Noncanonical circRNA biogenesis driven by alpha and gamma herpesviruses

Abstract

Herpesviruses express over 100 transcripts, including messenger RNAs, long noncoding RNAs, and microRNAs. Herein, we add to this list by performing circular RNA (circRNA) profiling for Herpes Simplex Virus-1, Kaposi sarcoma-associated herpesvirus (KSHV), and murine gammaherpesvirus 68. Using cell culture and animal models of lytic and latent infection, we identified thousands of back-splicing variants. This included circRNAs derived from viral latency genes (circK12, circLAT). During lytic infection circRNAs tiled the viral genome, with a transcriptional density 4,500-fold greater than the host. We characterized cis- and trans-elements controlling back-splicing and found that lytic infection promoted rampant, sequence-independent back-splicing. Using eCLIP and 4SU-Sequencing, we determined that the KSHV RNA binding protein (ORF57) preferentially bound viral circRNAs and globally promoted accumulation post-transcriptionally. Our work elucidates a unique splicing mechanism driven by late lytic replication and identifies a class of transcripts with potential to function in replication, persistence, or tumorigenesis.