A key role for the exoribonuclease XRN1 in regulating the hepatitis B viral transcriptome

Chronic hepatitis B virus (HBV) is a leading cause of liver disease and hepatocellular carcinoma that persists as a DNA mini-chromosome and replicates via genomic RNA intermediates. While HBV replication has been extensively studied, mechanisms governing viral RNA degradation remain unclear. Here, we identify a key role for the 5′–3′ exoribonuclease XRN1 in regulating the HBV transcriptome. Pharmacologic inhibition or genetic ablation of XRN1 increased HBV subgenomic RNAs without affecting pregenomic RNA (pgRNA) levels. Long-read RNA-seq showed that subgenomic RNAs, but not pgRNA, are degraded by XRN1, consistent with differential 5′ cap modification and processing (P-) body localization. HBV infection increased P-body number and size, and delivery of synthetic pgRNA demonstrated that active replication, not RNA expression alone, alters the abundance of P-bodies. These findings identify XRN1 as a key regulator of HBV RNA turnover and uncover a mechanism for viral replication to remodel host RNA dynamics.