Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
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.
Authors
- Guliang Wang
- Karen M. Vásquez (ORCID: https://orcid.org/0000-0002-6958-5073)
- Akshatha Nayak (ORCID: https://orcid.org/0000-0002-0536-2751)
- Chun Kit Kwok (ORCID: https://orcid.org/0000-0001-9175-8543)
- Austin Montgomery (ORCID: https://orcid.org/0000-0003-0374-4390)
- Eleni Aplakidou (ORCID: https://orcid.org/0009-0002-0737-4817)
- Fotis A. Baltoumas (ORCID: https://orcid.org/0000-0002-2870-2931)
- Wilfried M. Guiblet (ORCID: https://orcid.org/0000-0001-6319-3418)
- Ilias Georgakopoulos‐Soares (ORCID: https://orcid.org/0000-0003-3641-1488)
- Apostolos Zaravinos (ORCID: https://orcid.org/0000-0003-4625-5562)
- Nikol Chantzi (ORCID: https://orcid.org/0009-0005-4947-0745)
- Saiful Arefeen Sazed (ORCID: https://orcid.org/0000-0002-0919-4652)
- Panagiotis Karmiris-Obratański (ORCID: https://orcid.org/0000-0002-2507-0764)
- Camille Moeckel (ORCID: https://orcid.org/0009-0001-9808-4841)
- Georgios A. Pavlopoulos (ORCID: https://orcid.org/0000-0002-4577-8276)
- Ioannis Mouratidis (ORCID: https://orcid.org/0000-0002-1025-8780)
- Michail Patsakis
- Jesslyn Elvaretta Galuh
- Shiau Wei Liew
Institutions
- Austin College (US)
- Pennsylvania State University (US)
- University of Crete (GR)
- City University of Hong Kong (HK)
- European University Cyprus (CY)
- City University of Hong Kong, Shenzhen Research Institute (CN)
- Institute of Advanced Manufacturing Technology (PL)
- Frederick National Laboratory for Cancer Research (US)
- Alexander Fleming Biomedical Sciences Research Center (GR)
- AGH University of Krakow (PL)
- Penn State Milton S. Hershey Medical Center (US)
- The University of Texas at Austin (US)
Publication Details
- Journal
- Genome Research
- Published
- 2025-08-26
- DOI
- https://doi.org/10.1101/gr.279790.124
- Citations
- 2
- Primary Topic
- DNA and Nucleic Acid Chemistry
- Type
- article
Funders
- University of Pennsylvania
- City University of Hong Kong
- Pennsylvania State University
- Croucher Foundation
- National Natural Science Foundation of China
- Alexander S. Onassis Public Benefit Foundation
- Hellenic Foundation for Research and Innovation
- National Institutes of Health
- Huck Institutes of the Life Sciences
- Penn State College of Medicine
- National Cancer Institute
- National Institute of General Medical Sciences