Native G-quadruplexes Stabilization Impairs Transcription Initiation

G-quadruplexes (G4s) are noncanonical DNA secondary structures formed through the self-association of guanines. They are distributed genome-widely and participate in multiple biological processes including gene transcription, and quadruplex-targeted ligands serve as potential therapeutic agents for DNA-targeted therapies. However, the roles of G-quadruplexes in transcriptional regulation remains elusive. Here, we establish a sensitive G4-CUT&Tag method for genome-wide profiling of native G-quadruplexes with high resolution and specificity. We find that native G-quadruplex signals are cell-type specific and are associated with transcriptional regulatory elements with active epigenetic modifications. Promoter-proximal RNA polymerase II pausing promotes native G-quadruplex formation, oppositely, G-quadruplex stabilization by quadruplex-targeted ligands globally reduces RNA polymerase II occupancy at gene promoters as well as nascent RNA synthesis. Moreover, G-quadruplex stabilization modulates chromatin states and impedes transcription initiation via inhibiting the loading of general transcription factors to promoters.Together, these studies reveal a reciprocal regulation between native G-quadruplex dynamics and gene transcription in the genome, which will deepen our knowledge of G-quadruplex biology towards considering therapeutically targeting G-quadruplexes in human diseases. In this study, we firstly reported a native G-quadruplex profiling method, G4-CUT&Tag, by combining the G-quadruplex specific BG4 antibody with the sensitive CUT&Tag technique (Kaya-Okur et al. 2019; Wang et al. 2019).our studies provided a more effective strategy for comprehensively profiling native G-quadruplexes in the human genome and demonstrated that disruption of G-quadruplex dynamics could cause a rapid and genome-wide alteration in chromatin states and impairment of transcription initiation.These studies revealed the underlying mechanisms for the intertwinement of RNA polymeraseII, chromatin states, and native G-quadruplexes, providing a paradigm for functional studies of the noncanonical DNA secondary structures and advancing our understanding of quadruplex-targeting therapies.