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Updated: Jun 6, 2026
05:12
AQRNA-seq for Quantifying Small RNAs
Published on: February 2, 2024
Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across
Letong Xu1, Shenghai Shen2, Yizhou Zhang1
1Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.
Elife
|June 4, 2026
Summary
Pseudouridine (Ψ) modifications in bacteria, particularly in tRNA and mRNA, are mapped transcriptome-wide. These abundant RNA modifications impact bacterial gene expression and translation, with conserved features across species.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Pseudouridine (Ψ) is the most abundant RNA modification, crucial in eukaryotes but underexplored in bacteria.
- Understanding Ψ distribution and function in bacteria is vital for comprehending bacterial gene regulation.
Purpose of the Study:
- To perform the first transcriptome-wide, quantitative mapping of Ψ modifications in five bacterial species at single-base resolution.
- To investigate the functional significance and evolutionary conservation of bacterial Ψ modifications.
- To develop computational tools for predicting Ψ modification sites.
Main Methods:
- Optimized baBID-seq method for bacterial RNA analysis.
- Comparative genomics and transcriptomics across five bacterial species.
- Development of a deep learning framework (pseU_NN) integrating sequence and structure features.
Main Results:
- Revealed growth phase-dependent dynamics of pseudouridylation in bacterial tRNA and mRNA, especially in metabolic genes.
- Identified evolutionarily conserved features of Ψ modifications, including motif contexts and operon clustering.
- Demonstrated Ψ modifications influence mRNA stability, translation, and RNA-binding protein interactions.
- Established a deep learning model for accurate prediction of Ψ-modified sites.
Conclusions:
- Provides a comprehensive landscape of bacterial RNA Ψ modifications.
- Highlights the functional roles of Ψ in bacterial adaptation and gene expression.
- Establishes a foundation for future research into bacterial Ψ modification mechanisms and applications.
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