Fig. 3: Invasion of H3K27me3 into gene bodies following depletion of H3K36me.
From: H3K36 Methylation as a Guardian of Epigenome Integrity
a Metagene plots depicting the invasion of H3K27me within gene bodies. Protein-coding genes with gene lengths falling between the 25th and 75th percentiles and with FPKM values exceeding 0.1 were included. After filtering and stratifying into three quantiles, the bottom 2000 were classified as lowly expressed and the top 2000 as highly expressed genes. 2000 genes with zero expression were designated as silent genes. ChIP-seq H3K27me1/2/3 signals were MS-normalized as previously described. b Barplots of genome-wide prevalence of modifications based on mass spectrometry, showing progressive depletion of H3K27me1, and progressive increases in H3K27me2 and H3K27me3 levels in multi-KO conditions reaching approximately 1.5-fold and more than 2.5-fold, respectively. Error bars display the standard deviation around the mean. (n = 3 per condition). c Log2 fold changes of gene expression comparing PA to TKO, depicting 1.5-fold more genes being downregulated (609) than upregulated (391) following significant H3K27me3 invasion (adjusted p-value < 0.05) into their gene bodies compared to a randomized, control set of genes, which have similar numbers of genes up- (503) and down-regulated (497). Statistical significance was tested using a two-sided Wilcoxon rank-sum test. **** represents p-value = 4.9e-13. In the box plots, boxes span the lower (first quartile) and upper quartiles (third quartile), median is indicated with a center line, and whiskers extend to a maximum of 1.5 times the interquartile range. Source data are provided as a Source Data file.
