Fig. 1

Feasibility of the approach to identify TFs that induce binding site-directed DNA methylation. a Flowchart of the approach. The TF of interest is overexpressed in a lentivirus vector that co-expresses a puromycin-resistant marker in 293T cells. Puromycin selection is applied for 7 days; then, TF-overexpressing 293T cells are subjected to DNA methylation analysis to identify differentially methylated CpGs (DMCs). Corresponding TFBMs of overexpressed TF are identified and then assessed to determine whether they are overrepresented at DMC regions. b Scatter plot showing DMCs caused by SPI1 overexpression in 293T cells. X- and Y-axes show M-values for 293T-mock and SPI1-overexpressing 293T (293T-SPI1) cells, respectively. Dashed lines represent ΔM borders of > 2. Green, purple, and gray dots represent significantly methylated, demethylated, and insignificant probes, respectively. Numbers of DMCs are shown upper left (methylated) and bottom right (demethylated). c Distribution of enrichment scores for SPI1 binding motifs within ± 5000 bp of demethylated CpGs (left) and methylated CpGs (right) in SPI1-overexpressing 293T cells. X- and Y-axes show distance from probe CpG position and enrichment score, respectively. Horizontal line represents enrichment score = 0