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Related Experiment Video

Updated: Jan 14, 2026

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
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DirectRM: integrated detection of landscape and crosstalk between multiple RNA modifications using direct RNA

Yuxin Zhang1,2,3, Yuecheng Wu1, Jiongming Ma2,3

  • 1Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China.

Nature Communications
|October 28, 2025
PubMed
Summary

DirectRM enables simultaneous detection of six RNA modifications using nanopore sequencing. This tool reveals complex modification patterns, advancing epitranscriptome research.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA modifications play crucial roles in gene regulation.
  • Accurate profiling of multiple RNA modifications is challenging.
  • Nanopore direct RNA sequencing offers a promising avenue for native RNA analysis.

Purpose of the Study:

  • To develop a robust computational tool for simultaneous detection of multiple RNA modifications.
  • To leverage nanopore direct RNA sequencing for high-throughput epitranscriptomic profiling.
  • To investigate the co-occurrence and spatial relationships of RNA modifications.

Main Methods:

  • Developed DirectRM, a two-stage computational pipeline.
  • Utilized a binary classifier to identify candidate modified k-mers.
  • Employed an attention-based neural network for precise modification and position determination.
  • Trained and validated the model on native RNA samples from human cell lines and viral RNAs.

Main Results:

  • DirectRM accurately detects six abundant RNA modifications simultaneously in native RNAs.
  • The tool demonstrates high sensitivity, precision, and robustness, surpassing existing methods.
  • Revealed transcript-level proximity and molecule-level interference of adjacent RNA modifications.
  • Established associations between modifications at both transcript and molecule levels.

Conclusions:

  • DirectRM provides a powerful approach for comprehensive epitranscriptome analysis.
  • The findings offer new insights into the complex interplay of RNA modifications.
  • DirectRM is expandable for detecting additional RNA modifications in future studies.