IFN-α inhibits HBV transcription and replication in cell culture and in humanized mice by targeting the epigenetic regulation of the nuclear cccDNA minichromosome

HBV infection remains a leading cause of death worldwide. IFN-alpha inhibits viral replication in vitro and in vivo, and pegylated IFN-alpha is a commonly administered treatment for individuals infected with HBV. The HBV genome contains a typical IFN-stimulated response element (ISRE), but the molecular mechanisms by which IFN-alpha suppresses HBV replication have not been established in relevant experimental systems. Here, we show that IFN-alpha inhibits HBV replication by decreasing the transcription of pregenomic RNA (pgRNA) and sub-genomic RNA from the HBV covalently closed circular DNA (cccDNA) minichromosome, both in cultured cells in which HBV is replicating and in mice whose livers have been repopulated with human hepatocytes and infected with HBV. Administration of IFN-alpha resulted in cccDNA-bound histone hypoacetylation as well as active recruitment to the cccDNA of transcriptional corepressors. IFN-alpha treatment also reduced binding of the STAT1 and STAT2 transcription factors to active cccDNA. The inhibitory activity of IFN-alpha was linked to the IRSE, as IRSE-mutant HBV transcribed less pgRNA and could not be repressed by IFN-alpha treatment. Our results identify a molecular mechanism whereby IFN-alpha mediates epigenetic repression of HBV cccDNA transcriptional activity, which may assist in the development of novel effective therapeutics.