RNA-seq and ATAC-seq analysis of 5-azacytidine-treated HepG2 cells reveals epigenetic reactivation of BFL-1 and SQOR in hepatocellular carcinoma

Epigenetic silencing of tumor suppressor genes through promoter hypermethylation contributes to oncogenesis and resistance to cell death stimuli. We employed low-concentration 5-azacytidine (5-AZA) treatment to identify epigenetically silenced genes that modulate cell death susceptibility in HepG2 hepatocellular carcinoma cells without inducing baseline cytotoxicity.

HepG2 cells were treated with 0, 2, and 10 μM 5-azacytidine for 4 days, followed by integrative RNA-seq and ATAC-seq analysis to characterize transcriptomic changes and chromatin accessibility patterns. This approach revealed coordinated promoter opening and transcriptional reactivation of methylation-silenced genes, particularly BFL-1 (BCL2A1) and SQOR, whose reactivation enhanced cell death susceptibility to TNF-α/CHX and sorafenib treatments.