LiveG4ID-seq identifies the chromatin G-quadruplex landscape in living cells

G-quadruplex (G4) structures exist in single-stranded DNA of chromatins and regulate genome function. However, the native chromatin G4 landscape in living cells has yet to be fully characterized. Herein, we fused BG4 antibody and GFP-tag to construct a live-cell G4 identifier (LiveG4ID). We first displayed its function as a high-specificity chromatin G4 probe in living cells by Dox-induced expression LiveG4ID in HEK293T cells and detecting its cellular localization, biocompatibility and G4-binding specificity. By coupling LiveG4ID with CUT&Tag technology, we established LiveG4ID-seq, a method for mapping native chromatin G4 landscape in living cells. LiveG4ID-seq can identify more chromatin G4 motifs than traditional CUT&Tag and ChIP-seq methods. Using LiveG4ID-seq, we profiled the dynamic landscape of chromatin G4 structures during the cell cycle. These data demonstrate the capacity of LiveG4ID-seq to profile a more accurate G4 landscape in living cells and promote future study on chromatin G4 structures. Overall design: The chromatin G-quadruplex landscape was detected by LiveG4ID-seq and CUT&Tag in HEK293T cells. The binding specificity of LiveG4ID to chromatin G4 was evaluated with CUT&Tag by detecting the competitive binding of G-quadruplex antibody in LiveG4ID expressing cells. Transcriptome of HEK293T cells with different LiveG4ID expression levels were measured by RNA-seq. LiveG4ID-seq was further tested in human HeLa cells and mouse N2a cells. LiveG4ID-seq was also used to profile the dynamic landscape of chromatin G-quadruplexes during the cell cycles.