K. Shinozaki, K. Yamaguchi-shinozaki, and M. Seki, Regulatory network of gene expression in the drought and cold stress responses, Curr. Opin. Plant Biol, vol.6, pp.410-417, 2003.

E. H. Davidson, A genomic regulatory network for development, Science, vol.295, pp.1669-1678, 2002.

S. Huang, G. Eichler, Y. Bar-yam, and D. E. Ingber, Cell fates as highdimensional attractor states of a complex gene regulatory network, Phys. Rev. Lett, vol.94, p.128701, 2005.

T. Frum and A. Ralston, Cell signaling and transcription factors regulating cell fate during formation of the mouse blastocyst, Trends Genet. TIG, vol.31, pp.402-410, 2015.

D. Parfitt and M. M. Shen, From blastocyst to gastrula: gene regulatory networks of embryonic stem cells and early mouse embryogenesis, Philos. Trans. R. Soc. Lond. B. Biol. Sci, vol.369, p.20130542, 2014.

L. A. Boyer, Core transcriptional regulatory circuitry in human embryonic stem cells, Cell, vol.122, pp.947-956, 2005.

Y. Loh, The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells, Nat. Genet, vol.38, pp.431-440, 2006.

X. Chen, Integration of external signaling pathways with the core transcriptional network in embryonic stem cells, Cell, vol.133, pp.1106-1117, 2008.

J. Kim, J. Chu, X. Shen, J. Wang, and S. H. Orkin, An extended transcriptional network for pluripotency of embryonic stem cells, Cell, vol.132, pp.1049-1061, 2008.

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

J. Chew, 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.

H. Niwa, K. Ogawa, D. Shimosato, and K. Adachi, A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells, Nature, vol.460, pp.118-122, 2009.

D. Huang, LIF-activated Jak signaling determines Esrrb expression during late-stage reprogramming, Biol. Open, vol.7, p.29264, 2018.

I. Chambers, Functional expression cloning of nanog, a pluripotency sustaining factor in embryonic stem cells, Cell, vol.113, pp.643-655, 2003.

N. Festuccia, Esrrb is a direct nanog target gene that can substitute for nanog function in pluripotent cells, Cell Stem Cell, vol.11, pp.477-490, 2012.

V. Azuara, Chromatin signatures of pluripotent cell lines, Nat. Cell Biol, vol.8, pp.532-538, 2006.

B. E. Bernstein, A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell, vol.125, pp.315-326, 2006.

T. S. Mikkelsen, Genome-wide maps of chromatin state in pluripotent and lineage-committed cells, Nature, vol.448, pp.553-560, 2007.

L. A. Boyer, Polycomb complexes repress developmental regulators in murine embryonic stem cells, Nature, vol.441, pp.349-353, 2006.

D. Pasini, A. P. Bracken, J. B. Hansen, M. Capillo, and K. Helin, The polycomb group protein Suz12 is required for embryonic stem cell differentiation, Mol. Cell. Biol, vol.27, pp.3769-3779, 2007.

M. Leeb, Polycomb complexes act redundantly to repress genomic repeats and genes, Genes Dev, vol.24, pp.265-276, 2010.

M. E. Tanenbaum, L. A. Gilbert, L. S. Qi, J. S. Weissman, and R. D. Vale, A protein tagging system for signal amplification in gene expression and fluorescence imaging, Cell, vol.159, pp.635-646, 2014.

R. T. Utley, Transcriptional activators direct histone acetyltransferase complexes to nucleosomes, Nature, vol.394, pp.498-502, 1998.

A. Nishiyama, Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors, Cell Stem Cell, vol.5, pp.420-433, 2009.

L. Ho, An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network, Proc. Natl Acad. Sci, vol.106, pp.5187-5191, 2009.

B. L. Kidder, S. Palmer, and J. G. Knott, SWI/SNF-Brg1 regulates self-renewal and occupies core pluripotency-related genes in embryonic stem cells, Stem Cells, vol.27, pp.317-328, 2009.

Q. Ying, The ground state of embryonic stem cell self-renewal, Nature, vol.453, pp.519-523, 2008.

M. Sone, Hybrid cellular metabolism coordinated by Zic3 and Esrrb synergistically enhances induction of naive pluripotency, Cell Metab, vol.25, p.6, 2017.

C. Ballaré, Phf19 links methylated Lys36 of histone H3 to regulation of polycomb activity, Nat. Struct. Mol. Biol, vol.19, pp.1257-1265, 2012.

D. Acampora, L. G. Di-giovannantonio, and A. Simeone, Otx2 is an intrinsic determinant of the embryonic stem cell state and is required for transition to a stable epiblast stem cell condition, Development, vol.140, pp.43-55, 2013.

