Decoding the Architecture of the Varicella-Zoster Virus Transcriptome

Area of Science:

• Virology
• Molecular Biology
• Genomics

Background:

• Varicella-zoster virus (VZV) causes varicella and herpes zoster, with its complex transcriptome poorly defined.
• The VZV genome encodes numerous overlapping transcripts, but its full coding potential remains unknown.

Purpose of the Study:

• To comprehensively reannotate the lytic VZV transcriptome architecture.
• To identify all polyadenylated VZV RNAs, including canonical, noncanonical, fused ORFs, and noncoding RNAs (ncRNAs).
• To determine the kinetic class of all VZV transcripts and investigate gene expression regulation.

Main Methods:

• Integrated short-read and long-read RNA sequencing on VZV-infected cells.
• Precise mapping of transcription start sites, splice junctions, and polyadenylation sites.
• Analysis of VZV transcripts from two strains and two cell types.

Main Results:

• Identified 136 distinct polyadenylated VZV RNAs, expanding the known coding and noncoding repertoire.
• Characterized canonical ORFs, noncanonical ORFs, ORF fusions, and putative ncRNAs.
• Unexpectedly found that the ORF62 transcript, crucial for viral transactivation, exhibits late kinetic expression, unlike in other alphaherpesviruses.

Conclusions:

• The VZV transcriptome is highly complex, with a greater diversity of RNAs than previously known.
• The late kinetic expression of the ORF62 transcript challenges existing models of alphaherpesvirus gene regulation.
• This comprehensive resource facilitates future functional studies on VZV RNAs and regulatory mechanisms.