Fig. 3: H3K36me3 is unable to substitute for H3K27me3 in regulating gene expression and differentiation.

a Cluster heatmap (k-means, 4) of RNA-seq data analyzed with Deseq2 for differential expression (FDR < 0.05). Heatmap shows differentially expressed PRC2 target genes identified by H3K27me3 positive promoters in WT mESCs (n = 4986) in the indicated cell lines based on three independent biological replicates. b MA plots showing mean changes in gene expression from Deseq2 analysis based on three independent biological replicates (n = 3). Indicated with red dots are significantly upregulated genes in Suz12 KO mESCs filtered with log2 expression foldchange > 1 and FDR < 0.05. The mean expression of the upregulated genes in Suz12 KO mESCs are traced in the indicated cell lines. c Bar plot showing the fraction of the 1326 upregulated PRC2 target genes in Suz12 KO mESCs that are fully or partially rescued in the indicated cell lines (see methods for filtering criteria). Statistical significance was calculated using Fisher’s exact test, two-tailed (*p  <  0.05; **p  <  0.01; ***p  <  0.001, ****p  <  0.0001). Source data are provided as a Source Data file. d Bar plot showing the percentage of beating clusters identified on day 10 after induction of embryoid body differentiation in the indicated cell lines. The plot is representative of at least three independent experiments. e Mean H3K4me3 CUT&RUN signals (RPKM) (n = 2) in indicated cell lines within a 40 Kb window centered on 7732 H3K27me3 positive promoter peaks identified in WT mESCs. f Custom annotation based DMR methylation (%, see methods) at CpG islands for indicated cell lines (n = 3). The horizontal lines mark the median; the boxes mark the interquartile range (IQR) and whiskers extend up to 1.5 times the IQR; individual data points beyond this range are plotted. Statistical significance was calculated for the means using an unpaired two-sample t test, two-tailed (*p  <  0.05; **p  <  0.01; ***p  <  0.001, ****p  <  0.0001). Source data are provided as a Source Data file.