ArticleNature communications2023
Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome.Genomics, proteomics & bioinformatics · 2026Article
- Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.Nucleic acids research · 2026Article
- Integrating mass spectrometry with Nanopore direct RNA sequencing forbioRxiv : the preprint server for biology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- NanoCortex: A Unified Agentic System for Nanopore Sequencing Analysis.bioRxiv : the preprint server for biology · 2026Article
- Assessment of nanopore RNA modification calling in human cell lines and synthetic systems.Genome biology · 2026Article
- Systematic assessment of diverse RNA modifications using nanopore direct RNA sequencing.Nucleic acids research · 2026Article
- Cytoplasmic localization of pseudouridine synthase 7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance.Nature communications · 2026Article
- Multimodal profiling reveals cell type-specific pseudouridine modification and density-dependent translational regulation.Nucleic acids research · 2026Article
- 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
- Nanopore direct RNA sequencing for RNA modification analysis: workflow assessment and computational tool benchmarking.Advanced biotechnology · 2026Article
- Stoichiometry-preserving and stochasticity-aware identification of m6A from direct RNA sequencing.Briefings in bioinformatics · 2026Article
- Systematic evaluation of computational tools for multitype RNA modification detection using nanopore direct RNA sequencing.Nature methods · 2026Article
- Integrative analysis of nanopore direct RNA sequencing data reveals a global impact of pseudouridylation on mNPJ precision oncology · 2026Article
- Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing.Nature communications · 2026Article
- Comprehensive discovery of mNature communications · 2025Article
- Nanopore sequencing reveals operon-specific ribosome remodeling accompanying naphthyridone resistance inbioRxiv : the preprint server for biology · 2025Article
- Mechanistic insight into the pseudouridylation of RNA.RNA biology · 2025Review
- Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications.Nucleic acids research · 2025Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Here, we develop and apply a semi-quantitative method for the high-confidence identification of pseudouridylated sites on mammalian mRNAs via direct long-read nanopore sequencing. A comparative analysis of a modification-free transcriptome reveals that the depth of coverage and specific k-mer sequences are critical parameters for accurate basecalling. By adjusting these parameters for high-confidence U-to-C basecalling errors, we identify many known sites of pseudouridylation and uncover previously unreported uridine-modified sites, many of which fall in k-mers that are known targets of pseudouridine synthases. Identified sites are validated using 1000-mer synthetic RNA controls bearing a single pseudouridine in the center position, demonstrating systematic under-calling using our approach. We identify mRNAs with up to 7 unique modification sites. Our workflow allows direct detection of low-, medium-, and high-occupancy pseudouridine modifications on native RNA molecules from nanopore sequencing data and multiple modifications on the same strand.
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