TY  - JOUR
A1  - Chantzi, Nikol
A1  - Nayak, Akshatha
A1  - Baltoumas, Fotis A.
A1  - Aplakidou, Eleni
A1  - Liew, Shiau Wei
A1  - Galuh, Jesslyn Elvaretta
A1  - Patsakis, Michail
A1  - Montgomery, Austin
A1  - Moeckel, Camille
A1  - Mouratidis, Ioannis
A1  - Sazed, Saiful Arefeen
A1  - Guiblet, Wilfried
A1  - Karmiris-Obratański, Panagiotis
A1  - Wang, Guliang
A1  - Zaravinos, Apostolos
A1  - Vasquez, Karen M.
A1  - Kwok, Chun Kit
A1  - Pavlopoulos, Georgios A.
A1  - Georgakopoulos-Soares, Ilias
T1  - Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
Y1  - 2025/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 2578 
EP  - 2600 
DO  - 10.1101/gr.279790.124 
VL  - 35 
IS  - 11 
UR  - http://genome.cshlp.org/content/35/11/2578.abstract 
N2  - 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. 
ER  -