Comprehensive Transcriptomic and Epitranscriptomic Profiling of Hepatitis B Virus Transcripts in Two Hepatocellular...

Area of Science:

• Virology
• Molecular Biology
• Hepatology

Background:

• Hepatitis B virus (HBV) post-transcriptional regulation and epitranscriptomic modifications are not fully understood.
• Characterizing HBV's RNA landscape is crucial for understanding infection and developing treatments.

Purpose of the Study:

• To systematically profile the transcriptomic complexity and RNA modification landscape of HBV.
• To analyze HBV's complete transcriptome in hepatocellular carcinoma (HCC) models.

Main Methods:

• Transfection of HCC cell lines (PLC/PRF/5 and Huh7) with HBV replicon plasmid.
• Nanopore direct RNA sequencing of total nucleic acids.
• Bioinformatic analysis of alternative splicing, polyadenylation, and RNA modifications.

Main Results:

• Identified 34 distinct HBV splice variants, including 14 novel isoforms, with cell-type-specific expression.
• Detected 30 high-confidence RNA modification sites on HBV transcripts, with 93% conservation.
• Observed significant heterogeneity in poly(A) tail length distributions between cells.

Conclusions:

• PLC/PRF/5 cells may better mimic HBV immune evasion, while Huh7 cells show efficient replication due to longer poly(A) tails.
• Findings provide a benchmark for selecting appropriate HBV research models.
• Identified transcriptomic features offer potential targets for novel antiviral strategies.