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RMPore: a comprehensive database of single-molecule RNA modifications detected by Nanopore direct RNA sequencing.

Zhuobin Lin1, Xiaoqiong Bao1, Luowanyue Zhang2

  • 1Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China.

Nucleic Acids Research
|November 9, 2025
PubMed
Summary

RMPore is a new database analyzing RNA modifications using Nanopore direct RNA sequencing. It identifies millions of modification sites across species, advancing epitranscriptomics research.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA modifications are crucial for post-transcriptional regulation but are underexplored due to technological limits.
  • Nanopore direct RNA sequencing (DRS) offers a promising approach for transcriptome-wide RNA modification profiling with single-molecule resolution.

Purpose of the Study:

  • To develop a comprehensive database and analytical pipeline for single-molecule RNA modification detection.
  • To characterize RNA modification sites and their regulatory relationships across multiple species.

Main Methods:

  • Utilized Nanopore direct RNA sequencing (DRS) data from 958 samples across 34 species.
  • Developed RMPore, an analytical pipeline integrating 20 detection tools to identify and categorize RNA modification sites.
  • Performed advanced single-molecule analyses on correlated and haplotype-biased sites, incorporating molecular event annotations.

Main Results:

  • Identified over 65 million RNA modification sites spanning 25 types across 34 species.
  • Categorized modification sites into high, medium, and low confidence levels based on tool prediction and reproducibility.
  • Integrated annotations for splicing, RNA-binding protein interactions, RNA-RNA interactions, and circular RNAs.

Conclusions:

  • RMPore provides a valuable resource for single-molecule epitranscriptomics research.
  • The database and pipeline facilitate deeper understanding of RNA modification landscape and regulatory roles.
  • This work bridges critical gaps in RNA modification research by enabling comprehensive transcriptome-wide analysis.