Viral RNA structures and host proteins

RNA viruses have evolved to maximize their limited genetic space by incorporating regulatory elements within complex secondary RNA structures. For example, alphaviruses use specific RNA structures to optimize viral RNA synthesis, package their genomes, and evade the innate immune system. Flaviviruses are also well-known to use RNA structures to replicate through circularization and to avoid degradation by host factors. In the evolutionary arms race between innate defence mechanisms and viral evasion, many restriction factors target evolutionarily conserved viral structures such as the double-stranded RNA intermediate and the 5’ triphosphate. However, beyond these well-known viral features, not much is known about other viral RNA structures that are recognized by host RNA binding proteins and RNA helicases.

RNA viruses continue to be the main culprits for pandemics and re-emerging outbreaks all over the world. And while viruses acquire mutations at the sequence level to evade the host's innate immune system and respond to many other selective pressures, functional RNA structures embedded in their genomes may provide another avenue for the development of structure-based antivirals. In addition, knowledge of host proteins that recognize and modulate these conserved RNA structural features is also useful for the development of host-based therapeutics. Furthermore, given recent advances in technologies that reveal RNA secondary structures (icSHAPE, SHAPE-MaP, LASER) and map RNA-protein interactions (e.g. various CLIP protocols, SHAPE-eCLIP) much is to be gained by having a better understanding of host-viral RNA interactions. Therefore, in this Research Topic, we are interested in Original Research and Reviews that can improve and update our understanding of functional viral RNA structures, RNA-binding proteins, and helicases that recognize or alter these structures and the importance of interactions between hosts and structured viral RNA elements.

In this Research Topic, we are interested in an improved understanding of how viruses and host factors exploit conserved viral RNA structures. Submissions on the following themes are encouraged:

• Importance of specific viral RNA structures during viral replication.
• Interactions between RNA binding proteins, especially RNA helicases and viral RNAs.
• Mechanisms of RNA binding proteins targeting structures for antiviral or proviral actions
• Antivirals targeting conserved RNA structures on viruses or host proteins that modulate these structures.

Keywords: RNA structure, host factors, helicase, RNA binding proteins

Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.