AML1/ETO-repressed genes show more AML1/ETO binding and AML1/ETO-activated genes show more AML1 binding. (A) Correlation between the binding affinity ratio of AML1/ETO to AML1 and gene sets repressed or activated by AML1/ETO. FDR q-value, false discovery rate q value; NES, normalized enrichment score. (B) Association of the binding affinities of AML1/ETO and AML1 with the modulation of gene expression by AML1/ETO. Heat maps of AML1/ETO and AML1 ChIP-seq signals on AML1/ETO-regulated genes were sorted based on the ratio of the AML1/ETO binding affinity vs AML1 binding affinity in a 4-kb window centered on the AML1/ETO peak summit (left and center). In the gene expression panel (right), the blue indicates AML1/ETO-repressed genes and the yellow indicates AML1/ETO-activated genes. (C) Overview of the loci of representative AML1/ETO-repressed genes OGG1 and AML1/ETO-activated genes CTTN in Kasumi-1 and SKNO-1 cells. Blue, AML1/ETO ChIP-seq signals; red, AML1 ChIP-seq signals; black, RNA-seq signals before and after AML1/ETO knockdown. Refseq annotations are shown at the bottom. ChIP-seq and RNA-seq data used in this analysis were retrieved from the NCBI Gene Expression Omnibus database (ie, GSM1113430,¹⁶ GSM1113428,¹⁶ GSM585589,²⁵ GSM726978,²⁵ GSM1071857,¹⁴  and GSM1071852¹⁴ ). *GEO accession number GSE65427. (D) Validation for the expression changes of genes with higher AML1/ETO binding signals or genes with higher AML1 binding signals by real-time RT-PCR. Western blotting in the left panel showed the AML1/ETO knockdown efficiency. On AML1/ETO knockdown, genes with higher AML1/ETO binding signals (eg, OGG1, CTSG, PARVG, NKG7, and IL6R) were significantly upregulated, whereas genes with higher AML1 binding signals (eg, CTTN, YES1, CALM2, DUSP6, and PADI3) were significantly downregulated. The overview of the loci of those genes can be seen in Figure 6C and supplemental Figures 8 and 10. Error bars represent the SD of triplicate measurements. *P < .05; **P < .01; ***P < .001.