5-Hydroxymethylcytosine is a predominantly stable DNA modification, Nat Chem, vol.6, pp.1049-1055, 2014. ,
Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding, Mol Cell, vol.43, pp.145-155, 2011. ,
The dinucleotide CG as a genomic signaling module, J Mol Biol, vol.409, pp.47-53, 2011. ,
Modification of enhancer chromatin: what, how, and why, Mol Cell, vol.49, pp.825-837, 2013. ,
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. ,
PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation, Genome Biol, vol.14, p.99, 2013. ,
Stable expression of FoxA1 promotes pluripotent P19 embryonal carcinoma cells to be neural stem-like cells, Gene Expr, vol.15, pp.153-162, 2012. ,
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
Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages, Immunity, vol.32, pp.317-328, 2010. ,
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin, Genome Res, vol.17, pp.877-885, 2007. ,
,
Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor, Cell Rep, vol.21, pp.342-349, 2013. ,
STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Res, vol.43, pp.447-452, 2015. ,
, , 2012.
, Primer3--new capabilities and interfaces, Nucleic Acids Res, vol.40, p.115
Practical guidelines for the comprehensive analysis of ChIP-seq data, PLOS Comput. Biol, vol.9, p.11, 2013. ,
Is this the right normalization? A diagnostic tool for ChIP-seq normalization, BMC Bioinformatics, vol.16, p.150, 2015. ,
Quantitative ChIP-seq normalization reveals global modulation of the epigenome, Cell Reports, vol.9, p.1163, 2014. ,
A signal noise model for significance analysis of ChIP-seq with négative control, Nat. Biotechnol, vol.26, p.1199, 2008. ,
An integrated software system foa analysing ChIP-chip and ChIP-seq data, Nat. Biotechnol, vol.26, p.1293, 2008. ,
Normalization on ChIP-seq data with control, BMC Bioinformatics, vol.13, p.199, 2012. ,
Normalization, bias correction, and peak calling for ChIP-seq, Stat. Appl. Gen. Mol. Biol, p.11, 2012. ,
Cytosine modifications modulate the chromatin architecture of transcriptional enhancers ,
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets, Bioinformatics, vol.25, p.2730, 2009. ,
Non-linear total variation based noise removal algorithms, Physica D, vol.60, p.259, 1992. ,
Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-asociated enhancers, Nucleic Acid Res, vol.40, p.8255, 2012. ,
TM4: a free, open-source system for microarray data management and analysis, Biotechniques, vol.34, p.374, 2003. ,
Cistrome: an integrative platform for transcriptional regulation studies, Genome Biology, p.12, 2011. ,
Genome-wide protein DNA binding dynamics suggest a molecular clutch for transcription factor function, Nature, vol.484, p.251, 2012. ,
Extensive chromatin remodelling and establishment of transcription factor hotspots during early adipogenesis, The EMBO Journal, vol.30, p.1459, 2011. ,
Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative, Mol Cell Biol, vol.15, issue.3, pp.1405-1421, 1995. ,
Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans, Nat Rev Genet, vol.13, issue.10, pp.720-731, 2012. ,
Computational strategies for the genome-wide identification of cis-regulatory elements and transcriptional targets, Curr Top Dev Biol, vol.98, pp.121-145, 2012. ,
Transcriptional features of genomic regulatory blocks, Genome Biol, vol.10, issue.4, p.38, 2009. ,
The Mediator complex: a central integrator of transcription, Nat Rev Mol Cell Biol, vol.16, issue.3, pp.155-166, 2015. ,
,
An atlas of active enhancers across human cell types and tissues, Nature, vol.507, issue.7493, pp.455-461, 2014. ,
A unified architecture of transcriptional regulatory elements, Trends Genet, vol.31, issue.8, pp.426-433, 2015. ,
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. ,
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. ,
Genome-wide quantitative enhancer activity maps identified by STARR-seq, Science, vol.339, issue.6123, pp.1074-1077 ,
Fine tuning of craniofacial morphology by distant-acting enhancers, Science, vol.342, p.1241006, 2013. ,
EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos, Genome Res, 2015. ,
5-Formylcytosine can be a stable DNA modification in mammals, Nat Chem Biol, vol.11, issue.8, pp.555-557, 2015. ,
5-Hydroxymethylcytosine is a predominantly stable DNA modification, Nat Chem, vol.6, issue.12, pp.1049-55, 2014. ,
MEME SUITE: tools for motif discovery and searching, Nucleic Acids Res, vol.37, pp.202-208, 2009. ,
Searching for statistically significant regulatory modules, Bioinformatics, vol.19, pp.16-25, 2003. ,
Regulation of chromatin by histone modifications, Cell Res, vol.21, issue.3, pp.381-395, 2011. ,
Highresolution profiling of histone methylations in the human genome, Cell, vol.129, issue.4, pp.823-837, 2007. ,
Methylation-dependent and -independent genomic targeting principles of the MBD protein family, Cell, vol.153, issue.2, pp.480-492, 2013. ,
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. ,
FACT facilitates transcription-dependent nucleosome alteration, Science, vol.301, issue.5636, pp.1090-1093, 2003. ,
Sequentially acting Sox transcription factors in neural lineage development, Genes Dev, vol.25, issue.23, pp.2453-2464, 2011. ,
A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell, vol.125, issue.2, pp.315-326, 2006. ,
Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding, Mol Cell, vol.43, issue.1, pp.145-155, 2011. ,
Going the distance: a current view of enhancer action, Science, vol.281, issue.5373, pp.60-63, 1998. ,
ChIP-Seq identification of weakly conserved heart enhancers, Nat Genet, vol.42, issue.9, pp.806-810, 2010. ,
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. ,
Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes, PLoS Biol, vol.3, issue.5, p.157, 2005. ,
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. ,
Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution, Science, vol.336, issue.6083, pp.934-937, 2012. ,
Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution, Nat Chem, vol.6, issue.5, pp.435-440, 2014. ,
Targets and dynamics of promoter DNA methylation during early mouse development, Nat Genet, vol.42, issue.12, pp.1093-1100, 2010. ,
UHRF1 plays a role in maintaining DNA methylation in mammalian cells, Science, vol.317, issue.5845, pp.1760-1764, 2007. ,
Dnmt3L and the establishment of maternal genomic imprints, Science, vol.294, issue.5551, pp.2536-2539, 2001. ,
Die Blastomerenkerne von Ascaris megalocephala und die Theorie der Chromosomenindividualität, Arch Zellforsch, vol.3, pp.181-268, 1909. ,
DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein, Cell, vol.64, issue.6, pp.1123-1134, 1991. ,
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. ,
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. ,
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. ,
Sp1 elements protect a CpG island from de novo methylation, Nature, vol.371, issue.6496, pp.435-438, 1994. ,
Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond, Epigenetics Chromatin, vol.8, p.24, 2015. ,
Myc represses transcription through recruitment of DNA methyltransferase corepressor, EMBO J, vol.24, issue.2, pp.336-346, 2005. ,
The histone variant H2A.Z is an important regulator of enhancer activity, Nucleic Acids Res, vol.43, issue.20, pp.9742-9756, 2015. ,
