DNMT3B Regulates Cis-Regulatory Chromatin and Cell Cycle Programs in Acute Myeloid Leukemia

To investigate the epigenomic impact of DNMT3B inhibition, we treated KG1A AML cells with Nanaomycin A (NanA), a selective DNMT3B inhibitor, and performed genome-wide DNA methylation profiling using the Illumina MethylationEPIC v2.0 array. Following 48-hour exposure to NanA (50 nM), differentially methylated CpG sites were identified, with the majority exhibiting moderate hypomethylation (±25% Δβ-value).

These changes were enriched in promoter and gene body regions and overlapped with regions of altered chromatin accessibility. The resulting dataset provides a high-resolution view of DNMT3B-dependent methylation dynamics in AML and serves as a resource for understanding the epigenetic consequences of targeted methyltransferase inhibition.