ArticleNature communications2025
DirectRM: integrated detection of landscape and crosstalk between multiple RNA modifications using direct RNA sequencing.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Review
- DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- ModiCal: A Targeted Calibration Workflow for Site-Specific mACS chemical biology · 2026Article
- Sequence determinant and functional relevance of 8-oxoguanine RNA modification unveiled from foundation-model-based predictor.Molecular therapy. Nucleic acids · 2026Article
- MethyNano: supervised contrastive pretraining enables robust and generalizable methylation detection from nanopore sequencing.Bioinformatics (Oxford, England) · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Emerging roles of non-mNature plants · 2026Review
- Reprogramming of the mToxics · 2026Article
- Unravelling Multilayered RNA Modification Networks in Female Reproduction and Obstetric/Gynaecologic Disorders.Biomolecules · 2026Review
- Mke-resnet: a lightweight and interpretable deep learning framework for efficient RNA m6A site identification.BMC bioinformatics · 2026Article
- Emerging roles of mRNA acetylation in plants.Plant communications · 2026Article
- The changing landscape of gene expression analysis.Briefings in bioinformatics · 2026Review
- Domain-derived knowledge enabled machine learning and functional characterization of cancer-associated RNA methylation sites.BMC bioinformatics · 2026Article
- CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.Briefings in bioinformatics · 2026Article
- m6AHD: a new framework for identifying abnormal N6-methyladenosine (m6A) in heart diseases based on sequencing features.Frontiers in genetics · 2026Article
- THGC_MDA: a method for predicting the associations between mFrontiers in genetics · 2026Article
- N4-acetylcytidine modification bridges metabolic reprogramming and immune evasion in cancer: mechanisms and therapeutic implications.Frontiers in immunology · 2026Review
- m5C and m6A cooperatively stabilize EPHB4 to drive lymphatic metastasis in gastric cancer.Frontiers in genetics · 2026Article
- DirectRM: integrated detection of landscape and crosstalk between multiple RNA modifications using direct RNA sequencing.Nature communications · 2025Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Profiling RNA modifications is essential to understand their functions and interactions. By taking the advantages of nanopore direct RNA sequencing, we present DirectRM, enabling simultaneous detection of six abundant modifications (N4-acetylcytidine, 1-methyladenosine, 5-methylcytidine, N7-methlguanosine, N6-methyladenosine, and pseudouridine) in native RNAs. Its two-stage pipeline identifies candidate modified kmers using binary classifier, then determines specific modifications and positions using an attention-based neural network. Trained with molecule-level features extracted from native RNA samples and validated on human cell lines and viral RNAs, DirectRM demonstrates high sensitivity, precision and robustness, outperforming existing tools. Crucially, we reveal the associations between modifications at both transcript and molecule-level. Modifications tend to proximate to each other on the transcript level, while at the molecule level, the presence of one modification is likely to reduce the occurrence of modifications at adjacent positions. DirectRM offers a powerful approach for studying epitranscriptome complexity and is expandable for future research.
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