Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

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...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
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.
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 helps...

You might also read

Related Articles

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

Sort by
Same author

Embryo-scale Visual Cell Sorting reveals a conserved transcriptomic signature of nucleolar size linked to proteostasis.

bioRxiv : the preprint server for biology·2026
Same author

Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes.

bioRxiv : the preprint server for biology·2026
Same author

The WalRK two-component system in <i>Streptococcus pneumoniae</i> ensures robustness of secondary wall polymer attachment.

bioRxiv : the preprint server for biology·2026
Same author

Origin of replication discovery for environmentally isolated <i>Pantoea</i> strain enables expression of heterologous proteins, pathways and products.

iScience·2026
Same author

KBase: Open-source Platform for Collaborative Biological Data Analysis and Publication.

Journal of molecular biology·2026
Same author

Construction of a randomly barcoded insertional mutant library in the filamentous fungus <i>Trichoderma atroviride</i>.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: Jun 1, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension

Julius B Lucks1, Stefanie A Mortimer, Cole Trapnell

  • 1Department of Bioengineering, University of California, Berkeley, CA 94720, USA. jblucks@cornell.edu

Proceedings of the National Academy of Sciences of the United States of America
|June 7, 2011
PubMed
Summary

We developed SHAPE-Seq, a high-throughput method to rapidly characterize RNA structures. This technique provides single nucleotide resolution for complex RNA pools, advancing RNA biology and synthetic systems.

More Related Videos

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
11:58

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

Published on: January 30, 2019

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Related Experiment Videos

Last Updated: Jun 1, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
11:58

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

Published on: January 30, 2019

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Bioinformatics

Background:

  • Noncoding RNAs play crucial regulatory roles, with their function dependent on specific secondary and tertiary structures.
  • Characterizing RNA structures in complex populations requires advanced, high-throughput technologies.

Purpose of the Study:

  • To develop a high-throughput technique for rapid and accurate characterization of RNA secondary and tertiary structures.
  • To enable simultaneous structural analysis of multiple RNA molecules with single nucleotide resolution.

Main Methods:

  • SHAPE-Seq combines selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry with multiplexed paired-end deep sequencing.
  • Data analysis utilizes a fully automated pipeline based on a maximum likelihood model.

Main Results:

  • SHAPE-Seq accurately infers quantitative, single nucleotide-resolution secondary and tertiary structural information.
  • The method detects subtle conformational changes caused by single nucleotide mutations.
  • Simultaneous structural measurement of complex RNA pools is achieved.

Conclusions:

  • SHAPE-Seq significantly enhances the throughput and accessibility of RNA structure studies.
  • This technology supports fundamental biological research and the engineering of RNA for synthetic biology applications.