Long-read transcriptomics of caviid gammaherpesvirus 1: compiling a comprehensive RNA atlas

Area of Science:

• Virology
• Genomics
• Transcriptomics

Background:

• Caviid gammaherpesvirus 1 (CaGHV-1) is an oncogenic virus with a known genome but an uncharacterized transcriptome.
• Understanding gammaherpesvirus pathogenesis is hindered by limited animal models.

Purpose of the Study:

• To create the first comprehensive transcriptomic atlas of CaGHV-1.
• To identify viral mRNAs, non-coding RNAs, and regulatory elements.
• To establish CaGHV-1 as a model for gammaherpesvirus pathogenesis research.

Main Methods:

• Nanopore long-read RNA sequencing was employed to annotate the CaGHV-1 genome.
• Transcriptomic atlas construction and promoter element mapping were performed.
• Functional studies investigated the CaGHV-1 RTA transcription factor's activity.

Main Results:

• A detailed transcriptomic atlas of CaGHV-1, including diverse mRNAs and non-coding RNAs, was generated.
• Promoter elements for all viral genes were mapped.
• The CaGHV-1 RTA factor demonstrated self-activation and cross-activation of homologous gammaherpesvirus promoters, indicating conserved transcriptional mechanisms.
• Extensive transcriptional overlap within the viral genome was observed.

Conclusions:

• CaGHV-1 exhibits conserved RTA-mediated transcriptional mechanisms similar to other gammaherpesviruses.
• The study establishes CaGHV-1 as a valuable small animal model for studying gammaherpesvirus replication, regulation, and tumorigenesis.
• This research provides critical insights into gammaherpesvirus molecular biology and pathogenesis.