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Functions and therapeutic applications of pseudouridylation

Nature Reviews Molecular Cell Biology volume 26, pages 691–705 (2025)Cite this article

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Abstract

The success of using pseudouridine (Ψ) and its methylation derivative in mRNA vaccines against SARS-CoV-2 has sparked a renewed interest in this RNA modification, known as the ‘fifth nucleotide’ of RNA. In this Review, we discuss the emerging functions of pseudouridylation in gene regulation, focusing on how pseudouridine in mRNA, tRNA and ribosomal RNA (rRNA) regulates translation. We also discuss the effects of pseudouridylation on RNA secondary structure, pre-mRNA splicing, and in vitro mRNA stability. In addition to nuclear-genome-encoded RNAs, pseudouridine is also present in mitochondria-encoded rRNA, mRNA and tRNA, where it has different distributions and functions compared with their nuclear counterparts. We then discuss the therapeutic potential of programmable pseudouridylation and mRNA vaccine optimization through pseudouridylation. Lastly, we briefly describe the latest quantitative pseudouridine detection methods. We posit that pseudouridine is a highly promising modification that merits further epitranscriptomics investigation and therapeutic application.

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Fig. 1: Roles of pseudouridylation in translation regulation.
Fig. 2: Roles of pseudouridylation in RNA structure and pre-mRNA splicing.
Fig. 3: The landscape of pseudouridine in nuclear-genome-encoded RNA and mitochondria-encoded RNA.
Fig. 4: Programmable pseudouridylation for suppression of nonsense mutations.
Fig. 5: Pseudouridylation in mRNA vaccines suppresses mRNA sensing by innate immune factors.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (22425071 and 22337001 to C.Y., and 32200467 to Q.H.), the National Key R&D Program of China (2023YFC3402200 to C.Y. and 2021YFC2302400 to M.Z.), Beijing Municipal Science & Technology Commission (Z231100002723005 to C.Y.) and the Ministry of Agriculture and Rural Affairs of China (NK2022010102 to C.Y.). Q.H. was supported in part by the Postdoctoral Fellowship of Peking-Tsinghua Center for Life Sciences.

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  1. Meiling Zhang

    Present address: College of Biological Sciences, China Agricultural University, Beijing, China

  2. These authors contributed equally: Nan Luo, Qiang Huang, Meiling Zhang.

Authors and Affiliations

  1. State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China

    Nan Luo, Qiang Huang, Meiling Zhang & Chengqi Yi

  2. Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China

    Chengqi Yi

  3. Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, China

    Chengqi Yi

  4. Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China

    Chengqi Yi

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Glossary

Ψ-based RNA editors

A type of RNA single-base editor that introduce pseudouridine (Ψ) modifications at specific sites, thereby altering the function of RNA molecules.

Box H/ACA small nucleolar ribonucleoproteins

A complex responsible for RNA-dependent pseudouridylation, consisting of a H/ACA box small nucleolar RNA and four proteins: NHP2, NOP10, GAR1 and DKC1.

Box H/ACA small nucleolar RNA

Small nucleolar RNA that contain conserved H/ACA boxes for the recognition of partner proteins, and a pseudouridylation pocket, which directs base pairing with the substrate RNA.

Folding traps

A type of RNA folding problem of misfolding into inactive, often long-lived conformations, making the escape from these conformations a rate-limiting step in the folding process.

Near-cognate tRNAs

Endogenous tRNAs whose anticodon forms partial base pairing with a specific codon on the mRNA, allowing the incorporation of non-canonical amino acids during translation.

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Luo, N., Huang, Q., Zhang, M. et al. Functions and therapeutic applications of pseudouridylation. Nat Rev Mol Cell Biol 26, 691–705 (2025). https://doi.org/10.1038/s41580-025-00852-1

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