Supplementary Figure 2: Hypermethylation of bivalent promoters after TET inactivation.

a, GO analysis for genes associated with hypermethylated bivalent promoters (n = 1,693), genes associated with hypermethylated poised enhancers (n = 3,570) and genes associated with hypermethylated active enhancers (n = 3,805). FDR < 0.01 was set as a cutoff for bivalent promoters and poised enhancers, and FDR < 0.05 was set as a cutoff for active enhancers. Developmental categories are in red. b, Fraction of genomic regions showing a >5% increase in 5mC (Hyper) or a >5% decrease in 5mC (Hypo) for TKO versus WT hESCs by ERRBS of HUES8 and MEL-1 WT and TKO hESCs; n = 2 independent experiments. c, DNA methylation change between TKO and WT MEL-1 hESCs by ERRBS at different promoter types. Box-and-whisker plots were generated using the methylation change at individual promoters. The error bars show 10% and 90% confidence intervals. The lower and upper limits of the box represent the first and third quartile, respectively, and the bar at the center of the plot box indicates the median. The promoters are divided into four groups based on histone modification patterns. The details of promoter definitions can be found in the Methods; n = 2 independent experiments. Statistical analysis was performed by one-way ANOVA: **P < 0.01, ****P < 0.0001. d, Representation of bivalent promoters among promoters that show different degrees of methylation change between TKO and WT MEL-1 hESCs by ERRBS; n indicates the total number of promoters in each DNA methylation change group, with n = 2 independent experiments. e, Correlation between the methylation level at bivalent promoters in HUES8 WT, MEL-1 WT, HUES8 TKO and MEL-1 TKO hESCs by ERRBS; n = 2 independent experiments. f, Overlap between all hyper-DMR-associated bivalent promoters in mESCs¹¹ and their human counterparts in hESCs (by ERRBS, n = 2 independent experiments). The odds ratio and P value are given (Fisher’s exact test)