Ribosomal DNA arrays are the most H-DNA rich element in the human genome.

Repetitive DNA sequences can form noncanonical structures such as H-DNA. The new telomere-to-telomere genome assembly for the human genome has eliminated gaps, enabling examination of highly repetitive regions including centromeric and pericentromeric repeats and ribosomal DNA arrays. We find that H-DNA appears once every 25 000 base pairs in the human genome. Its distribution is highly inhomogeneous with H-DNA motif hotspots being detectable in acrocentric chromosomes. Ribosomal DNA arrays are the genomic element with a 40.94-fold H-DNA enrichment. Across acrocentric chromosomes, we report that 54.82% of H-DNA motifs found in these chromosomes are in rDNA array loci. We discover that binding sites for the PRDM9-B allele, a variant of the PRDM9 protein, are enriched for H-DNA motifs. We further investigate these findings through an analysis of PRDM-9 ChIP-seq data across various PRDM-9 alleles, observing an enrichment of H-DNA motifs in the binding sites of A-like alleles (including A, B, and N alleles), but not C-like alleles (including C and L4 alleles). The enrichment of H-DNA motifs at ribosomal DNA arrays is consistent in nonhuman great ape genomes. We conclude that ribosomal DNA arrays are the most enriched genomic loci for H-DNA sequences in human and other great ape genomes.