Many pathogenic viruses have RNA genomes (e.g. influenza, Hepatitis C virus) and as expected these contain all the required elements for the viral lifecycles. These elements may be structured or unstructured. In addition, viruses with DNA genomes often have key regulatory RNA elements in their genomes (e.g. HIV, hepatitis B virus).
Here we report approaches we are developing and using to discover novel functional elements in viral genomes. These have been applied to model the functional elements in HBV. Notably, HBV contains a complex post-transcriptional regulatory element that inhibits splicing and promotes the export of unspliced RNA. This element has rtecently been shown to be able to be targeted by antiviral drugs. This element contains a combination of structured and unstructured elements that regulate this process.
We are also investigating the roles of RNA-RNA interactions in the CRISPR-Cas antiviral response. To facilitate this we have developed publicly available software available through bioanalysis.otago.ac.nz