Boonchuen, P. | Search bioRxiv

bioRxiv2023

Virus-derived circular RNAs populate hepatitis C virus-infected cells

It is known that pre-mRNAs in eukaryotic cells can be processed to circular RNAs by a back- splicing mechanism. Circular RNAs have great stability and can sequester proteins or small RNAs to exert functions on cellular pathways. Because viruses often exploit host pathways, we explored whether the RNA genome of the cytoplasmic hepatitis C virus is processed to yield virus-derived circRNAs (vcircRNAs). Computational analyses of RNA-seq experiments predicted that the viral RNA genome is fragmented to generate hundreds of vcircRNAs. More than a dozen of them were experimentally verified by rolling-circle amplification. VcircRNAs that contained the viral internal ribosome entry site were found to be translated into novel proteins that displayed pro-viral functions. Furthermore, a highly abundant, non-translated vcircRNA was shown to enhance viral RNA abundance. These findings argue that novel vcircRNA molecules modulate viral amplification in cells infected by a cytoplasmic RNA virus. Significance StatementProcessing of an RNA viral genome into hundreds of circular RNAs provides novel pro-viral functions and can promote translation of novel viral peptides.

microbiology↗

bioRxiv2020

Host-derived Circular RNAs Display Proviral Activities in Hepatitis C Virus - Infected Cells

Viruses subvert macromolecular pathways in infected host cells to aid in viral gene amplification or to counteract innate immune responses. Roles for host-encoded RNAs, including microRNAs, have been found to provide pro- and anti-viral functions. Recently, circular RNAs (circRNAs), that are generated by a nuclear back-splicing mechanism of pre-mRNAs, have been implicated to have roles in DNA virus-infected cells. This study examines the circular RNA landscape in uninfected and hepatitis C virus (HCV)-infected liver cells. Results showed that the abundances of distinct classes of circRNAs were up-regulated or down-regulated in infected cells. Identified circRNAs displayed pro-viral effects. One particular up-regulated circRNA, circPSD3, displayed a very pronounced effect on viral RNA abundances in both hepatitis C virus- and Dengue virus-infected cells. Surprisingly, circPSD3 also inhibited the cellular nonsense-mediated decay (NMD) pathway in liver cells. Thus, enhanced abundance of circPSD3 in virus-infected cells aids in viral replication and likely contributes to the known inhibition of NMD in HCV-infected cells. Findings from the global analyses of the circular RNA landscape argue pro-, and likely, anti-viral functions are executed by circRNAs that modulate both viral gene expression as well as host pathways. Because of their long half-lives, circRNAs likely play hitherto unknown, important roles in viral pathogenesis. Author SummaryUsually, cells are infected by one or a few virus particles that carry genomes with limited expression capacity. Thus, the expression of viral genomes has to compete with a sea of cellular components that aid in viral translation, replication and virion production. Depending on their lifestyle, viruses have evolved to avoid or to subvert cellular pathways, especially those that display anti-viral functions. Host-derived circular RNA molecules have recently been discovered in the cytoplasm of cells, although, as-of yet, few functions have been assigned to them. Here, we describe alterations in the circular RNA landscape in hepatitis C virus-infected liver cells. Up-regulated and down-regulated circular RNAs were identified, and three of the upregulated RNAs were shown to promote HCV infection. One of them, circPSD3, inhibited the cellular nonsense-mediated RNA decay that is a powerful antiviral response in infected cells. Because circular RNAs are more stable than linear RNAs, they may have important functions during viral infection, dictating the outcomes of innate immune responses and viral pathogenesis.

microbiology↗