CRBI Seminar – Dr. Qili Feng Professor in School of Life Sciences, South China Normal University, Guangzhou, China

Gene transcription regulation by DNA advanced structures

DNA advanced structures such as G4 and i-motif, have been found to play important roles in multiple biological processes. A large-scale genomic analysis of distribution and evolution of the DNA secondary structures in 37 representative species revealed that the number, density and ratios of advanced structures in the genomes gradually increased with evolution and enriched in the upstream regulatory regions of many genes, particularly transcription factor genes, suggesting that these DNA structures may have developed into an epigenetic regulation mechanism for gene transcription in genomes. Methylation modification and advanced structures in DNA molecules are two epigenetic regulation mechanisms for gene transcription. We found that the 5mC modification in G4 forming sequences inhibited the folding of the sequences into G4s. Suppression of whole-genome methylation led to a genome-wide increase in the abundance of G4s. Whole-genome bisulfite sequencing (WGBS) and G4 CUT&Tag data from HeLa and K562 cells revealed that the hypomethylated sequences around transcriptional start sites (TSSs) had a much higher abundance of G4s than the hypermethylated sequences, suggesting a negative relationship between these two epigenetic mechanisms. G4 and i-motif structures were identified in the promoter of the transcription factor gene BmPOUM2, which regulates the expression of the wing disc cuticle protein gene (BmWCP4) during metamorphosis in Bombyx mori. Disruption or deletion of the G4 and i-motif structures by base mutation, anti-sense oligonucleotides (ASOs) , inhibitory ligands or knockout resulted in significant decrease in the activity of the BmPOUM2 promoter. Two transcription factors (BmLARK and BmILF) were was identified by pull-down experiment and proved to specifically bind to the G4 and i-motif structures, respectively, and activated the transcription of BmPOUM2.  All the data indicate that DNA advanced structures function as an epigenetic regulation mechanism for gene transcription and participate in regulation of insect development.