G4Atlas: a comprehensive transcriptome-wide G-quadruplex database

Abstract

RNA G-quadruplex (rG4) is a vital RNA tertiary structure motif that involves the base pairs on both Hoogsteen and Watson-Crick faces of guanines. rG4 is of great importance in the post-transcriptional regulation of gene expression. Experimental technologies have advanced to identify in vitro and in vivo rG4s across diverse transcriptomes. Building on these recent advances, here we present G4Atlas, the first transcriptome-wide G-quadruplex database, in which we have collated, classified, and visualized transcriptome rG4 experimental data, generated from rG4-seq, chemical profiling and ligand-binding methods. Our comprehensive database includes transcriptome-wide rG4s generated from 82 experimental treatments and 238 samples across ten species. In addition, we have also included RNA secondary structure prediction information across both experimentally identified and unidentified rG4s to enable users to display any potential competitive folding between rG4 and RNA secondary structures. As such, G4Atlas will enable users to explore the general functions of rG4s in diverse biological processes. In addition, G4Atlas lays the foundation for further data-driven deep learning algorithms to examine rG4 structural features.

PlantRNA-FM: An Interpretable RNA Foundation Model for Exploration Functional RNA Motifs in Plants

“…We first obtained all rG4 motifs in the 5’ UTRs from our G4Atlas database 33 . Subsequently, we identified all rG4 motifs associated with translation using our model’s attention contrast matrix across the transcriptome ( Methods ).…”

“…We obtained all potential rG4 in rice from our G4Atlas database 33 . Next, we aligned the rG4 sequences with the corresponding attention contrast matrix and employed the paired t -test to assess the statistical significance.…”

“…RNA G-quadruplexes (rG4s) are one of the RNA tertiary structure motifs formed by the stacking of two or more G-quartets, composed of four guanines held together by both Watson-Crick and Hoogsteen hydrogen bonds 8,32,33 . Previous studies have demonstrated the important role of individual rG4s in repressing translation 34 .…”

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

“…A trio of new nucleic acid quadruplex-related databases also feature. 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.…”

The entangled world of DNA quadruplex folds

“…Besides the right-handed double helical structure [1,2], nucleic acids can fold into a variety of secondary structures like hairpin, triplex, quadruplex, i-motif, etc [3][4][5][6][7][8][9]. Multiple pieces of evidence unfold the instrumental role of quadruplex in regulating the biological processes across all the domains of life [10][11][12][13][14][15][16][17][18][19][20][21][22]. This class of thermodynamically stable alternative structure encompasses four guanine-rich strands [23] (thus the name quadruplex or tetraplex), stabilized by planar G-tetrads (Figure 1A) that stack on each other (Figure 1B, 1C).…”