Genome-wide DNA methylation profiling of DNMT3A-knockout SW620 colorectal cancer cells.

To characterize DNMT3A-dependent changes in the DNA methylation landscape, genome-wide DNA methylation profiling was performed in control and DNMT3A-knockdown SW620 colorectal cancer cells using the Infinium MethylationEPIC BeadChip array. Comparative analysis identified 14,390 differentially methylated regions, of which 12,059 were annotated to known genes.

These methylation alterations were predominantly localized to promoter-associated regions, including TSS1500, TSS200, and 5′ untranslated regions. DNMT3A loss reduced promoter methylation at genes involved in TNFα- and IFNγ-related signaling pathways, including TNFRSF1A and TNFRSF1B. These data define the DNMT3A-dependent DNA methylation landscape in SW620 cells and support a role for DNMT3A-mediated promoter methylation in the transcriptional regulation of tumor immune signaling pathways.