{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T19:00:13Z","timestamp":1772305213352,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,8,16]],"date-time":"2022-08-16T00:00:00Z","timestamp":1660608000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003151","name":"Fonds de recherche du Quebec Nature et technologies","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003151","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["NSERC RGPIN-155219-17"],"award-info":[{"award-number":["NSERC RGPIN-155219-17"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-05552-17"],"award-info":[{"award-number":["RGPIN-05552-17"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>G-quadruplexes (G4) are 3D structures that are found in both DNA and RNA. Interest in this structure has grown over the past few years due to both its implication in diverse biological mechanisms and its potential use as a therapeutic target, to name two examples. G4s in humans have been widely studied; however, the level of their study in other species remains relatively minimal. That said, progress in this field has resulted in the prediction of G4s structures in various species, ranging from bacteria to eukaryotes. These predictions were analysed in a previous study which revealed that G4s are present in all living kingdoms. To date, eleven different databases have grouped the various G4s depending on either their structures, on the proteins that might bind them, or on their location in the various genomes. However, none of these databases contains information on their location in the transcriptome of many of the implicated species. The GAIA database was designed so as to make this data available online in a user-friendly manner. Through its web interface, users can query GAIA to filter G4s, which, we hope, will help the research in this field. GAIA is available at: https:\/\/gaia.cobius.usherbrooke.ca<\/jats:p>","DOI":"10.1093\/nar\/gkac657","type":"journal-article","created":{"date-parts":[[2022,8,16]],"date-time":"2022-08-16T06:08:51Z","timestamp":1660630131000},"page":"D135-D140","source":"Crossref","is-referenced-by-count":6,"title":["GAIA: G-quadruplexes in alive creature database"],"prefix":"10.1093","volume":"51","author":[{"given":"Ana\u00efs","family":"Vannutelli","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Functional Genomics , Facult\u00e9 de m\u00e9decine et des sciences de la sant\u00e9, Universit\u00e9 de Sherbrooke, QC J1E 4K8, Canada"},{"name":"Department of Computer Science , Facult\u00e9 des sciences, Universit\u00e9 de Sherbrooke, QC J1K 2R1, Canada"}]},{"given":"Lauriane\u00a0Lucienne\u00a0Noele","family":"Schell","sequence":"additional","affiliation":[{"name":"Department of Computer Science , Facult\u00e9 des sciences, Universit\u00e9 de Sherbrooke, QC J1K 2R1, Canada"}]},{"given":"Jean-Pierre","family":"Perreault","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Functional Genomics , Facult\u00e9 de m\u00e9decine et des sciences de la sant\u00e9, Universit\u00e9 de Sherbrooke, QC J1E 4K8, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2040-4948","authenticated-orcid":false,"given":"A\u00efda","family":"Ouangraoua","sequence":"additional","affiliation":[{"name":"Department of Computer Science , Facult\u00e9 des sciences, Universit\u00e9 de Sherbrooke, QC J1K 2R1, Canada"}]}],"member":"286","published-online":{"date-parts":[[2022,8,16]]},"reference":[{"key":"2023010804324550900_B1","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/351331a0","article-title":"Tetramerization of an RNA oligonucleotide containing a GGGG sequence","volume":"351","author":"Kim","year":"1991","journal-title":"Nature"},{"key":"2023010804324550900_B2","doi-asserted-by":"crossref","first-page":"8406","DOI":"10.1021\/bi00151a003","article-title":"Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures","volume":"31","author":"Cheong","year":"1992","journal-title":"Biochemistry"},{"key":"2023010804324550900_B3","doi-asserted-by":"crossref","first-page":"21751","DOI":"10.1074\/jbc.M116.744839","article-title":"Irregular G-quadruplexes found in the untranslated regions of human mRNAs influence translation","volume":"291","author":"Bolduc","year":"2016","journal-title":"J. Biol. Chem."},{"key":"2023010804324550900_B4","doi-asserted-by":"crossref","first-page":"5017","DOI":"10.1021\/ja310251r","article-title":"Bulges in G-Quadruplexes: broadening the definition of G-Quadruplex-Forming sequences","volume":"135","author":"Mukundan","year":"2013","journal-title":"J. Am. Chem. Soc."},{"key":"2023010804324550900_B5","doi-asserted-by":"crossref","first-page":"4301","DOI":"10.1021\/ja807503g","article-title":"Structure of the human telomere in K+ solution: a stable basket-type G-Quadruplex with only two G-Tetrad layers","volume":"131","author":"Lim","year":"2009","journal-title":"J. Am. Chem. Soc."