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Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome.

Xiaochen Wang1,2, Jinjing Luo3,4, Xiaoqiang Lang3,5

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Pseudouridine (Ψ) is a common RNA modification enhancing RNA structure and function. The new Ψ-Atlas database provides a comprehensive resource for studying pseudouridylation across diverse RNA types and species.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Pseudouridine (Ψ) is the most abundant RNA modification, crucial for RNA structural integrity and function.
  • Despite its prevalence, a centralized, intuitive database for Ψ modifications across species and RNA types is lacking.

Purpose of the Study:

  • To develop and present Ψ-Atlas, a comprehensive and integrated database for RNA pseudouridine modifications.
  • To provide a user-friendly platform with visualization and analytical tools for studying pseudouridylation.

Main Methods:

  • Compilation of 554,895 Ψ modification sites from 78 species and various RNA categories (mRNA, ncRNA, tRNA, rRNA).
  • Integration of data generated by next-generation sequencing (e.g., Ψ-Seq, Pseudo-Seq) and third-generation sequencing (Direct RNA sequencing).
  • Development of an intuitive interface with analytical tools like PsiVar and PsiFinder.

Main Results:

  • Ψ-Atlas is the most extensive and integrated resource for RNA pseudouridine modifications to date.
  • The database covers a wide range of RNA types and species, offering a holistic view of pseudouridylation.
  • Includes advanced analytical tools for in-depth pseudouridine research.

Conclusions:

  • Ψ-Atlas serves as a robust search and visualization tool for the study of pseudouridylation in epitranscriptomics.
  • This resource facilitates a deeper understanding of the roles and patterns of pseudouridine modifications in diverse biological contexts.