PRC2 members associate with repressed genes in AML-HSPCs. (A) Schematic of hematopoietic differentiation of control- and AML-iPSCs with days indicating time points at which samples were harvested for CAGE sequencing. (B) Heat map showing unsupervised clustering of the 100 most variable genes in control- and AML-iPSCs during hematopoietic specifications with cells harvested at the indicated time points (n = 4). (C) Heat map depicting dynamic changes in motif activity in promoters between control- and AML-iPSC differentiation as inferred from CAGE data using MARA. (D) Individual motif activity profiles of ARNT_ARNT2_BHLHB2_MAX_MYC_USF1; ETS1,2; LMO2; TFCP2; SNAI1..3; SPI1; NFY(A,B,C); and ZEB1 promoters between control and AML differentiation as inferred from CAGE data using MARA. Data are presented as mean ± SEM and analyzed using unpaired t test for each time point. (E) Box plots showing expression levels (log₂[CPM + 1]) of MYC and NFYA from RNA-seq of control and AML cells at iPSC and HSPC stages. Boxes represent interquartile range with whiskers extending to 1.5× interquartile range and horizontal lines denoting median values. Outliers are shown as individual points. Adjusted P values (FDR) derived from DESeq2 results. (F) Heat map of unsupervised clustering of candidate ChIP-seq signatures from ChIP-Atlas, showing differential patterns between control- and AML-HSPCs across days 8, 10, and 12 of hematopoietic differentiation. (G) STRING network of TFs with differential motif activity and direct interaction to PRC1/2 members (circled in black). Nodes in the network represent proteins, and edges represent predicted associations based on various sources of evidence, which include curated databases (light blue), performed experiments (purple), text-mining (yellow), coexpression (black), and homology (dark blue). ∗P ≤ .05; ∗∗P ≤ .01; ∗∗∗P ≤ .001. ns, not significant; CPM, counts per million; FDR, false discovery rate; TPM, transcripts per million.