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 transcription factor-based mechanism for mouse heterochromatin formation, Nat Struct Mol Biol, vol.19, issue.10, pp.1023-1030, 2012. ,
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. ,
Superfamily 2 helicases. Front Biosci (Landmark Ed, vol.17, pp.2070-2088, 2012. ,
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. ,
RSC, an essential, abundant chromatin-remodeling complex, Cell, vol.87, issue.7, pp.1249-1260, 1996. ,
Modification of enhancer chromatin: what, how, and why?, Mol Cell, vol.49, issue.5, pp.825-837, 2013. ,
Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks, Curr Biol, vol.26, issue.1, pp.38-51, 2016. ,
Genome-wide analysis of mammalian promoter architecture and evolution, Nat Genet, vol.38, issue.6, pp.626-635, 2006. ,
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
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. ,
Identification of TET1 Partners That Control Its DNA-Demethylating Function, Genes Cancer, vol.4, issue.5-6, pp.235-241, 2013. ,
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. ,
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. ,
TET2 promotes histone O-GlcNAcylation during gene transcription, Nature, vol.493, issue.7433, pp.561-564, 2013. ,
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. ,
Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4, Mol Cell, vol.9, issue.2, pp.279-289, 2002. ,
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. ,
Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis, Genome Res, vol.20, issue.10, pp.1383-1390, 2010. ,
Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes, Hum Genet, vol.83, issue.2, pp.181-188, 1989. ,
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. ,
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters, Science, vol.322, issue.5909, pp.1845-1848, 2008. ,
Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability, Nature Feb, vol.470, issue.7334, pp.419-423, 2011. ,
Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair, Cell, vol.146, issue.1, pp.67-79, 2011. ,
NANOG-dependent function of TET1 and TET2 in establishment of pluripotency, Nature, vol.495, issue.7441, pp.370-374, 2013. ,
Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF protein complex, Science, vol.265, issue.5168, pp.53-60, 1994. ,
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. ,
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. ,
Differences in the localization and morphology of chromosomes in the human nucleus, J Cell Biol, vol.145, issue.6, pp.1119-1131, 1999. ,
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. ,
Molecular mechanisms of gene silencing mediated by DNA methylation, Mol Cell Biol, vol.22, issue.9, pp.3157-3173, 2002. ,
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. ,
A large fraction of extragenic RNA pol II transcription sites overlap enhancers, PLoS Biol, vol.8, issue.5, p.1000384, 2010. ,
, CTCF Binding Polarity Determines Chromatin Looping. Mol Cell, vol.60, issue.4, pp.676-684, 2015.
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. ,
TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS, EMBO J, vol.32, issue.5, pp.645-55, 2013. ,
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. ,
Constitutive heterochromatin: a surprising variety of expressed sequences, Chromosoma, vol.118, issue.4, pp.419-435, 2009. ,
Enhanced chromatin dynamics by FACT promotes transcriptional restart after UV-induced DNA damage, Mol Cell, vol.51, issue.4, pp.469-479, 2013. ,
Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, vol.485, issue.7398, pp.376-380, 2012. ,
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
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
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. ,
The active spatial organization of the beta-globin locus requires the transcription factor EKLF, Genes Dev, vol.18, issue.20, pp.2485-2490, 2004. ,
Promoter escape by RNA polymerase II, Biochim Biophys Acta, vol.1577, issue.2, pp.208-223, 2002. ,
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. ,
Activity-dependent phosphorylation of MeCP2 threonine 308 regulates interaction with NCoR, Nature, vol.499, issue.7458, pp.341-345, 2013. ,
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. ,
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
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. ,
An integrated encyclopedia of DNA elements in the human genome, Nature, vol.489, issue.7414, pp.57-74, 2012. ,
Discovery and characterization of chromatin states for systematic annotation of the human genome, Nat Biotechnol, vol.28, issue.8, pp.817-825, 2010. ,
Mapping and analysis of chromatin state dynamics in nine human cell types, Nature, vol.473, issue.7345, pp.43-49, 2011. ,
Mediator-dependent recruitment of TFIIH modules in preinitiation complex, Mol Cell, vol.31, issue.3, pp.337-346, 2008. ,
G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis, Nat Cell Biol, vol.8, issue.2, pp.188-194, 2006. ,
Conservation and divergence of methylation patterning in plants and animals, Proc Natl Acad Sci U S A, vol.107, pp.8689-8694, 2010. ,
DNA methylation supports intrinsic epigenetic memory in mammalian cells, PLoS Genet, vol.2, issue.4, p.65, 2006. ,
Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms, J. Mol. Biol, vol.374, issue.3, pp.563-579, 2007. ,
Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation, Nature, vol.473, issue.7347, pp.398-402, 2011. ,
Systematic protein location mapping reveals five principal chromatin types in Drosophila cells, Cell, vol.143, issue.2, pp.212-224, 2010. ,
Recruitment to the nuclear periphery can alter expression of genes in human cells, PLoS Genet, vol.4, issue.3, p.1000039, 2008. ,
H2B ubiquitylation plays a role in nucleosome dynamics during transcription elongation, Mol Cell, vol.31, issue.1, pp.57-66, 2008. ,
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. ,
Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain, PLoS One, vol.6, issue.6, p.21306, 2011. ,
Cytidine deaminases: AIDing DNA demethylation?, Genes Dev, vol.24, pp.2107-2114, 2010. ,
PPAR -induced PARylation promotes local DNA demethylation by production of 5-hydroxymethylcytosine, Nat Commun, vol.4, p.2262, 2013. ,
GlcNAcylation of histone H2B facilitates its monoubiquitination, Nature, vol.480, issue.7378, pp.557-560, 2011. ,
Methylation-mediated transcriptional silencing in euchromatin by methyl-CpG binding protein MBD1 isoforms, Mol Cell Biol, vol.19, issue.9, pp.6415-6426, 1999. ,
DNA methyltransferase Dnmt1 associates with histone deacetylase activity, Nat Genet, vol.24, issue.1, pp.88-91, 2000. ,
The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase, Nucleic Acids Res, vol.31, issue.9, pp.2305-2312, 2003. ,
An oestrogen-receptor-alpha-bound human chromatin interactome, Nature, vol.462, issue.7269, pp.58-64, 2009. ,
Role for DNA methylation in the control of cell type specific maspin expression, Nat Genet, vol.31, issue.2, pp.175-179, 2002. ,
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. ,
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. ,
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. ,
Insulators: exploiting transcriptional and epigenetic mechanisms, Nat Rev Genet, issue.9, pp.703-713, 2006. ,
Chromatin targeting of de novo DNA methyltransferases by the PWWP domain, J Biol Chem, vol.279, issue.24, pp.25447-25454, 2004. ,
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. ,
Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages, Immunity, vol.32, issue.3, pp.317-328, 2010. ,
Domainwide regulation of gene expression in the human genome, Genome Res, vol.17, issue.9, pp.1286-1295, 2007. ,
Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates, PLoS One, vol.5, issue.12, p.15367, 2010. ,
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. ,
Distinct factors control histone variant H3.3 localization at specific genomic regions, Cell, vol.140, issue.5, pp.678-691, 2010. ,
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. ,
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. ,
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. ,
Environment drives selection and function of enhancers controlling tissuespecific macrophage identities, Cell, vol.159, issue.6, pp.1327-1340, 2014. ,
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function, Cell, vol.162, issue.4, pp.900-910, 2015. ,
Enhancer transcripts mark active estrogen receptor binding sites, Genome Res, vol.23, issue.8, pp.1210-1223, 2013. ,
CTCF-mediated functional chromatin interactome in pluripotent cells, Nat Genet, vol.43, issue.7, pp.630-638, 2011. ,
Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence, Genes Dev, vol.28, issue.20, pp.2304-2313, 2014. ,
ATP-dependent chromatin remodeling activities, Cell Mol Life Sci, vol.58, issue.5-6, pp.673-682, 2001. ,
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. ,
Nucleosome dynamics define transcriptional enhancers, Nat Genet, vol.42, issue.4, pp.343-347, 2010. ,
Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA, Science, vol.333, issue.6047, pp.1303-1307, 2011. ,
Determinants of myogenic specificity within MyoD are required for noncanonical E box binding, Mol Cell Biol, vol.27, issue.16, pp.5910-520, 2007. ,
Histone modifications at human enhancers reflect global cell-typespecific gene expression, Nature, vol.459, issue.7243, pp.108-120, 2009. ,
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. ,
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome, Nat Genet, vol.39, issue.3, pp.311-318, 2007. ,
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. ,
The selection and function of cell type-specific enhancers, Nat Rev Mol Cell Biol, vol.16, issue.3, pp.144-154, 2015. ,
Identification and characterization of a family of mammalian methyl-CpG binding proteins, Mol Cell Biol, vol.18, issue.11, pp.6538-6547, 1998. ,
The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites, Nature, vol.401, issue.6750, pp.301-304, 1999. ,
Three-dimensional positioning of genes in mouse cell nuclei, Chromosoma, vol.117, issue.6, pp.535-551, 2008. ,
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. ,
Dnmt3/transcription factor interactions as crucial players in targeted DNA methylation, Epigenetics, vol.4, issue.7, pp.487-499, 2009. ,
Super-enhancers in the control of cell identity and disease, Cell, vol.155, issue.4, pp.934-947, 2013. ,
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. ,
Discovery and annotation of functional chromatin signatures in the human genome, PLoS Comput Biol, vol.5, issue.11, p.1000566, 2009. ,
5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation, Mol Cell, vol.56, issue.2, pp.286-297, 2014. ,
Shadow enhancers as a source of evolutionary novelty, Science, vol.321, issue.5894, p.1314, 2008. ,
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
Structural insight into substrate preference for TET-mediated oxidation, Nature, vol.527, issue.7576, pp.118-122, 2015. ,
FOXA1 is a key determinant of estrogen receptor function and endocrine response, Nat Genet, vol.43, issue.1, pp.27-33, 2011. ,
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. ,
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. ,
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine, Science, vol.333, issue.6047, pp.1300-1303, 2011. ,
ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor, Cell, vol.90, issue.1, pp.145-155, 1997. ,
A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation, Genome Biol, vol.14, issue.10, p.119, 2013. ,
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. ,
Structure and function of a human TAFII250 double bromodomain module, Science, vol.288, issue.5470, pp.1422-1425, 2000. ,
Nucleosome stability mediated by histone variants H3.3 and H2A, Z. Genes Dev, vol.21, issue.12, pp.1519-1529, 2007. ,
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
A highresolution map of the three-dimensional chromatin interactome in human cells, Nature, vol.503, issue.7475, pp.290-294, 2013. ,
Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm, Bioinformatics, vol.19, pp.169-176, 2003. ,
Rethinking how DNA methylation patterns are maintained, Nat Rev Genet, vol.10, issue.11, pp.805-811, 2009. ,
Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription, Nat Genet, vol.19, issue.2, pp.187-191, 1998. ,
Mediator and cohesin connect gene expression and chromatin architecture, Nature, vol.467, issue.7314, pp.430-435, 2010. ,
Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription, Mol Cell, vol.51, issue.3, pp.310-325, 2013. ,
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. ,
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. ,
Transient cyclical methylation of promoter DNA, Nature, vol.452, issue.7183, pp.112-115, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00266286
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. ,
Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation, Cell, vol.155, issue.7, pp.1507-1520, 2013. ,
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome, Cell, vol.128, issue.6, pp.1231-1245, 2007. ,
Widespread transcription at neuronal activity-regulated enhancers, Nature, vol.465, issue.7295, pp.182-187, 2010. ,
Architectural and Functional Commonalities between Enhancers and Promoters, Cell, vol.162, issue.5, pp.948-959, 2015. ,
Chromatin looping and eRNA transcription precede the transcriptional activation of gene in the -globin locus, Biosci Rep, vol.35, issue.2, p.179, 2015. ,
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. ,
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. ,
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. ,
Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX, Nature, vol.497, issue.7447, pp.122-126, 2013. ,
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. ,
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. ,
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
CAGE: cap analysis of gene expression, Nat Methods, vol.3, issue.3, pp.211-222, 2006. ,
An RNA polymerase II holoenzyme responsive to activators, Nature, vol.368, issue.6470, pp.466-469, 1994. ,
Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development, Science, vol.296, issue.5565, pp.158-62, 2002. ,
The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain, Science, vol.324, issue.5929, pp.929-930, 2009. ,
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. ,
Transcription through chromatin by RNA polymerase II: histone displacement and exchange, Mutat Res, vol.618, issue.1-2, pp.116-129, 2007. ,
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. ,
Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex, Nature, vol.370, issue.6489, pp.477-481, 1994. ,
Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins, Nature, vol.410, issue.6824, pp.116-120, 2001. ,
