Extended Data Fig. 8: FOXA2 induces regional DNA demethylation during NET of PCa.

a, The mA and mCpG profiling on single DNA molecules spanning FOXA2 peak center at 4 quartiles of FOXA2 peaks as in Fig. 6b in D2 LNCaP⁺FOXA2 cells. Aggregate curves (top) for each quartile were created with a 50-bp rolling window. Base density across the 2-kb region for each quartile is indicated in the one-dimensional heatmaps (bottom); the scale bars indicate the number of adenine bases and CG dinucleotides sequenced at each position relative to FOXA2 peaks center as in Fig. 6b. Color scales are shown as in Fig. 6a. b, GO analyses by MSigDB of the top 200 genes associated with hyper-DMRs (left) and hypo-DMRs (right) between D2 and D28 LNCaP⁺FOXA2 cells. Top enriched molecular concepts are shown on the y axis, while the x axis indicates enrichment significance in −log₁₀(p value); p values were calculated by the one-sided hypergeometric test. c, PCA analyses of CRPC/NEPC PDX and patient samples using the top 200 genes as in b. d,e, Aggregated mCpG intensity plots showing the DNA methylation profiles of CRPC PDX (d) and NEPC PDX (e) at previously reported NE-CREs and Ad-CREs¹¹.