Skip to main content
. 2022 Jan 1;36(1-2):38–52. doi: 10.1101/gad.348983.121

Figure 2.

Figure 2.

Direct CDX2 occupancy at intestinal enhancers in stomach cells. (A) CDX2 binding sites in adult mouse intestinal villus cells, determined by CUT&RUN (CnR), show evidence for direct or indirect DNA occupancy based on the presence of footprints at the CDX2 consensus motif. Cdx2−/− villi lacked signals at CDX2 binding sites. Direct and indirect sites gave similar signals in ATAC-seq and H3K7ac ChIP-seq. (B) In CDX2+ stomach organoids, the TF occupies a large fraction of intestinal cis-elements that bind CDX2 with direct DNA contact (3438 out of 10,573) but few of the 18,626 sites where it binds DNA indirectly in the intestine in vivo. Pre-existing chromatin accessibility is common at indirectly bound CDX2 sites, but chromatin at most direct sites is closed in stomach organoids, and CDX2 expression opens that chromatin. (C) In stomach organoids, CDX2 occupies 3438 intestinal cis-elements that bind CDX2 with direct DNA contact in the native intestine in vivo, whereas most sites that bind CDX2 indirectly in the intestine lack CDX2 binding. All bound sites in stomach organoids, even those that show faint occupancy in the intestine, leave strong footprints at the CDX2 motif (TTTATDR), implying close DNA contact. (D) Schematic showing direct and indirect DNA contact by CDX2 in different contexts.