{"doi":"10.1101/2024.07.09.602008","title":"Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life","abstract":"G-quadruplex DNA structures exhibit a profound influence on essential biological processes, including transcription, replication, telomere maintenance, and genomic stability. These structures have demonstrably shaped organismal evolution. However, a comprehensive, organism-wide G-quadruplex map encompassing the diversity of life has remained elusive. Here, we introduce Quadrupia, the most extensive and well-characterized G-quadruplex database to date, facilitating the exploration of G-quadruplex structures across the evolutionary spectrum. Quadrupia has identified G-quadruplex sequences in 108,449 reference genomes, with a total of 140,181,277 G-quadruplexes. The database also hosts a collection of 319,784 G-quadruplex clusters of 20 or more members, annotated by taxonomic distributions, multiple sequence alignments, profile Hidden Markov Models and cross-references to G-quadruplex 3D structures. Examination of G-quadruplexes across functional genomic elements in different taxa indicates preferential orientation and positioning, with significant differences between individual taxonomic groups. For example, we find that G-quadruplexes in bacteria with a single replication origin display profound preference for the leading orientation. Finally, we experimentally validate the most frequently observed G-quadruplexes using CD-spectroscopy, UV melting, and fluorescent-based approaches. Quadrupia is publicly available through https://www.pavlopoulos-lab.org/quadrupia.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":491384,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8583,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1273798,"name":"Akshatha Nayak","orcid":null,"position":1,"is_corresponding":false},{"id":1016100,"name":"Fotis A. Baltoumas","orcid":"0000-0002-2870-2931","position":2,"is_corresponding":false},{"id":1336984,"name":"Eleni Aplakidou","orcid":"0009-0002-0737-4817","position":3,"is_corresponding":false},{"id":1336985,"name":"Shiau Wei Liew","orcid":"0000-0002-2424-9084","position":4,"is_corresponding":false},{"id":1337351,"name":"Jesslyn Elvaretta Galuh","orcid":null,"position":5,"is_corresponding":false},{"id":1273797,"name":"Michail Patsakis","orcid":null,"position":6,"is_corresponding":false},{"id":1112734,"name":"Camille Moeckel","orcid":"0009-0001-9808-4841","position":7,"is_corresponding":false},{"id":1273314,"name":"Ioannis Mouratidis","orcid":"0000-0002-1025-8780","position":8,"is_corresponding":false},{"id":827857,"name":"Saiful Arefeen Sazed","orcid":"0000-0002-0919-4652","position":9,"is_corresponding":false},{"id":632274,"name":"Wilfried M. Guiblet","orcid":"0000-0001-6319-3418","position":10,"is_corresponding":false},{"id":766618,"name":"Austin Montgomery","orcid":"0000-0003-0374-4390","position":11,"is_corresponding":false},{"id":1336986,"name":"Panagiotis Karmiris-Obratański","orcid":"0000-0002-2507-0764","position":12,"is_corresponding":false},{"id":1337352,"name":"Wang Guliang","orcid":null,"position":13,"is_corresponding":false},{"id":1336987,"name":"Apostolos Zaravinos","orcid":"0000-0003-4625-5562","position":14,"is_corresponding":false},{"id":294124,"name":"Karen M. Vásquez","orcid":"0000-0002-6958-5073","position":15,"is_corresponding":false},{"id":112352,"name":"Chun Kit Kwok","orcid":"0000-0001-9175-8543","position":16,"is_corresponding":false},{"id":328498,"name":"Georgios A. Pavlopoulos","orcid":"0000-0002-4577-8276","position":17,"is_corresponding":false},{"id":38299,"name":"Ilias Georgakopoulos-Soares","orcid":"0000-0003-3641-1488","position":18,"is_corresponding":false},{"id":1273313,"name":"Nikol Chantzi","orcid":"0009-0005-4947-0745","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:08:45.247225Z","pmid":null,"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":[]}