J. Dekker and L. Mirny, The 3D genome as moderator of chromosomal communication, Cell, vol.164, pp.1110-1121, 2016.

J. R. Dixon, D. U. Gorkin, and B. Ren, Chromatin domains: the unit of chromosome organization, Mol. Cell, vol.62, pp.668-680, 2016.

J. R. Dixon, Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, vol.485, pp.376-380, 2012.

D. M. Knipe, Snapshots: chromatin control of viral infection, Virology, vol.435, pp.141-156, 2013.

J. Beck and M. Nassal, Hepatitis B virus replication, World J. Gastroenterol, vol.13, pp.48-64, 2007.

J. E. Newbold, The covalently closed duplex form of the hepadnavirus genome exists in situ as a heterogeneous population of viral minichromosomes, J. Virol, vol.69, pp.3350-3357, 1995.

M. Levrero, Control of cccDNA function in hepatitis B virus infection, J. Hepatol, vol.51, pp.581-592, 2009.

A. J. Berk, in Fields Virology, vol.2, pp.2355-2394, 2007.

E. Lieberman-aiden, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, vol.326, pp.289-293, 2009.

L. Riviere, HBx relieves chromatin-mediated transcriptional repression of hepatitis B viral cccDNA involving SETDB1 histone methyltransferase, J. Hepatol, vol.63, pp.1093-1102, 2015.

A. Cournac, H. Marie-nelly, M. Marbouty, R. Koszul, and J. Mozziconacci, Normalization of a chromosomal contact map, BMC Genom, vol.13, p.436, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-00769663

S. S. Rao, A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping, Cell, vol.159, pp.1665-1680, 2014.

P. Tropberger, Mapping of histone modifications in episomal HBV cccDNA uncovers an unusual chromatin organization amenable to epigenetic manipulation, Proc. Natl Acad. Sci. USA, vol.112, pp.5715-5724, 2015.

B. Mifsud, Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C, Nat. Genet, vol.47, pp.598-606, 2015.

E. P. Consortium, An integrated encyclopedia of DNA elements in the human genome, Nature, vol.489, pp.57-74, 2012.
URL : https://hal.archives-ouvertes.fr/inserm-02187850

X. Li, The function of targeted host genes determines the oncogenicity of HBV integration in hepatocellular carcinoma, J. Hepatol, vol.60, pp.975-984, 2014.

T. Tu, M. A. Budzinska, N. A. Shackel, and S. Urban, HBV DNA integration: molecular mechanisms and clinical implications, Viruses, vol.9, p.75, 2017.

B. Van-steensel and A. S. Belmont, Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression, Cell, vol.169, pp.780-791, 2017.

A. M. Deaton and A. Bird, CpG islands and the regulation of transcription, Genes Dev, vol.25, pp.1010-1022, 2011.

F. Oriente, Prep1 controls insulin glucoregulatory function in liver by transcriptional targeting of SHP1 tyrosine phosphatase, Diabetes, vol.60, pp.138-147, 2011.

K. Wang and A. X. Holterman, Pathophysiologic role of hepatocyte nuclear factor 6, Cell Signal, vol.24, pp.9-16, 2012.

J. P. Thomson, CpG islands influence chromatin structure via the CpGbinding protein Cfp1, Nature, vol.464, pp.1082-1086, 2010.

D. A. Brown, The SET1 complex selects actively transcribed target genes via multivalent interaction with CpG island chromatin, Cell Rep, vol.20, pp.2313-2327, 2017.

V. Alarcon, The enzymes LSD1 and Set1A cooperate with the viral protein HBx to establish an active hepatitis B viral chromatin state, Sci. Rep, vol.6, p.25901, 2016.

Y. Guo, Y. Li, S. Mu, J. Zhang, and Z. Yan, Evidence that methylation of hepatitis B virus covalently closed circular DNA in liver tissues of patients with chronic hepatitis B modulates HBV replication, J. Med. Virol, vol.81, pp.1177-1183, 2009.

Y. H. Guo, Y. N. Li, J. R. Zhao, J. Zhang, and Z. Yan, HBc binds to the CpG islands of HBV cccDNA and promotes an epigenetic permissive state, Epigenetics, vol.6, pp.720-726, 2011.

J. Lucifora, Hepatitis B virus X protein is essential to initiate and maintain virus replication after infection, J. Hepatol, vol.55, pp.996-1003, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00850162

L. Belloni, Nuclear HBx binds the HBV minichromosome and modifies the epigenetic regulation of cccDNA function, Proc. Natl Acad. Sci. USA, vol.106, 2009.

D. Cougot, Inhibition of PP1 phosphatase activity by HBx: a mechanism for the activation of hepatitis B virus transcription, Sci. Signal, vol.5, p.1, 2012.

D. Cougot, The hepatitis B virus X protein functionally interacts with CREB-binding protein/p300 in the regulation of CREB-mediated transcription, J. Biol. Chem, vol.282, pp.4277-4287, 2007.

F. Guerrieri, Genome-wide identification of direct HBx genomic targets. BMC Genom, vol.18, p.184, 2017.
URL : https://hal.archives-ouvertes.fr/inserm-01470815

D. L. Miller, C. L. Myers, B. Rickards, H. A. Coller, and S. J. Flint, Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival, Genome Biol, vol.8, p.58, 2007.

