Suz12 inactivation causes loss of the H3K27me3 repression mark and increased chromatin accessibility. (A) Centered heat maps of the ChIP-seq Suz12 signals in the different leukemia conditions, centered on Suz12 peaks in J control leukemias. (B-C) Global Suz12 and H3K27me3 signal densities comparing J+S1 vs J and S1 vs WT. J, JAK3(M511I) leukemia; J+S1, JAK3(M511I)+Suz12gRNA leukemia; S1, Suz12gRNA leukemia; WT, wild-type cells. (D) Principle component analysis (PCA) plot showing clustering of RNA samples according to genotype and immunophenotype (SP = CD8 single positive vs DP = CD8/CD4 double positive). (E) Volcano plots showing the significance of the differential gene expression vs fold change. Red dots are upregulated genes with a disappearing Suz12 (left) or H3K27me3 (right) peak; blue dots are downregulated genes with a disappearing Suz12 (left) or H3K27me3 (right) peak. (F) GSEA showing significant positive enrichment of genes with a disappearing H3K27me3 peak in the ranked list of differentially expressed genes in J+S1 vs J (SP background) and S1 vs WT (DP background). (G) GSEA showing significant positive enrichment of genes with an appearing ATAC-seq peak in the ranked list of differentially expressed genes in J+S1 vs J (SP background) and S1 vs WT (DP background). (H) GSEA showing significant positive enrichment of PRC2 target genes²⁵  in the ranked list of differentially expressed genes in J+S1 vs J (SP background) and S1 vs WT (DP background). NES, normalized enrichment score; p, nominal P value. (I) RNA-seq counts show upregulation of canonical PRC2 targets Hoxa3 and Hoxa5 on Suz12 loss (S1, J+S1). Expression (mean with SEM) is relative to wild-type (WT) levels. P values, calculated with 2-tailed unpaired Student t test, denote significant differences between J+S1 vs J cells and S1 vs J cells.