Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans, Nat Rev Genet, vol.13, pp.720-731, 2012. ,
Network motifs: theory and experimental approaches, Nat Rev Genet, vol.8, pp.450-461, 2007. ,
Multipotent cell lineages in early mouse development depend on SOX2 function, Genes Dev, vol.17, pp.126-140, 2003. ,
Computational discovery of gene modules and regulatory networks, Nat Biotechnol, vol.21, pp.1337-1342, 2003. ,
Synergy of SF1 and RAR in activation of Oct-3/4 promoter, J Biol Chem, vol.275, pp.6608-6619, 2000. ,
An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level, Science, vol.342, pp.253-257, 2013. ,
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences, Cell, vol.133, pp.1266-1276, 2008. ,
, The NIH Roadmap Epigenomics Mapping Consortium, vol.28, pp.1045-1048, 2010.
Molecular signals of epigenetic states, Science, vol.330, pp.612-616, 2010. ,
Core transcriptional regulatory circuitry in human embryonic stem cells, Cell, vol.122, pp.947-956, 2005. ,
Mechanisms and models of somatic cell reprogramming, Nat Rev Genet, vol.14, pp.427-439, 2013. ,
Conserved POU binding DNA sites in the Sox2 upstream enhancer regulate gene expression in embryonic and neural stem cells, J Biol Chem, vol.279, pp.41846-41857, 2004. ,
Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells, Cell, vol.113, pp.643-655, 2003. ,
Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma, Cancer Cell, vol.24, pp.777-790, 2013. ,
Myb controls intestinal stem cell genes and self-renewal, Stem Cells, vol.29, pp.2042-2050, 2011. ,
Transcriptional regulatory networks in embryonic stem cells, Cold Spring Harb Symp Quant Biol, vol.73, pp.203-209, 2008. ,
Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells, Mol Cell Biol, vol.25, pp.6031-6046, 2005. ,
A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity, Nature, vol.468, pp.316-320, 2010. ,
Origins and activity of the Mediator complex, Semin Cell Dev Biol, vol.22, pp.729-734, 2011. ,
Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits, Genome Res, vol.24, pp.1-13, 2014. ,
Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression, Nat Genet, vol.44, pp.1191-1198, 2012. ,
Emerging properties of animal gene regulatory networks, Nature, vol.468, pp.911-920, 2010. ,
The pluripotent genome in three dimensions is shaped around pluripotency factors, Nature, vol.501, pp.227-231, 2013. ,
Zic3 enhances the generation of mouse induced pluripotent stem cells, Stem Cells Dev, vol.22, pp.2017-2025, 2013. ,
Chromatin architecture reorganization during stem cell differentiation, Nature, vol.518, pp.331-336, 2015. ,
Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors, Cell Stem Cell, vol.13, pp.459-470, 2013. ,
Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes, Cell, vol.159, pp.374-387, 2014. ,
A gene ontology inferred from molecular networks, Nat Biotechnol, vol.31, pp.38-45, 2013. ,
Genetic and epigenetic fine mapping of causal autoimmune disease variants, Nature, vol.518, pp.337-343, 2015. ,
Sox2 deficiency causes neurodegeneration and impaired neurogenesis in the adult mouse brain, Development, vol.131, pp.3805-3819, 2004. ,
Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers, Am J Hum Genet, vol.92, pp.489-503, 2013. ,
Architecture of the human regulatory network derived from ENCODE data, Nature, vol.489, pp.91-100, 2012. ,
Distinct properties of cell-type-specific and shared transcription factor binding sites, Mol Cell, vol.52, pp.25-36, 2013. ,
Transcriptional and epigenetic dynamics during specification of human embryonic stem cells, Cell, vol.153, pp.1149-1163, 2013. ,
Forcing cells to change lineages, Nature, vol.462, pp.587-594, 2009. ,
SOX2 functions to maintain neural progenitor identity, Neuron, vol.39, pp.749-765, 2003. ,
