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

RNA-seq

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...

Ribosome Profiling

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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

You might also read

Related Articles

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

Sort by

Same author

Investigation of TRMT61B methyltransferase activity on mRNA and its effects on translation.

Nucleic acids research·2026

Same author

The atypical E3 ligase HOIL-1 safeguards the ribosome during cellular stress.

Nature cell biology·2026

Same author

Discovery and Optimization of Thienopyrazine RNA-Splicing Modulators for the Treatment of Huntington's Disease.

Journal of medicinal chemistry·2026

Same author

Investigation of TRMT61B methyltransferase activity on mRNA and its effects on translation.

bioRxiv : the preprint server for biology·2025

Same author

A ribosome-bound pseudoknot in the HCV coding region stimulates viral growth by tuning viral translation.

Cell reports·2025

Same author

Inhibition of immune response reduces pathology in dorsal root ganglia and peripheral nerves in cynomolgus macaques following AAV gene therapy.

Molecular therapy. Methods & clinical development·2025

Same journal

Nondenaturing Polyacrylamide Gel Electrophoresis: Preparation and Analysis of DNA.

Current protocols in molecular biology·2021

Same journal

Purification and Concentration of DNA from Aqueous Solutions: Preparation and Analysis of DNA.

Current protocols in molecular biology·2021

Same journal

Expression of Proteins Using Semliki Forest Virus Vectors: Protein Expression.

Current protocols in molecular biology·2021

Same journal

Methylation and Uracil Interference Assays for Analysis of Protein-DNA Interactions: DNA-Protein Interactions.

Current protocols in molecular biology·2021

Same journal

Separation of Double- and Single-Stranded Nucleic Acids Using Hydroxylapatite Chromatography: Preparation and Analysis of DNA.

Current protocols in molecular biology·2021

Same journal

Pulsed-Field Gel Electrophoresis: Preparation and Analysis of DNA.

Current protocols in molecular biology·2021

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 1, 2026

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Transcriptome-Wide Identification of Pseudouridine Modifications Using Pseudo-seq.

Thomas M Carlile¹, Maria F Rojas-Duran¹, Wendy V Gilbert¹

¹Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.

Current Protocols in Molecular Biology

|October 2, 2015

Summary

This summary is machine-generated.

Researchers developed Pseudo-seq, a method to identify pseudouridines (Ψ) in messenger RNAs (mRNAs). This technique enables genome-wide discovery of these important RNA modifications in various organisms, advancing our understanding of post-transcriptional regulation.

Keywords:

RNA modification next-generation sequencing pseudouridine

More Related Videos

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

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

Related Experiment Videos

Last Updated: Apr 1, 2026

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

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

Area of Science:

Molecular Biology
Genomics
RNA Biology

Background:

RNA molecules undergo diverse post-transcriptional modifications across all life domains.
Modified sites in abundant noncoding RNAs are well-known, but discovery in less abundant mRNAs is emerging.
Recent studies identified numerous novel pseudouridines (Ψ) in mRNAs, highlighting dynamic regulation.

Purpose of the Study:

To introduce Pseudo-seq, an efficient and high-resolution method for genome-wide pseudouridine identification.
To enable the discovery of novel pseudouridylation sites in messenger RNAs.
To provide a versatile tool applicable to any organism or cell type.

Main Methods:

Isolation of RNA from S. cerevisiae.
Preparation of Pseudo-seq libraries from RNA samples.
Bioinformatic analysis for identifying pseudouridylation sites from sequencing data.

Main Results:

Demonstration of Pseudo-seq as an efficient method for genome-wide Ψ identification.
Successful application of the method to identify pseudouridylation sites.
Establishment of a protocol applicable across different organisms and cell types.

Conclusions:

Pseudo-seq facilitates the rapid and high-resolution identification of novel pseudouridylation events in mRNAs.
The method significantly advances the study of RNA modifications in less abundant transcripts.
Pseudo-seq is a valuable tool for exploring the landscape of mRNA pseudouridylation genome-wide.