TIGP (BIO)—Viral epitranscriptomics: reverse transcribing viruses utilizing RNA methylations for efficient replication

Abstract

The outcome of viral infections is not solely dependent on genomic sequences per se, as it is subject to additional regulation not directly encoded in the viral genome. One example is epitranscriptomic RNA modifications, such as N⁶-methyladenosine (m⁶A), where covalent modifications added to individual nucleotides on RNA can regulate RNA metabolism and function, mostly through the recruitment or dismissal of functional RNA binding proteins. We believe that viruses have evolved to enrich for RNA modifications that are beneficial to viral replication. In support of this hypothesis, I will present examples of how RNA modifications enhance support the replication of the reverse transcribing viruses HIV-1 and Human Hepatitis B virus (HBV). First of all, we have found that the RNA of HIV-1 and HBV are both highly enriched with multiple modifications at stoichiometries much higher than that on host cellular mRNAs, suggesting potential positive selection for highly modified RNA during the rapid evolution of these viruses. Specifically for HIV-1, we have found that distinct adenosine residues on the viral RNA are m⁶A methylated. These m⁶A can stabilize viral RNA when m⁶A is recognized by the host cytosolic reader protein YTHDF2, while the host nuclear reader protein YTHDC1 binds m⁶A on viral RNA to fine tune viral RNA alternative splicing. Thus, by regulating RNA-protein interactions, the presence of m⁶A ensures the stability and proper processing of HIV-1 viral RNAs to facilitate viral replication. In addition, we have recently found evidence that cytidines on the RNA of Human Hepatitis B virus (HBV) can be methylated as 5-methylcytidine (m⁵C), with the deposition of this methylation dependent on the cellular RNA methyltransferase NSUN2. m⁵C was mapped to key packaging signals on the HBV genomic RNA (pgRNA), and HBV replication in NSUN2 knocked out cells showed a ~50% drop in viral capsid protein (HBc) translation, a similar drop in packaged RNA in viral particles, and a near-complete loss of the reverse-transcribed viral genomic DNA, implicating m⁵C methylations to be required for the production of infectious viral particles. Overall, evidence from this and other labs has shown that diverse pathogenic viruses utilize host RNA modification mechanisms to enhance viral replication and fitness. Efforts are underway to better elucidate how these modifications support viruses and how this knowledge may contribute to future efforts to control viral diseases.

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