Promoter G-quadruplex structure as an epigenetic regulator of tissue-specific development and functional formation in Bombyx mori [CUT&Tag]

Cell differentiation, tissue development and functional formation rely on the precise activation of specific gene expression which regulated by the interaction of epigenetic modifications and transcription factors. DNA G-quadruplex structures (G4s) have emerged as important regulators of gene transcription. Here, by nuclear G4-CUT&Tag, ATAC-seq, and histone modification data, we demonstrate that G4s in Bombyx mori are primarily located in promoter regions and are associated with active chromatin marks. Comparative analyses of G4 distribution in the brain and fat body revealed that identical promoter sequences can adopt distinct G4 folding states in different tissues. Notably, the presence of folded G4s strongly correlated with high transcriptional activity of genes essential for tissue-specific functions. Furthermore, treatment with G4-stabilizing ligands disrupted energy metabolism and significantly delayed neurodevelopment in B.mori.. In summary, our findings emphasize G4s as critical epigenetic regulators in maintaining tissue development and functional formation in insects. G4-CUT&Tag to detect G4 structures in the brain, fat body, and ovarian cell line BmN of silkworms