O. Alder, R. Cullum, S. Lee, A. C. Kan, W. Wei et al., Hippo Signaling Influences HNF4A and FOXA2 Enhancer Switching during Hepatocyte Differentiation, Cell Reports, vol.9, issue.1, pp.261-271, 2014.
DOI : 10.1016/j.celrep.2014.08.046

URL : https://doi.org/10.1016/j.celrep.2014.08.046

J. P. Babeu and F. Boudreau, Hepatocyte nuclear factor 4-alpha involvement in liver and intestinal inflammatory networks, World Journal of Gastroenterology, vol.20, issue.1, pp.22-30, 2014.
DOI : 10.3748/wjg.v20.i1.22

URL : http://doi.org/10.3748/wjg.v20.i1.22

M. J. Bonder, S. Kasela, M. Kals, R. Tamm, K. Lokk et al., , 2014.

, Genetic and epigenetic regulation of gene expression in fetal and adult human livers, BMC Genomics, vol.15

N. Briançon, A. Bailly, F. Clotman, P. Jacquemin, F. P. Lemaigre et al., Expression of the ??7 Isoform of Hepatocyte Nuclear Factor (HNF) 4 Is Activated by HNF6/OC-2 and HNF1 and Repressed by HNF4??1 in the Liver, Journal of Biological Chemistry, vol.1, issue.32, pp.33398-33408, 2004.
DOI : 10.1093/nar/gkh581

F. Cabillic and A. Corlu, Regulation of Transdifferentiation and Retrodifferentiation by??Inflammatory Cytokines in Hepatocellular Carcinoma, Gastroenterology, vol.151, issue.4, pp.607-615, 2016.
DOI : 10.1053/j.gastro.2016.06.052

URL : https://hal.archives-ouvertes.fr/hal-01398435

V. Cerec, D. Glaise, D. Garnier, S. Morosan, B. Turlin et al., Transdifferentiation of hepatocyte-like cells from the human hepatoma HepaRG cell line through bipotent progenitor, Hepatology, vol.103, issue.4, pp.957-967, 2007.
DOI : 10.1007/s004180100310

URL : https://hal.archives-ouvertes.fr/hal-00690471

S. Chahar, V. Gandhi, S. Yu, K. Desai, R. Cowper-sal-lari et al., , 2014.

, Chromatin profiling reveals regulatory network shifts and a protective role for hepatocyte nuclear factor 4a during colitis, Mol. Cell. Biol, vol.34, pp.3291-3304

C. G. Chapman, C. J. Mariani, F. Wu, K. Meckel, F. Butun et al., TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer, 2015.

. Sci and . Rep,

K. Chellappa, P. Deol, J. R. Evans, L. M. Vuong, G. Chen et al., Opposing roles of nuclear receptor HNF4a isoforms in colitis and colitis-associated colon cancer. Elife 5, 2016.

H. Chiba, T. Itoh, S. Satohisa, N. Sakai, H. Noguchi et al., Activation of p21CIP1/WAF1 gene expression and inhibition of cell proliferation by overexpression of hepatocyte nuclear factor-4??, Experimental Cell Research, vol.302, issue.1, pp.11-21, 2005.
DOI : 10.1016/j.yexcr.2004.08.014

P. Du, W. A. Kibbe, L. , and S. M. , lumi: a pipeline for processing Illumina microarray, Bioinformatics, vol.36, issue.2, pp.1547-1548, 2008.
DOI : 10.1093/nar/gkm1075

H. Dubois-pot-schneider, K. Fekir, C. Coulouarn, D. Glaise, C. Aninat et al., Inflammatory cytokines promote the retrodifferentiation of tumor-derived hepatocyte-like cells to progenitor cells, Hepatology, vol.7, issue.29, pp.2077-2090, 2014.
DOI : 10.1016/j.stem.2010.08.008

URL : https://hal.archives-ouvertes.fr/hal-01134747

C. M. Greco, P. Kunderfranco, M. Rubino, V. Larcher, P. Carullo et al., DNA hydroxymethylation controls cardiomyocyte gene expression in development and hypertrophy, Nature Communications, vol.53, 2016.
DOI : 10.1002/anie.201308469

P. Gripon, S. Rumin, S. Urban, L. Seyec, J. Glaise et al., Infection of a human hepatoma cell line by hepatitis B virus, Proc. Natl. Acad. Sci. USA 99, pp.15655-15660, 2002.

