Figure 3 |. Co-factor expression modulates FOXA2 enrichment at a subset of target sites.

a) Differential motif analysis displaying –log₁₀ p-value of enriched motifs in dEN exclusive sites versus BJ^FOXA2 exclusive sites with the most significant motifs on the left. Expression (log₂ FPKM) of the TFs associated with the listed motif in both BJ^FOXA2 and dEN. Of note, while there are many significant differential motifs observed in dEN exclusive sites, not all motifs are associated with factors that display differential expression.

b) Simplified schematic of ectopic expression system used to co-express GATA4 in BJ^FOXA2. Immunostaining of FOXA2 and V5-GATA4 in co-infected BJ^FOXA2 fibroblasts. White scale bar is equal to 345nm.

c) Bean plot comparing FOXA2 enrichments at all dEN exclusive co-bound sites when FOXA2 is expressed independently versus when FOXA2 and GATA4 are co-expressed. Thick black bars represent average. Blue lines indicate data points within the distribution while teal bars represent data points outside of the distribution.

d) Scatter plot comparing FOXA2 enrichment of co-bound dEN exclusive sites in BJ^FOXA2 fibroblasts compared to BJ^FOXA2-GATA4 fibroblasts. Red dots indicate regions that gain at least 2 fold enrichment and are above RPKM of 1 in BJ^FOXA2-GATA4 fibroblasts. P-value 2e⁻¹⁶.

e) Box plots displaying the RPKM of FOXA2 enrichment in BJ^FOXA2 and BJ^FOXA2-GATA4 at the subset of regions that are GATA4 stabilized compared to the non-enriched subset. Boxes indicate interquartile range and whiskers show maximum and minimum values. Outliers are removed.

f) Representative IGV browser tracks displaying FOXA2 and GATA4 enrichment in dEN and the various fibroblasts as indicated on the left. Gray bar highlights a region that shows the co-factor mediated recruitment of FOXA2 to two of its dEN targets chr13:76,031,782–76,039,815 and chr17:14,352,627–14,360,300.