Figure 5.

Pioneer-like activity of CDX2 at select intestinal enhancers. (A) CDX2 binding determined by CnR in gastric organoids overlapped most with binding sites in adult intestines and poorly with binding in embryonic tissues. Data tracks for CDX2 binding show shared binding sites with adult intestines (red boxes) and others unique to stomach organoids (gray box). In embryonic tissues, CDX2 binds at sites distinct from these. (B) K-means clustering of ATAC data at the 3438 cis-elements with direct CDX2 binding shared with native intestines. Sites with the highest pre-existing access in stomach organoids are mainly promoters. CDX2 increased access at 737 and opened the chromatin at 2449 enhancers. Gene set enrichment analysis shows that both types of increased chromatin access are linked to genes that increase expression in CDX2⁺ organoids. The Epcam locus exemplifies increased chromatin access at previously open (light blue) and closed (dark blue) sites. (C) Summation of ATAC-seq signals over cis-elements previously inaccessible in stomach organoids: 2449 sites where CDX2 binding is shared with normal intestines (black curve; cluster 3 in Fig. 2C) and 5546 sites unique to gastric organoids (blue curve; cluster 3 in Supplemental Fig. S4D). Shared sites gained more access than unique sites.