Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Mismatch Repair

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...

Mismatch Repair

Mismatch Repair

Homologous Recombination

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

Long-patch Base Excision Repair

Long-patch Base Excision Repair

Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:

Nucleotide Excision Repair

Nucleotide Excision Repair

DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

<i>YoyoMut</i>: Interactive Exploration of SARS-CoV-2 Mutation Fixation and Reversion Through Time.

Life (Basel, Switzerland)·2026

Same author

Unveiling the Impact of Drug-Sensitive Mutations on HIV-1 Protease Dynamics: A Molecular Dynamics Simulation Study of the T12A, L63Q, and H69N Variants.

International journal of molecular sciences·2026

Same author

Loss of function of retinol dehydrogenase 11 causes a recessive syndrome characterized by myopathy, retinal dystrophy, juvenile cataracts, and microcephaly.

Genetics in medicine : official journal of the American College of Medical Genetics·2026

Same author

Exploring Genomic Variability in the Mediterranean Buffalo Breed: A Step Towards Custom SNP Array.

Animals : an open access journal from MDPI·2026

Same author

Enhanced Untargeted Metabolomics Based on High-Resolution Mass Spectrometry Reveals Global Rewiring Due to Mitochondrial Dysfunction in Yeast.

International journal of molecular sciences·2026

Same author

Single-cell transcriptomic profiling of human fetal neural stem cells isolated from the subventricular zone.

Frontiers in cell and developmental biology·2026

Same journal

Tracking Synthetic Adhesins on Bacterial Surfaces with Immunofluorescence Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Engineering and Adapting Disulfide-Containing Proteins to Enable Intracellular Functionality.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

AI-Driven Protein Research: From Prediction to Design.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for the In Vitro Selection of Protein and Peptide Libraries Using mRNA Display.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Nov 9, 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

RNA Editing Detection in HPC Infrastructures.

Claudio Lo Giudice¹, Luigi Mansi¹, Tiziano Flati²

¹Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.

Methods in Molecular Biology (Clifton, N.J.)

|April 9, 2021

Summary

This summary is machine-generated.

This study introduces REDItools v2, a faster computational tool for identifying RNA editing events. It efficiently detects A-to-I modifications in large RNA sequencing datasets using High Performance Computing.

Keywords:

A-to-I editing Bioinformatics DNAseq Deep sequencing Genomics HPC MPI RNA editing RNAseq Transcriptomics

More Related Videos

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Related Experiment Videos

Last Updated: Nov 9, 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

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

Adenosine-to-Inosine (A-to-I) RNA editing is a crucial co/posttranscriptional modification mediated by ADAR enzymes.
Dysregulation of A-to-I editing is implicated in human diseases like neurological disorders and cancer.
Detecting RNA editing variants in large-scale RNA sequencing (RNAseq) data presents significant computational challenges.

Purpose of the Study:

To develop a computationally efficient method for identifying A-to-I RNA editing events.
To enable the analysis of massive RNAseq datasets for RNA editing variant detection.
To demonstrate the application of REDItools v2 on High Performance Computing (HPC) infrastructures.

Main Methods:

Development of a novel version of REDItools (v2) optimized for speed.
Implementation of High Performance Computing (HPC) strategies for large-scale data processing.
Utilizing REDItools v2 for the identification of A-to-I RNA editing events in RNAseq data.

Main Results:

REDItools v2 significantly reduces computing times for RNA editing variant detection.
The tool effectively identifies A-to-I RNA editing events in large RNAseq datasets.
Successful application of REDItools v2 on HPC systems is demonstrated.

Conclusions:

REDItools v2 offers a powerful and efficient solution for analyzing RNA editing in large transcriptome sequencing experiments.
The enhanced computational performance facilitates the study of RNA editing's role in human health and disease.
This tool supports large-scale genomic research by enabling faster and more comprehensive RNA editing analysis.