Fig. 4.

Maturation-enriched regions of accessible enhancer chromatin show loss of accessibility in the intestinal epithelium of Cdx2^KO and Hnf4αγ^DKO mutants. (A) The intestinal chromatin (GSE115541, n=2 biological replicates) becomes more accessible at maturation-enriched regions and less accessible at embryo-enriched regions (ATAC-seq regions defined in Fig. 1A) from E11.5 embryo to adult. (B-E) The intestinal chromatin accessibility at the maturation-enriched sites is compromised upon depletion (Shh-Cre) of Cdx2 (B,C; GSE115314) or Hnf4 genes (D,E) in E16.5 embryos, whereas promoter regions are relatively unaffected and serve as an internal control (n=2 wild-type controls, 1 Hnf4g^+/− control, 2 Cdx2^KO mutants and 2 Hnf4αγ^DKO mutants; whole small intestine epithelium).