{"doi":"10.1093/nargab/lqaf012","title":"Ribosomal DNA arrays are the most H-DNA rich element in the human genome","abstract":"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.","journal":"NAR Genomics and Bioinformatics","year":2025,"id":529991,"datarank":0.29188652235829704,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.0,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9302,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":464213,"name":"Candace S. Y. Chan","orcid":"0000-0001-9667-7996","position":1,"is_corresponding":false},{"id":1273797,"name":"Michail Patsakis","orcid":null,"position":2,"is_corresponding":false},{"id":1273798,"name":"Akshatha Nayak","orcid":null,"position":3,"is_corresponding":false},{"id":766618,"name":"Austin Montgomery","orcid":"0000-0003-0374-4390","position":4,"is_corresponding":false},{"id":1273314,"name":"Ioannis Mouratidis","orcid":"0000-0002-1025-8780","position":5,"is_corresponding":false},{"id":38299,"name":"Ilias Georgakopoulos-Soares","orcid":"0000-0003-3641-1488","position":6,"is_corresponding":false},{"id":1273313,"name":"Nikol Chantzi","orcid":"0009-0005-4947-0745","position":0,"is_corresponding":true}],"reference_count":63,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:51:01.235017Z","pmid":"40041207","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}