Fig. 4: PR regulation of BCK expression through binding at a CTCF-driven chromatin loop.

a, b Enrichment levels of CTCF gene signature in MCF7 ESR1 mutant cells (n = 4) (a) and ESR1 WT (n = 44) and mutant (n = 7) metastases (b). Box plots span the upper quartile (upper limit), median (center) and lower quartile (lower limit). Whiskers extend a maximum of 1.5× IQR. Dunnett’s test (two-sided) (a) and Mann–Whitney U-test (two-sided) was used. c, d Genomic track illustrating the CTCF and cohesion complex (c) binding and CTCF-driven chromatin loops (d) at KRT14/16/17 proximal genomic region in MCF7 cells. CTCF motif orientations of each peak is labeled with arrows. Y-axis represents signal intensity of each track. e CTCF binding events at binding sites 1 and 5 in c. Each bar represents mean ± SD of fold enrichment normalized to IgG from three independent experiments. Pair-wise t-test (two-sided) was performed. f Genomic track view of PR ChIP-seq in MCF7 cells under R5020 and progesterone treatments. Y-axis represents signal intensity under the same scale. Super enhancer range is highlighted. g KRT14, 16, and 17 mRNA levels in MCF7 ESR1 WT and mutant cells with PGR siRNA knockdown for 7 days. Each bar represents mean ± SD of fold changes normalized to WT cells with three biological replicates as a representative from three independent experiments. Student’s t-test (two-sided) was used. h KRT16 and 17 mRNA levels in MCF7 ESR1 WT and mutant cells treated with 0.1% EtOH, 100 nM P4 or 1 μM RU486 for 3 days. Each bar represents mean ± SD of fold changes normalized to WT cells with three biological replicates as a representative from three independent experiments. Dunnett’s (two-sided) test was used. i Representative images of immunofluorescence staining of CK5 and CK16 in MCF7 WT and ESR1 mutant cells after 3 day treatment with 1% EtOH or 1 μM RU486. j Quantification of CK positive cells in i. Each bar represents mean ± SD from eight different regions combining from two independent experiments. Student’s t-test (two-sided) was used. Source data are provided as a Source Data file for a, b, e, g, h, j.