Association of histone modifications with transcription factor binding sites of different specimen groups. (A) Association of transcription factor binding sites with histone modification changes was analyzed. Overall, 150 bp enclosing each oligonucleotide was screened with high stringency for approximately 600 bona fide transcription factor binding sites. GSA was used to identify associations between transcription factor binding sites and histone modification changes. (B) GSA analyses were performed independently for regions with different distances to the TSSs. Approximately 600 bona fide transcription factor binding sites (TRANSFAC database) were analyzed by GSA in the H3K9me3 dataset of AML versus CD34⁺ in different promoter regions, and the number of resulting P values in each range was plotted. A shift to lower P values indicates an association between the presence of specific transcription factor binding sites and changes in H3K9me3 levels in the core promoter region. (C) Among the overrepresented transcription factor binding sites, ETS and CRE binding elements were most prominently altered in different datasets. AML specimens consistently showed decreased levels of H3K9me3 at binding sites for most ETS factors and CREB.