H. Hernandez-vargas, M. P. Lambert, L. Calvez-kelm, F. Gouysse, G. Mckay-chopin et al., Hepatocellular Carcinoma Displays Distinct DNA Methylation Signatures with Potential as Clinical Predictors, PLoS ONE, vol.5, issue.3, 2010.
DOI : 10.1371/journal.pone.0009749.s008

M. Ivanov, M. Kals, M. Kacevska, I. Barragan, K. Kasuga et al., , 2013.

. Ontogeny, distribution and potential roles of 5-hydroxymethylcy- tosine in human liver function, Genome Biol, vol.14

M. Iwafuchi-doi and K. S. Zaret, Pioneer transcription factors in cell reprogramming, Genes & Development, vol.28, issue.24, pp.2679-2692, 2014.
DOI : 10.1101/gad.253443.114

A. A. Khan, M. V. Shaik, N. Parveen, A. Rajendraprasad, M. A. Aleem et al., Human fetal liver derived stem cell transplantation as supportive modality in the management of end stage decompensated liver cirrhosis, Cell Transplantation, vol.19, pp.409-418, 2010.
DOI : 10.3727/096368910X498241

K. Kim, A. Doi, B. Wen, K. Ng, R. Zhao et al., Epigenetic memory in induced pluripotent stem cells, Nature, vol.23, issue.7313, pp.285-290, 2010.
DOI : 10.1186/gb-2001-2-10-research0042

N. L. Lazarevich, O. A. Cheremnova, E. V. Varga, D. A. Ovchinnikov, E. I. Kudrjavtseva et al., Progression of HCC in mice is associated with a downregulation in the expression of hepatocyte nuclear factors, Hepatology, vol.968, issue.4, pp.1038-1047, 2004.
DOI : 10.1111/j.1749-6632.2002.tb04324.x

R. Lister, M. Pelizzola, Y. S. Kida, R. D. Hawkins, J. R. Nery et al., Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells, Nature, vol.133, issue.7336, pp.68-73, 2011.
DOI : 10.1016/j.cell.2008.03.029

B. Lucas, K. Grigo, S. Erdmann, J. Lausen, L. Klein-hitpass et al., HNF4?? reduces proliferation of kidney cells and affects genes deregulated in renal cell carcinoma, Oncogene, vol.24, issue.42, pp.6418-6431, 2005.
DOI : 10.1093/nar/29.11.e53

URL : http://www.nature.com/onc/journal/v24/n42/pdf/1208794a.pdf

A. Miyajima, M. Tanaka, and T. Itoh, Stem/Progenitor Cells in Liver Development, Homeostasis, Regeneration, and Reprogramming, Cell Stem Cell, vol.14, issue.5, pp.561-574, 2014.
DOI : 10.1016/j.stem.2014.04.010

URL : https://doi.org/10.1016/j.stem.2014.04.010

F. Mohn, M. Weber, M. Rebhan, T. C. Roloff, J. Richter et al., Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors, Molecular Cell, vol.30, issue.6, pp.755-766, 2008.
DOI : 10.1016/j.molcel.2008.05.007

X. Mu, R. Español-suñer, I. Mederacke, S. Affò, R. Manco et al., , 2015.

, Hepatocellular carcinoma originates from hepatocytes and not from the progenitor/biliary compartment, J. Clin. Invest, vol.125, pp.3891-3903

F. Neri, D. Incarnato, A. Krepelova, D. Dettori, S. Rapelli et al., TET1 is controlled by pluripotency-associated factors in ESCs and downmodulated by PRC2 in differentiated cells and tissues, Nucleic Acids Research, vol.2011, issue.14, pp.6814-6826, 2015.
DOI : 10.1128/MCB.01172-14

C. E. Nestor, A. Lentini, C. Hägg-nilsson, D. R. Gawel, M. Gustafsson et al., 5-Hydroxymethylcytosine Remodeling Precedes Lineage Specification during Differentiation of Human CD4 + T Cells, Cell Reports, vol.16, issue.2, pp.559-570, 2016.
DOI : 10.1016/j.celrep.2016.05.091

R. Parent and L. Beretta, Translational control plays a prominent role in the hepatocytic differentiation of HepaRG liver progenitor cells, Genome Biology, vol.9, issue.1, 2008.
DOI : 10.1186/gb-2008-9-1-r19

F. Parviz, C. Matullo, W. D. Garrison, L. Savatski, J. W. Adamson et al., Hepatocyte nuclear factor 4?? controls the development of a hepatic epithelium and liver morphogenesis, Nature Genetics, vol.20, issue.3, pp.292-296, 2003.
DOI : 10.1128/MCB.20.14.5175-5183.2000

T. J. Peters, M. J. Buckley, A. L. Statham, R. Pidsley, K. Samaras et al., De novo identification of differentially methylated regions in the human genome, Epigenetics Chromatin, vol.8, 2015.

