Fig. 4

FOXA1 KD in MCF-7 cells leads to local DNA methylation increase. A Heatmap depicting DNA methylation β-values at 228 CpGs (rows) in DMRs (the mean β-value at the control replicates are subtracted to the β-value of each CpG, see "Materials and methods" section). Blue indicates demethylation when compared to the control replicates and red indicates increased methylation. See Additional file 3: Fig. S19 for immunoblotting evaluation of the three conditions (control, KD, and rescue). B, C, D Genomic context and methylation information at 3 of the 229 identified DMRs, which correspond to the promoter regions of the GREB1 (B), TFF1 (C), and BRIP1 (D) genes. The upper panels provide the location in the corresponding chromosome. The second panel from the top provides the beta-values at the CpGs in the regions (blue for control samples, purple for knock-down (KD), and green for transient rescue). The third panel from the top indicates in green the significant CpGs used to predict the DMR, while the non-significant CpGs are depicted in red