Fig. 3

H3.3 G34R triggers gains in H3K9me3 and genocopies KDM4 A/B/C triple-knockout. a Normalised H3K9me3 ChIP-seq reads across all H3K9me3-enriched genes in WT and G34R cells. b Normalised H3K9me3 read counts at KDM4 A/B/C depleted (n = 2953) and enriched (n = 4761) genomic regions. c, d Heatmaps of c H3K9me3 and d H3K36me3 ChIP-seq reads at sites which gain (>1.5-fold) H3K9me3 (n = 927) or H3K36me3 (n = 439) in KDM4-tKO mutants (±1 kb) with profiles of corresponding regions in WT and G34R cells. e Representative screenshots of genes (Repin1, Zfp787, Ankrd13a) enriched for KDM4 which gain H3K9me3 and H3K36me3 in both KDM4-tKO cells and G34R mutants. H3K9me3 and H3K36me3 ChIP-seq in KDM4-tKO³⁶ were obtained from GEO (accession number GSE64252). f H3K9me3 ChIP-qPCR in WT and G34R cells. Results are normalised for input and bars represent mean enrichment of three independent experiments, calculated relative to a negative control (β-actin promoter). Error bars represent standard deviation of three independent experiments (n = 3). P-values calculated using Student’s T-test (*P < 0.05, **P < 0.01, ***P < 0.0001). g Heatmap of log₂ (G34R/WT RPKM) of genes which were downregulated in KDM4-tKO (n = 933) compared against a random selection (n = 933) of genes. h log₂ (RPKM) of WT vs G34R RNA-seq of genes downregulated in KDM4-tKO (n = 933). i Representative screenshot of a gene which is downregulated in KDM4-tKO. j Heatmap of log₂ (G34R/WT RPKM) of genes which were upregulated in KDM4-tKO (n = 1099) compared against a random selection (n = 1099) of genes. k log₂ (RPKM) of WT vs G34R RNA-seq of genes upregulated in KDM4-tKO (n = 1099). l Representative screenshot of a gene which is upregulated in KDM4-tKO. Red and blue circles indicate genes which are >2-fold up or downregulated in G34R relative to WT. Boxes represent 25th, median and 75th percentile; whiskers represent 10th and 90th percentiles