Extended Data Fig. 5: NKX2-1 is induced by FOXA2 and required for FOXA2-driven NET.
a, RT–PCR analysis of NKX2-1 mRNA in time-course LNCaP+FOXA2 cells and LuNE cells. Data were normalized to GAPDH. Shown are the mean ± s.e.m. of technical replicates from one of three (n = 3) independent experiments. P values by two-sided t test. b, Genome browser view of FOXA2 ChIP–seq signal around the NKX2-1 gene in NEPC cells (NCI-H660, LuCaP145.2). c,d, Hi-C contact maps (5 kb resolution) of NKX2-1 gene region in time-course LNCaP+FOXA2 cells (c), NCI-H660 and LuCaP PDX (d). The mRNA expression of NKX2-1 in the indicated samples is shown on the bottom right. Gene boxes and 1D ChIP–seq tracks of matched models are aligned at the bottom. Black arrows indicate enhancer–promoter loops at NKX2-1 locus. Enhancers are highlighted in light blue, and promoters in light orange color. FOXA2, NKX2-1, H3K27ac, H3K4me1, H3K27me3 and CTCF tracks under the D0 contact map used their corresponding ChIP–seq performed in closely related D2 cells. All others were done in conditions exactly matched to Hi-C. The scale bars indicate ICE-normalized contact frequency. e, Heatmap showing active (H3K27ac) enhancer (H3K4me1) and promoter (H3K4me3) marks at NKX2-1-only, FOXA2-only and shared binding sites in NCI-H660 cells. Scale bar: enrichment intensity. f, Pie chart showing the genomic distribution of FOXA2-only, NKX2-1-only and shared binding sites identified in NCI-H660 cells. g, TF motifs that significantly enriched at NKX2-1-only, FOXA2-only binding sites in NCI-H660 (top) and LuCaP145.1 (bottom). P values by two-sided hypergeometric test with Benjamini–Hochberg correction. h, The number of chromatin loops anchored by FOXA2 and NKX2-1 in time-course LNCaP+FOXA2 Hi-C samples.