C. Buecker, Reorganization of enhancer patterns in transition from naive to primed pluripotency, Cell Stem Cell, vol.14, pp.838-853, 2014.

D. Acampora, Functional antagonism between OTX2 and NANOG specifies a spectrum of heterogeneous identities in embryonic stem cells, Stem Cell Rep, vol.9, pp.1642-1659, 2017.

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

D. Shlyueva, G. Stampfel, and A. Stark, Transcriptional enhancers: from properties to genome-wide predictions, Nat. Rev. Genet, vol.15, pp.272-286, 2014.

H. W. King and R. J. Klose, The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells, vol.6, p.22631, 2017.

I. Chambers, Nanog safeguards pluripotency and mediates germline development, Nature, vol.450, pp.1230-1234, 2007.

P. Navarro, Molecular coupling of Xist regulation and pluripotency, Science, vol.321, pp.1693-1695, 2008.

P. Navarro, 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

M. Zhang, Esrrb complementation rescues development of Nanog-null germ cells, Cell Rep, vol.22, pp.332-339, 2018.

J. Silva, Nanog is the gateway to the pluripotent ground state, Cell, vol.138, pp.722-737, 2009.

H. T. Stuart, NANOG amplifies STAT3 activation and they synergistically induce the naive pluripotent program, Curr. Biol, vol.24, pp.340-346, 2014.

A. C. Carter, B. N. Davis-dusenbery, K. Koszka, J. K. Ichida, and K. Eggan, Nanog-independent reprogramming to iPSCs with canonical factors, Stem Cell Rep, vol.2, pp.119-126, 2014.

B. A. Schwarz, O. Bar-nur, J. C. Silva, and K. Hochedlinger, Nanog is dispensable for the generation of induced pluripotent stem cells, Curr. Biol, vol.24, pp.347-350, 2014.

N. Konstantinides, Phenotypic convergence: distinct transcription factors regulate common terminal features, Cell, vol.174, pp.1-14, 2018.

D. Acampora, Forebrain and midbrain regions are deleted in Otx2-/-mutants due to a defective anterior neuroectoderm specification during gastrulation, Dev. Camb. Engl, vol.121, pp.3279-3290, 1995.

X. Gao, Reprogramming to pluripotency using designer TALE transcription factors targeting enhancers, Stem Cell Rep, vol.1, pp.183-197, 2013.

J. G. Doench, Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation, Nat. Biotechnol, vol.32, pp.1262-1267, 2014.

P. D. Hsu, DNA targeting specificity of RNA-guided Cas9 nucleases, Nat. Biotechnol, vol.31, pp.827-832, 2013.

F. Mueller, FISH-quant: automatic counting of transcripts in 3D FISH images, Nat. Methods, vol.10, pp.277-278, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01622707

J. Buenrostro, B. Wu, H. Chang, and W. Greenleaf, ATAC-seq: a method for assaying chromatin accessibility genome-wide, Curr. Protoc. Mol. Biol, vol.109, pp.21-29, 2015.

C. Galonska, M. J. Ziller, R. Karnik, and A. Meissner, Ground state conditions induce rapid reorganization of core pluripotency factor binding before global epigenetic reprogramming, Cell Stem Cell, vol.17, pp.462-470, 2015.

A. Marson, Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells, Cell, vol.134, pp.521-533, 2008.

W. A. Whyte, Master transcription factors and mediator establish superenhancers at key cell identity genes, Cell, vol.153, pp.307-319, 2013.

B. Lee, Tgif1 counterbalances the activity of core pluripotency factors in mouse embryonic stem cells, Cell Rep, vol.13, pp.52-60, 2015.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat. Methods, vol.9, pp.357-359, 2012.

A. Dobin and T. R. Gingeras, Mapping RNA-seq reads with STAR, Curr. Protoc. Bioinforma, vol.51, pp.11-14, 2015.

B. Li and C. N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinforma, vol.12, p.323, 2011.

J. Feng, T. Liu, B. Qin, Y. Zhang, and X. S. Liu, Identifying ChIP-seq enrichment using MACS, Nat. Protoc, vol.7, pp.1728-1740, 2012.

W. M. Rand, Objective criteria for the evaluation of clustering methods, J. Am. Stat. Assoc, vol.66, pp.846-850, 1971.
DOI : 10.1080/01621459.1971.10482356

URL : http://arxiv.org/pdf/1704.01036

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.
DOI : 10.1101/002832

URL : https://www.biorxiv.org/content/biorxiv/early/2014/11/17/002832.full.pdf