R. Pidsley, C. C. Wong, Y. Volta, M. Lunnon, K. Mill et al., A data-driven approach to preprocessing Illumina 450K methylation array data, BMC Genomics, vol.14, issue.1, 2013.
DOI : 10.1093/ije/dyr225

S. Ruiz, D. Diep, A. Gore, A. D. Panopoulos, N. Montserrat et al., Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells, Proc. Natl. Acad. Sci. USA, pp.16196-16201, 2012.
DOI : 10.1038/nbt.1503

M. Santiago, C. Antunes, M. Guedes, N. Sousa, and C. J. Marques, TET enzymes and DNA hydroxymethylation in neural development and function ??? How critical are they?, Genomics, vol.104, issue.5, pp.334-340, 2014.
DOI : 10.1016/j.ygeno.2014.08.018

D. Schübeler, Function and information content of DNA methylation, Nature, vol.62, issue.7534, pp.321-326, 2015.
DOI : 10.1038/ng.2442

G. K. Smyth, Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments, Statistical Applications in Genetics and Molecular Biology, vol.3, issue.1, pp.1544-6115, 2004.
DOI : 10.2202/1544-6115.1027

W. Sun, M. Guan, L. , and X. , 5-Hydroxymethylcytosine-Mediated DNA Demethylation in Stem Cells and Development, Stem Cells and Development, vol.23, issue.9, pp.923-930, 2014.
DOI : 10.1089/scd.2013.0428

W. Sun, L. Zang, Q. Shu, L. , and X. , From development to diseases: The role of 5hmC in brain, Genomics, vol.104, issue.5, pp.347-351, 2014.
DOI : 10.1016/j.ygeno.2014.08.021

T. Tanaka, S. Jiang, H. Hotta, K. Takano, H. Iwanari et al., Dysregulated expression of P1 and P2 promoter-driven hepatocyte nuclear factor-4?? in the pathogenesis of human cancer, The Journal of Pathology, vol.326, issue.5, pp.662-672, 2006.
DOI : 10.5551/jat.9.233

, Stem Cell Reports j, vol.9, 2017277.

M. E. Torres-padilla, C. Fougère-deschatrette, and M. C. Weiss, Expression of HNF4?? isoforms in mouse liver development is regulated by sequential promoter usage and constitutive 3??? end splicing, Mechanisms of Development, vol.109, issue.2, pp.183-193, 2001.
DOI : 10.1016/S0925-4773(01)00521-4

L. Vallier, Heps with Pep: Direct Reprogramming into Human Hepatocytes, Cell Stem Cell, vol.14, issue.3, pp.267-269, 2014.
DOI : 10.1016/j.stem.2014.02.010

O. Wallerman, M. Motallebipour, S. Enroth, K. Patra, M. S. Bysani et al., Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing, Nucleic Acids Research, vol.21, issue.22, pp.7498-7508, 2009.
DOI : 10.1093/bioinformatics/bti1043

S. Wallner, C. Schröder, E. Leitão, T. Berulava, C. Haak et al., Epigenetic dynamics of monocyte-to-macrophage differentiation, Epigenetics & Chromatin, vol.38, issue.1, 2016.
DOI : 10.1093/nar/gkq537

A. Wang, F. Yue, Y. Li, R. Xie, T. Harper et al., Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates, Cell Stem Cell, vol.16, issue.4, pp.386-399, 2015.
DOI : 10.1016/j.stem.2015.02.013

A. J. Watt, W. D. Garrison, D. , and S. A. , HNF4: A central regulator of hepatocyte differentiation and function, Hepatology, vol.20, issue.6, pp.1249-1253, 2003.
DOI : 10.1128/MCB.20.14.5175-5183.2000

A. A. Wilson, L. Ying, M. Liesa, C. Segeritz, J. A. Mills et al., Emergence of a Stage-Dependent Human Liver Disease Signature with Directed Differentiation of Alpha-1 Antitrypsin-Deficient iPS Cells, Stem Cell Reports, vol.4, issue.5, pp.873-885, 2015.
DOI : 10.1016/j.stemcr.2015.02.021

Y. A. Yang, J. C. Zhao, K. W. Fong, J. Kim, S. Li et al., FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function, Nucleic Acids Research, vol.5, issue.17, pp.8153-8164, 2016.
DOI : 10.1093/nar/gku372

B. Yu, Z. He, P. You, Q. Han, D. Xiang et al., Reprogramming Fibroblasts into Bipotential Hepatic Stem Cells by Defined Factors, Cell Stem Cell, vol.13, issue.3, pp.328-340, 2013.
DOI : 10.1016/j.stem.2013.06.017

S. Zhu, M. Rezvani, J. Harbell, A. N. Mattis, A. R. Wolfe et al., Mouse liver repopulation with hepatocytes generated from human fibroblasts, Nature, vol.161, issue.7494, pp.93-97, 2014.
DOI : 10.1016/S0002-9440(10)64212-5