Fig. 3

Effect size of CpG methylation on DNA shape features. Methylation-induced changes were analyzed for four shape features: a, e roll, b, f propeller twist (ProT), c, g helix twist (HelT), d, h minor groove width (MGW). For each shape feature, values for pentamers from the DNAshape query table for unmethylated DNA were plotted against values for corresponding pentamers from the methyl-DNAshape query table for methylated DNA. For simplicity, pentamers with one and only one CpG/mpg step (where “m” represents 5-methylcytosine and “g” represents G base-paired with “m” on the reverse-complement strand) were considered, for a total of 116 occurrences (Additional file 1). For bp step features Roll and HelT, values at bp steps 2–3 of each pentamer were used. For MGW and ProT, values at the central bp of each pentamer were used. CpG methylation increased Roll by an order of magnitude (light-orange dots). The opposite was observed when methylation occurred at the immediate next bp step (light-blue dots). Presence of a methyl group at the central bp, either on the forward (light-blue dots) or reverse (light-orange dots) strand caused a decrease in ProT