Secondary structure prediction for RNA sequences including N6-methyladenosine

Abstract

There is increasing interest in the roles of covalently modified nucleotides in RNA. There has been, however, an inability to account for modifications in secondary structure prediction because of a lack of software and thermodynamic parameters. We report the solution for these issues for N⁶-methyladenosine (m⁶A), allowing secondary structure prediction for an alphabet of A, C, G, U, and m⁶A. The RNAstructure software now works with user-defined nucleotide alphabets of any size. We also report a set of nearest neighbor parameters for helices and loops containing m⁶A, using experiments. Interestingly, N⁶-methylation decreases folding stability for adenosines in the middle of a helix, has little effect on folding stability for adenosines at the ends of helices, and increases folding stability for unpaired adenosines stacked on a helix. We demonstrate predictions for an N⁶-methylation-activated protein recognition site from MALAT1 and human transcriptome-wide effects of N⁶-methylation on the probability of adenosine being buried in a helix.