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Updated: Oct 10, 2025

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RNA modifications detection by comparative Nanopore direct RNA sequencing.

Adrien Leger1,2, Paulo P Amaral3,4,5, Luca Pandolfini3,6

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

Nature Communications
|December 11, 2021
PubMed
Summary
This summary is machine-generated.

We developed Nanocompore, a new tool to detect RNA modifications using direct-RNA sequencing. This framework profiles N6-methyladenosine (m6A) in yeast and human cells, revealing co-occurrence of modifications.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA molecules are chemically modified after transcription (post-transcriptional modifications, PTMs), altering their function.
  • High-throughput sequencing methods are increasingly used to map these RNA PTMs.
  • Oxford Nanopore direct-RNA sequencing shows sensitivity to RNA modifications.

Purpose of the Study:

  • To develop and validate Nanocompore, a robust analytical framework for identifying RNA modifications from direct-RNA sequencing data.
  • To profile N6-methyladenosine (m6A) modifications in vivo in yeast and human RNAs.
  • To investigate the co-occurrence of multiple modified residues on individual RNA molecules.

Main Methods:

  • Development of Nanocompore, a comparative analytical framework using non-modified control samples.
  • Application of Nanocompore to analyze direct-RNA sequencing data from yeast and human cells.
  • Validation of Nanocompore results using orthogonal experimental methods.

Main Results:

  • Nanocompore accurately detects various RNA modifications with precise positional information in vitro.
  • The framework successfully profiled m6A modifications in vivo in yeast and human RNAs, including targeted non-coding RNAs.
  • Novel insights into the co-occurrence of multiple modified residues on single RNA molecules were obtained.

Conclusions:

  • Nanocompore is a validated and robust framework for identifying RNA modifications from direct-RNA sequencing data.
  • The tool enables in vivo profiling of specific RNA modifications like m6A.
  • The study provides new understanding of the combinatorial nature of RNA modifications within individual RNA molecules.