LiveG4ID‐Seq for Profiling the Dynamic Landscape of Chromatin G‐Quadruplexes During Cell Cycle in Living Cells

Abstract

AbstractG‐quadruplex (G4) structures exist in the single‐stranded DNA of chromatin and regulate genome function. However, the native chromatin G4 landscape in living cells has yet to be fully characterized. Herein, a genetic‐encoded live‐cell G4 identifier probe (LiveG4ID) is constructed and its cellular localization, biocompatibility, and G4‐binding specificity is evaluated. By coupling LiveG4ID with cleavage under targets and tagmentation (CUT&Tag), LiveG4ID‐seq, a method for mapping native chromatin G4 landscape in living cells with high accuracy is established. Compared to the conventional G4 CUT&Tag method, LiveG4ID‐seq can identify more chromatin G4 signals and have a higher ratio of true positive signals. Using LiveG4ID‐seq, the dynamic landscape of chromatin G4 structures during the cell cycle is profiled. It is discovered that chromatin G4 structures are prevalent in the promoter regions of cell cycle‐specific genes, even in the early M phase when the chromatin is condensed. These data demonstrate the capacity of LiveG4ID‐seq to profile a more accurate G4 landscape in living cells and promote future studies on chromatin G4 structures.