Cross-Species Insights Into Gamma Herpesvirus Transcriptomes: Long-Read and Multi-Omics Perspectives

Comparative transcriptome analyses of gamma herpesviruses have been revolutionized by long-read sequencing and integrative multi-omics approaches, enabling unprecedented resolution of viral gene expression. Cross-species studies of Kaposi's sarcoma-associated herpesvirus (KSHV), Epstein-Barr virus (EBV), and murine gamma herpesvirus 68 (MHV68) have uncovered a vast diversity of transcript isoforms, including alternative 5'/3' UTR variants, alternative splice isoforms, and transcripts encoding truncated or extended coding sequences. These efforts revealed novel transcript isoforms harboring partial open reading frames, entirely new ORFs, and an expanding repertoire of viral non-coding RNAs. Additional regulatory mechanisms, such as promoter dependence on viral replication factors, selective polyadenylation site usage, frameshifting via alternative splicing, and extensive readthrough transcription, further illustrate the complex strategies governing gamma herpesvirus transcriptomes. This review synthesizes these discoveries, highlighting transcriptional strategies employed by gamma herpesviruses for persistence through different phases of replication, while outlining how integrative transcriptomics has reshaped our understanding of herpesvirus gene regulation.