Quantitative and sensitive methods for the detection of pseudouridine (Ψ) have been lacking. Now, a method termed 2-bromoacrylamide-assisted cyclization sequencing (BACS) has been developed that enables the accurate quantification of Ψ stoichiometry, precise identification of Ψ positions and robust detection of densely modified Ψ sites.
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References
Borchardt, E. K., Martinez, N. M. & Gilbert, W. V. Regulation and function of RNA pseudouridylation in human cells. Annu. Rev. Genet. 54, 309–336 (2020). This review summarizes the regulation and biological functions of Ψ in human cells.
Carlile, T. M. et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515, 143–146 (2014). This paper reports a CMC-based method (Pseudo-seq) for transcriptome-wide mapping of Ψ.
Schwartz, S. et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159, 148–162 (2014). This paper reports a CMC-based method (Ψ-seq) for transcriptome-wide mapping of Ψ.
Khoddami, V. et al. Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution. Proc. Natl Acad. Sci. USA. 116, 6784–6789 (2019). This paper reports an early bisulfite-based method (RBS-seq) for transcriptome-wide mapping of Ψ.
Dai, Q. et al. Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution. Nat. Biotechnol. 41, 344–354 (2023). This paper reports an optimized bisulfite-based method (BID-seq) for transcriptome-wide mapping of Ψ.
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This is a summary of: Xu, H. et al. Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome. Nat. Methods https://doi.org/10.1038/s41592-024-02439-8 (2024).
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A method for quantitative and base-resolution sequencing of pseudouridine. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02466-5
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DOI: https://doi.org/10.1038/s41592-024-02466-5
