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RNA Editing

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...

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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.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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Related Experiment Video

Updated: Jul 15, 2025

A Nonsequencing Approach for the Rapid Detection of RNA Editing

A Nonsequencing Approach for the Rapid Detection of RNA Editing

Published on: April 21, 2022

Benchmarking RNA Editing Detection Tools.

David Rodríguez Morales¹, Sarah Rennie¹, Shizuka Uchida²

¹Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.

Biotech (Basel (Switzerland))

|September 27, 2023

Summary

This summary is machine-generated.

Epitranscriptomics research is growing, with RNA editing being a key focus. This study benchmarks bioinformatic tools for detecting RNA editing sites (RES) from RNA sequencing data to guide researchers.

Keywords:

RNA editing RNA sequencing databases epitranscriptomics tools

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Last Updated: Jul 15, 2025

A Nonsequencing Approach for the Rapid Detection of RNA Editing

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RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Over 170 RNA modifications exist, creating the field of epitranscriptomics.
RNA editing, particularly adenosine to inosine (A-to-I) and cysteine to uracil (C-to-U), is frequent in mammalian transcriptomes.
RNA editing is detectable from RNA sequencing (RNA-seq) data, offering insights into the epitranscriptome.

Purpose of the Study:

To benchmark bioinformatic tools for detecting RNA editing sites (RES) from RNA-seq data.
To provide a comprehensive comparison of available tools for RES detection.
To offer recommendations for selecting appropriate tools for future studies.

Main Methods:

Benchmarking of various bioinformatic tools designed for RES detection.
Utilizing previously published RNA-seq datasets for performance evaluation.
Comparative analysis of tool performance based on established criteria.

Main Results:

Each bioinformatic tool exhibits distinct advantages and disadvantages.
Performance variations among tools were observed when analyzing RNA-seq data.
The study provides a detailed performance overview of each tool.

Conclusions:

Selecting the right bioinformatic tool for RES detection is crucial for researchers and clinicians.
This benchmarking study aids in choosing the most suitable tool for specific research needs.
Recommendations are provided to facilitate the effective utilization of RNA-seq data for epitranscriptomic analysis.