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Related Concept Videos

RNA Editing02:23

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...
RNA-seq03:21

RNA-seq

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

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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Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

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: May 15, 2026

A Nonsequencing Approach for the Rapid Detection of RNA Editing
08:50

A Nonsequencing Approach for the Rapid Detection of RNA Editing

Published on: April 21, 2022

Identifying RNA editing sites using RNA sequencing data alone.

Gokul Ramaswami1, Rui Zhang, Robert Piskol

  • 1Department of Genetics, Stanford University, Stanford, California, USA.

Nature Methods
|January 8, 2013
PubMed
Summary
This summary is machine-generated.

High-confidence RNA editing sites were identified using RNA sequencing across multiple samples, eliminating the need for matched DNA. This study nearly doubles known human protein recoding events and reveals neuronal functions for genes with conserved editing sites.

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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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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA editing is a crucial post-transcriptional modification.
  • Accurate identification of RNA editing sites is essential for understanding gene function.
  • Current methods often require matched genomic DNA, limiting scalability.

Purpose of the Study:

  • To develop and validate a method for high-confidence RNA editing site detection using only RNA sequencing data.
  • To identify novel RNA editing sites in humans and Drosophila.
  • To investigate the functional implications of conserved RNA editing sites in human genes.

Main Methods:

  • Utilized RNA sequencing data from multiple individuals and species.
  • Developed computational algorithms to identify RNA editing sites without matched genomic DNA.
  • Performed comparative analysis across species and investigated gene enrichment for specific editing site characteristics.

Main Results:

  • Achieved high confidence in calling RNA editing sites solely from RNA sequencing data.
  • Identified a substantial number of previously unknown RNA editing sites in both human and Drosophila.
  • Nearly doubled the number of known human protein recoding events.
  • Discovered an enrichment of neuronal functions in human genes containing conserved editing sites within Alu repeats.

Conclusions:

  • RNA sequencing data alone is sufficient for confident RNA editing site identification.
  • The findings significantly expand the landscape of known RNA editing events, particularly in humans.
  • Conserved RNA editing sites in Alu repeats are linked to neuronal gene functions, suggesting a role in nervous system biology.