Y. Hayashizaki, A promoter-level mammalian expression atlas 505 19. Encode Project Consortium. 2012. An integrated encyclopedia of DNA elements in the 506 human genome, Nature Nature, vol.507, issue.20, pp.462-47057, 2014.

F. Muller, F. Consortium, A. Forrest, P. Carninci, M. Rehli et al., An atlas of 514 active enhancers across human cell types and tissues, Nature, vol.507, issue.21, pp.455-461, 2014.

G. Natoli, M. Buendia, J. Faivre, and P. Carninci, CAGE profiling of ncRNAs in 518 hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus- 519 induced tumors, Genome Res, vol.25, issue.22, pp.1812-1824, 2015.

N. Sharopova, M. Kimura, and M. Feolo, NCBI's Database of Genotypes and Phenotypes: 522 dbGaP, Nucleic Acids Res, vol.42, issue.523, pp.975-979, 2014.

H. Li, R. Durbin, A. Hasegawa, C. Daub, P. Carninci et al., Fast and accurate short read alignment with Burrows-Wheeler 524 transform MOIRAI: a 526 compact workflow system for CAGE analysis, Bioinformatics BMC Bioinformatics, vol.25, issue.527, pp.1754-1760144, 2009.

J. Hayer, F. Jadeau, G. Deleage, A. Kay, F. Zoulim et al., HBVdb: a knowledge database for Hepatitis B Virus, Nucleic Acids Research, vol.41, issue.D1, pp.566-570, 2013.
DOI : 10.1093/nar/gks1022
URL : https://hal.archives-ouvertes.fr/hal-00965883

M. Frith, E. Valen, A. Krogh, Y. Hayashizaki, P. Carninci et al., A code for 538 transcription initiation in mammalian genomes Integrative Genomics Viewer (IGV): 540 high-performance genomics data visualization and exploration, Genome Nat Genet Genome Res Brief Bioinform, vol.536, issue.541, pp.626-635, 2008.

S. Ladner, M. Otto, C. Barker, K. Zaifert, G. Wang et al., Inducible expression of human hepatitis B virus (HBV) in stably transfected 543 hepatoblastoma cells: a novel system for screening potential inhibitors of HBV replication, Antimicrob Agents Chemother, vol.542, issue.545, pp.1715-1720, 1997.

M. Buendia and C. Neuveut, Inhibition of PP1 phosphatase activity by HBx: a 547 mechanism for the activation of hepatitis B virus transcription, Sci Signal, vol.5, issue.548, pp.1-31, 2012.

H. Guo, D. Jiang, T. Zhou, A. Cuconati, T. Block et al., Characterization of the Intracellular Deproteinized Relaxed Circular DNA of Hepatitis B Virus: an Intermediate of Covalently Closed Circular DNA Formation, Journal of Virology, vol.81, issue.22, pp.12472-12484, 2007.
DOI : 10.1128/JVI.01123-07

J. Lucifora, S. Arzberger, D. Durantel, L. Belloni, M. Strubin et al., Hepatitis B virus X protein is essential to initiate and maintain virus replication after infection, Journal of Hepatology, vol.55, issue.5, pp.996-1003, 2011.
DOI : 10.1016/j.jhep.2011.02.015
URL : https://hal.archives-ouvertes.fr/hal-00850162

S. Dion, M. Bourgine, O. Godon, F. Levillayer, and M. Michel, Adeno-Associated Virus-Mediated Gene Transfer Leads to Persistent Hepatitis B Virus Replication in Mice Expressing HLA-A2 and HLA-DR1 Molecules, Journal of Virology, vol.87, issue.10, pp.5554-5563, 2013.
DOI : 10.1128/JVI.03134-12

F. Zoulim, Persistence of cccDNA during the natural history of chronic hepatitis B and 560 decline during adefovir dipivoxil therapy, Gastroenterology, vol.126, issue.561, pp.1750-1758, 2004.

C. Laurent, A. Laurent, P. Bioulac-sage, J. Calderaro, and J. Zucman-rossi, Integration 563 of tumour and viral genomic characterizations in HBV-related hepatocellular carcinomas, Gut, vol.564, issue.565, pp.820-829, 2015.

S. Murakami, T. Nomura, Y. Lin, D. Dorjsuren, S. Ohno et al., Hepatitis B virus X protein: structure, function and biology Human 571 hepatitis B virus X protein is detectable in nuclei of transfected cells, and is active for 572 transactivation, Intervirology Biochim Biophys Acta, vol.569, issue.573, pp.81-99330, 1999.

J. Williams, O. Andrisani, A. Mercier, M. Robinson, W. Zhong et al., The hepatitis B virus X protein targets the basic region-leucine zipper domain of CREB., Proceedings of the National Academy of Sciences, vol.92, issue.9, pp.3819-3823, 1995.
DOI : 10.1073/pnas.92.9.3819

Y. Zheng, J. Riegler, J. Wu, and T. Yen, Novel short transcripts of hepatitis B virus X 580 gene derived from intragenic promoter, J Biol Chem, vol.269, issue.581, pp.22593-22598, 1994.

L. Kwee, R. Lucito, B. Aufiero, and R. Schneider, Alternate translation initiation on 582 hepatitis B virus X mRNA produces multiple polypeptides that differentially transactivate 583 class II and III promoters, J Virol, vol.66, issue.584, pp.4382-4389, 1992.

C. Seeger, W. Mason, W. Sung, H. Zheng, S. Li et al., Hepatitis B Virus Biology, Microbiology and Molecular Biology Reviews, vol.64, issue.1, pp.51-68, 2000.
DOI : 10.1128/MMBR.64.1.51-68.2000

C. Zhang, J. Hardwick, C. Buser, J. Xu, Z. Kan et al., Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma, p.590

C. Guettier, E. Dussaix, D. Castaing, C. Brechot, D. Samuel et al., Hepatocellular carcinoma 593 is associated with an increased risk of hepatitis B virus recurrence after liver transplantation Serum hepatitis B virus RNA levels as an early predictor of hepatitis B envelope 597 antigen seroconversion during treatment with polymerase inhibitors Hepatitis B virus particles of plasma and liver 599 contain viral DNA-RNA hybrid molecules, Gastroenterology Hepatology Virology, vol.594, issue.600, pp.1890-1899, 1984.

Y. Kawakami, Y. Fujimoto, H. Ochi, H. Abe, T. Maekawa et al., Serum HBV RNA is a predictor of early 603 emergence of the YMDD mutant in patients treated with lamivudine, Hepatology, vol.45, issue.605, pp.1179-604, 2007.

J. Wang, T. Shen, X. Huang, G. Kumar, X. Chen et al., Serum hepatitis B virus RNA is encapsidated pregenome RNA, 2016.