Eukaryotic transcription factors, Biochem J, vol.270, issue.2, pp.281-2819, 1990. ,
Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment, Cell, vol.159, issue.6, pp.1312-1326, 2014. ,
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. ,
ATG deserts define a novel core promoter subclass, Genome Res, vol.15, issue.9, pp.1189-1197, 2005. ,
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. ,
Metazoan promoters: emerging characteristics and insights into transcriptional regulation, Nat Rev Genet, vol.13, issue.4, pp.233-245, 2012. ,
A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei, Cell, vol.71, issue.5, pp.865-873, 1992. ,
Requirement of RSF and FACT for transcription of chromatin templates in vitro, Science, vol.282, issue.5395, pp.1900-1904, 1998. ,
Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA, Cell, vol.69, issue.6, pp.905-914, 1992. ,
Role for DNA methylation in genomic imprinting, Nature, vol.366, issue.6453, pp.362-365, 1993. ,
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation, Cell, vol.148, issue.1-2, pp.84-98, 2012. ,
Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation, Nature, vol.498, issue.7455, pp.516-520, 2013. ,
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
Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation, Cell, vol.151, issue.7, pp.1608-1616, 2012. ,
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. ,
Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, vol.326, issue.5950, pp.289-293, 2009. ,
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. ,
Human DNA methylomes at base resolution show widespread epigenomic differences, Nature, vol.462, issue.7271, pp.315-322, 2009. ,
Cistrome: an integrative platform for transcriptional regulation studies, Genome Biol, vol.12, issue.8, p.83, 2011. ,
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. ,
ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection, Biochem Soc Trans, vol.41, issue.3, pp.727-740, 2013. ,
Selective inhibition of tumor oncogenes by disruption of super-enhancers, Cell, vol.153, issue.2, pp.320-334, 2013. ,
Role of Tet proteins in enhancer activity and telomere elongation, Genes Dev, vol.28, pp.2103-2119, 2014. ,
A computational investigation on the substrate preference of ten-eleven-translocation 2 (TET2), Phys Chem Chem PhysJan, vol.22, 2016. ,
Crystal structure of the nucleosome core particle at 2.8 A resolution, Nature, vol.389, issue.6648, pp.251-260, 1997. ,
Chz1, a nuclear chaperone for histone H2AZ, Mol Cell, vol.25, issue.3, pp.357-368, 2007. ,
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. ,
Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions, Cell, vol.161, issue.5, pp.1012-1025, 2015. ,
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription, Cell, vol.132, issue.6, pp.958-970, 2008. ,
Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor, Nat Neurosci, vol.16, issue.7, pp.898-902, 2013. ,
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. ,
PBX1 genomic pioneer function drives ER? signaling underlying progression in breast cancer, PLoS Genet, vol.7, issue.11, p.1002368, 2011. ,
DNA demethylation by TET proteins: a potential therapeutic target in cancer, Epigenetic Diagnosis & Therapy, vol.1, pp.49-59, 2015. ,
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. ,
TRANSFAC: transcriptional regulation, from patterns to profiles, Nucleic Acids Res, vol.31, issue.1, pp.374-378, 2003. ,
Conserved role of intragenic DNA methylation in regulating alternative promoters, Nature, vol.466, issue.7303, pp.253-257, 2010. ,
Common themes and cell type specific variations of higher order chromatin arrangements in the mouse, BMC Cell Biol, vol.6, p.44, 2005. ,
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. ,
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. ,
Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs, Cell, vol.58, issue.3, pp.499-507, 1989. ,
Genome-scale DNA methylation maps of pluripotent and differentiated cells, Nature, vol.454, issue.7205, pp.766-770, 2008. ,
Discovery of active enhancers through bidirectional expression of short transcripts, Genome Biol, vol.12, issue.11, p.113, 2011. ,
MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system, Cell, vol.151, issue.7, pp.1417-1430, 2012. ,
Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro, Biochim Biophys Acta, vol.1839, issue.11, pp.1323-1329, 2014. ,
Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells, Dev Cell, vol.10, issue.1, pp.105-116, 2006. ,
Cyclical DNA methylation of a transcriptionally active promoter, Nature, vol.452, issue.7183, pp.45-50, 2008. ,
Mapping cis-and trans-chromatin interaction networks using chromosome conformation capture (3C), Methods Mol Biol, vol.464, pp.105-126, 2009. ,
Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster, EMBO J, vol.28, issue.9, pp.1234-1245, 2009. ,
Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet, vol.37, issue.10, pp.1090-1097, 2005. ,
ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex, Science, vol.303, issue.5656, pp.343-348, 2004. ,
Reactivation of an inactive human X chromosome: evidence for X inactivation by DNA methylation, Science, vol.211, issue.4480, pp.393-396, 1981. ,
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. ,
A regulatory archipelago controls Hox genes transcription in digits, Cell, vol.147, issue.5, pp.1132-1145, 2011. ,
Master transcription factors determine cell-type-specific responses to TGF-signaling, Cell, vol.147, issue.3, pp.565-576, 2011. ,
TET-mediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent gene reactivation, Nucleic Acids Res, vol.42, issue.13, pp.8592-8604, 2014. ,
Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, Chemistry, vol.17, issue.49, pp.13782-13788, 2011. ,
Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex, Nature, vol.393, issue.6683, pp.386-389, 1998. ,
Noncoding transcription at enhancers: general principles and functional models, Annu Rev Genet, vol.46, pp.1-19, 2012. ,
An expansive human regulatory lexicon encoded in transcription factor footprints, Nature, vol.489, issue.7414, pp.83-90, 2012. ,
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. ,
MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex, Nat Genet, vol.23, issue.1, pp.58-61, 1999. ,
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. ,
Scanning human gene deserts for long-range enhancers, Science, vol.302, issue.5644, p.413, 2003. ,
Spatial partitioning of the regulatory landscape of the X-inactivation centre, Nature, vol.485, issue.7398, pp.381-385, 2012. ,
ANP32E is a histone chaperone that removes H2A.Z from chromatin, Nature, vol.505, issue.7485, pp.648-653, 2014. ,
Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution, BMC Bioinformatics, vol.11, 2010. ,
Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases, Nat Genet, vol.19, issue.3, pp.219-220, 1998. ,
DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development, Cell, vol.99, issue.3, pp.247-257, 1999. ,
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. ,
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. ,
Enhancer function: new insights into the regulation of tissue-specific gene expression, Nat Rev Genet, vol.12, issue.4, pp.283-93, 2011. ,
DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA, Nature, vol.448, issue.7154, pp.714-717, 2007. ,
The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins, Nature, vol.400, issue.6741, pp.284-288, 1999. ,
