Expression of G-quadruplex coordinates BRCA1, CDH1, and RASSF1 via DNA methylation in mouse breast cancer cells

G-quadruplex (G4) structures are enriched in key genomic regions and regulate gene expression and chromosomal stability. However, their role in de novo DNA methylation remains unclear. DNA methyltransferase 3A (DNMT3A) and DNA methyltransferase 3B (DNMT3B) are vital for cancer initiation and progression. This study investigated the role of G4 structures in regulating DNMT3A and DNMT3B expression and their epigenetic function in breast cancer. G4 structures in DNMT3A and DNMT3B were identified using Quadruplex forming G-Rich Sequences Mapper, circular dichroism, and gel mobility shift assays. The effects of the G4 stabilizer pyridostatin on breast cancer 4T1 cell proliferation, migration, DNMT3A and DNMT3B expression, and promoter methylation of Breast Cancer 1 (BRCA1), E-cadherin (CDH1), and Ras Association Domain Family Member 1 (RASSF1) were evaluated. G4-forming sequences were found in the core promoter regions of DNMT3A and DNMT3B. They formed parallel G4 structures in vitro. Pyridostatin enhanced G4 stability, inhibited 4T1 cell proliferation and migration, downregulated DNMT3A and DNMT3B expression, reduced promoter methylation of BRCA1 and RASSF1, and altered target gene expression. Promoter G4 structures actively regulate gene expression by modulating de novo DNA methylation, suggesting that targeting G4s may represent a novel therapeutic strategy for breast cancer. Specific regions of DNA are capable of folding into a distinctive structure called a G-quadruplex (G4). These structures act like switches, controlling whether genes are turned on or off and helping to maintain chromosome stability. However, the role of these factors in the DNA methylation process remains unclear. Two key enzymes, DNA methyltransferase 3A (DNMT3A) and DNA methyltransferase 3B (DNMT3B), are responsible for these modifications, and their activity has been associated with cancer development. In this study, the effects of G4 structures on the expression of DNMT3A and DNMT3B, and consequently on breast cancer-related genes, were examined. G4 structures were detected in the regulatory regions of both DNMT3A and DNMT3B. When these G4 structures were stabilized using a chemical compound, the activities of the enzymes were altered, resulting in changes in the expression of breast cancer-related genes. These results indicate that gene expression and DNA methylation can be regulated by G4 structures in DNA, and it is suggested that targeting these structures may provide a novel strategy for breast cancer treatment.