Fig. 3

In BM-CD34+ cells, 5hmC associates with increased binding of FLI1 and RUNX1. Binding of FLI1 (a, e, i), RUNX1 (b, f, j), GATA2 (c, g, h) and ERG (d, h, l) at regulatory elements positive (red line) or negative (blue line) for 5hmC in BM-CD34+ cells. Regulatory regions were defined by chromatin enrichment with a specific histone modification or the ChromHMM, chromosome segmentation and Hidden Markov Model of Ernst and Kellis. Putative active enhancers were defined by H3K27ac ChIP-seq peaks or H3K4me1/H3K27ac ChIP-seq peaks. Poised enhancers were defined by H3K4me1 ChIP-seq peaks. A specific regulatory region was considered positive for 5hmC if it contained at least one hydroxymethylated cytosine. Since regulatory regions throughout the genome defined by ChIP-seq peaks or ChromHMM were of different lengths, we scaled regulatory regions to the same length (scaled ChIP-seq peaks, x-axis) and analyzed TF occupancies (y-axis; read coverage patterns). Differences between TF enrichment were assessed using the Kolmogorov–Smirnov test to quantify the distance between the empirical distribution function of the TF enrichment in regulatory regions positive versus negative for 5hmC, *significant differences in TF occupancy with D > 0.45 and p < 10⁻¹⁰