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

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

You might also read

Related Articles

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

Sort by

Same author

Enhanced Environmental PFAS Characterization Using a Virtual High-Resolution Mass Spectral Library Generated by Transfer Learning-Based Neural Network.

Environmental science & technology·2026

Same author

Machine-learning prediction of 30-day infection-related hospitalization in advanced CKD.

BMC infectious diseases·2026

Same author

Integration of AHRR methylation, heavy metals, and clinical characteristics for urothelial carcinoma risk stratification: An explainable artificial intelligence approach.

Environmental pollution (Barking, Essex : 1987)·2026

Same author

Microplastics induce mitochondrial dysfunction and accelerate cardiovascular pathogenesis.

Archives of toxicology·2026

Same author

SGLT2 Inhibitors Mitigate Contrast-Induced Acute Kidney Injury in Diabetes: Clinical and Experimental Evidence.

International journal of molecular sciences·2026

Same author

SGLT2 Inhibitor Use and Cardiorenal Outcomes in Type 2 Diabetes With Liver Cirrhosis.

JAMA network open·2026

Same journal

Optimized tRNA structure-seq reveals robust tRNA secondary structures in <i>S. cerevisiae</i> under mild stress conditions.

RNA (New York, N.Y.)·2026

Same journal

SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs.

RNA (New York, N.Y.)·2026

Same journal

Reduced Sensitivity to RNA Structural Differences Distinguishes Eukaryotic Pus4 from Bacterial TruB.

RNA (New York, N.Y.)·2026

Same journal

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.

RNA (New York, N.Y.)·2026

Same journal

RBM38 Regulates HORMAD1 Splicing to Enhances MEK Inhibitor Sensitivity in Breast Cancer.

RNA (New York, N.Y.)·2026

Same journal

EF-P Inhibits Ribosomal α-Hydroxy Acid Incorporation: Strategic tRNA Body Selection for Co-incorporating α-Hydroxy Acids and Nonproteinogenic Amino Acids into Depsipeptides.

RNA (New York, N.Y.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 9, 2026

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

MUTACLASH: identifying functional small RNA target sites using crosslinking-induced mutations.

Wei-Sheng Wu¹, Dong-En Lee¹, Chi-Jung Chung¹

¹Department of Electrical Engineering, National Cheng Kung University, Tainan 701, Taiwan.

RNA (New York, N.Y.)

|December 2, 2025

Summary

This summary is machine-generated.

We developed MUTACLASH to analyze crosslinking-induced mutations (CIMs) in CLASH experiments. This tool identifies functional small RNA binding sites on target mRNAs, revealing insights into gene regulation.

Keywords:

Argonaute CLASH PIWI piRNA small RNA

More Related Videos

Site-Directed Mutagenesis for In Vitro and In Vivo Experiments Exemplified with RNA Interactions in Escherichia Coli

Site-Directed Mutagenesis for In Vitro and In Vivo Experiments Exemplified with RNA Interactions in Escherichia Coli

Published on: February 5, 2019

A Standard Methodology to Examine On-site Mutagenicity As a Function of Point Mutation Repair Catalyzed by CRISPR/Cas9 and SsODN in Human Cells

A Standard Methodology to Examine On-site Mutagenicity As a Function of Point Mutation Repair Catalyzed by CRISPR/Cas9 and SsODN in Human Cells

Published on: August 25, 2017

Related Experiment Videos

Last Updated: Jan 9, 2026

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Site-Directed Mutagenesis for In Vitro and In Vivo Experiments Exemplified with RNA Interactions in Escherichia Coli

Site-Directed Mutagenesis for In Vitro and In Vivo Experiments Exemplified with RNA Interactions in Escherichia Coli

Published on: February 5, 2019

A Standard Methodology to Examine On-site Mutagenicity As a Function of Point Mutation Repair Catalyzed by CRISPR/Cas9 and SsODN in Human Cells

A Standard Methodology to Examine On-site Mutagenicity As a Function of Point Mutation Repair Catalyzed by CRISPR/Cas9 and SsODN in Human Cells

Published on: August 25, 2017

Area of Science:

Molecular Biology
Bioinformatics
Genetics

Background:

Small RNAs are crucial regulators of gene expression.
Crosslinking, ligation, and sequencing of hybrids (CLASH) reveals RNA-binding protein targets.
Argonaute and PIWI proteins bind diverse mRNA targets with varying rules.

Purpose of the Study:

To develop a bioinformatics tool, MUTACLASH, for analyzing crosslinking-induced mutations (CIMs) in CLASH data.
To use CIMs as molecular footprints to identify functional small RNA binding sites on target mRNAs.
To investigate the functional relevance of non-canonical small RNA interactions.

Main Methods:

Development of the MUTACLASH bioinformatics tool.
Systematic analysis of CIMs in small RNA CLASH datasets (miRNA and piRNA).
Statistical enrichment analysis of CIMs at Argonaute binding sites.

Main Results:

CIMs serve as molecular footprints for Argonaute binding on target mRNAs.
CIMs are enriched at the center of small RNA binding sites and at mismatched piRNA interaction sites.
mRNAs with CIM-marked non-canonical binding sites show stronger regulatory effects.

Conclusions:

MUTACLASH effectively identifies functional small RNA binding sites, including overlooked ones.
CIM analysis provides single-nucleotide resolution insights into RNA-binding protein interactions.
Understanding these interactions is key to deciphering gene regulation by small RNAs.