Fig. 5
From: Pan-cancer predictions of transcription factors mediating aberrant DNA methylation
Gain of DNA methylation upon FOXA1 or GATA3 removal in HCC1954 breast cancer cells. a Western blot analysis of FOXA1 protein levels in parental HCC1954 cells (WT), a control clone (Ctrl) and two FOXA1 KO clones (KO1 and KO2). GAPDH was used as an internal control for equal loading. b Western blot analysis of GATA3 protein levels in parental HCC1954 cells (WT), a control clone (Ctrl) and two GATA3 KO clones (KO1 and KO2). GAPDH was used as an internal control for equal loading. Star indicates nonspecific bands. c DNA methylation levels in HCC1954 FOXA1 KO cells compared to HCC1954 cells (mean across samples) in 200 bp windows around FOXA1 peak summits that contain at least 2 CpGs and overlapping a matching FOXA1 motif (n = 4473). d DNA methylation levels in HCC1954 GATA3 KO cells compared to HCC1954 cells around GATA3 peak summits as in c. (n = 1598). e Genome browser view (chr19:16093263-16093982) of an hyper-methylated DMR in HCC1954 FOXA1 KO cells compared to HCC1954 cells matching hypo-methylated DMR in HCC1954 vs HME1 and FOXA1 binding sites and motif. f Genome browser views (chr1:214377303-214378552 and chr8:42296869-42299784) as in e of two hyper-methylated DMRs in HCC1954 GATA3 KO cells compared to HCC1954 cells