ArticleNature biotechnology2023
Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers.
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Who cites it
168 citing papers in PubMed, 229 citations in OpenAlex.
- The role of RNA modifications in cancer translational control.RNA biology · 2026Review
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- Advances in mutant characterization for detecting causal mutations in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Comprehensive post-transcriptional modification profiles in individual Staphylococcus aureus tRNA species.Nucleic acids research · 2026Article
- RModBlock antisense oligonucleotides as a universal tool for precise and efficient inhibition of RNA modifications.Nature biomedical engineering · 2026Article
- Systems-level analysis predicts no autotrophy-linked protein-RNA interactions in Clostridium autoethanogenum.Nature communications · 2026Article
- High-throughput Profiling of Pseudouridines in Microbiome-derived Bacterial RNA.Current protocols · 2026Article
- The impact of psuedouridine modification on human tRNA.Biochemical Society transactions · 2026Review
- Article
- Integrating mass spectrometry with Nanopore direct RNA sequencing forbioRxiv : the preprint server for biology · 2026Article
- Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.Nature chemical biology · 2026Article
- A Ψ-Ψ codon-anticodon pairing in nonsense suppression and translational recoding.Nature chemical biology · 2026Article
- Regulatory elements on chromatin-associated RNA 15 years beyond RNA epigenetics.Nature chemical biology · 2026Review
- Trub1-mediated pseudouridylation is dispensable for immune cell development and homeostasis.Genes and immunity · 2026Article
- Assessment of nanopore RNA modification calling in human cell lines and synthetic systems.Genome biology · 2026Article
- Emerging roles of non-mNature plants · 2026Review
- Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples.Nature biotechnology · 2026Article
- Cytoplasmic localization of pseudouridine synthase 7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance.Nature communications · 2026Article
108 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors at 3 institutions in 2 countries.
Funding
Abstract
Functional characterization of pseudouridine (Ψ) in mammalian mRNA has been hampered by the lack of a quantitative method that maps Ψ in the whole transcriptome. We report bisulfite-induced deletion sequencing (BID-seq), which uses a bisulfite-mediated reaction to convert pseudouridine stoichiometrically into deletion upon reverse transcription without cytosine deamination. BID-seq enables detection of abundant Ψ sites with stoichiometry information in several human cell lines and 12 different mouse tissues using 10-20 ng input RNA. We uncover consensus sequences for Ψ in mammalian mRNA and assign different 'writer' proteins to individual Ψ deposition. Our results reveal a transcript stabilization role of Ψ sites installed by TRUB1 in human cancer cells. We also detect the presence of Ψ within stop codons of mammalian mRNA and confirm the role of Ψ in promoting stop codon readthrough in vivo. BID-seq will enable future investigations of the roles of Ψ in diverse biological processes.
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