The Role of BAZ2-dependent Chromatin Remodeling in Suppressing G4 DNA Structures and Associated Genomic Instability [INDUCE-seq]

DNA G-quadruplexes (G4s) are secondary structures with significant roles in regulating genome function and stability. Dysregulation of the dynamic formation of G4s is linked to genomic instability and disease, but the underlying mechanisms are not fully understood. In this study, we conducted a screen of chromatin-modifying enzymes and identified nine potential inhibitors of G4 formation, including seven that were not previously characterized. Among these, we highlight the role of BAZ2 chromatin remodelers as key suppressors of G4 DNA and G4-related genome instability. Depletion of BAZ2 subunits led to increased G4 formation, especially at transcriptional regulatory elements. BAZ2B was found to associate with G4 loci, suggesting that it plays a direct role in suppressing G4s. While BAZ2-deficient cells exhibited modest genomic instability, treatment with the G4-stabilizing ligand BRACO19 exacerbated double-strand breaks (DSBs), highlighting its utility as a tool to study G4-dependent genome instability. DSB profiling using INDUCE-seq uncovered distinct breakage patterns around G4s, further underscoring the impact of G4s on genome integrity. Notably, we found that within G4s, G repeats were more susceptible to DSBs than loops. These results establish BAZ2 chromatin remodeling complexes as direct regulators of G4 dynamics and provide new insights into G4-dependent genome instability. INDUCE-seq performed on A549 cells following different siRNA treatments and BRACO19 treatment.

DNA G-四链体（DNA G-quadruplexes, G4s）是一类在调控基因组功能与稳定性中发挥关键作用的二级结构。G4动态形成过程的失调与基因组不稳定性及疾病密切相关，但其潜在分子机制尚未完全阐明。本研究针对染色质修饰酶开展筛选，鉴定出9种潜在的G4形成抑制剂，其中7种此前未被报道过。其中，我们重点阐释了BAZ2家族染色质重塑因子作为G4 DNA及G4相关基因组不稳定性关键抑制因子的作用。BAZ2亚基的敲低会导致G4形成水平升高，尤其是在转录调控元件区域。研究发现BAZ2B可与G4位点结合，提示其在抑制G4形成中发挥直接作用。尽管BAZ2缺陷细胞仅表现出轻度的基因组不稳定性，但经G4稳定配体BRACO19处理后，双链断裂（double-strand breaks, DSBs）水平显著升高，这表明BRACO19可作为研究G4依赖型基因组不稳定性的有效工具。通过INDUCE-seq进行的双链断裂谱分析揭示了G4周围独特的断裂模式，进一步证实了G4对基因组完整性的影响。值得注意的是，我们发现在G4结构内部，G重复序列相较于环区更易发生双链断裂。上述研究结果确定BAZ2染色质重塑复合物为G4动态平衡的直接调控因子，为理解G4依赖型基因组不稳定性提供了新的研究视角。本数据集为经不同小干扰RNA（small interfering RNA, siRNA）处理及BRACO19处理后的A549细胞的INDUCE-seq实验数据。