KSHV-mediated dysregulation of circRNAs and RNA processing

The majority of the human genome is actively transcribed into RNAs with no obvious coding capacity, termed non-coding RNAs (ncRNAs). It is now widely accepted that ncRNAs have crucial roles in many aspects of cell regulation and as such their dysregulation has been implicated in the development of a wide variety of diseases. Non-coding RNAs include long non-coding RNAs, microRNAs (miRNAs) and circular RNAs (circRNAs). Originally it was thought that each ncRNA species worked independently, however there is emerging evidence that different ncRNAs can interact with each other through RNA:RNA interactions, affecting their function, in what is now known as a ‘ncRNA regulatory network’. circRNAs are formed through a unique backsplice mechanism and have crucial roles in these ncRNA regulatory networks through their miRNA sponging function. Though research is still in its infancy, evidence suggests circRNA levels are tightly regulated in the cell, with dysregulated circRNA levels being implicated in a range of diseases including viral infection. We have investigated the role of cellular circRNAs in Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) infection. Like all herpesviruses, it has two distinct phases of its life cycle: lytic replication and latency. Chapters 3 and 4 highlight that the cellular circRNA,circHIPK3, is dysregulated during KSHV lytic replication and this dysregulation is important for successful viral replication. Furthermore, a novel non-coding RNA regulatory network is identified, composed of circHIPK3:miR-30c:DLL4, with all aspects of this network contributing to successful KSHV lytic replication. Collectively this data shows how the virus-mediated circRNA dysregulation allows critical regulation of downstream targets essential for viral replication. Following these findings, Chapter 5 aimed to elucidate how cellular circRNAs are dysregulated during KSHV lytic replication. This led to the analysis and characterisation of the host cell RNA binding protein SFPQ, during KSHV infection. Results demonstrate that SFPQ forms novel viral-induced condensates, reminiscent of modified paraspeckles during KSHV lytic replication. Further analysis suggest these condensates are likely to have essential roles in RNA processing, including circRNA biogenesis