ArticleNature chemical biology2023
Quantitative profiling of pseudouridylation landscape in the human transcriptome.
Article in Nature chemical biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
What it found
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Who cites it
92 citing papers in PubMed, 130 citations in OpenAlex.
- Reduced sensitivity to RNA structural differences distinguishes eukaryotic Pus4 from bacterial TruB.RNA (New York, N.Y.) · 2026Article
- Review
- High-throughput Profiling of Pseudouridines in Microbiome-derived Bacterial RNA.Current protocols · 2026Article
- Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome.Genomics, proteomics & bioinformatics · 2026Article
- Trub1-mediated pseudouridylation is dispensable for immune cell development and homeostasis.Genes and immunity · 2026Article
- RNA modifications in cancer and their detection: a review.Japanese journal of clinical oncology · 2026Review
- Assessment of nanopore RNA modification calling in human cell lines and synthetic systems.Genome biology · 2026Article
- Multimodal profiling reveals cell type-specific pseudouridine modification and density-dependent translational regulation.Nucleic acids research · 2026Article
- Roles and related underlying mechanisms of mitochondrial RNA modification in cancer progression.Acta pharmacologica Sinica · 2026Review
- Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications.Nature communications · 2026Article
- Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing.RNA (New York, N.Y.) · 2026Review
- Targeting RNA binding proteins with small-molecule inhibitors: Advances, challenges, and therapeutic opportunities.Acta pharmaceutica Sinica. B · 2026Review
- Review
- Quantitative mapping of pseudouridines in bacterial RNA.Nature communications · 2026Article
- Decoding human tRNA modifications and crosstalk by enhanced single-read analysis.Genome biology · 2026Article
- Quantitative analysis of small RNA pseudouridylation reveals interplay of PUS enzymes in tRNA anticodon stem-loop.Nature communications · 2026Article
- Integrative analysis of nanopore direct RNA sequencing data reveals a global impact of pseudouridylation on mNPJ precision oncology · 2026Article
- Epitranscriptomic control of cancer hallmarks: Functions, mechanisms, and therapeutics of RNA modifications.Cancer cell · 2026Review
- RNA modification systems as therapeutic targets.Nature reviews. Drug discovery · 2026Review
- PUS1 Drives Renal Cancer Progression by Preventing Formation of Endogenous Double-stranded RNAs.International journal of biological sciences · 2026Article
32 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pseudouridine (Ψ) is an abundant post-transcriptional RNA modification in ncRNA and mRNA. However, stoichiometric measurement of individual Ψ sites in human transcriptome remains unaddressed. Here we develop 'PRAISE', via selective chemical labeling of Ψ by bisulfite to induce nucleotide deletion signature during reverse transcription, to realize quantitative assessment of the Ψ landscape in the human transcriptome. Unlike traditional bisulfite treatment, our approach is based on quaternary base mapping and revealed an ~10% median modification level for 2,209 confident Ψ sites in HEK293T cells. By perturbing pseudouridine synthases, we obtained differential mRNA targets of PUS1, PUS7, TRUB1 and DKC1, with TRUB1 targets showing the highest modification stoichiometry. In addition, we quantified known and new Ψ sites in mitochondrial mRNA catalyzed by PUS1. Collectively, we provide a sensitive and convenient method to measure transcriptome-wide Ψ; we envision this quantitative approach would facilitate emerging efforts to elucidate the function and mechanism of mRNA pseudouridylation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.