library_construction_protocol: In vivo MNase-seq was performed on purified nuclei at different timepoints after transfection with HBV cccDNA or on in vitro reconstituted chromatin. For MNase-seq on in vitro reconstituted chromatin, titration of MNase was performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested chromatin arrays. Chromatinized DNA (100 ng) was digested using MNase (NEB) in 25 µL reactions with 2.5–25 units of enzymes that was incubated for 5 minutes at 37°C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37°C. The reaction was stopped by adding 20 mM EDTA and 1% SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index Barcodes or Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out using only 5 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). For MNase-seq on cell cultured samples, HEK293T cells were transfected with recombinant cccDNA 4 or 24-hours prior to harvest for MNase-seq. The nuclei of HEK293, HepG2.2.15, and HepAD38 cells were purified by incubating cells in Nuclei isolation buffer for 10 minutes (0.1% Igepal, 0.1% Triton X -100, 1 mM DTT in 1 X PBS), mechanically lysing with 10 strokes of loose (A) pestle Dounce homogenizer, and washing nuclei twice in 10 mL of Wash Buffer with Tween (10 mM Tris-HCl pH 7.5, 2.5 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Titration of MNase was similarly performed to determine enzyme concentrations that yielded partial- , fully-, or over-digested genomic DNA. MNase (NEB) was added to 2 x 106 nuclei in 50 µL reaction volume with 125–2000 units of enzyme that was incubated for 5 minutes at 37 °C before 1 mM of CaCl2 was added and incubation continued for another 5 minutes at 37 °C. The reaction was stopped by adding 20 mM EDTA and 1 % SDS. DNA was subsequently purified using Clean and Concentrated-5 DNA columns (Zymo). Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit – DNA repair, End Prep, USER, and Ligation of Unique Dual Index UMI Adaptors (NEB). Barcoding PCR was consistently carried out with NEBNext High-Fidelity 2X PCR Mix and subsequent size selection using agarose gel or beads (Ampure XP). Libraries were then pooled and enriched for HBV-containing reads using custom-designed xGen Lockdown probes (Integrated DNA Technology) of 60 bp each tiling the entire HBV genome and oligo capture protocol was followed per manufacture's protocol. Enriched libraries were subsequently amplified using 11 PCR cycles with NEBNext High-Fidelity 2X PCR Mix and purified using Ampure XP beads. Following assembly, HBV minichromosomes were submitted at MSKCC's Epigenetics Research Innovation Lab for processing. ATAC-seq was carried out as previously described with minor modifications using in house prepared transposase (Tn5) enzyme. Upon Mg precipitation, two replicates were used and analyzed for each condition. Briefly, a total of 130 ng chromatinized material was reconstituted in 50 μL transposition buffer containing 25 μL TD buffer (2 0mM Tris HCl pH 7.5, 10 mM MgCl2, 20 % Dimethyl Formamide), 2.5 μL Tn5 transposase, 0.1 % Tween20, 0.01 % Digitonin, 16.5 µl 1X PBS and 5.4 μL ddH2O. Samples were then incubated at 37 °C for 25 min. DNA was isolated using a ZYMO Kit (D4014). ATAC-seq libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541), a uniquely barcoded primer per sample, and a universal primer. Samples were first subjected to 5 cycles of initial amplification in order to identify the number or cycles needed for each partially amplified library. Upon completion of final amplification, samples were subject to a dual size selection (0.55x–1.5x) using SPRIselect beads (Beckman Coulter, B23317). Fragment distribution of libraries was assessed with an Agilent Bioanalyzer and the sequencing libraries were sent to the MSKCC Integrated Genomics Operation core facility for sequencing on a NovaSeq 6000 flow cell in a 50 bp paired-end (50PE) mode.