3D RNA from evolutionary couplings

Abstract

Non-protein-coding RNAs are ubiquitous in cell physiology, with a diverse repertoire of known functions. In fact, the majority of the eukaryotic genome does not code for proteins, and thousands of conserved long non-protein-coding RNAs of currently unkown function have been identified. When available, knowledge of their 3D structure is very helpful in elucidating the function of these RNAs. However, despite some outstanding structure elucidation of RNAs using X-ray crystallography, NMR and cryoEM, learning RNA 3D structures remains low-throughput. RNA structure prediction in silico is a promising alternative approach and works well for double-helical stems, but full 3D structure determination requires tertiary contacts outside of secondary structures that are difficult to infer from sequence information. Here, based only on information from RNA multiple sequence alignments, we use a global statistical sequence probability model of co-variation in a pairs of nucleotide positions to detect 3D contacts, in analogy to recently developed breakthrough methods for computational protein folding. In blinded tests on 22 known RNA structures ranging in size from 65 to 1800 nucleotides, the predicted contacts matched physical nucleotide interactions with 65-95% true positive prediction accuracy. Importantly, we infer many long-range tertiary contacts, including non-Watson-Crick interactions, where secondary structure elements assemble in 3D. When used as restraints in molecular dynamics simulations, the inferred contacts improve RNA 3D structure prediction to a coordinate error as low as 6 - 10 [A] rmsd deviation in atom positions, with potential for further refinement by molecular dynamics. These contacts include functionally important interactions, such as those that distinguish the active and inactive conformations of four riboswitches. In blind prediction mode, we present evolutionary couplings suitable for folding simulations for 180 RNAs of unknown structure, available at https://marks.hms.harvard.edu/ev_rna/. We anticipate that this approach can help shed light on the structure and function of non-protein-coding RNAs as well as 3D-structured mRNAs.