CBFA2T3 marks LSC gene signatures and opposingly regulates HSC/LSC and antiproliferative genes. (A) Volcano plot of gene expression changes (fold changes ≥1.5, adjusted P ≤ .05) in high-CBFA2T3 vs low-CBFA2T3 patient samples in the GSE14468 dataset. High and low CBFA2T3 expression is relative to the median level in all patient samples (n = 526). Also shown are Gene Ontology functions of the downregulated (left, blue) and upregulated (right, red) genes. (B) GSEA showing association of HSC/LSC gene signatures with high-level CBFA2T3 expression in the patient samples. NES, normalized enrichment score. The colored bar at the bottom shows ranked gene expression based on fold changes and P value. Red indicates upregulation in high-CBFA2T3 samples, whereas blue indicates downregulation in high-CBFA2T3 samples. (C) A Venn diagram showing overlap of CBFA2T3-occupied genes in HSCs and Kasumi-1 cells. Also shown are log2 fold changes of CBFA2T3 cis-repressome genes (blue) and cis-actome genes (red) and the biological functions of the CBFA2T3-binding sites at these genes identified by GREAT.58 (D) RT-qPCR showing effects of CBFA2T3 knockdown on messenger RNA expression of the indicated genes in human HSPCs. (E) Cell cycle phase quantification modeled from propidium iodide–stained DNA content histograms. Error bars represent the 95% confidence interval, calculated by bootstrap resampling of the original events. P values were calculated by permutation tests (n = 1000).