GAIA: G-quadruplexes in alive creature database

Abstract

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

Toward a Better Understanding of G4 Evolution in the 3 Living Kingdoms

“…The primary explanation for these results is that only 26 rG4s were predicted in Scer . 70 With such a small number, the proportion range varied greatly, from −28% to 44%. Importantly, these results do not appear to be the result of poor random generation, as demonstrated in Supplemental Figures 9 and 10 .…”

“…Hence, the number of prG4s of each species was retrieved from the GAIA database ( https://gaia.cobius.usherbrooke.ca/ ) and was randomly relocated in the transcripts of the species, creating a “fake prG4” dataset. 70 Then, the fake prG4s were randomly selected, and their locations were randomly allocated throughout the transcriptome. The random data set was generated 10 times, and Figure 2C provides a simplified illustration of the concept.…”

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

“…G4Atlas ( 5 ) focuses on experimentally determined RNA G-quadruplexes (rG4s) across transcriptomes, determined by a variety of experimental methods, and accompanied by their classification into canonical and other types. QUADRAtlas ( 6 ) similarly focuses on rG4s, covering both experimental and predicted structures and including information on rG4-binding proteins, while GAIA ( 7 ) surveys predicted quadruplexes in both genomes and transcriptomes across all three kingdoms. RNA modifications are also addressed by three new databases.…”

Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life

“…To date, there are a few databases available incorporating the identification of potential G4 DNA-forming sequences in different organisms; however, all available datasets cover a small number of species. Zhong et al (2023) constructed G4Bank, a G4 database containing six million G4s across thirteen species (54), while GAIA currently harbors G4s for 61 different organismal genomes (55). Another database named G4Atlas contains only 238 experimental G4s from 10 species (56).…”