Hepatitis B Virus Episome DNA Localizes To the Vicinity of Chromosome 19 In 3D Host Genome Upon Infection

Hepatitis B virus (HBV) infects 240 million people worldwide. The infection requires establishment and persistence of a viral episome, the covalently closed circular (ccc) DNA, in the nucleus. Here we studied cccDNA spatial localization in the 3D host genome by using chromosome conformation capture based sequencing analysis and fluorescence in situ hybridization (FISH). We show cccDNA is not randomly distributed in host nucleus, rather, it is preferentially accumulated at specialized areas, particularly in regions close to chromosome 19 (chr.19). Activation of cccDNA appears to be associated with its re-localization from a heterochromatin hub pre-established by 5 regions of chr.19 to transcriptionally active regions formed by chromosomes in close proximity to chr.19 including chr. 16, 17, 20, 22. This active versus inactive positioning at discrete regions of host genome is primarily controlled by viral HBx protein and host factors including the structural maintenance of chromosomes protein 5/6 (SMC5/6) complex. HBV-4C was used to study HBV cccDNA spatial localization in the 3D host nucleus using de novo HBV infection model. Hi-C was used to analyze overall host chromatin organization. Transcriptional activity was analyzed by combing RNA-seq.