Genome-wide mapping of native G-loops in living cells

G-quadruplex (G4) are four-stranded DNA secondary structures that form in guanine-rich regions of the genome, which can enhance or repress gene expression. An R-loop is a special triple-stranded nucleic acid structure formed when nascent RNA invades double-stranded DNA (dsDNA) during transcription. G-loops are constituted by one or more DNA G4 on one strand and a stable RNA/DNA hybrid on the other. We developed the HepG4-seq for mapping the native G4s and the HBD-seq for mapping native R-loops. We combined the HepG4-seq and HBD-seq to profile the genomic native G-loops, which are regions co-occupied by both native G4s and R-loops, in both HEK293 cells and mouse embryonic stem cells (mESCs). Overall design: Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping G4 and R-loop in HEK293 and mESC cells.