Fig. 1

Current statistics of available structures and abundance of CpG dinucleotides in TF binding sites. a Count statistics of protein–DNA complex and unbound DNA structures available in the PDB as of 31 May 2017. Counts of subsets of structures (right two bars) containing methylated DNA at CpG site(s) or in other sequence contexts were two orders of magnitude lower than the count of structures containing unmethylated DNA. Systematic profiling of the effect of methylation on three-dimensional DNA structure would require a substantially larger number of structures. Counts include structures solved by X-ray crystallography and NMR spectroscopy. b Abundance of CpG steps in TF binding motifs in HT-SELEX data for human TF datasets [29], derived using MotifDb [51]. CpG dinucleotides can be observed in binding sites irrespective of TF family. Five largest human TF families (based on number of binding sites containing at least one CpG step) are specified. Almost 90% of ETS family motifs contain CpG steps. Numbers on each bar represent counts of motifs containing CpG or no CpG steps