TF-binding motif analysis of genomic regions in which DNA methylation was different between FLT3-ITD⁺ and FLT3-ITD⁻ AMLs. (A) The 3 TFs were confirmed by HOMER in the genomic regions ±200 bp in length adjacent to each of the 1243 CpG sites with a P value <1e−50. (B) hierarchical clustering of methylation levels at 135 CpG sites in the STAT5-binding sites was classified in 8 patients of cluster A in the first trunk. Eight patients with AML with FLT3-ITD in cluster A in Figure 3A are indicated by red arrows. (C) Genetic localization of 135 CpG sites for which the STAT5-binding motif existed nearby. (D) Annotation of candidate cis-regulatory elements (cCREs) in the gene body and intergenic CpG sites close to STAT5-binding motifs. (E) Chromatin accessibility of the genomic regions where STAT5 binds close to the methylation-changed CpG sites was analyzed in 5 patients using ATAC-seq. Some open chromatin regions in the HOXB-AS3 gene were identified only in patients with FLT3-ITD and high PRDM16 gene expression. Annotations of cCREs are described in panel D.