Chantzi Nikol, Liew Shiau Wei, Wijaya Aurell, Chan Candace, Mouratidis Ioannis, Santana Amaral Emilyane de Oliveira, Uzun Yasin, Hemberg Martin, Vasquez Karen M, Kwok Chun Kit, Georgakopoulos-Soares Ilias
Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong Hong Kong SAR 999077, China.
bioRxiv. 2025 Jun 25:2025.06.17.660256. doi: 10.1101/2025.06.17.660256.
G-quadruplexes (G4s) are alternative DNA structures with diverse biological roles, but their examination in highly repetitive parts of the human genome has been hindered by the lack of reliable sequencing technologies. Recent long-read based genome assemblies have enabled their characterization in previously inaccessible parts of the human genome. Here, we examine the topography and genomic instability of potential G4-forming sequences in the gap-less, reference human genome assembly and in 88 haplotypes of diverse ancestry. We report that G4s are highly enriched in specific repetitive regions, including in certain centromeric and pericentromeric repeat types, and in ribosomal DNA arrays, and experimentally validate the most prevalent G4s detected. G4s tend to have lower methylation than expected throughout the human genome and are genomically unstable, showing an excess of all mutation types, including substitutions, insertions and deletions and most prominently structural variants. Finally, we show that G4s are consistently enriched at PRDM9 binding sites, a protein involved in meiotic recombination. Together, our findings establish G4s as dynamic and functionally significant elements of the human genome and highlight new avenues for investigating their contributions to human disease and evolution.
G-四链体（G4s）是具有多种生物学作用的替代性DNA结构，但由于缺乏可靠的测序技术，对其在人类基因组高度重复部分的研究受到了阻碍。最近基于长读长的基因组组装使得在人类基因组以前无法进入的部分对其进行表征成为可能。在这里，我们研究了无间隙参考人类基因组组装以及88种不同祖先单倍型中潜在G4形成序列的拓扑结构和基因组不稳定性。我们报告称，G4s在特定的重复区域高度富集，包括某些着丝粒和近着丝粒重复类型以及核糖体DNA阵列，并通过实验验证了检测到的最普遍的G4s。在整个人类基因组中，G4s的甲基化程度往往低于预期，并且在基因组上不稳定，表现出所有突变类型的过量，包括替换、插入和缺失，最显著的是结构变异。最后，我们表明G4s在PRDM9结合位点持续富集，PRDM9是一种参与减数分裂重组的蛋白质。总之，我们的研究结果将G4s确立为人类基因组中动态且具有功能重要性的元件，并突出了研究它们对人类疾病和进化贡献的新途径。
