Fig. 2: Differentiation-specific hyper-DMRs show reduced chromatin activity at pioneer TF-binding sites.

a Volcano plot of WGBS data illustrating differentially methylated CpGs (DMCs) identified in TKO_PP compared with WT_PP. Red and blue represent increased and decreased 5mC in TKO_PP cells, respectively (credible methylation difference >0.2). b Heatmap illustrating methylation difference between TKO_PP and WT_PP at centers of annotated genomic features (±5 kb) for chromatin accessibility (ATAC), hydroxylation (5hmC), TF binding (FOXA2, GATA4, and GATA6), bivalent promoters, poised enhancers, and active enhancers. Average 5mC signals of every 100-bp bin were calculated. c Classification of TKO hyper-DMRs based on 5mC levels in hESCs (green), WT_PP cells (blue), and TKO_PP cells (red). d Average density plots and heatmaps of FOXA2, GATA4, GATA6, PDX1, and HNF6 signals at differentiation-specific hyper-DMRs or non-differentiation hyper-DMRs in pancreatic progenitors. The statistical significance was calculated using the student’s unpaired two-tailed t-test without multiple test correction. e Average density plots and heatmaps of ATAC-seq reads at differentiation-specific hyper-DMRs or non-differentiation hyper-DMRs in PP for WT (green) or TKO (orange) cells. f Enrichment profile of methylation ratio (5mC/C) at proximal (≤1 kb from TSS) and distal (>1 kb from TSS) decreased accessible regions in PP for WT (green) and TKO (orange) cells. g Genome-browser view of the PDX1/PDX1-AS1 locus. A specific TKO hyper-DMR showing decreased 5hmC, ATAC-seq, and H3K27ac signals is highlighted in pink.