Dominant and Genome-Wide Formation of DNA:RNA Hybrid G-Quadruplexes in Living Yeast Cells

Abstract

Four-stranded G-quadruplex (G4) structures formed by guanine-rich nucleic acids play a role in many essential physiological processes. To date, studies have focused almost exclusively on monomeric intramolecular G4s with three or more G-tetrads. Based on the analysis of Okazaki fragment syntheses and G4 probing, we report here a massive genome-wide formation of a hybrid type of G4s (hG4s), composed of G-tracts from both DNA and RNA, in the genome of live yeast cells. We found that hG4s can form with as few as one G-tract in DNA, increasing the total number of G4 sites from 38 to 127841. Furthermore, we also effectively detected hG4s of two G-tetrads, bringing the total number of G4 sites to a final of 587694, an increase of >15,000-fold. We even found that hG4s dominate in DNAs capable of forming the canonical intramolecular DNA G4s by themselves. Taken together, our results reveal a previously unrecognized rule governing G4 formation in eukaryotic genomes that makes hG4s the overwhelmingly dominant G4 species. They are present in all genes, with greater structural diversity and a wider dynamic range. More importantly, the involvement of RNA gives hG4s the ability to function in a transcription-dependent manner. These new findings thus emphasize a complete renewal and expansion of our current perspective on the existence and functional role of G4s in eukaryotic cells.

G-Quadruplexes in Human Telomere: Structures, Properties, and Applications

“…Telomere RNA plays a crucial role in the “capping” of telomeres through the formation of telomeric DNA:RNA G-quadruplexes [ 20 , 124 , 125 , 126 ]. This argument is supported by insights from a single-molecule FRET study examining the folding patterns of telomere DNA in conjunction with telomere RNA.…”

“…Their formation is dependent on the negative supercoiling generated by RNA polymerases. Genome-wide occurrence of DNA:RNA hybrid G-quadruplexes has been also indicated [ 126 ]. The biological roles of DNA:RNA hybrid G-quadruplexes are gradually getting clearer.…”