2. Academic Validation
  3. DirectRM: integrated detection of landscape and crosstalk between multiple RNA modifications using direct RNA sequencing

DirectRM: integrated detection of landscape and crosstalk between multiple RNA modifications using direct RNA sequencing

  • Nat Commun. 2025 Oct 27;16(1):9450. doi: 10.1038/s41467-025-64495-8.
Yuxin Zhang # 1 2 3,  Yuecheng Wu # 1,  Jiongming Ma 2 3,  Yiyu Wu 1,  Liying Li 1,  Haozhe Wang 2,  Guifang Jia 4,  Daniel J Rigden 3,  Jia Meng 5 6,  Daiyun Huang 7,  Kunqi Chen 8 9 10
Affiliations

Affiliations

  • 1 Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China.
  • 2 Suzhou Key Laboratory of Cancer Biology and Chronic Diseases, Department of Biosciences and Bioinformatics, Center for Intelligent RNA Therapeutics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China.
  • 3 Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
  • 4 Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
  • 5 Suzhou Key Laboratory of Cancer Biology and Chronic Diseases, Department of Biosciences and Bioinformatics, Center for Intelligent RNA Therapeutics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China. jia.meng@xjtlu.edu.cn.
  • 6 Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK. jia.meng@xjtlu.edu.cn.
  • 7 Wisdom Lake Academy of Pharmacy, Center for Intelligent RNA Therapeutics, Xi'an Jiaotong-Liverpool University, Suzhou, China. daiyun.huang02@xjtlu.edu.cn.
  • 8 Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China. kunqi.chen@fjmu.edu.cn.
  • 9 Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China. kunqi.chen@fjmu.edu.cn.
  • 10 School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China. kunqi.chen@fjmu.edu.cn.
  • # Contributed equally.
PMID: 41145497 DOI: 10.1038/s41467-025-64495-8
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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