Dominant Formation of DNA:RNA Hybrid G-Quadruplexes in the Genomes of Living Human and Mouse Cells

Abstract

Guanine-rich nucleic acids can form four-stranded structures known as G-quadruplexes (G4s), which play critical roles in essential cellular activities. Putative G-quadruplex-forming sequences (PQSs) are abundant in the genomes of animal cells. To date, research on G4s has focused primarily on intramolecular G4s formed by four contiguous G-tracts from the same nucleic acid strand. However, our recent study indicates that a hybrid type of G4s, DNA:RNA hybrid G4s (hG4s), comprising G-tracts from both DNA and RNA, is, in fact, the most abundant G4 species found in the genomes of living yeast cells. Here, we demonstrate that hG4s also readily form and predominate in the genomes of living human and mouse cells, with an abundance several orders of magnitude greater than that of intramolecular DNA G4s (dG4s). Furthermore, each individual G-tract in a PQS tends to form an hG4 independent of adjacent G-tracts. This independence of DNA G-tracts is maintained even in PQSs containing four G-tracts, despite their potential to form intramolecular DNA G4s only by themselves. Collectively, our studies demonstrate that hG4s are the predominant physiological G4 structures in the genomes of eukaryotic organisms. Given that hG4s differ significantly from intramolecular dG4s in terms of structural form, formation mechanism, abundance, and association with transcription, there is a clear need for a comprehensive revision of our current understanding of genomic G4s and their functional roles. We hypothesize that hG4 formation may serve as a global sensing mechanism to monitor RNA levels in cells to maintain transcriptional homeostasis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/630557v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@6a9f0org.highwire.dtl.DTLVardef@17f02f8org.highwire.dtl.DTLVardef@19bfd10org.highwire.dtl.DTLVardef@34f4b_HPS_FORMAT_FIGEXP M_FIG C_FIG