Fig. 4: Tests of the m6A nearest neighbor parameters and RNAstructure software.
From: Secondary structure prediction for RNA sequences including N6-methyladenosine
A The structure of MALAT1 RNA. The predicted secondary structure for the HNRNPC binding site is the closed conformation both with and without N6-methylation at A22 (green arrow). This is also supported by the NMR NOESY walk (Supplementary Fig. S4) and the similar chemical shifts for imino proton resonances with and without methylation (Supplementary Fig. S6). We model the binding of HNRNPC protein as the conformation that exposes the recognition sequence (marked in red nucleotides). When A22 is methylated to m6A, we estimate the cost of opening the binding site is reduced by 0.6 kcal/mol as compared to the unmethylated sequence. B The average probability that A or m6A are buried in a helix at the position of high-confidence m6A sites in the human transcriptome. The mean probability that an A or m6A is base paired and stacked between two adjacent pairs for 18,026 sites of N6-methylation, as estimated by RNAstructure. Position 0 is the site of methylation. N6-methylation is estimated to further open the structure at the methylation site. C The average PARS scores for accessibility for the 18,026 sites of N6-methylation in the human transcriptome. Lower PARS scores indicate higher counts of nuclease S1 cleavage relative to nuclease V1 cleavage and therefore a higher likelihood of being unpaired. The RNAstructure predictions and the PARS data both show considerable single-stranded character at the site of N6-methylation.
