Enrichment of G4 DNA motif in transcriptional regulatory region of chicken genome

G-quadruplex or G4 DNA is a stable, four-stranded DNA structure formed from guanine-rich regions. Based on the hypothesis that G4 DNA participated in the regulation of transcription, we analyzed G4 DNA in 5 kb 5′ flanking regions of 2892 chicken RefSeq genes with annotated transcription start sites (TSS). In total, 4769 distinct putative G4 DNA motifs (G4M) were identified in 1880 (65%) genes. The pattern of distribution of the G4M showed a gradient along the 5′ flanking regions; from −5 to −4 kb, to −1 kb to the TSS, the frequency (number of G4M per kilobase) increased significantly from 0.192 to 0.768, and 62.56% of the G4M in the 1 kb upstream regions were located in the region −400 to the TSS, where a core promoter is always present. Thus, 38.24% of the analyzed genes contained at least one G4M in the 400 bp upstream region. Our findings support the hypothesis that G4M are involved in gene transcription.