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bioRxiv · 10.1101/2025.05.07.652742

m5C RNA Methylation Is Dysregulated by Oncogenic Herpesviruses via c-Myc Signaling to Counteract Host Antiviral Factors

Wu, Z.·Zhou, D.·He, Z.·Fiches, G.·Park, Y.·He, J.·Chen, J.·Shanaka, K.·Lepcha, T. T.·Desai, P. J.·Zhu, J.·Santoso, N.
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Abstract

Herpesviruses are a group of double-stranded DNA viruses known to develop versatile viral strategies to escape host immune surveillance for promoting their replication and propagation. This is illustrated by Kaposis sarcoma-associated herpesvirus (KSHV), an oncogenic gamma-herpesvirus that overcomes host immune suppression by multiple mechanisms. In this study, we reported that KSHV dysregulates 5-methylcytosine (m5C) modification and mRNA stability of host antiviral factors to benefit its lytic replication. KSHV lytic reactivation or de novo challenge led to downregulation of m5C RNA methyltransferases, NSUN2 and NSUN1 (NSUN2/1), while NSUN2/1 depletion promoted KSHV lytic replication. Such KSHV-mediated downregulation of NSUN2/1 is via suppression of the transcriptional factor c-Myc. We further performed the RNA bisulfite sequencing (RNA-BS-seq) to identify KSHV-dependent m5C modification of host mRNAs. KSHV lytic reactivation led to the significant reduction of m5C methylation and mRNA stability of TRIM25, a key activator of the RIG-I pathway, while TRIM25 depletion indeed promoted KSHV lytic replication. These host-virus interaction events were also observed in the infection of another oncogenic gamma-herpesvirus Epstein-Barr virus (EBV). Overall, our results highlighted a new strategy for human gamma-herpesviruses to counteract host antiviral factors and promote their lytic replication by manipulating host m5C RNA methylation. Significance StatementOur study has identified a novel viral mechanism of human gamma-herpesviruses to manipulate host RNA methylation machineries to subvert immune defenses and enhance viral lytic replication. In particular, our new data showed that KSHV/EBV downregulate the key 5-methylcytosine (m5C) RNA writers NSUN2/1 via c-Myc, and thus decrease m5C modification and stability of TRIM25 mRNA. As TRIM25 is a key E3 ubiquitin ligase in RIG-I signal transduction, its inhibition disrupts RIG-I mediated antiviral sensing and thus favors viral lytic replication. As human gamma-herpesviruses are critical pathogens that highly associate with multiple human diseases especially certain tumors, such studies are significant to shed light in improving the fundamental understanding of virus-host interactions and identifying new host targets for future translational applications.

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Wu, Z., Zhou, D., He, Z., Fiches, G., Park, Y., He, J., Chen, J., Shanaka, K., Lepcha, T. T., Desai, P. J., Zhu, J., Santoso, N.. 2025-05-08. m5C RNA Methylation Is Dysregulated by Oncogenic Herpesviruses via c-Myc Signaling to Counteract Host Antiviral Factors. https://doi.org/10.1101/2025.05.07.652742

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