G-quadruplexes (G4s) are noncanonical DNA secondary structures formed through the self-association of guanines, and G4s are distributed widely across the genome. G4 participates in multiple biological processes including gene transcription, and G4-targeted ligands serve as potential therapeutic agents for DNA-targeted therapies. However, genome-wide studies of the exact roles of G4s in transcriptional regulation are still lacking. Here, we establish a sensitive G4-CUT&Tag method for genome-wide profiling of native G4s with high resolution and specificity. We find that native G4 signals are cell type–specific and are associated with transcriptional regulatory elements carrying active epigenetic modifications. Drug-induced promoter-proximal RNA polymerase II pausing promotes nearby G4 formation. In contrast, G4 stabilization by G4-targeted ligands globally reduces RNA polymerase II occupancy at gene promoters as well as nascent RNA synthesis. Moreover, ligand-induced G4 stabilization modulates chromatin states and impedes transcription initiation via inhibition of general transcription factors loading to promoters. Together, our study reveals a reciprocal genome-wide regulation between native G4 dynamics and gene transcription, which will deepen our understanding of G4 biology toward therapeutically targeting G4s in human diseases.

中文翻译：

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配体诱导的天然 G-四链体稳定会损害转录起始

G-四链体 (G4s) 是通过鸟嘌呤的自缔合形成的非经典 DNA 二级结构，G4s 在基因组中广泛分布。G4 参与多种生物过程，包括基因转录，而 G4 靶向配体可作为 DNA 靶向治疗的潜在治疗剂。然而，仍然缺乏对 G4 在转录调控中的确切作用的全基因组研究。在这里，我们建立了一种敏感的 G4-CUT&Tag 方法，用于对具有高分辨率和特异性的天然 G4 进行全基因组分析。我们发现天然 G4 信号是细胞类型特异性的，并且与携带主动表观遗传修饰的转录调控元件相关。药物诱导的启动子近端 RNA 聚合酶 II 暂停促进附近 G4 的形成。相比之下，G4 靶向配体的 G4 稳定性在全球范围内减少了 RNA 聚合酶 II 在基因启动子处的占有率以及新生 RNA 合成。此外，配体诱导的 G4 稳定通过抑制加载到启动子的一般转录因子来调节染色质状态并阻碍转录起始。总之，我们的研究揭示了天然 G4 动力学和基因转录之间的互惠全基因组调控，这将加深我们对 G4 生物学的理解，以治疗靶向人类疾病中的 G4。