FIMO: scanning for occurrences of a given motif, Bioinformatics, vol.27, pp.1017-1018, 2011. ,
A genome-wide screen in EpiSCs identifies Nr5a nuclear receptors as potent inducers of ground state pluripotency, Development, vol.137, pp.3185-3192, 2010. ,
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency, Cell Res, vol.21, pp.1393-1409, 2011. ,
Super-enhancers in the control of cell identity and disease, Cell, vol.155, pp.934-947, 2013. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02871951
Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers, Mol Cell, vol.58, pp.362-370, 2015. ,
Estrogen receptor ? (ESR1) gene amplification is frequent in breast cancer, Nat Genet, vol.39, pp.655-660, 2007. ,
Experimental conversion of liver to pancreas, Curr Biol, vol.13, pp.105-115, 2003. ,
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions, Nucleic Acids Res, vol.43, pp.117-122, 2015. ,
Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors, Cell, vol.142, pp.375-386, 2010. ,
Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming, Cell, vol.132, pp.567-582, 2008. ,
DNA-binding specificities of human transcription factors, Cell, vol.152, pp.327-339, 2013. ,
Insulin-promoter-factor 1 is required for pancreas development in mice, Nature, vol.371, pp.606-609, 1994. ,
Mediator and cohesin connect gene expression and chromatin architecture, Nature, vol.467, pp.430-435, 2010. ,
KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Res, vol.40, pp.109-114, 2012. ,
Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors, Cell, vol.157, pp.740-752, 2014. ,
The role of site accessibility in microRNA target recognition, Nat Genet, vol.39, pp.1278-1284, 2007. ,
The citric acid cycle and the Szent-Györgyi cycle in pigeon breast muscle, Biochem J, vol.34, pp.775-779, 1940. ,
Deconstructing transcriptional heterogeneity in pluripotent stem cells, Nature, vol.516, pp.56-61, 2014. ,
Transposable elements have rewired the core regulatory network of human embryonic stem cells, Nat Genet, vol.42, pp.631-634, 2010. ,
Octamer and Sox elements are required for transcriptional cis regulation of Nanog gene expression, Mol Cell Biol, vol.25, pp.2475-2485, 2005. ,
Sox2 acts through Sox21 to regulate transcription in pluripotent and differentiated cells, Curr Biol, vol.22, pp.1705-1710, 2012. ,
Targeting transcription regulation in cancer with a covalent CDK7 inhibitor, Nature, vol.511, pp.616-620, 2014. ,
Transcriptional regulation and its misregulation in disease, Cell, vol.152, pp.1237-1251, 2013. ,
Transcriptional regulatory networks in Saccharomyces cerevisiae, Science, vol.298, pp.799-804, 2002. ,
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers, Mol Syst Biol, vol.6, p.377, 2010. ,
Looping back to leap forward: transcription enters a new era, Cell, vol.157, pp.13-25, 2014. ,
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, vol.120, pp.15-20, 2005. ,
The SOX17/miR-371-5p/SOX2 axis inhibits EMT, stem cell properties and metastasis in colorectal cancer, Oncotarget, vol.6, pp.9099-9112, 2015. ,
Conditional c-myb knockout in adult hematopoietic stem cells leads to loss of self-renewal due to impaired proliferation and accelerated differentiation, Proc Natl Acad Sci, vol.106, pp.21689-21694, 2009. ,
Zic3 is required for maintenance of pluripotency in embryonic stem cells, Mol Biol Cell, vol.18, pp.1348-1358, 2007. ,
Browning of human adipocytes requires KLF11 and reprogramming of PPAR? superenhancers, Genes Dev, vol.29, pp.7-22, 2015. ,
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells, Nat Genet, vol.38, pp.431-440, 2006. ,
Selective inhibition of tumor oncogenes by disruption of super-enhancers, Cell, vol.153, pp.320-334, 2013. ,
Direct conversion of mouse fibroblasts to self-renewing, tripotent neural precursor cells, Proc Natl Acad Sci, vol.109, pp.2527-2532, 2012. ,