},{"key":"2023010804324550900_B6","doi-asserted-by":"crossref","first-page":"6239","DOI":"10.1093\/nar\/gkp630","article-title":"Sequence variant (CTAGGG)n in the human telomere favors a G-quadruplex structure containing a G.C.G.C tetrad","volume":"37","author":"Lim","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B7","doi-asserted-by":"crossref","first-page":"2908","DOI":"10.1093\/nar\/gki609","article-title":"Prevalence of quadruplexes in the human genome","volume":"33","author":"Huppert","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B8","doi-asserted-by":"crossref","first-page":"W676","DOI":"10.1093\/nar\/gkl253","article-title":"QGRS mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences","volume":"34","author":"Kikin","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B9","doi-asserted-by":"crossref","first-page":"7022","DOI":"10.1093\/nar\/gkq557","article-title":"5\u2032-UTR G-quadruplex structures acting as translational repressors","volume":"38","author":"Beaudoin","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B10","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1093\/nar\/gkt904","article-title":"New scoring system to identify RNA G-quadruplex folding","volume":"42","author":"Beaudoin","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B11","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.biochi.2018.06.002","article-title":"G4RNA screener web server: user focused interface for RNA G-quadruplex prediction","volume":"151","author":"Garant","year":"2018","journal-title":"Biochimie."},{"key":"2023010804324550900_B12","doi-asserted-by":"crossref","first-page":"1746","DOI":"10.1093\/nar\/gkw006","article-title":"Re-evaluation of G-quadruplex propensity with G4Hunter","volume":"44","author":"Bedrat","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B13","doi-asserted-by":"crossref","first-page":"767","DOI":"10.3390\/ijms21030767","article-title":"Characterization of a G-Quadruplex structure in Pre-mirna-1229 and in its alzheimer's disease-associated variant rs2291418: implications for miRNA-1229 maturation","volume":"21","author":"Imperatore","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"2023010804324550900_B14","doi-asserted-by":"crossref","first-page":"6442","DOI":"10.1093\/nar\/gkw432","article-title":"Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome","volume":"44","author":"De\u00a0Nicola","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B15","doi-asserted-by":"crossref","first-page":"lqaa035","DOI":"10.1093\/nargab\/lqaa035","article-title":"Where are G-quadruplexes located in the human transcriptome","volume":"2","author":"Vannutelli","year":"2020","journal-title":"NAR Genomics Bioinformatics"},{"key":"2023010804324550900_B16","doi-asserted-by":"crossref","first-page":"lqac010","DOI":"10.1093\/nargab\/lqac010","article-title":"G-Quadruplex occurrence and conservation: more than just a question of guanine-cytosine content","volume":"4","author":"Vannutelli","year":"2022","journal-title":"NAR Genomics Bioinformatics"},{"key":"2023010804324550900_B17","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1089\/cmb.2019.0010","article-title":"Plant-GQ: an integrative database of G-Quadruplex in plant","volume":"26","author":"Ge","year":"2019","journal-title":"J. Comput. Biol."},{"key":"2023010804324550900_B18","doi-asserted-by":"crossref","first-page":"S9","DOI":"10.1186\/1471-2164-10-S3-S9","article-title":"TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome","volume":"10","author":"Jenjaroenpun","year":"2009","journal-title":"BMC Genomics"},{"key":"2023010804324550900_B19","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkm982","article-title":"GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs","volume":"36","author":"Kikin","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B20","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1109\/69.50912","article-title":"The implementation of POSTGRES","volume":"2","author":"Stonebraker","year":"1990","journal-title":"IEEE Trans. Knowledge Data Eng."},{"key":"2023010804324550900_B21","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1101\/gr.073585.107","article-title":"EnsemblCompara genetrees: complete, duplication-aware phylogenetic trees in vertebrates","volume":"19","author":"Vilella","year":"2009","journal-title":"Genome Res."},{"key":"2023010804324550900_B22","doi-asserted-by":"crossref","first-page":"bav059","DOI":"10.1093\/database\/bav059","article-title":"G4RNA: an RNA G-quadruplex database","volume":"2015","author":"Garant","year":"2015","journal-title":"Database (Oxford)"},{"key":"2023010804324550900_B23","doi-asserted-by":"crossref","first-page":"aaf5371","DOI":"10.1126\/science.aaf5371","article-title":"RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria","volume":"353","author":"Guo","year":"2016","journal-title":"Science"},{"key":"2023010804324550900_B24","doi-asserted-by":"crossref","first-page":"38144","DOI":"10.1038\/srep38144","article-title":"G4IPDB: a database for G-quadruplex structure forming nucleic acid interacting proteins","volume":"6","author":"Mishra","year":"2016","journal-title":"Scientific Rep."