Mapping the temporal transcriptomic signature of a viral pathogen through CAGE and nanopore sequencing.
Authors: Tombácz Dóra, Kakuk Balázs, Torma Gábor, Fülöp Ádám, Dörmő Ákos, Gulyás Gábor, Csabai Zsolt, Boldogkői Zsolt
Journal: PloS one
Summary
# Editorial Summary: Temporal Transcriptomic Mapping of Equid Alphaherpesvirus 1 Equid alphaherpesvirus 1 (EHV-1) remains a significant challenge for the equine industry, yet our understanding of how the virus regulates its gene expression throughout infection has been incomplete. Researchers combined two complementary sequencing approaches—CAGE (Cap Analysis of Gene Expression) on the Illumina platform to pinpoint transcript start sites, and Oxford Nanopore long-read sequencing to capture full-length viral transcripts—sampling across nine timepoints during the viral replication cycle and using protein synthesis inhibition to identify immediate-early genes. The study substantially refined the EHV-1 transcriptome annotation, revealing multiple isoforms per gene and previously unidentified transcripts that reflect a far more complex regulatory architecture than previously recognised. These findings suggest EHV-1 achieves remarkable genomic efficiency through dynamic transcript isoform switching, allowing the virus to precisely calibrate gene expression according to replication stage and host cell environment. For equine practitioners, this deeper knowledge of viral transcriptional control may eventually inform the development of more effective vaccines and antivirals by identifying critical regulatory nodes and stage-specific vulnerabilities in the EHV-1 lifecycle.
Read the full abstract on PubMed
Practical Takeaways
- •Improved understanding of EHV-1 gene expression patterns may support development of more targeted antivirals and vaccines against this economically significant equine pathogen
- •The virus's capacity for transcript isoform diversity suggests potential therapeutic targets during specific stages of infection that could be exploited for intervention
Key Findings
- •CAGE and nanopore sequencing identified multiple novel EHV-1 transcripts and refined existing transcriptome annotations with improved accuracy for full-length transcript detection
- •Time-course analysis across nine viral lifecycle stages revealed kinetic classification of viral transcripts with shifting isoform patterns indicating sophisticated gene expression regulation
- •Multiple transcript isoforms per gene enable EHV-1 to modulate gene expression at different replication stages, enhancing genomic efficiency and host adaptation