ArticleNature communications2024
Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed.
- Advanced deep learning strategies in nanopore RNA sequencing.RNA biology · 2026Review
- The role of RNA modifications in cancer translational control.RNA biology · 2026Review
- Review
- Compendium of RNA modifications for bacterial stress adaptation.Microbiology and molecular biology reviews : MMBR · 2026Review
- Transcriptional architecture of African swine fever virus.PLoS pathogens · 2026Article
- The Hidden Layer of MicroRNA Regulation in Gynecologic Cancers: IsomiRs, Arm Switching, and RNA Epitranscriptomic Modifications.International journal of molecular sciences · 2026Review
- Review
- ShapeRNA: an integrated web server for RNA secondary structure, ensemble, and functional analysis.Nucleic acids research · 2026Article
- Single-molecule mbioRxiv : the preprint server for biology · 2026Article
- Epigenetic orchestration of sugar signaling in plant development and stress adaptation.Horticulture research · 2026Article
- ModiCal: A Targeted Calibration Workflow for Site-Specific mACS chemical biology · 2026Article
- Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.Nucleic acids research · 2026Article
- The Role of NMedComm · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Cold storage delays peach fruit softening via mMolecular horticulture · 2026Article
- Emerging roles of non-mNature plants · 2026Review
- Pseudouridylation landscape across 42bioRxiv : the preprint server for biology · 2026Article
- Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell.Nature methods · 2026Article
- Isoform-specific m6A deposition and coordinated splicing shape mammalian transcriptome evolution.Nature communications · 2026Article
- RNA N6-methyladenosine (m6A) regulates cell cycle progression in diffuse midline glioma (DMG) and confers sensitivity to FTO inhibition.Cell death & disease · 2026Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
23 authors.
Funding
Abstract
The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.
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