Key result
The computational method RNA GUESS identified previously known and novel evolutionarily conserved RNA secondary structures in Enterovirus 71, including a potential RNA switch.
Why the study?
Little is known about the contribution of RNA structure to viral replication and evolution in viral RNAs.
The computational tool RNA GUESS identified both known and novel evolutionarily conserved RNA secondary structures in Enterovirus 71, providing new targets for physical and genetic studies of viral replication.
RNA GUESS extends computational RNA structure prediction in viruses; leaves open functional validation and therapeutic relevance in EV71.
Viral RNAs store information in their sequence and structure. Little, however is known about the contribution of RNA structure to viral replication and evolution. We previously described RNA ISRAEU to computationally identify structured regions in viral RNA based on evolutionary conservation of predicted structures. Here, we apply RNA GUESS (Generator of Uniformly Evolved Secondary Structures) to better understand enterovirus 71, a highly pathogenic human picornavirus. RNA GUESS identified previously known evolutionarily conserved picornavirus RNA structures, and uniquely predicted RNA structures with significant structural conservation despite the lack of an obvious sequence conservation. One structure consists of a stretch of obligatorily unpaired nucleotides that can potentially interact with RNA-binding proteins and siRNAs. Another, forms a potential RNA switch that can form two alternative structures while the third and fourth constitute hairpin-like structures. These findings provide a launching point for physical and genetic studies regarding the function and structures of these RNA elements.
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Fridlyand et al. (2018) studied Enterovirus 71 (n=94). RNA GUESS computational method was evaluated on Identification of evolutionarily conserved RNA secondary structures. The computational method RNA GUESS identified previously known and novel evolutionarily conserved RNA secondary structures in Enterovirus 71, including a potential RNA switch.
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