Single-nucleotide-resolution mapping of HBV promoters in infected human livers and hepatocellular carcinoma

Abstract : Hepatitis B virus (HBV) is a major cause of liver diseases including hepatocellular carcinoma (HCC), and more than 650,000 people die annually due to HBV-associated liver failure. Extensive studies of individual promoters have revealed that heterogeneous RNA 5' -ends contribute to the complexity of HBV transcriptome and proteome. Here we provide a comprehensive map of HBV transcription start sites (TSSs) in human liver, HCC and blood, as well as several experimental replication systems, at single nucleotide resolution. Using CAGE analysis of 16 HCC/non-tumor liver pairs, we identify 17 robust TSSs, including a novel promoter for the X gene located in the middle of the gene body, which potentially produces a shorter X protein translated from the conserved second start codon, and two minor anti-sense transcripts that might represent viral ncRNAs. Interestingly, transcription profiles were similar in HCC and non-tumor livers, although quantitative analysis revealed highly variable patterns of TSS usage among clinical samples, reflecting precise regulation of HBV transcription initiation at each promoter. Unlike the variety of TSSs found in liver and HCC, the vast majority of transcripts detected in HBV-positive blood samples are pgRNA, most likely generated and released from liver. Our quantitative TSS mapping using the CAGE technology will allow better understanding of HBV transcriptional responses in further studies aimed at eradicating HBV in chronic carriers.