Fig. 4: AHR restricts genomic accessibility to Yap/Tead targets.

a Deeptools heatmap showing accessibility data of differentially expressed peaks identified in d4 ENR AHR KO vs WT organoids across samples (FDR < 0.05) (b) GO gene ontology (biological process) was conducted on genes that overlap between differentially accessible targets identified by ATAC-seq and differentially upregulated or downregulated genes in AHR KO vs WT organoids grown in D4 ENR conditions as determined by RNA-seq (FDR < 0.05). Statistical significance was determined by permutation testing of the overlap between the datasets (p value <0.00001). c IgV images of accessibility peaks (open regions) of known Yap/Tead targets (Ctgf, Cyr61, Amotl2) and fetal-like genes (Clu, Tacstd2, Ly6a) in d4 ENR WT and AHR KO organoids (d) Pairwise comparison of TF activity between differentiated AHR KO and WT organoids (d4 ENR). The volcano plots show the differential binding activity against the –log10 (p value) of all investigated TF motifs represented by a dot. Only the top 5% (both by fold-change, -log10 p value) of TF motifs identified are highlighted in red. TFs belonging to Tead and Ets-1 like family of factors are bolded. e Motif sequences of some identified TFs belonging to Tead (Tead 3, Tead4, Tead1) and Ets-1 family are shown, and the dotted line highlights the similarity in the binding sequence of these factors (f) Top 5% of identified motifs were aligned to each other and matched to an archetypal consensus motif. The color represents the fold-change (Red to grey – highest to lowest) in differential binding score between d4 AHR KO vs WT organoids. Source data for (4b, d) are provided with this paper in the source data file.