Fig. 4

Reprogramming of CpG methylation status between ESCs and adult tissue occurs only at a small fraction of CpGs at binding sites for specific TFs. a Heatmap of CpG methylation percentage from BS-seq data in E7.5 embryos and adult intestine. Only CpGs with at least 10 BS-seq reads are displayed. The heatmaps are divided as follows: CpGs at E14.5m PGC DNase-Hi sites with high methylation (> 80%) in E7.5 embryos, sorted by % methylation in intestine (top left); CpGs at E14.5m PGC DNase-Lo sites with very low methylation (< 20%) in E7.5, sorted by methylation in intestine (bottom left); CpGs at E14.5m PGC DNase-Hi sites with very high methylation in E7.5, sorted by methylation in intestine (top right); and CpGs at E14.5m PGC DNase-Lo sites with very low methylation in E7.5, sorted by methylation in intestine (bottom right). The number of CpGs in each category is shown in the matrix to the right. The heatmaps at DNase-Hi sites are scaled separately from those at DNase-Lo sites to allow viewing of each class. The relative heights of the DNase-Hi heatmaps are scaled according to the relative number of CpGs at each, and the DNase-Lo heatmaps are scaled to each other similarly. b Heatmap of a subset of the sites shown in a, containing only the sites that overlap ATAC-seq peaks during embryonic, fetal, and adult intestine development. c Heatmap of all CpGs genome-wide with at least 10 BS-seq reads in both samples that have either high or low methylation in E7.5 embryos. d An example of a region with a CpG at a binding sequence for the putative reprogramming TF Tcfap2a that has high methylation in E7.5 and low methylation in the adult intestine. e Bar plots showing the number of motifs and the statistical significance of motif enrichment for the indicated TFs. f Venn diagram showing the overlap of sites that have high DNA methylation (> 80%) in E7.5 embryos and low methylation (< 20%) in either adult intestine, neonatal heart, or neonatal forebrain