Regulation of gene expression by epigenetic modifiers

Abstract

Over 60% of human genes contain CpG islands in their promoter regions, making DNA methylation one of the most widespread mechanisms of transcriptional control. This research examined the molecular mechanisms through which epigenetic modifiers regulate gene expression patterns in mammalian cells. Using a combination of chromatin immunoprecipitation sequencing and RNA sequencing approaches, we investigated the effects of DNA methyltransferase inhibitors and histone deacetylase inhibitors on genome-wide expression profiles in HeLa and HEK293 cell lines. The research was conducted at Stockholm Institute of Applied Sciences between January 2022 and November 2023. Treatment with 5-azacytidine resulted in demethylation of 2,847 CpG sites across 1,456 gene promoters, with corresponding upregulation of 892 previously silenced genes. Histone deacetylase inhibition with trichostatin A produced distinct but overlapping effects, activating 1,124 genes through increased histone H3 and H4 acetylation. Combined treatment demonstrated synergistic effects, with 3.2-fold greater gene reactivation compared to either agent alone. Pathway analysis revealed enrichment for tumor suppressor genes, cell cycle regulators, and apoptotic mediators among reactivated transcripts. These findings establish that coordinated epigenetic modifications function as master regulators of gene expression programs and suggest therapeutic potential for epigenetic modifier combinations in restoring normal gene expression patterns.