Characterization of MLL fusion type–specific chromatin binding sites. (A) Heat map showing the indicated chromatin immunoprecipitation sequencing (ChIP-seq) signals at fusion-specific and common binding sites in model ALL cells. Window shows ±5 kb from the peak center. (B) Genomic locations of fusion-specific and common binding peaks. (C) Average read density metaplots showing the indicated signals in each leukemia type at fusion-specific binding sites over a ±5 kb window from the peak center. (D) Gene set enrichment analysis (GSEA) demonstrating the association of fusion-specific binding targets with upregulated gene expression in the corresponding ALL type. (E) RNA sequence analysis showing differential expression of PROM1 and IKZF2 between paired ALLs (left). Each individual point represents one sample. P values were calculated by DESeq2. ChIP-seq tracks showing MLL-Af4 and MLL-AF9 binding and the associated histone modifications at PROM1 and IKZF2 loci (right). NES, normalized enrichment score; RPKM, reads per kilobase per million mapped reads.