Latent enhancers activated by stimulation in differentiated cells, Cell, vol.152, issue.1-2, pp.157-171, 2013. ,
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. ,
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. ,
Tissue-specific spatial organization of genomes, Genome Biol, vol.5, issue.7, p.44, 2004. ,
Cohesins functionally associate with CTCF on mammalian chromosome arms, Cell, vol.132, issue.3, pp.422-433, 2008. ,
Nucleosome assembly protein 1 exchanges histone H2A-H2B dimers and assists nucleosome sliding, J Biol Chem, vol.280, issue.3, pp.1817-1825, 2005. ,
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells, Nature, vol.473, issue.7347, pp.394-397, 2011. ,
TATA element recognition by the TATA box-binding protein has been conserved throughout evolution, Genes Dev, vol.13, issue.24, pp.3217-3230, 1999. ,
MacroH2A, a core histone containing a large nonhistone region, Science, vol.257, issue.5075, pp.1398-1400, 1992. ,
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
In vivo enhancer analysis of human conserved non-coding sequences, Nature, vol.444, issue.7118, pp.499-502, 2006. ,
Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation, Mol Cell, vol.38, issue.4, pp.603-613, 2010. ,
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles, Nucleic Acids Res, vol.38, pp.105-110, 2010. ,
What are super-enhancers?, Nat Genet, vol.47, issue.1, pp.8-12, 2015. ,
CXXC domain of human DNMT1 is essential for enzymatic activity, Biochemistry, vol.47, issue.38, pp.10000-10009, 2008. ,
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
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. ,
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. ,
, 1885. Über Zelltheilung. Morph Jb, vol.10, pp.214-330
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level, PLoS Genet, vol.7, issue.1, p.1001274, 2011. ,
A unique chromatin signature uncovers early developmental enhancers in humans, Nature, vol.470, issue.7333, pp.279-283, 2011. ,
Dnmt2-dependent methylomes lack defined DNA methylation patterns, Proc Natl Acad Sci U S A, vol.110, issue.21, pp.8627-8631, 2013. ,
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. ,
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping, Cell, vol.159, issue.7, pp.1665-1680, 2014. ,
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.
DNA methylation and human disease, Nat Rev Genet, vol.6, issue.8, pp.597-610, 2005. ,
The role of general initiation factors in transcription by RNA polymerase II, Trends Biochem Sci, vol.21, issue.9, pp.327-335, 1996. ,
Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping, Genes Dev, vol.19, issue.5, pp.542-552, 2005. ,
Core promoters in transcription: old problem, new insights, Trends Biochem Sci, vol.40, issue.3, pp.165-171, 2015. ,
CTCF physically links cohesin to chromatin, Proc Natl Acad Sci U S A, vol.105, issue.24, pp.8309-8314, 2008. ,
Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells, Development, vol.139, issue.1, pp.15-31, 2012. ,
Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification, Cell, vol.151, issue.1, pp.153-166, 2012. ,
The long-range interaction landscape of gene promoters, Nature, vol.489, issue.7414, pp.109-113 ,
Monoubiquitylation of H2A.Z distinguishes its association with euchromatin or facultative heterochromatin, Mol Cell Biol, vol.27, issue.18, pp.6457-6468, 2007. ,
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. ,
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. ,
Genome-wide control of RNA polymerase II activity by cohesin, PLoS Genet, vol.9, issue.3, p.1003382, 2013. ,
Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity, Genome Res, vol.19, issue.7, pp.1165-1174, 2009. ,
ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions, Methods, vol.48, issue.3, pp.240-248, 2009. ,
ESCI award lecture: regulation, function and biomarker potential of DNA methylation, Eur J Clin Invest, vol.45, issue.3, pp.288-293, 2015. ,
Promoter features related to tissue specificity as measured by Shannon entropy, Genome Biol, vol.6, issue.4, p.33, 2005. ,
Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages, Science, vol.265, issue.5178, pp.1573-1577, 1994. ,
Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin, Mol Cell, vol.58, issue.6, pp.1101-1112, 2015. ,
Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers, Nucleic Acids Res, vol.40, issue.17, pp.8255-8265, 2012. ,
Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers, Genome Res, vol.21, issue.4, pp.555-565, 2011. ,
Three-dimensional folding and functional organization principles of the Drosophila genome, Cell, vol.148, issue.3, pp.458-472, 2012. ,
Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion, Mol Cell Biol, vol.35, issue.6, pp.1014-1039, 2015. ,
The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA, Nature, vol.450, issue.7171, pp.908-912, 2007. ,
Genomewide profiling of DNA methylation reveals a class of normally methylated CpG island promoters, PLoS Genet, vol.3, issue.10, pp.2023-2036, 2007. ,
Genome-wide analysis reveals TET-and TDG-dependent 5-methylcytosine oxidation dynamics, Cell, vol.153, issue.3, pp.692-706, 2013. ,
A chromatin remodelling complex involved in transcription and DNA processing, Nature, vol.406, issue.6795, pp.541-544, 2000. ,
A map of the cis-regulatory sequences in the mouse genome, Nature, vol.488, issue.7409, pp.116-120, 2012. ,
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. ,
Drosophila Brahma complex remodels nucleosome organizations in multiple aspects, Nucleic Acids Res, vol.42, issue.15, pp.9730-9739, 2014. ,
Guanine-5-carboxylcytosine base pairs mimic mismatches during, DNA replication. Sci Rep, vol.4, p.5220, 2014. ,
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes, Genome Res, vol.15, issue.8, pp.1034-1050, 2005. ,
Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis, EMBO J, vol.30, issue.8, pp.1459-1472, 2011. ,
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. ,
DNA methylation: roles in mammalian development, Nat Rev Genet, vol.14, issue.3, pp.204-220, 2013. ,
Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming, Cell, vol.153, issue.3, pp.678-691, 2013. ,
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine, Nat Biotechnol, vol.29, issue.1, pp.68-72, 2011. ,
Tissue specific differentially methylated regions (TDMR): Changes in DNA methylation during development, Genomics, vol.93, issue.2, pp.130-139, 2009. ,
The dynamics of chromosome organization and gene regulation, Annu Rev Biochem, vol.72, pp.573-608, 2003. ,
Evidence for large domains of similarly expressed genes in the Drosophila genome, J Biol, vol.1, issue.1, p.5, 2002. ,
Long-range intrachromosomal interactions in the T helper type 2 cytokine locus, Nat Immunol, vol.5, issue.10, pp.1017-1027, 2004. ,
Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives, Cell, vol.152, issue.5, pp.1146-1159, 2013. ,
Visualization of interphase chromosomes, J Cell Sci, vol.26, pp.281-299, 1977. ,
DNA-binding factors shape the mouse methylome at distal regulatory regions, Nature, vol.480, issue.7378, pp.490-495, 2011. ,
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells, Genome Biol, vol.12, issue.6, p.54, 2011. ,
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. ,
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
Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells, PLoS Genet, vol.7, issue.6, p.1002154, 2011. ,
Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA, Nucleic Acids Res, vol.38, p.181, 2010. ,
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. ,
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1, Science, vol.324, issue.5929, pp.930-935, 2009. ,
TET2 repression by androgen hormone regulates global hydroxymethylation status and prostate cancer progression, Nat Commun, vol.6, p.8219, 2015. ,
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. ,
Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development, Genome Res, vol.24, issue.8, pp.1285-1295, 2014. ,
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. ,
Chromatin deacetylation by an ATPdependent nucleosome remodelling complex, Nature, vol.395, issue.6705, pp.917-921, 1998. ,
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. ,
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. ,
Purification and properties of an ATP-dependent nucleosome remodeling factor, Cell, vol.83, issue.6, pp.1011-1020, 1995. ,
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. ,
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 ,
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
Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II, Nature, vol.388, issue.6642, pp.598-602, 1997. ,
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
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. ,
Histone exchange, chromatin structure and the regulation of transcription, Nat Rev Mol Cell Biol, vol.16, issue.3, pp.178-189, 2015. ,
Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4, Cell, vol.131, issue.1, pp.58-69, 2007. ,
ChIP-seq accurately predicts tissue-specific activity of enhancers, Nature, vol.457, issue.7231, pp.854-858, 2009. ,
VISTA Enhancer Browser--a database of tissuespecific human enhancers, Nucleic Acids Res, vol.35, pp.88-92, 2007. ,
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. ,
Transcription of IAP endogenous retroviruses is constrained by cytosine methylation, Nat Genet, vol.20, issue.2, pp.116-117, 1998. ,
Computational identification of active enhancers in model organisms, Genomics Proteomics Bioinformatics, vol.11, issue.3, pp.142-150, 2013. ,
A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth, Mol Cell, vol.27, issue.3, pp.380-392, 2007. ,
Combinatorial patterns of histone acetylations and methylations in the human genome, Nat Genet, vol.40, issue.7, pp.897-903, 2008. ,
Stage-and cell-specific expression of Dnmt3a and Dnmt3b during embryogenesis, Mech Dev, vol.118, issue.1-2, pp.187-190, 2002. ,
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 ,
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome, Nat Genet, vol.39, issue.4, pp.457-466, 2007. ,
Cohesin mediates transcriptional insulation by CCCTC-binding factor, Nature, vol.451, issue.7180, pp.796-801, 2008. ,
Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming, Nat Commun, vol.5, p.4719, 2014. ,
Master transcription factors and mediator establish super-enhancers at key cell identity genes, Cell, vol.153, issue.2, pp.307-319, 2013. ,
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. ,
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity, Nature, vol.473, issue.7347, pp.343-348, 2011. ,
Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus, J Cell Sci, vol.119, pp.132-140, 2006. ,
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 ,
Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells, Nature, vol.473, issue.7347, pp.389-393, 2011. ,
Cloning, expression and chromosome locations of the human DNMT3 gene family, Gene, vol.236, issue.1, pp.87-95, 1999. ,
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. ,
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. ,
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. ,
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. ,
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. ,
NURD, a novel complex with both ATPdependent chromatin-remodeling and histone deacetylase activities, Mol Cell, vol.2, issue.6, pp.851-861, 1998. ,
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. ,
Involvement of crosstalk between Oct4 and Meis1a in neural cell fate decision, PLoS One, vol.8, issue.2, p.56997, 2013. ,
NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation, Cell, vol.97, issue.1, pp.41-51, 1999. ,
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. ,
Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4, Mol Cell, vol.19, issue.4, pp.535-545, 2005. ,
Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300, Cell, vol.93, issue.3, pp.361-372, 1998. ,
Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells, Cell, vol.147, issue.7, pp.1498-1510, 2011. ,
N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso, Mol Cell, vol.12, issue.3, pp.723-734, 2003. ,
Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome, Cell, vol.149, issue.6, pp.1368-1380, 2012. ,
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo, Nat Genet, vol.39, issue.12, pp.1512-1516, 2007. ,
Genome-wide evolutionary analysis of eukaryotic DNA methylation, Science, vol.328, issue.5980, pp.916-919, 2010. ,
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions, Genome Res, vol.21, issue.8, pp.1273-1283, 2011. ,
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. ,
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. ,
Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6, Nature, vol.525, issue.7569, pp.389-393, 2015. ,
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. ,
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. ,
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. ,
Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations, Nature, vol.504, issue.7479, pp.306-310, 2013. ,
Genome-wide chromatin state transitions associated with developmental and environmental cues, Cell, vol.152, issue.3, pp.642-654, 2013. ,
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks, Nature, vol.456, issue.7218, pp.125-129, 2008. ,
Charting a dynamic DNA methylation landscape of the human genome, 2013. ,
The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain, Science, vol.324, pp.929-959, 2009. ,
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1, Science, vol.324, pp.930-935, 2009. ,
Prediction of novel enzymes involved in oxidative and other complex modifications of bases in nucleic acids, Cell cycle, vol.8, pp.1698-710, 2009. ,
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. ,
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. ,
Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation, Cell, vol.19, pp.1545-55, 2013. ,
Structure of a Naegleria Tetlike dioxygenase in complex with 5-methylcytosine DNA, Nature, vol.506, pp.391-396, 2014. ,
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. ,
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine, Science, vol.333, pp.1300-1303, 2011. ,
Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA, Science, vol.333, pp.1303-1310, 2011. ,
Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates, PLoS One, vol.5, p.15367, 2010. ,
Quantification of the sixth DNA base hydroxymethylcytosine in the brain, Angew Chem Int Ed Engl, vol.49, pp.5375-5382, 2010. ,
Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA, Nucleic Acids Res, vol.38, p.181, 2010. ,
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine ,
, Nat Biotechnol, vol.29, pp.68-72, 2011.
Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation, Oncogene, vol.32, pp.663-672, 2013. ,
Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming, Cell, vol.153, pp.678-91, 2013. ,
Genome-wide analysis reveals TETand TDG-dependent 5-methylcytosine oxidation dynamics, Cell, vol.153, pp.692-706, 2013. ,
Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution, Nat Chem, vol.6, pp.435-475, 2014. ,
Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development, Cell Res, vol.21, pp.1670-1676, 2011. ,
Genomic DNA methylation: the mark and its mediators, Trends Biochem Sci, vol.31, pp.89-97, 2006. ,
DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development, Cell, vol.99, pp.247-57, 1999. ,
Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos, Science, vol.334, p.194, 2011. ,
Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine, Science, vol.339, pp.448-52, 2013. ,
Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1, Cancer Res, vol.67, pp.946-50, 2007. ,
Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation, Nucleic Acids Res, vol.40, pp.4841-4850, 2012. ,
Cell cycle-dependent turnover of 5-hydroxymethyl cytosine in mouse embryonic stem cells, PLoS One, vol.8, p.82961, 2013. ,
Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain, PLoS One, vol.6, p.21306, 2011. ,
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. ,
TETmediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent gene reactivation, Nucleic Acids Res, vol.4, pp.8592-604, 2014. ,
Mechanism and stemcell activity of 5-carboxycytosine decarboxylation determined by isotope tracing, Angew Chem Int Ed Engl, vol.51, pp.6516-6536, 2012. ,
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. ,
Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain, Cell, vol.145, pp.423-457, 2011. ,
Thymine DNA glycosylase is essential for active DNA demethylation by linked deaminationbase excision repair, Cell, vol.146, pp.67-79, 2011. ,
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. ,
AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation, Nat Chem Biol, vol.8, pp.751-759, 2012. ,
Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA, Nat Chem Biol, vol.10, pp.574-81, 2014. ,
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. ,
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. ,
Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation, Nature, vol.473, pp.398-402, 2011. ,
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity, Nature, vol.473, pp.343-351, 2011. ,
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells, Genome Biol, vol.12, p.54, 2011. ,
Genomic mapping of 5-hydroxymethylcytosine in the human brain, Nucleic Acids Res, vol.39, pp.5015-5039, 2011. ,
Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers, Nucleic Acids Res, vol.40, pp.8255-65, 2012. ,
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells, Nature, vol.473, pp.394-401, 2011. ,
The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine, Nat Protoc, vol.7, pp.1909-1926, 2012. ,
Direct detection of DNA methylation during single-molecule, real-time sequencing, Nat Methods, vol.7, pp.461-466, 2010. ,
High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells, Cell Rep, vol.3, pp.567-76, 2013. ,
RRHP: a tag-based approach for 5-hydroxymethylcytosine mapping at single-site resolution, Genome Biol, vol.15, p.456, 2014. ,
The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing, PLoS One, vol.5, p.8888, 2010. ,
Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution, Science, vol.336, pp.934-941, 2012. ,
Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine, Nat Protoc, vol.8, pp.1841-51, 2013. ,
Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome, Cell, vol.149, pp.1368-80, 2012. ,
Chemical modification-assisted bisulfite sequencing (CAB-Seq) for 5-carboxylcytosine detection in DNA, J Am Chem Soc, vol.135, pp.9315-9322, 2013. ,
Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing, Nat Biotechnol, 2014. ,
Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells, Nature, vol.473, pp.389-93, 2011. ,
Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells, PLoS Genet, vol.7, p.1002154, 2011. ,
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.
MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system, Cell, vol.151, pp.1417-1447, 2012. ,
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. ,
TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS, EMBO J, vol.32, pp.645-55, 2013. ,
Identification of TET1 Partners That Control Its DNADemethylating Function, Genes Cancer, vol.4, pp.235-276, 2013. ,
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. ,
Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells, Cell, vol.147, pp.1498-510, 2011. ,
Tet proteins connect the Olinked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells, Mol Cell, vol.49, pp.645-56, 2013. ,
TET2 promotes histone O-GlcNAcylation during gene transcription, Nature, vol.493, pp.561-565, 2013. ,
TET3-OGT interaction increases the stability and the presence of OGT in chromatin, Genes Cells, vol.19, pp.52-65, 2014. ,
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. ,
Cycling of O-linked beta-Nacetylglucosamine on nucleocytoplasmic proteins, Nature, vol.446, pp.1017-1039, 2007. ,
Loss of Tet enzymes compromises proper differentiation of embryonic stem cells, Dev Cell, vol.29, pp.102-113, 2014. ,
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. ,
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. ,
Oct4 and the small molecule inhibitor, SC1, regulates Tet2 expression in mouse embryonic stem cells ,
, Mol Biol Rep, vol.40, pp.2897-906, 2013.
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. ,
Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development, Cell, vol.151, pp.1200-1213, 2012. ,
,
Dynamics of 5-hydroxymethylcytosine and chromatin marks in Mammalian neurogenesis, Cell Rep, vol.3, pp.291-300, 2013. ,
Tet1 regulates adult hippocampal neurogenesis and cognition, Cell Stem Cell, vol.13, pp.237-282, 2013. ,
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. ,
PPAR?-induced PARylation promotes local DNA demethylation by production of 5-hydroxymethylcytosine, Nat Commun, vol.4, p.2262, 2013. ,
1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation ,
, Genome Biol, vol.14, p.99, 2013.
Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis, Cell Rep, vol.6, pp.231-275, 2014. ,
TET2 plays an essential role in erythropoiesis by regulating lineage-specific genes via DNA oxidative demethylation in a zebrafish model ,
Dynamics of ten-eleven translocation hydroxylase family proteins and 5-hydroxymethylcytosine in oligodendrocyte differentiation, Glia, vol.62, pp.914-940, 2014. ,
DNA demethylation, Tet proteins and 5-hydroxymethylcytosine in epigenetic reprogramming: An emerging complex story, Genomics, issue.14, pp.154-156, 2014. ,
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. ,
The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes, Nature, vol.477, pp.606-616, 2011. ,
5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming, Nat Commun, vol.2, p.241, 2011. ,
PGC7 suppresses TET3 for protecting DNA methylation, Nucleic Acids Res, vol.42, pp.2893-905, 2014. ,
PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos, Nature, vol.486, pp.415-424, 2012. ,
Role of Tet1 in erasure of genomic imprinting, Nature, vol.504, pp.460-464, 2013. ,
NANOG-dependent function of TET1 and TET2 in establishment of pluripotency, Nature, vol.495, pp.370-374, 2013. ,
Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2, Nature, vol.488, pp.652-657, 2012. ,
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. ,
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. ,
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. ,
Mutations in TET2 in meyloid cancers, N Engl J Med, vol.360, pp.2289-301, 2009. ,
Genetic characterization of TET1, TET2, and TET3 mutations in myeloid malignancies, Blood, vol.114, pp.144-151, 2009. ,
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2, Nature, vol.468, pp.839-882, 2010. ,
Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation, Cancer Cell, vol.20, pp.11-24, 2011. ,
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. ,
Clinical and biological implications of driver mutations in myelodisplastic syndromes, Blood, vol.122, pp.3616-3643, 2013. ,
TET2 mutation is an unfavorable prognostic factor in acute myeloid leukemia patients with intermediate-risk cytogenetics, Blood, vol.118, pp.3803-3813, 2011. ,
Landscape of genetic lesions in 944 patients with myelodysplastic syndromes, Leukemia, vol.28, pp.241-248, 2014. ,
Concurrent loss of Ezh2 and Tet2 cooperates in the pathogenesis of myelodisplastic disorders, J Exp Med, vol.210, pp.2627-2666, 2013. ,
Indentification of a melanoma susceptibility locus and somatic mutation in TET2, Carcinogenesis, vol.35, pp.2097-101, 2014. ,
Recurrent R-spondin fusions in colon cancer, Nature, vol.488, pp.660-664, 2012. ,
Integrated molecular analysis of clear-cell renal cell carcinoma, Nat Genet, vol.45, pp.860-867, 2013. ,
The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website, Br J Cancer, vol.91, pp.355-363, 2004. ,
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. ,
Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma, Cell, vol.150, pp.1135-1181, 2012. ,
TET2 promoter methylation in low-grade diffuse gliomas lacking IDH1/2 mutations, J Clin Pathol, vol.64, pp.850-852, 2011. ,
TET2 promoter DNA methylation and expression analysis in pediatric Bcell acute lymphoblastic leukemia, Hematol Rep, vol.6, p.5333, 2014. ,
DNA-binding factors shape the mouse methylome at distal regulatory regions, Nature, vol.480, pp.490-495, 2011. ,
HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis, Proc Natl Acad Sci, vol.110, pp.9920-9925, 2013. ,
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. ,
miR-29 represses the activities of DNA methyltransferases and DNA demethylases, Int J Mol Sci, vol.14, pp.14647-58, 2013. ,
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. ,
MicroRNA-antagonism regulates breast cancer stemness and metastasis vie TET-familydependent chromatin remodeling, Cell, vol.154, pp.311-335, 2013. ,
An extensive network of TET2-targeting MicroRNAs regulates malignant hematopoiesis, Cell Rep, vol.5, pp.471-81, 2013. ,
Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX, Nature, vol.497, pp.122-128, 2013. ,
Differentiation of tubular and villous adenomas based on Wnt pathway-related gene expression profiles, Int J Mol Med, vol.26, pp.121-126, 2010. ,
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.
Regulation of TET protein stability by calpains, Cell Rep, vol.6, pp.278-284, 2013. ,
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. ,
IDH1 and IDH2 mutations in gliomas, N Engl J Med, vol.360, pp.765-73, 2009. ,
Recurring mutations found by sequencing an acute myeloid leukemia genome, N Engl J Med, vol.361, pp.1058-66, 2009. ,
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. ,
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate, Nature, vol.462, pp.739-783, 2009. ,
Transformation by the (R)-enantiomer of 2-hydroxyglutarate linked to EGLN activation, Nature, vol.483, pp.484-492, 2012. ,
R)-2-hydroxyglutarate is sufficient to promote leukemogenesis and its effects are reversible, Science, vol.339, pp.1621-1626, 2013. ,
The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases, EMBO Rep, vol.12, pp.463-472, 2011. ,
IDH mutation impairs histone demethylation and results in a block to cell differentiation, Nature, vol.483, pp.474-482, 2012. ,
Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of ?-ketoglutarate-depedent dioxygenases, Cancer Cell, vol.19, pp.17-30, 2011. ,
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. ,
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. ,
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. ,
SDH mutations in cancer, Biochem Biophys Acta, vol.1807, pp.1432-1475, 2011. ,
TET1 suppresses cancer invasion by activation the tissue inhibitors of metalloproteinases, Cell Rep, vol.2, pp.568-79, 2012. ,
Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation, Science, vol.340, pp.622-628, 2013. ,
An inhibitor of mutant IDH1 delays growth and promotes differentiation of glioma cells, Science, vol.340, pp.626-656, 2013. ,
The calpain system and cancer, Nat Rev Cancer, vol.11, pp.364-74, 2011. ,
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. ,
Group B Streptococcus induces macrophage apoptosis by calpain activation, J Immunol, vol.176, pp.7542-56, 2006. ,
Calpain-1 cleaves and activates caspase-7, J Biol Chem, vol.284, pp.25441-25450, 2009. ,
Anti-breast cancer effects of histone deacetylase inhibitors and calpain inhibitor, Anticancer Res, vol.32, pp.2523-2532, 2012. ,
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. ,
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. ,
MicroRNA-26a acts as a tumor suppressor inhibiting gallbladder cancer cell proliferation directly targeting HMGA2, Int J Oncol, vol.44, pp.2050-2058, 2014. ,
Human HMGA2 protein overexpressed in mice induces precursor T-cell lymphoblastic leukemia, Blood Cancer, vol.4, p.227, 2014. ,
Ascorbate induces teneleven translocation (Tet) methylcytosine dioxygenase-mediated generation of 5-hydroxymethylcytosine, J Biol Chem, vol.288, pp.13669-74, 2013. ,
Ascorbic acid enhances Tetmediated 5-methylcytosine oxidation and promotes DNA demethylation in mammals, J Am Chem Soc, vol.135, pp.10396-403, 2013. ,
Vitamin C induces Tetdependent DNA demethylation and a blastocyst-like state in ES cells, Nature, vol.500, pp.222-228, 2013. ,
Vitamin C modulates TET1 function during somatic cell reprogramming, Nat Genet, vol.45, pp.1504-1513, 2013. ,
Vitamin C and survival among women with breast cancer: a meta-analysis, Eur J Cancer, vol.50, pp.1223-1254, 2014. ,
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. ,