Small genomes, big lessons: What viruses teach us about structure-based riboregulation

RNA viruses encode multiple layers of information within a single molecule, which functions simultaneously as a template for protein synthesis and as a structured regulatory RNA. These structures control key aspects of viral gene expression, govern host interactions, and mediate immune evasion. Although the prevalence of RNA structure in viral genomes is now well established, only recently have functional and mechanistic studies begun to uncover how these elements act as regulatory modules that shape infection outcomes. With their compact genomes and experimentally tractable life cycles, RNA viruses represent powerful model systems for uncovering the fundamental building blocks of riboregulation and illuminating principles of gene control conserved across eukaryotes. Here, we review current mechanistic understanding of RNA structure-based regulation across diverse viral families and draw parallels to structure-mediated gene control in eukaryotic transcriptomes, highlighting RNA structure as a central regulatory layer in gene expression with broad therapeutic and synthetic biology potential.