Landscape and mutational dynamics of G-quadruplexes across the complete human genome

Abstract Background 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. Results 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 and are genomically unstable, showing an excess of insertions and deletions. Finally, we show that G4-forming motifs are consistently enriched at meiotic DSB hotspots across individuals with different PRDM9 genotypes. Conclusions 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.