Virus Dataset Detail

> Detail information for each sample

Dataset Information
Accession GSE100400
Status 2018/4/30
Title Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx
Organism Homo sapiens;Mus musculus
Experiment type Expression profiling by high throughput sequencing;Genome binding/occupancy profiling by high throughput sequencing;Other
Summary In hepatocyte nuclei, hepatitis B virus (HBV) genomes occur episomally as covalently closed circular DNA (cccDNA). The HBV X protein (HBx) is required to initiate and maintain HBV replication and acts as host gene trans-regulator. However, functionally relevant spatiotemporal localization and interactions of cccDNA and HBx remain to be understood. This is the first study utilizing circularized chromosome conformation capture (4C) to identify regional virus-host genome interactions. We combined 4C with RNA-seq and ChIP-seq to illuminate the nuclear landscape associated with HBV episomes and HBx. Moreover, we functionally studied HBx-binding to episomal HBV DNA. In human HBV-positive HepaRG hepatocytes, 4C and ChIP revealed specific nuclear localization of HBV episomes and HBx associated with actively transcribed nuclear domains correlating well in size with constrained topological units built up by chromatin fibre loops, which are believed to constitute fundamental cell nuclear architectural units. Interestingly, HBx alone occupied transcribed chromatin domains, and its binding to HBV episomes depended on its C-terminus in vitro. In conclusion, HBx and HBV DNA similarly follow higher-order nuclear assembly patterns, specifically favoring transcriptionally active nuclear compartments. These novel observations may shed light on important unsolved problems: to understand the long-term episomal stability and the facilitation of viral persistence.
Samples
GSM ID Sample info Characteristics Description
GSM2680341 mRNA-seq HepaRG t3 tumour stage:primary cell-like; source:liver -
GSM2680342 mRNA-seq HepG2.2.15 tumour stage:transformed; source:liver -
GSM2680343 mRNA-seq HepG2 H1.3 tumour stage:transformed; source:liver -
GSM2680313 murine hepatocytes (MMH-D3) Pol2 tumour stage:non-transformed; source:liver; antibody:Pol2 -
GSM2680314 murine hepatocytes (MMH-D3) NLS-HBx-RFP tumour stage:non-transformed; source:liver; antibody:NLS-HBx-RFP -
GSM2680315 murine hepatocytes (MMH-D3) H3K36me3 tumour stage:non-transformed; source:liver; antibody:H3K36me3 -
GSM2680316 murine hepatocytes (MMH-D3) H3K36ac tumour stage:non-transformed; source:liver; antibody:H3K36ac -
GSM2680317 murine hepatocytes (MMH-D3) H3K27me3 tumour stage:non-transformed; source:liver; antibody:H3K27me3 -
GSM2680318 murine hepatocytes (MMH-D3) H3K27ac tumour stage:non-transformed; source:liver; antibody:H3K27ac -
GSM2680319 murine hepatocytes (MMH-D3) H3K9me3 tumour stage:non-transformed; source:liver; antibody:H3K9me3 -
GSM2680320 murine hepatocytes (MMH-D3) H3K9ac tumour stage:non-transformed; source:liver; antibody:H3K9ac -
GSM2680321 murine hepatocytes (MMH-D3) H3K4me3 tumour stage:non-transformed; source:liver; antibody:H3K4me3 -
GSM2680322 murine hepatocytes (MMH-D3) H3K4me1 tumour stage:non-transformed; source:liver; antibody:H3K4me1 -
GSM2680323 human hepatocytes (HepG2.2.15) Pol2 tumour stage:transformed; source:liver; antibody:Pol2 -
GSM2680324 human hepatocytes (HepG2 H1.3) Pol2 tumour stage:transformed; source:liver; antibody:Pol2 -
GSM2680325 human hepatocytes (HepaRG) Pol2 tumour stage:primary cell-like; source:liver; antibody:Pol2 -
GSM2680326 human hepatocytes (HepG2.2.15) HBx tumour stage:transformed; source:liver; antibody:HBx -
GSM2680327 human hepatocytes (HepG2 H1.3) HBx tumour stage:transformed; source:liver; antibody:HBx -
GSM2680328 human hepatocytes (HepaRG) HBx tumour stage:primary cell-like; source:liver; antibody:HBx -
GSM2680329 human hepatocytes (HepG2.2.15) H3K36me3 tumour stage:transformed; source:liver; antibody:H3K36me3 -
GSM2680330 human hepatocytes (HepG2 H1.3) H3K36me3 tumour stage:transformed; source:liver; antibody:H3K36me3 -
GSM2680331 human hepatocytes (HepaRG) H3K36me3 tumour stage:primary cell-like; source:liver; antibody:H3K36me3 -
GSM2680332 human hepatocytes (HepG2.2.15) H3K4me3 tumour stage:transformed; source:liver; antibody:H3K4me3 -
GSM2680333 human hepatocytes (HepG2 H1.3) H3K4me3 tumour stage:transformed; source:liver; antibody:H3K4me3 -
GSM2680334 human hepatocytes (HepaRG) H3K4me3 tumour stage:primary cell-like; source:liver; antibody:H3K4me3 -
GSM2680335 4C_cccDNA-HepaRG tumour stage:primary cell-like; source:liver -
GSM2680336 4C_cccDNA-HepG2.2.15 tumour stage:transformed; source:liver -
GSM2680337 4C_cccDNA-HepG2 H1.3 tumour stage:transformed; source:liver -
GSM2680338 mRNA-seq HepaRG t0 tumour stage:primary cell-like; source:liver -
GSM2680339 mRNA-seq HepaRG t1 tumour stage:primary cell-like; source:liver -
GSM2680340 mRNA-seq HepaRG t2 tumour stage:primary cell-like; source:liver -
Platform GPL18573  GPL19057  : Illumina NextSeq 500 (Homo sapiens);Illumina NextSeq 500 (Mus musculus)
Literature 29933745  
Download Download xCell Data  Download Expression Analysis Data  Download Genome Binding/Occupancy Profiling Analysis Data
xCell Plot
* p<0.05 ** p<0.01