Pseudouridine (Ψ) is a C5 glycoside isomer of uridine, formed by breaking the N1 glycosyl bond and undergoing a 180° base rotation. This modification stands as 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, bestows unique structural and functional attributes upon the RNA molecules it adorns, and facilitates additional hydrogen bonding. Here, we present the Ψ-Atlas, an extensive database meticulously curated for the comprehensive collection and annotation of RNA pseudouridine. This database encompasses 40,000 pseudouridine modification sites across various RNA categories, including mRNA, ncRNA, tRNA, rRNA, and others, in 20 distinct species reported in current literature.

The sequencing methodologies employed comprise second-generation techniques such as Ψ-seq, Pseudo-seq, CeU-Seq, PSI-seq, RBS-Seq, HydraPsiSeq, as well as third-generation sequencing methods like Direct RNA sequencing (DRS). The Ψ-Atlas offers an intuitive interface for information display and a myriad of analytical tools, including RMlevelDiff, RMplantVar, RNAmodNet, and Blast (for functional analysis). Additionally, it provides resources such as mRNAbrowse, RNAlollipop, JBrowse, and Integrative Genomics Viewer (for data visualization). In essence, these resources present unparalleled opportunities for exploring the epitranscriptomics of pseudouridine.

Ψ-Atlas: an integrated database for pseudouridine epitranscriptome

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