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

Nonsense-mediated mRNA Decay

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,...

Nonsense-mediated mRNA Decay

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,...

Experimental RNAi

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...

RNA Interference

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...

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...

Biosynthesis of Nucleic Acids

Biosynthesis of Nucleic Acids

Nucleic acid biosynthesis is a fundamental biochemical process that produces the purine and pyrimidine nucleotides essential for DNA and RNA synthesis. This pathway maintains a balanced nucleotide pool, preventing imbalances that could jeopardize genetic integrity and cellular function. Given the crucial role of nucleotides, their synthesis is tightly regulated to ensure proper cellular homeostasis.Purine BiosynthesisThe biosynthesis of purine nucleotides begins with ribose-5-phosphate, a...

You might also read

Related Articles

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

Sort by

Same author

The aryl hydrocarbon receptor (AhR) activity and DNA-damaging effects of chlorinated polycyclic aromatic hydrocarbons (Cl-PAHs).

Chemosphere·2018

Same author

A nuclear-encoded protein, mTERF6, mediates transcription termination of rpoA polycistron for plastid-encoded RNA polymerase-dependent chloroplast gene expression and chloroplast development.

Scientific reports·2018

Same author

Cumulative metabolic effects of low-dose benzo(<i>a</i>)pyrene exposure on human cells.

Toxicology research·2018

Same author

New MS network analysis pattern for the rapid identification of constituents from traditional Chinese medicine prescription Lishukang capsules in vitro and in vivo based on UHPLC/Q-TOF-MS.

Talanta·2018

Same author

Efficient Catalytic Performance for Acylation-Nazarov Cyclization Based on an Unusual Postsynthetic Oxidization Strategy in a Fe(II)-MOF.

Inorganic chemistry·2018

Same author

A prospective, mixed-methods, before and after study to identify the evidence base for the core components of an effective Paediatric Early Warning System and the development of an implementation package containing those core recommendations for use in the UK: Paediatric early warning system - utilisation and mortality avoidance- the PUMA study protocol.

BMC pediatrics·2018

Search research articles

Related Experiment Video

Updated: May 23, 2026

Investigation of RNA Synthesis Using 5-Bromouridine Labelling and Immunoprecipitation

Investigation of RNA Synthesis Using 5-Bromouridine Labelling and Immunoprecipitation

Published on: May 3, 2018

Inducing nonsense suppression by targeted pseudouridylation.

Chao Huang¹, Guowei Wu, Yi-Tao Yu

¹Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA.

Nature Protocols

|March 31, 2012

Summary

Researchers developed a method to precisely add pseudouridine modifications to RNA molecules using engineered box H/ACA RNAs. This technique enables the study of RNA modifications and offers potential therapeutic applications for diseases caused by premature translation termination.

More Related Videos

Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil (Ers4tU)

Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil (Ers4tU)

Published on: August 22, 2019

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

Published on: February 1, 2019

Related Experiment Videos

Last Updated: May 23, 2026

Investigation of RNA Synthesis Using 5-Bromouridine Labelling and Immunoprecipitation

Investigation of RNA Synthesis Using 5-Bromouridine Labelling and Immunoprecipitation

Published on: May 3, 2018

Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil (Ers4tU)

Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil (Ers4tU)

Published on: August 22, 2019

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

Published on: February 1, 2019

Area of Science:

Biochemistry
Molecular Biology
RNA Biology

Background:

Pseudouridylation, the isomerization of uridine to pseudouridine, is crucial for RNA function and is primarily mediated by box H/ACA small ribonucleoproteins (RNPs).
The specificity of pseudouridylation is dictated by base-pairing between the guide sequence of box H/ACA RNA and the target RNA substrate.
Engineered box H/ACA RNAs can direct site-specific pseudouridylation to various RNA types, facilitating research into RNA modification effects.

Purpose of the Study:

To present a protocol for designing box H/ACA RNAs for site-specific pseudouridylation of target RNAs, using TRM4 mRNA as an example.
To explore the potential of pseudouridylation in suppressing nonsense-mediated mRNA decay and treating diseases linked to premature termination codons (PTCs).

Main Methods:

Design of a novel box H/ACA RNA with an artificial guide sequence complementary to the target RNA substrate.
Application of the engineered box H/ACA RNA to site-specifically introduce pseudouridine into TRM4 mRNA.
Evaluation of the protocol's efficacy and potential therapeutic applications.

Main Results:

Demonstration of a protocol to engineer box H/ACA RNAs for site-specific pseudouridylation.
Successful pseudouridylation of TRM4 mRNA at a targeted location.
Identification of pseudouridylation at PTCs as a potential strategy for nonsense suppression.

Conclusions:

Engineered box H/ACA RNAs provide a versatile tool for site-specific RNA pseudouridylation.
This methodology enables fundamental research on the functional impact of RNA modifications.
The protocol offers a promising avenue for developing novel therapeutic strategies for PTC-related genetic disorders.