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Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing
Aaron M Fleming1, Cynthia J Burrows1
1Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA afleming@chem.utah.edu burrows@chem.utah.edu.
RNA (New York, N.Y.)
|January 14, 2026
Summary
Nanopore direct RNA sequencing (DRS) offers a powerful method for studying RNA modifications. This technique provides whole transcriptome insights, enabling detailed analysis of epitranscriptomics.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- The epitranscriptome, encompassing RNA modifications, plays a crucial role in gene regulation.
- Analyzing RNA modifications is essential for understanding cellular processes and disease.
- Traditional methods for studying RNA modifications can be complex and labor-intensive.
Purpose of the Study:
- To review the capabilities and applications of Nanopore direct RNA sequencing (DRS) for epitranscriptomic analysis.
- To highlight the advantages of DRS, including minimal RNA handling and long read lengths.
- To discuss current challenges and future prospects of Nanopore DRS in RNA research.
Main Methods:
- Nanopore direct RNA sequencing involves minimal RNA manipulation.
- A single round of reverse transcription creates a DNA:RNA duplex for sequencing.
- Library preparation allows direct reading of nucleotides and their modifications via a protein nanopore.
Main Results:
- Nanopore DRS provides simultaneous sequencing of hundreds of RNA strands, offering whole transcriptome data.
- Long read lengths enable operon-specific epitranscriptomics, such as analyzing ribosomal RNA modifications under cellular stress.
- The method allows monitoring of interplay between different RNA modifications and correlations across RNAs within a cell type.
Conclusions:
- Nanopore DRS is a revolutionary tool for comprehensive epitranscriptomic analysis.
- Its ability to provide whole transcriptome information with long reads opens new avenues for biological discovery.
- Further development is expected to address current challenges and expand the applications of Nanopore DRS.
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