Extended Data Fig. 6: Effect of H2A.Z DKO in H2AK119ub1 and H3K27me3 in FGOs.
a, b, Scatter plots showing the correlations between biological duplicates of H3K27me3 (a) and H2AK119ub1 (b) CATCH-seq in H2A.Z control and DKO FGOs. c, Heatmaps showing the signal intensity of H2A.Z, H3K4me3, H3K27me3, and H2AK119ub1 at all genes in H2A.Z control and H2A.Z DKO FGOs. Actively expressed genes are defined by [RPKM > 1], while lowly expressed genes are [0.1 < RPKM < 1], and inactive genes are [RPKM < 0.1] in all stages, respectively. The remaining genes are defined as variably expressed genes. The RNA-seq datasets are from Veselovska et al.41. d, Box plots showing the signal intensity of H2A.Z, H3K4me3, H3K27me3, and H2AK119ub1 at promoters in H2A.Z control and DKO FGOs. The center lines in the boxes represent median values. The box edges, upper and lower whiskers indicate the interquartile range (IQR, from the 25th to 75th percentile), the maximal value smaller than 1.5 x the IQR above the 75th percentile, and the minimal value larger than 1.5 x the IQR below the 25th percentile, respectively (n = 1 as biological replicates were combined). P-value was calculated by two-sided t-test. e, Heatmaps (left panel) showing the signal intensity of indicated histone modifications at H2AK119ub1/H3K4me3-harbored promoters. The line plots at right show the average signal profiles of H2K119ub1 and H3K4me3 around TSSs in H2A.Z control and DKO FGOs. f, Genome browser views of representative genes that show a reduction of H2AK119ub1 at active genes in H2A.Z DKO FGOs. g, Heatmaps showing the signal intensity of indicated histone modifications at ‘H3K4me3-lost’, ‘Intermediate’, and ‘H3K4me3-unchanged’ promoters in H2A.Z control and DKO FGOs. h, Box plots showing the signal intensity of H2AK119ub1 and H3K4me3 at ‘H3K4me3-lost’, ‘Intermediate’, and ‘H3K4me3-unchanged’ regions in H2A.Z control and DKO FGOs. The definitions of lines, box edges, whiskers, and n are the same as panel d. P-value was calculated by two-sided t-test.
