RT Journal Article
SR Electronic
T1 Computational Discovery of Evolutionary Conserved Enterovirus 71 RNA Secondary Structures
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 495507
DO 10.1101/495507
A1 Nathan Fridlyand
A1 Alexander N Lukashev
A1 Andrey Chursov
A1 Franco M Venanzi
A1 Jonathan W Yewdell
A1 Albert A Sufianov
A1 Alexander Shneider
YR 2018
UL http://biorxiv.org/content/early/2018/12/17/495507.abstract
AB 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.