Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome

Pseudouridine (Ψ) is a C5 glycosidic isomer of uridine, formed by breaking the N1 glycosyl bond and undergoing a 180° base rotation. This modification is one of the most widespread post-transcriptional alterations in RNA and is universally distributed among diverse RNA species. The pervasiveness of this modification enhances RNA structural integrity, confers unique structural and functional attributes upon the RNA molecules it adorns, and facilitates additional hydrogen bonding. However, a convenient, integrated, and intuitive visualization database that includes all currently reported species and RNA types is lacking. Here, we present Ψ-Atlas, an extensive database meticulously curated for the comprehensive collection and annotation of RNA pseudouridine. This database encompasses 554,895 Ψ modification sites across various RNA categories, including mRNA, non-coding RNA (ncRNA), tRNA, and rRNA, in 77 distinct species reported in the current literature. The sequencing methodologies employed comprise next-generation sequencing techniques such as Ψ-Seq, Pseudo-Seq, CeU-Seq, PSI-Seq, RBS-Seq, HydraPsiSeq, BID-Seq, and PRAISE-Seq, as well as third-generation sequencing methods like direct RNA sequencing. Ψ-Atlas is the most comprehensive and integrated resource for RNA Ψ modifications to date. Ψ-Atlas offers an intuitive interface for information display and a myriad of analytical tools, including PsiVar and PsiFinder. Overall, this platform serves as a robust search and visualization tool for the study of pseudouridylation in epitranscriptomics. Ψ-Atlas is available at https://rnainformatics.org.cn/PsiAtlas.