Epigenetic therapy targets DNA methylation, histone modifications and microRNAs. The FDA-approved DNA hypomethylating agents (DHAs) like 5-azacytidine (5AC) and decitabine (DAC) demonstrated efficacy in the treatment of hematologic malignancies. DHAs are broadly classified into nucleoside and non-nucleoside analogues. In this study, we are providing evidence that the nucleoside analogues DHAs (DAC and 5AC) increase the enzymatic activity of the histone deacetylase (HDAC) enzyme SIRT6 in leukemia cells. To investigate the consequences of such activation, we used ChIP-Seq to analyze the genome-wide effect of DHAs on the acetylation of H3K9, the physiological substrate of SIRT6, using bone marrow cells derived from leukemia patients. Significant H3K9 acetylation decrease was observed in 102 genes at different loci confirming the activation of SIRT6. This is the first report to identify the nucleoside analogs DHAs as activators of SIRT6. The consequences of SIRT6 activation will affect the use of DHAs in combination therapy.