Exploring the architecture of viral RNA genomes

•Sequences and structures in the genomes of RNA viruses play important regulatory roles.•Different methods allow for the determination of higher-order structures of complete RNA genomes.•Global genomic structural analyses have provided important new insights into virus replication.

The genomes of RNA viruses contain local structural elements and long-range interactions that control various steps in virus replication. While many individual RNA elements have been characterized, it remains less clear how the structure and activity of such elements are integrated and regulated within the complex context of complete viral genomes. Recent technical advances, particularly the development of high-throughput solution structure mapping methods, have made secondary structural analysis of entire viral RNA genomes feasible. As a consequence, whole-genome structural models have been deduced for a number of plus-strand RNA viruses and retroviruses and these structures have provided intriguing functional and evolutionary insights into global genome architecture.