Fig. 4

FOXA1 and GATA3 bind hypo-methylated regions in HCC1954 breast cancer cells. a Expression levels of FOXA1 and GATA3 in hTERT-HME1 and HCC1954 cells by RT-qPCR (mean ± SEM, n = 3 independent replicates; relative to RPL13A expression). b Protein levels of FOXA1 and GATA3 in hTERT-HME1 and HCC1954 cells by western blotting. GAPDH was used as an internal control for equal loading. Stars indicate nonspecific bands. c Genome browser view (chr14:75521286-75521809) of an hypo-methylated DMR in HCC1954 breast cancer cells compared to hTERT-HME1 normal cells matching a TCGA BRCA hypo-methylated DMR, FOXA1 ChIP-seq signal in HCC1954 cells in two replicates and location of FOXA1 motifs. d Genome browser view (chr2:27209983-27210462) as in c matching a GATA3 binding sites and motif. e Number of FOXA1 and GATA3 binding peaks in the different genomic categories: CpG-poor distal from gene TSS, CpG-poor proximal, CpG-rich distal or CpG-rich proximal. f Boxplots of mean DNA methylation in HCC1954 and hTERT-HME1 cells in 200 bp windows around FOXA1 or GATA3 HCC1954 peak summits that contain at least 2 CpGs and overlapping a matching FOXA1 or GATA3 motif (FOXA1 n = 4709; GATA3 n = 1671) or in all 200 bp consecutive windows along the hg38 genome containing at least 2 CpGs (n = 5,867,466). Wilcoxon p-values are indicated