Secondary structure prediction for RNA sequences including N6-methyladenosine

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 N-6-methyladenosine (m(6)A), allowing secondary structure prediction for an alphabet of A, C, G, U, and m(6)A. 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 m(6)A, using experiments. Interestingly, N-6-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 N-6-methylation-activated protein recognition site from MALAT1 and human transcriptome-wide effects of N-6-methylation on the probability of adenosine being buried in a helix. RNA folding free energy nearest neighbor parameters were determined for sequences with the nucleotide m(6)A. The RNAstructure software package can accommodate modified nucleotides, enabling secondary structure prediction of sequences with m(6)A.

Automated summary

This study addresses the issue of predicting the secondary structure of RNA with covalently modified nucleotides. The researchers developed software and determined thermodynamic parameters to enable the prediction of secondary structure for sequences containing N-6-methyladenosine (m(6)A). The study also revealed the effects of N-6-methylation on folding stability in different contexts.