Alternative splicing and circRNA biogenesis driven by alpha and gamma herpesviruses

Abstract

Herpesviruses rely on the host transcriptional machinery for expression of their >100 different transcripts. To prioritize viral transcripts, herpesviruses affect significant changes in all stages of gene expression. Herein, we examined how herpesviruses alter circular RNA (circRNA) synthesis resulting in distinct characteristics for those expressed from the host or viral genome. CircRNA were identified with our Circrnas in Host And viRuses anaLysis pIpEline (CHARLIE) capable of de novo annotation using aggregated calls from five distinct tools. Comparative profiling for Herpes Simplex Virus-1, Kaposi sarcoma-associated herpesvirus, and murine gammaherpesvirus 68 identified thousands of back splicing variants, including circRNA species commonly expressed in all phases of infection. CircRNA expression was highest during lytic infection, with a transcriptional density 500-fold greater than the host. We characterized cis- and trans-elements controlling back splicing and found viral circRNAs are generally resistant to spliceosome inhibition or depletion, with >90% lacking canonical splice donor-acceptor sites. Using eCLIP and 4sU-Sequencing, we determined that the viral RNA binding protein, ORF57, enhanced synthesis for a subset of viral and host circRNAs. 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.