Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

TL;DR

This study reveals that viral genomes contain more thermodynamically predicted RNA hairpin structures than expected by chance, with conserved structures found across different virus types and regions, indicating functional significance.

Contribution

It provides a comprehensive analysis of RNA secondary structure abundance and conservation in viral genomes, highlighting their potential functional roles beyond noncoding regions.

Findings

Hairpin structures are more abundant than expected in viral genomes.

RNA secondary structures are conserved in both coding and noncoding regions.

Conserved structures are identified in herpesvirus genomes.

Abstract

By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.