G-quadruplexes (G4s) are non-canonical four-stranded DNA structures and emerging as key regulators in a variety of cellular processes. Sporadic cases have reported their positive or repressive effect on gene expression, while exact roles of G4s remain to be studied genome-wide. Meanwhile, G4s could also trigger genome instability (copy number variations, single-nucleotide variations) and contribute to several diseases and cancers. Double-edged sword of G4s in gene regulation and genome evolution make themselves face different selection pressures but their evolutionary analysis is still in its infancy. Here, we conducted a comprehensive analysis of G4 genomic pattern, evolution, and function in fly genome. We found an enrichment of G4s in genic regions across twenty drosophila species. Drosophila-specific overrepresentation of G4s on the X chromosome, and longer length and higher structural stability of X-linked ones suggested that they were under selection and might have function. Integrating large-scale transcriptome data and G4-target-ligand experiment, we found that G4 stabilization mainly reduced gene expression level in a ligand-concentration-dependent manner. Directly quantifying the expression abundance of G4s in both sexes revealed paucity of G4s with male-biased expression on the X chromosome, suggesting G4 might suppress dosage compensation. By adopting quantitative G4 ChIP–seq (qG4-ChIP–seq) data, we observed the paucity of G4s at high affinity sites (HAS) and H4 lysine 16 acetylation (H4K16ac) regions but the enrichment at boundary of these regions and proposed that structurally stable G4s function as insulators in dosage compensation.
 

Non-B DNA,G-quadruplex,Dosage compensation