mutation without FLT3 internal tandem duplication, J Clin Oncol, vol.28, pp.3636-3679, 2010.

L. Dang, D. W. White, and S. Gross, Cancer-associated IDH1 mutations produce 2-hydroxyglutarate, Nature, vol.462, pp.739-783, 2009.

P. Koivunen, S. Lee, and C. G. Duncan, Transformation by the (R)-enantiomer of 2-hydroxyglutarate linked to EGLN activation, Nature, vol.483, pp.484-492, 2012.

J. A. Losman, R. E. Looper, and P. Koivunen, R)-2-hydroxyglutarate is sufficient to promote leukemogenesis and its effects are reversible, Science, vol.339, pp.1621-1626, 2013.

R. Chowdhury, K. K. Yeoh, and Y. M. Tian, The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases, EMBO Rep, vol.12, pp.463-472, 2011.

C. Lu, P. S. Ward, and G. S. Kapoor, IDH mutation impairs histone demethylation and results in a block to cell differentiation, Nature, vol.483, pp.474-482, 2012.

W. Xu, H. Yang, and Y. Liu, Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of ?-ketoglutarate-depedent dioxygenases, Cancer Cell, vol.19, pp.17-30, 2011.

M. Xiao, H. Yang, and W. Xu, Inhibition of ?-KG-dependent histone and DNA demethylases by fumarate and succinate accumulated in mutation of FH and SDH tumor suppressors, Genes Dev, vol.26, pp.1326-1364, 2012.

P. J. Pollard, J. J. Brière, and N. A. Alam, Accumulation of Krebs cycle intermediate and over-expression of HIF1alpha in tumors which result from germline FH and SDH mutations, Hum Mol Genet, vol.14, pp.2231-2240, 2005.

J. P. Bayley, V. Launonen, and I. P. Tomlinson, The FH mutation database: an online database of fumarate hydratase mutations involved in the MCUL (HLRCC) tumor syndrome and congenital fumarase deficiency, BMC Med Genet, vol.9, p.20, 2008.

C. Bardella, P. J. Pollard, and I. Tomlinson, SDH mutations in cancer, Biochem Biophys Acta, vol.1807, pp.1432-1475, 2011.

C. H. Hsu, K. L. Peng, and M. L. Kang, TET1 suppresses cancer invasion by activation the tissue inhibitors of metalloproteinases, Cell Rep, vol.2, pp.568-79, 2012.

F. Wang, J. Travins, and B. Delabarre, Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation, Science, vol.340, pp.622-628, 2013.

D. Rohle, J. Popovici-muller, and N. Palaskas, An inhibitor of mutant IDH1 delays growth and promotes differentiation of glioma cells, Science, vol.340, pp.626-656, 2013.

S. J. Storr, N. O. Carragher, and M. C. Frame, The calpain system and cancer, Nat Rev Cancer, vol.11, pp.364-74, 2011.

H. Toyota, N. Yanase, T. Yoshimoto, M. Moriyama, T. Sudo et al., Calpain-induced Bax-cleavage product is a more potent inducer of apoptotic cell death than wild-type Bax, Cancer Lett, vol.189, pp.221-251, 2003.

K. Fettucciari, I. Fetriconi, and R. Mannucci, Group B Streptococcus induces macrophage apoptosis by calpain activation, J Immunol, vol.176, pp.7542-56, 2006.

J. Gafni, X. Cong, S. F. Chen, B. W. Gibson, and L. M. Ellerby, Calpain-1 cleaves and activates caspase-7, J Biol Chem, vol.284, pp.25441-25450, 2009.

M. A. Mataga, S. Rosenthal, and S. Heerboth, Anti-breast cancer effects of histone deacetylase inhibitors and calpain inhibitor, Anticancer Res, vol.32, pp.2523-2532, 2012.

S. Lee, J. W. Jung, and S. B. Park, Histone deacetylase regulates high mobility group A2-targeting microRNAs in human cord bloodderived multipotent stem cell aging, Cell Mol Life Sci, vol.68, pp.325-361, 2011.

D. Fazio, P. Montalbano, R. Neureiter, and D. , Downregulation of HMGA2 by the pan-deacetylase inhibitor panobinostat is dependent on hsa-let-7b expression in liver cancer cell lines, Exp Cell Res, vol.318, pp.1832-1875, 2012.

H. Zhou, W. Guo, and Y. Zhao, MicroRNA-26a acts as a tumor suppressor inhibiting gallbladder cancer cell proliferation directly targeting HMGA2, Int J Oncol, vol.44, pp.2050-2058, 2014.

A. Efanov, N. Zanesi, and V. Coppola, Human HMGA2 protein overexpressed in mice induces precursor T-cell lymphoblastic leukemia, Blood Cancer, vol.4, p.227, 2014.

E. A. Minor, B. L. Court, J. I. Young, and G. Wang, Ascorbate induces teneleven translocation (Tet) methylcytosine dioxygenase-mediated generation of 5-hydroxymethylcytosine, J Biol Chem, vol.288, pp.13669-74, 2013.

R. Yin, S. Q. Mao, and B. Zhao, Ascorbic acid enhances Tetmediated 5-methylcytosine oxidation and promotes DNA demethylation in mammals, J Am Chem Soc, vol.135, pp.10396-403, 2013.

K. Blaschke, K. T. Ebata, and M. M. Karimi, Vitamin C induces Tetdependent DNA demethylation and a blastocyst-like state in ES cells, Nature, vol.500, pp.222-228, 2013.

J. Chen, L. Guo, and L. Zhang, Vitamin C modulates TET1 function during somatic cell reprogramming, Nat Genet, vol.45, pp.1504-1513, 2013.

H. R. Harris, N. Orsini, and A. Wolk, Vitamin C and survival among women with breast cancer: a meta-analysis, Eur J Cancer, vol.50, pp.1223-1254, 2014.

X. Xu, E. Yu, and L. Liu, Dietary intake of vitamins A, C, and E and the risk of colorectal adenoma: a meta-analysis of observational studies, Eur J Cancer Prev, vol.22, pp.529-568, 2013.