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| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
| Published: |
Genome research
2025
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| Subjects: | |
| Online Access: | https://pubmed.ncbi.nlm.nih.gov/40858360/ |
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| author | Chantzi, Nikol Nayak, Akshatha Baltoumas, Fotis A Aplakidou, Eleni Liew, Shiau Wei Galuh, Jesslyn Elvaretta Patsakis, Michail Montgomery, Austin Moeckel, Camille Mouratidis, Ioannis Sazed, Saiful Arefeen Guiblet, Wilfried Karmiris-Obratański, Panagiotis Wang, Guliang Zaravinos, Apostolos Vasquez, Karen M Kwok, Chun Kit Pavlopoulos, Georgios A Georgakopoulos-Soares, Ilias |
| author_facet | Chantzi, Nikol Nayak, Akshatha Baltoumas, Fotis A Aplakidou, Eleni Liew, Shiau Wei Galuh, Jesslyn Elvaretta Patsakis, Michail Montgomery, Austin Moeckel, Camille Mouratidis, Ioannis Sazed, Saiful Arefeen Guiblet, Wilfried Karmiris-Obratański, Panagiotis Wang, Guliang Zaravinos, Apostolos Vasquez, Karen M Kwok, Chun Kit Pavlopoulos, Georgios A Georgakopoulos-Soares, Ilias Chantzi, Nikol Nayak, Akshatha Baltoumas, Fotis A Aplakidou, Eleni Liew, Shiau Wei Galuh, Jesslyn Elvaretta Patsakis, Michail Montgomery, Austin Moeckel, Camille Mouratidis, Ioannis Sazed, Saiful Arefeen Guiblet, Wilfried Karmiris-Obratański, Panagiotis Wang, Guliang Zaravinos, Apostolos Vasquez, Karen M Kwok, Chun Kit Pavlopoulos, Georgios A Georgakopoulos-Soares, Ilias |
| collection | PubMed - marine biology |
| contents | Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life. Chantzi, Nikol Nayak, Akshatha Baltoumas, Fotis A Aplakidou, Eleni Liew, Shiau Wei Galuh, Jesslyn Elvaretta Patsakis, Michail Montgomery, Austin Moeckel, Camille Mouratidis, Ioannis Sazed, Saiful Arefeen Guiblet, Wilfried Karmiris-Obratański, Panagiotis Wang, Guliang Zaravinos, Apostolos Vasquez, Karen M Kwok, Chun Kit Pavlopoulos, Georgios A Georgakopoulos-Soares, Ilias G-Quadruplexes Evolution, Molecular Humans Genome 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. |
| format | Artículo científico |
| id | pubmed_40858360 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Genome research |
| record_format | pubmed |
| spellingShingle | Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life. Chantzi, Nikol Nayak, Akshatha Baltoumas, Fotis A Aplakidou, Eleni Liew, Shiau Wei Galuh, Jesslyn Elvaretta Patsakis, Michail Montgomery, Austin Moeckel, Camille Mouratidis, Ioannis Sazed, Saiful Arefeen Guiblet, Wilfried Karmiris-Obratański, Panagiotis Wang, Guliang Zaravinos, Apostolos Vasquez, Karen M Kwok, Chun Kit Pavlopoulos, Georgios A Georgakopoulos-Soares, Ilias G-Quadruplexes Evolution, Molecular Humans Genome Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life. Chantzi, Nikol Nayak, Akshatha Baltoumas, Fotis A Aplakidou, Eleni Liew, Shiau Wei Galuh, Jesslyn Elvaretta Patsakis, Michail Montgomery, Austin Moeckel, Camille Mouratidis, Ioannis Sazed, Saiful Arefeen Guiblet, Wilfried Karmiris-Obratański, Panagiotis Wang, Guliang Zaravinos, Apostolos Vasquez, Karen M Kwok, Chun Kit Pavlopoulos, Georgios A Georgakopoulos-Soares, Ilias G-Quadruplexes Evolution, Molecular Humans Genome 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. |
| title | Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life. |
| topic | G-Quadruplexes Evolution, Molecular Humans Genome |
| url | https://pubmed.ncbi.nlm.nih.gov/40858360/ |