RNA Viruses: RNA Roles in Pathogenesis, Coreplication and Viral Load

Poltronieri, Palmiro; Sun, Binlian; Mallardo, Massimo

RNA can both store information in its linear sequence and take on critical structural and catalytic roles in the cell, such as during the translation of messenger RNA into proteins [15] . These latter functions depend on the complex higher-order structures RNA is able to form. Homan et al. reported a method to probe the intricate conformational states in the analysis of HIV-1 NL4-3 RNA genome [15] . They chemically modified exposed segments of three complex RNA structures. They then sequenced the RNA to map the locations of the multiple modifications in each individual linear RNA molecule. This allowed the researchers to deduce interactions in three-dimensional space, and to uncover the local conformation, providing valuable information on the folding and function of RNAs [15] . Single-molecule RNA structure was tagged, i.e. multiple sites were chemically modified are identified by massively parallel sequencing of single RNA strands, and then analyzed for correlated and clustered interactions. The strategy thus identified RNA interaction groups by mutational profiling (RING-MaP) and made possible two applications. Firstly, through space interactions, 3D models were created for RNAs, spanning 80-265 nucleotides, and intramolecular interactions that stabilize RNA were characterized. Secondly, distinct conformations in solution were identified and revealed previously undetected hidden states and large-scale structural reconfigurations that occur in unfolded RNAs relative to native states. RING-MaP analysis of single-molecule nucleic acid structure enabled a novel view of the global architecture and multiple conformations that govern the functions in RNAs.