},{"key":"2023010804324550900_B25","doi-asserted-by":"crossref","first-page":"E1711","DOI":"10.3390\/molecules24091711","article-title":"The presence and localization of G-Quadruplex forming sequences in the domain of bacteria","volume":"24","author":"Bartas","year":"2019","journal-title":"Molecules"},{"key":"2023010804324550900_B26","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.3390\/biom10091349","article-title":"G-Quadruplexes in the Archaea domain","volume":"10","author":"Br\u00e1zda","year":"2020","journal-title":"Biomolecules"},{"key":"2023010804324550900_B27","doi-asserted-by":"crossref","first-page":"3862","DOI":"10.1093\/nar\/gkz179","article-title":"Whole genome experimental maps of DNA G-quadruplexes in multiple species(2019)","volume":"47","author":"Marsico","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B28","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1038\/s42003-020-01643-4","article-title":"Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution","volume":"4","author":"Wu","year":"2021","journal-title":"Commun. Biol."},{"key":"2023010804324550900_B29","doi-asserted-by":"crossref","first-page":"6098","DOI":"10.1093\/nar\/gkz463","article-title":"Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species","volume":"47","author":"Puig\u00a0Lombardi","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B30","doi-asserted-by":"crossref","first-page":"15679","DOI":"10.1038\/s41598-018-33944-4","article-title":"Case studies on potential G-quadruplex-forming sequences from the bacterial orders deinococcales and thermales derived from a survey of published genomes","volume":"8","author":"Ding","year":"2018","journal-title":"Sci. Rep."},{"key":"2023010804324550900_B31","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.biochi.2021.01.017","article-title":"G-quadruplex motifs are functionally conserved in cis-regulatory regions of pathogenic bacteria: an in-silico evaluation","volume":"184","author":"Dey","year":"2021","journal-title":"Biochimie"},{"key":"2023010804324550900_B32","doi-asserted-by":"crossref","first-page":"e1006675","DOI":"10.1371\/journal.pcbi.1006675","article-title":"G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide","volume":"14","author":"Lavezzo","year":"2018","journal-title":"PLoS Comput. Biol."},{"key":"2023010804324550900_B33","doi-asserted-by":"crossref","first-page":"2333","DOI":"10.1093\/nar\/gkab039","article-title":"DNA G-quadruplexes for native mass spectrometry in potassium: a database of validated structures in electrospray-compatible conditions","volume":"49","author":"Ghosh","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B34","doi-asserted-by":"crossref","first-page":"D381","DOI":"10.1093\/nar\/gkm781","article-title":"QuadBase: genome-wide database of G4 DNA\u2013occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes","volume":"36","author":"Yadav","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B35","doi-asserted-by":"crossref","first-page":"W277","DOI":"10.1093\/nar\/gkw425","article-title":"QuadBase2: web server for multiplexed guanine quadruplex mining and visualization","volume":"44","author":"Dhapola","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B36","doi-asserted-by":"crossref","first-page":"D372","DOI":"10.1093\/nar\/gkm787","article-title":"Greglist: a database listing potential G-quadruplex regulated genes","volume":"36","author":"Zhang","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B37","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1080\/15476286.2021.1989200","article-title":"RR3DD: an RNA global structure-based RNA three-dimensional structural classification database(2021)","volume":"18","author":"Hong","year":"2021","journal-title":"RNA Biol."},{"key":"2023010804324550900_B38","doi-asserted-by":"crossref","first-page":"D1115","DOI":"10.1093\/nar\/gks1101","article-title":"G4LDB: a database for discovering and studying G-quadruplex ligands","volume":"41","author":"Li","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023010804324550900_B39","doi-asserted-by":"crossref","first-page":"D150","DOI":"10.1093\/nar\/gkab952","article-title":"G4LDB 2.2: a database for discovering and studying G-quadruplex and i-Motif ligands(2022)","volume":"50","author":"Wang","year":"2021","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D135\/48441494\/gkac657.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D135\/48441494\/gkac657.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T04:36:58Z","timestamp":1673152618000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D135\/6667654"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8,16]]},"references-count":39,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2022,8,16]]},"published-print":{"date-parts":[[2023,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac657","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,6]]},"published":{"date-parts":[[2022,8,16]]}}}