Extended Data Fig. 7: FOXA1 binds hyperaccessible promoters with low affinity upon overexpression in MCF-7.

(a) Heatmap showing the matched epigenome dynamics at sites with high-confidence \(K_d^{Apps}\) fitted for FOXA1 at either gained or retained sites after FOXA1 overexpression. Signal of ChIP-seq and ATAC-seq tracks for MCF-7 is shown as log₂ fold change over the mean signal in matched control tracks, sites are ranked by apparent binding affinity (second column), and assigned regulatory features are depicted in the first column to the left. (b) Overlap of gained or retained FOXA1 binding sites with known regulatory features. (c - e) Boxplots representing the log₂ fold change of ATAC-seq, H3K4me1 ChIP-seq or H3K4me3 ChIP-seq signal over the mean signal in matched control tracks, separated by sites being gained and retained sites after FOXA1 overexpression. n = numbers of gained or retained sites overlapping with FOXA1 high confidence sites. p-values of a two-sided Wilcoxon test are reported. (f) Boxplots representing the FOXA1 motif z-score at gained or retained sites after FOXA1 overexpression. p-values of a two-sided Wilcoxon test are reported. (g) Distance (bp) of gained or retained sites to the nearest transcription start site (TSS). Box plots were drawn with the center line as the median, the hinges as the first and third quartiles, and with the whiskers extending to the lowest and highest values that were within 1.5 × interquartile range.