An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element, Science, vol.346, pp.1373-1377, 2014. ,
Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells, Nat Cell Biol, vol.9, pp.625-635, 2007. ,
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles, Nucleic Acids Res, vol.42, pp.142-147, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00943558
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes, Nucleic Acids Res, vol.34, pp.108-110, 2006. ,
Systematic localization of common disease-associated variation in regulatory DNA, Science, vol.337, pp.1190-1195, 2012. ,
Mir-290-295 deficiency in mice results in partially penetrant embryonic lethality and germ cell defects, Proc Natl Acad Sci, vol.108, pp.14163-14168, 2011. ,
The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells, Cell, vol.113, pp.631-642, 2003. ,
A blueprint for engineering cell fate: current technologies to reprogram cell identity, Cell Res, vol.23, pp.33-48, 2013. ,
Induction of diverse cardiac cell types by reprogramming fibroblasts with cardiac transcription factors, Development, vol.141, pp.4267-4278, 2014. ,
OCT4/SOX2-independent Nanog autorepression modulates heterogeneous Nanog gene expression in mouse ES cells, EMBO J, vol.31, pp.4547-4562, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02025074
Circuitry and dynamics of human transcription factor regulatory networks, Cell, vol.150, pp.1274-1286, 2012. ,
Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4, Cell, vol.95, pp.379-391, 1998. ,
Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells, Nat Genet, vol.24, pp.372-376, 2000. ,
Densely interconnected transcriptional circuits control cell states in human hematopoiesis, Cell, vol.144, pp.296-309, 2011. ,
Control of pancreas and liver gene expression by HNF transcription factors, Science, vol.303, pp.1378-1381, 2004. ,
Core transcriptional regulatory circuitry in human hepatocytes, Mol Syst Biol, vol.2, p.17, 2006. ,
Oct-3/4 and Sox2 regulate Oct-3/4 gene in embryonic stem cells, J Biol Chem, vol.280, pp.5307-5317, 2005. ,
Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages, EMBO J, vol.30, pp.494-509, 2011. ,
Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants, Proc Natl Acad Sci, vol.110, pp.17921-17926, 2013. ,
Predictive computation of genomic logic processing functions in embryonic development, Proc Natl Acad Sci, vol.109, pp.16434-16442, 2012. ,
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data, Genome Res, vol.21, pp.447-455, 2011. ,
Dramatic repositioning of c-Myb to different promoters during the cell cycle observed by combining cell sorting with chromatin immunoprecipitation, PLoS One, vol.6, p.17362, 2011. ,
The emergence of lineage-specific chromosomal topologies from coordinate gene regulation, Proc Natl Acad Sci, vol.106, pp.6679-6684, 2009. ,
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions, Nucleic Acids Res, vol.39, pp.124-128, 2011. ,
Transcriptional regulation of Nanog by OCT4 and SOX2, J Biol Chem, vol.280, pp.24731-24737, 2005. ,
Transcriptional regulation and the role of diverse coactivators in animal cells, FEBS Lett, vol.579, pp.909-915, 2005. ,
A proteome-scale map of the human interactome network, Cell, vol.159, pp.1212-1226, 2014. ,
Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia, Cancer Cell, vol.22, pp.209-221, 2012. ,
Acute TNF-induced repression of cell identity genes is mediated by NF?B-directed redistribution of cofactors from super-enhancers, 2015. ,
, Genome Res, vol.25, pp.1281-1294
Molecular architecture of transcription factor hotspots in early adipogenesis, Cell Rep, vol.7, pp.1434-1442, 2014. ,
Transcription factor cooperativity in early adipogenic hotspots and super-enhancers, Cell Rep, vol.7, pp.1443-1455, 2014. ,
