Extended Data Fig. 9: Dynamics of H3K4me3 and H3K27me3 resetting during the naïve-to-primed transition in human embryonic stem cells (hESCs).

a. Heatmaps showing the dynamics of H3K27me3 and H3K4me3 at the promoters of H3K27me3-only and H3K4me3-only genes identified in hESCs during the naive to primed transition. b. Expression levels of H3K4me3-only and H3K4me3-only genes during the transition from naïve to primed states in hESCs. The box represents the interquartile range (IQR), with the lower and upper bounds indicating the 25th and 75th percentiles respectively. The median is shown by the line inside the box. Whiskers extend to the minimum and maximum values within 1.5 times the IQR. c. Bubble plot showing statistically significant overlaps between hTB-, hCB-, H3K27me3-only, H3K4me3-only, and other-marked gene sets in hESCs and pluripotency-specific gene sets. Color represents P-value, and bubble size indicates the number of overlapping genes. Primed-specific genet sets were defined as the top 200 highly expressed genes in H9 primed hESC compared to cRH9 D0 hESC. Naïve-specific genet sets were defined as the top 200 highly expressed genes in cRH9 D0 hESC compared to H9 primed hESC. d. Enrichment of histone modifications at the promoters of hTB- and hCB-marked genes in hESCs. All datasets were obtained from the ENCODE project using H9 cell line cultured in mTeSER medium. e. Venn diagrams showing the overlap of orthologous genes between those marked as hTB and mTB. Among these shared TB-marked genes, an IGV genome browser view shows the dynamics of H3K4me3 and H3K27me3 during pluripotency progression at four hTB-marked genes. P-value was calculated by Monte Carlo simulation with 10,000 iterations followed by a z-test. f. Venn diagrams showing the overlap of orthologous genes between those marked as hTB and mCB. P-value was calculated by Monte Carlo simulation with 10,000 iterations followed by a z-test. Source numerical data are available in source data.