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Related Concept Videos

RNA-seq03:21

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Updated: Jan 17, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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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
PubMed
Summary
This summary is machine-generated.

Nanopore direct RNA sequencing (DRS) offers a powerful method for studying RNA modifications. This technique provides whole transcriptome insights, enabling detailed analysis of epitranscriptomics.

Keywords:
RNA modificationsepitranscriptomicsnanopore sequenceribosomal RNA

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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.