Nanog is the gateway to the pluripotent ground state, Cell, vol.138, pp.722-737, 2009. ,
Role of SOX2 mutations in human hippocampal malformations and epilepsy, Epilepsia, vol.47, pp.534-542, 2006. ,
Heart repair by reprogramming non-myocytes with cardiac transcription factors, Nature, vol.485, pp.599-604, 2012. ,
Transcription factors: from enhancer binding to developmental control, Nat Rev Genet, vol.13, pp.613-626, 2012. ,
Conservation of trans-acting circuitry during mammalian regulatory evolution, Nature, vol.515, pp.365-370, 2014. ,
Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors, Science, vol.338, pp.1360-1363, 2012. ,
Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, vol.126, pp.663-676, 2006. ,
Nanog overcomes reprogramming barriers and induces pluripotency in minimal conditions, Curr Biol, vol.21, pp.65-71, 2011. ,
Identification of Sox-2 regulatory region which is under the control of Oct-3/4-Sox-2 complex, Nucleic Acids Res, vol.30, pp.3202-3213, 2002. ,
Transcription factor binding dynamics during human ES cell differentiation, Nature, vol.518, pp.344-349, 2015. ,
The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling, Nat Genet, vol.41, pp.885-890, 2009. ,
Mutation of GATA3 in human breast tumors, Oncogene, vol.23, pp.7669-7678, 2004. ,
Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer, J Clin Invest, vol.122, pp.2519-2530, 2012. ,
A census of human transcription factors: function, expression and evolution, Nat Rev Genet, vol.10, pp.252-263, 2009. ,
Rapid and efficient reprogramming of somatic cells to induced pluripotent stem cells by retinoic acid receptor ? and liver receptor homolog 1, Proc Natl Acad Sci, vol.108, pp.18283-18288, 2011. ,
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo, EMBO J, vol.29, pp.2147-2160, 2010. ,
Myb is required for self-renewal in a model system of early hematopoiesis, Oncogene, vol.19, pp.1196-1205, 2000. ,
Master transcription factors and mediator establish super-enhancers at key cell identity genes, Cell, vol.153, pp.307-319, 2013. ,
miRDB: an online resource for microRNA target prediction and functional annotations, Nucleic Acids Res, vol.43, pp.146-152, 2015. ,
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites, Cell, vol.154, pp.801-813, 2013. ,
Transcriptional regulation of human Oct4 by steroidogenic factor-1, J Cell Biochem, vol.101, pp.1198-1209, 2007. ,
Dynamic regulatory network controlling T H 17 cell differentiation, Nature, vol.496, pp.461-468, 2013. ,
Control of the embryonic stem cell state, Cell, vol.144, pp.940-954, 2011. ,
Induced pluripotent stem cell lines derived from human somatic cells, Science, vol.318, pp.1917-1920, 2007. ,
Model-based analysis of ChIP-Seq (MACS), Genome Biol, vol.9, p.137, 2008. ,
FOXO1 is an essential regulator of pluripotency in human embryonic stem cells, Nat Cell Biol, vol.13, pp.1092-1099, 2011. ,
Predicting tissue specific transcription factor binding sites, BMC Genomics, vol.14, p.796, 2013. ,
In vivo reprogramming of adult pancreatic exocrine cells to ?-cells, Nature, vol.455, pp.627-632, 2008. ,
RNA polymerase II elongation control, Annu Rev Biochem, vol.81, pp.119-143, 2012. ,
Smad3 mutant mice develop metastatic colorectal cancer, Cell, vol.94, pp.703-714, 1998. ,
Dissecting neural differentiation regulatory networks through epigenetic footprinting, Nature, vol.518, pp.355-359, 2014. ,
An integrated approach to dissecting oncogene addiction implicates a Myb-coordinated self-renewal program as essential for leukemia maintenance, Genes Dev, vol.25, pp.1628-1640, 2011. ,
,
, Access the most recent version at doi, vol.26, pp.385-396, 2016.
, Genome Res
Models of human core transcriptional regulatory circuitries Material Supplemental ,