ArticleNucleic acids research2023
Nanopore sequencing for N1-methylpseudouridine in RNA reveals sequence-dependent discrimination of the modified nucleotide triphosphate during transcription.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed, 17 citations in OpenAlex.
- VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.Nucleic acids research · 2026Article
- Systematic assessment of diverse RNA modifications using nanopore direct RNA sequencing.Nucleic acids research · 2026Article
- Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing.RNA (New York, N.Y.) · 2026Review
- Unlocking the regulatory code of RNA: launching the Human RNome Project.Genome biology · 2025Article
- Multimodal zero-shot learning of previously unseen epitranscriptomes from RNA-seq data.Briefings in bioinformatics · 2025Article
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation.Cell genomics · 2025Article
- Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications.Nature communications · 2024Article
- Nanopore Direct RNA Sequencing for Modified Uridine Nucleotides Yields Signals Dependent on the Physical Properties of the Modified Base.Israel journal of chemistry · 2024Article
- Influence of N1-Methylpseudouridine in Guide RNAs on CRISPR/Cas9 Activity.International journal of molecular sciences · 2023Article
- Advantages and challenges associated with bisulfite-assisted nanopore direct RNA sequencing for modifications.RSC chemical biology · 2023Article
- Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in theACS chemical biology · 2023Article
- Bisulfite and Nanopore Sequencing for Pseudouridine in RNA.Accounts of chemical research · 2023Article
- Modification mapping by nanopore sequencing.Frontiers in genetics · 2022Review
- Detecting RNA modification using direct RNA sequencing: A systematic review.Computational and structural biotechnology journal · 2022Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Direct RNA sequencing with a commercial nanopore platform was used to sequence RNA containing uridine (U), pseudouridine (Ψ) or N1-methylpseudouridine (m1Ψ) in >100 different 5-nucleotide contexts. The base calling data for Ψ or m1Ψ were similar but different from U allowing their detection. Understanding the nanopore signatures for Ψ and m1Ψ enabled a running start T7 RNA polymerase assay to study the selection of UTP versus ΨTP or m1ΨTP competing mixtures in all possible adjacent sequence contexts. A significant sequence context dependency was observed for T7 RNA polymerase with insertion yields for ΨTP versus UTP spanning a range of 20-65%, and m1ΨTP versus UTP producing variable yields that differ by 15-70%. Experiments with SP6 RNA polymerase, as well as chemically-modified triphosphates and DNA templates provide insight to explain the observations. The SP6 polymerase introduced m1ΨTP when competed with UTP with a smaller window of yields (15-30%) across all sequence contexts studied. These results may aid in future efforts that employ RNA polymerases to make therapeutic mRNAs with sub-stoichiometric amounts of m1Ψ.
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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 Socratic graph.