Epigenetic profile of two classes of CTCF binding regions in BORIS-negative cells (GM12878). a Average tag density (tags/10 million) of CTCF, RNAPII, DNaseI digestion, H3K4me3, H3K27ac, and RAD21 (mapped by ChIP-seq in GM12878 cells, ENCODE data) at 2xCTSes (blue) and 1xCTSes (red). The data were normalized to the number of mapped reads and binding regions. b Upper panel: scatter plot shows overlapping of 2xCTSes (y-axis) and 1xCTSes (x-axis) with multiple ENCODE data available for GM12878. Similar to CTCF&BORIS and CTCF-only bound regions in K562 (Fig. S7c, left panel in Additional file 7), no correlation (R2 = 0.41) was found between 2xCTSes and 1xCTSes with respect to co-occupancy with the majority of transcription factors, histone modifications, and chromatin remodeling factors. Middle panel: scatter plot shows an overlapping of 1xCTSes mapped in K562 (y-axis) and in GM12878 cells (x-axis) with ENCODE data for K562 and GM12878 cells, respectively. 1xCTSes of GM12878 and K562 cells were correlated with each other (R2 = 0.98) with respect to co-occupancy with the majority of ENCODE data common for the two cell lines. Lower panel: scatter plot shows the overlapping of 2xCTSes in K562 (y-axis) and in GM12878 (x-axis) with ENCODE data for K562 and GM12878 cells (R2 = 0.93), respectively. (PPTX 220 kb)