Fig. 5: Altered Cdx2 binding in adult cells revives developmental Ctcf recruitment.

a Heatmap showing significant (q < 0.05, 1.5×) gain or reduction of Cdx2 binding in Eed^−/− cells as compared to the native villus cells (WT). b Profile plots showing Cdx2 signal at loci with gain and loss of Cdx2 binding in Eed^−/− cells from embryonic (E12.5), fetal (E16.5), adult villus, and Eed^−/− epithelium. c Profile plots showing DNA methylation signal at loci with gain or reduction of Cdx2 binding in Eed^−/− cells from embryonic (E6.5 and E12.5), fetal (E16.5), adult villus, and Eed^−/− epithelium. d Fractional methylation change at CpG at the 4th position within Cdx2 motif shows gain of methylation in Eed^−/− cells at the sites (panel a) with altered Cdx2 binding. The horizontal bars within the box plots represent medians, the tops and bottoms of the boxes represent the 75th and 25th percentiles, respectively, and the upper and lower whiskers extend to the maximum and minimum values, respectively. The outliers are indicated by dots. e A model showing DNA methylation-based Cdx2 binding at developmental target loci; Cdx2 is recruited to developmental sites upon gain of methylation of CpG (at 4th position) within the Cdx2 motif in adult Eed^−/− cells. f Heatmap showing chromatin accessibility dynamics at sites with gain or reduction of Cdx2 binding in Eed^−/− cells as compared to WT cells (as in a); chromatin accessibility at developmental Cdx2 target loci is lost with lack of Cdx2 binding in adult cells (as seen in a) and rebinding of Cdx2 to such loci in Eed^−/− cells reinduces open chromatin formation. g Genomic tracks showing recruitment of Cdx2 to developmental site in Eed^−/− cells accompanied by gain of chromatin accessibility and increase in DNA methylation at the Cdx2 binding locus; dot plot at the bottom shows methylated (solid black dots) or unmethylated (white dots) status of the CpG in Cdx2 motif (4th position) in 6 independent sequencing reads from WT and Eed^−/− WGBS data. h Heatmap showing alterations in active enhancer mark H3K27ac at the sites with Cdx2 gain or reduction in Eed^−/− cells as compared to WT cells (as in a); enhancer activity from developmental Cdx2 target loci is lost with lack of Cdx2 binding in adult cells (as seen in a) and rebinding of Cdx2 to such loci in Eed^−/− cells reactivates these enhancers. Source data are provided as a Source Data file.