R. Ferrari, Adenovirus small E1A employs the lysine acetylases p300/ CBP and tumor suppressor Rb to repress select host genes and promote productive virus infection, Cell. Host. Microbe, vol.16, pp.663-676, 2014.

R. Ferrari, Epigenetic reprogramming by adenovirus e1a, Science, vol.321, pp.1086-1088, 2008.

S. Radko, R. Jung, O. Olanubi, and P. Pelka, Effects of Adenovirus Type 5 E1A Isoforms on Viral Replication in Arrested Human Cells, PLoS. ONE, vol.10, p.140124, 2015.

M. Iwafuchi-doi, The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation, Mol. Cell, vol.62, pp.79-91, 2016.

H. Schrem, J. Klempnauer, and J. Borlak, Liver-enriched transcription factors in liver function and development. Part I: the hepatocyte nuclear factor network and liver-specific gene expression, Pharmacol. Rev, vol.54, pp.129-158, 2002.

M. Fournier, FOXA and master transcription factors recruit mediator and cohesin to the core transcriptional regulatory circuitry of cancer cells, Sci. Rep, vol.6, p.34962, 2016.

A. J. Berk, Recent lessons in gene expression, cell cycle control, and cell biology from adenovirus. Oncogene, vol.24, pp.7673-7685, 2005.

C. S. Young, The structure and function of the adenovirus major late promoter, Curr. Top. Microbiol. Immunol, vol.272, pp.213-249, 2003.

E. S. Gushchanskaya, The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes, Epigenetics, vol.9, pp.951-963, 2014.

S. Schoenfelder, Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells, Nat. Genet, vol.42, pp.53-61, 2010.

E. Apostolou and D. Thanos, Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression, Cell, vol.134, pp.85-96, 2008.

M. Merkenschlager, Cohesin: a global player in chromosome biology with local ties to gene regulation, Curr. Opin. Genet. Dev, vol.20, pp.555-561, 2010.

A. N. Engelman and P. K. Singh, Cellular and molecular mechanisms of HIV-1 integration targeting, Cell. Mol. Life Sci, vol.75, pp.2491-2507, 2018.

C. T. Bock, P. Schranz, C. H. Schroder, and H. Zentgraf, Hepatitis B virus genome is organized into nucleosomes in the nucleus of the infected cell, Virus Genes, vol.8, pp.215-229, 1994.

Y. Guo, Hepatitis B viral core protein disrupts human host gene expression by binding to promoter regions, BMC Genom, vol.13, p.563, 2012.

M. Du and L. Bai, 3D clustering of co-regulated genes and its effect on gene expression, Curr. Genet, vol.63, pp.1017-1021, 2017.

G. Li, Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation, Cell, vol.148, pp.84-98, 2012.

S. Fanucchi, Y. Shibayama, S. Burd, M. S. Weinberg, and M. M. Mhlanga, Chromosomal contact permits transcription between coregulated genes, Cell, vol.155, pp.606-620, 2013.

S. K. Ladner, Inducible expression of human hepatitis B virus (HBV) in stably transfected hepatoblastoma cells: a novel system for screening potential inhibitors of HBV replication, Antimicrob. Agents Chemother, vol.41, pp.1715-1720, 1997.

Y. Ni, Hepatitis B and D viruses exploit sodium taurocholate cotransporting polypeptide for species-specific entry into hepatocytes, Gastroenterology, vol.146, pp.1070-1083, 2014.

R. W. King, Inhibition of human hepatitis B virus replication by AT-61, a phenylpropenamide derivative, alone and in combination with (-)beta-L-2?,3?-dideoxy-3?-thiacytidine, Antimicrob. Agents Chemother, vol.42, pp.3179-3186, 1998.

S. Benhenda, The PRMT1 methyltransferase is a binding partner of HBx and a negative regulator of hepatitis B virus transcription, J. Virol, vol.87, pp.4360-4371, 2013.

S. Cairo, Hepatic stem-like phenotype and interplay of Wnt/beta-catenin and Myc signaling in aggressive childhood liver cancer, Cancer Cell, vol.14, pp.471-484, 2008.

M. Marbouty, Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms, vol.3, p.3318, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01316684

M. Imakaev, Iterative correction of Hi-C data reveals hallmarks of chromosome organization, Nat. Methods, vol.9, pp.999-1003, 2012.

A. Cournac, M. Marbouty, J. Mozziconacci, and R. Koszul, Generation and analysis of chromosomal contact maps of yeast species, Methods Mol. Biol, vol.1361, pp.227-245, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01419912

C. Levy-leduc, M. Delattre, T. Mary-huard, and S. Robin, Twodimensional segmentation for analyzing Hi-C data, Bioinformatics, vol.30, pp.386-392, 2014.

W. Huang-da, B. T. Sherman, and R. A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc, vol.4, pp.44-57, 2009.

S. Heinz, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol. Cell, vol.38, pp.576-589, 2010.

E. Eisenberg and E. Y. Levanon, Human housekeeping genes, revisited, Trends Genet, vol.29, pp.569-574, 2013.

D. Kim, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol, vol.14, p.36, 2013.