Helicases DDX5 and DDX17 promote heterogeneity in HBV transcription termination in infected human hepatocytes

J Hepatol. 2024 May 21:S0168-8278(24)00351-9. doi: 10.1016/j.jhep.2024.05.016. Online ahead of print.

Abstract

Background & aims: Transcription termination fine tunes gene expression and contributes to specify the function of RNAs in eukaryotic cells. Transcription termination of hepatitis B virus (HBV) is subjected to the recognition of the canonical polyadenylation signal (cPAS) common to all viral transcripts. The regulation of the usage of this cPAS and its impact on viral gene expression and replication is currently unknown.

Approach & results: To unravel the regulation of HBV transcript termination, we implemented a 3' RACE-PCR assay coupled to single molecule sequencing both in in vitro infected hepatocytes and in chronically infected patients. The detection of a previously unidentified transcriptional readthrough indicated that the cPAS was not systematically recognized during HBV replication in vitro and in vivo. Gene expression downregulation experiments demonstrated a role for the RNA helicases DDX5 and DDX17 in promoting viral transcriptional readthrough, which was, in turn, associated to HBV RNA destabilization and decreased HBx protein expression. RNA and chromatin immunoprecipitation, together with mutation of cPAS sequence, suggested a direct role of DDX5 and DDX17 in functionally linking cPAS recognition to transcriptional readthrough, HBV RNA stability and replication.

Conclusions: Our findings identify DDX5 and DDX17 as crucial determinants for HBV transcriptional fidelity and as host restriction factors for HBV replication.

Impact and implications: Hepatitis B virus (HBV) covalently closed circular (ccc)DNA degradation or functional inactivation remains the holy grail to be attained to achieve HBV cure. Transcriptional fidelity is a cornerstone in gene expression regulation. Here, we demonstrate that two helicases, DDX5 and DDX17, inhibit the recognition of HBV polyadenylation signal and transcriptional termination, thus decreasing HBV RNA stability and acting as restriction factors for efficient cccDNA transcription and viral replication. The observation that DDX5 and DDX17 are downregulated in HBV chronically infected patients suggests a role for the helicases in HBV persistence in vivo. These results open new perspectives for researchers aiming at identifying new targets to neutralise cccDNA transcription.

Keywords: HBV; RNA helicases; RNA polyadenylation; RNA stability; transcription termination.