Fig 2: ?Np63 regulates a common set of enhancer-associated genes in tracheal basal cells, AT2 cells and LUAD.a Venn diagram overlaying the genes associated with the top 2000 enhancers in AT2 and basal cells. b Schematic of dCas9-p300 and dCas9-?Np63 sgRNA experiment. c–e Relative expression levels of ETV5 (c), BCL9L (d) and KRT5 (e) in 293 T cells over-expressing the indicated constructs. Data were mean ± SD, n = 3, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001, two-tailed Student’s t-test. f–h qRT-PCR of ChIP assays for p300, H3K27ac and ?Np63 at the indicated sites. Data were mean ± SD, n = 3, * vs. shNT, P < 0.05, two-tailed Student’s t-test. Source data are provided as a Source Data file.

Fig 3: ?Np63 regulates the enhancer landscape of cell identity genes in basal cells of the trachea.a Schematic of isolation of ?Np63fl/fl;RosaM/M and ?Np63?/?;Rosa?/? basal cells for RNA-seq and ChIP-seq. b Pathway analysis of differentially expressed genes between ?Np63fl/fl;RosaM/M and ?Np63?/?; Rosa?/? basal cells. c ?Np63 motif derived from basal cell ?Np63 ChIP-seq compared to published p63 motif. d H3K27ac ChIP-seq signal area under peak for top 500 enhancers in the indicated samples. Data were mean ± SD, n = 3, **** vs. respective ?Np63fl/fl;RosaM/M, P < 10-6, two-tailed Student’s t-test. e Ranking of top 2000 enhancers based on H3K27ac ChIP-seq in ?Np63fl/fl;RosaM/M (blue) and ?Np63?/?;Rosa?/? (red) basal cells. f qRT-PCR of the indicated genes in ?Np63fl/fl;RosaM/M and ?Np63?/?;Rosa?/? basal cells. Data were mean ± SD, n = 3, * vs. ?Np63fl/fl;RosaM/M, P < 0.05, *** vs. ?Np63fl/fl;RosaM/M, P < 0.0001, two-tailed Student’s t-test. g, h ChIP-seq profiles of ?Np63fl/fl;RosaM/M basal cells for the indicated tracks in the Krt5 (g) and Bcl9l (h) loci. Source data are provided as a Source Data file.

Fig 4: BCL9L mediates the oncogenic activities of ?Np63 and is critical for maintenance of LUSC and LUAD.a Quantification of colony formation efficiency in soft agar of H520 LUSC cells and H358 LUAD cells infected with the indicated shRNAs. Data were mean ± SD, n = 3, *P < 0.05, **P < 0.01, ****P < 0.0001, vs. respective shNT, two-tailed Student’s t-test. b Tumour volume quantification of xenograft tumours derived from the indicated cell lines. Boxplots represent the individual data points, median and whiskers (min to max method) are shown, n = 5, * vs. respective shNT, P < 0.05, two-tailed Student’s t-test. c Quantification of colony formation efficiency in soft agar of H520 LUSC cells and H358 LUAD cells transfected with the indicated constructs. Boxplots represent the individual data points, median and whiskers (min to max method) are shown, n = 3, *P < 0.05, **P < 0.01, vs. respective siNT/empty, two-tailed Student’s t-test. d Venn diagram overlaying genes associated with the top 2000 enhancers in AT2 cells and LUAD derived from KrasG12D/+ mice. e, f Kaplan–Meier curves of overall lung adenocarcinoma survival data based on the levels of BCL9L in the indicated cohorts. Source data are provided as a Source Data file.