Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry

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.