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Related Concept Videos

RNA-seq03:21

RNA-seq

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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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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Related Experiment Video

Updated: Oct 19, 2025

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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Computational methods for RNA modification detection from nanopore direct RNA sequencing data.

Mattia Furlan1, Anna Delgado-Tejedor2,3, Logan Mulroney1,4

  • 1Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy.

RNA Biology
|September 24, 2021
PubMed
Summary
This summary is machine-generated.

Detecting RNA modifications is crucial for understanding cellular processes. Nanopore direct RNA sequencing offers single-molecule resolution, but analyzing its data for RNA modification detection remains challenging, with many tools available.

Keywords:
RNA modificationsdirect rna sequencingepitranscriptomenanoporesoftware

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA modifications are vital for cellular regulation across all RNA types.
  • Accurate mapping of RNA modifications is essential but technically challenging.
  • Nanopore direct RNA sequencing enables native RNA analysis at single-molecule resolution.

Purpose of the Study:

  • To review existing approaches for detecting RNA modifications using nanopore sequencing.
  • To outline the principles behind current algorithms for nanopore RNA modification analysis.
  • To address the complexities and challenges in analyzing nanopore RNA sequencing data for modifications.

Main Methods:

  • Review of diverse computational and experimental approaches for RNA modification detection.
  • Analysis of algorithms designed for nanopore direct RNA sequencing data.
  • Comparison of tool features and performance in identifying RNA modifications.

Main Results:

  • Nanopore sequencing provides a direct method for detecting RNA modifications.
  • A variety of tools and algorithms exist for analyzing nanopore RNA data.
  • Challenges remain in the comprehensive and accurate detection of RNA modifications.

Conclusions:

  • Despite challenges, nanopore direct RNA sequencing is a powerful tool for studying RNA modifications.
  • Further development of analytical methods is needed to fully leverage nanopore sequencing for RNA epitranscriptomics.
  • This review provides an overview of current strategies and principles in the field.