ArticleRNA biology2018
Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing.
Article in RNA biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Long Noncoding RNA Isoform Specificity and Chemical Modification on tRNA-Derived Fragments Leading to Divergent Functions.The American journal of pathology · 2026Review
- Direct RNA Sequencing Reveals Stress-Dependent and Pathway-Specific rRNA Modification Reprogramming during 50S Biogenesis.Biochemistry · 2026Article
- Decoding human tRNA modifications and crosstalk by enhanced single-read analysis.Genome biology · 2026Article
- Quantitative CRACI reveals transcriptome-wide distribution of RNA dihydrouridine at base resolution.Nature communications · 2025Article
- Epitranscriptomic alterations induced by environmental toxins: implications for RNA modifications and disease.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2025Review
- Post-Transcriptional Modifications of the Large Ribosome Subunit Assembly Intermediates inBiochemistry · 2025Article
- Article
- Pseudouridine guides germline small RNA transport and epigenetic inheritance.Nature structural & molecular biology · 2025Article
- Deaminase-Driven Reverse Transcription Mutagenesis in Oncogenesis: Critical Analysis of Transcriptional Strand Asymmetries of Single Base Substitution Signatures.International journal of molecular sciences · 2025Review
- Promoted read-through and mutation against pseudouridine-CMC by an evolved reverse transcriptase.Communications biology · 2025Article
- Promoted Read-through and Mutation Against Pseudouridine-CMC by an Evolved Reverse Transcriptase.bioRxiv : the preprint server for biology · 2024Article
- A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS.RNA (New York, N.Y.) · 2024Article
- General Principles and Limitations for Detection of RNA Modifications by Sequencing.Accounts of chemical research · 2024Article
- Benchmarking RNA Editing Detection Tools.Biotech (Basel (Switzerland)) · 2023Review
- A dual-purpose polymerase engineered for direct sequencing of pseudouridine and queuosine.Nucleic acids research · 2023Article
- Determining RNA Natural Modifications and Nucleoside Analog-Labeled Sites by a Chemical/Enzyme-Induced Base Mutation Principle.Molecules (Basel, Switzerland) · 2023Review
- Data Analysis Pipeline for Detection and Quantification of Pseudouridine (ψ) in RNA by HydraPsiSeq.Methods in molecular biology (Clifton, N.J.) · 2023Article
- RNA Post-Transcriptional Modifications in Two Large Subunit Intermediates Populated inBiochemistry · 2022Article
- RNA modification mapping with JACUSA2.Genome biology · 2022Article
- Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling.Genome biology · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The abundant RNA modification pseudouridine (Ψ) has been mapped transcriptome-wide by chemically modifying pseudouridines with carbodiimide and detecting the resulting reverse transcription stops in high-throughput sequencing. However, these methods have limited sensitivity and specificity, in part due to the use of reverse transcription stops. We sought to use mutations rather than just stops in sequencing data to identify pseudouridine sites. Here, we identify reverse transcription conditions that allow read-through of carbodiimide-modified pseudouridine (CMC-Ψ), and we show that pseudouridines in carbodiimide-treated human ribosomal RNA have context-dependent mutation and stop rates in high-throughput sequencing libraries prepared under these conditions. Furthermore, accounting for the context-dependence of mutation and stop rates can enhance the detection of pseudouridine sites. Similar approaches could contribute to the sequencing-based detection of many RNA modifications.
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