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 Stability01:53

RNA Stability

33.8K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
33.8K
Ribosome Profiling02:24

Ribosome Profiling

3.6K
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...
3.6K
RNA-seq03:21

RNA-seq

10.3K
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...
10.3K
Nuclear Export of mRNA02:31

Nuclear Export of mRNA

7.8K
Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
7.8K
Translational Regulation01:29

Translational Regulation

75
Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
75
Types of RNA01:20

Types of RNA

6.0K
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA Performs Diverse...
6.0K

You might also read

Related Articles

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

Sort by
Same author

High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.

Nucleic acids research·2026
Same author

An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.

Genome biology·2026
Same author

What does it take to learn the rules of RNA base pairing? A lot less than you may think.

Communications biology·2026
Same author

Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain.

bioRxiv : the preprint server for biology·2026
Same author

High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.

bioRxiv : the preprint server for biology·2025
Same author

All-at-once RNA folding with 3D motif prediction framed by evolutionary information.

Nature methods·2025

Related Experiment Video

Updated: Aug 18, 2025

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
07:24

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Published on: July 9, 2021

2.5K

Thirteen dubious ways to detect conserved structural RNAs.

William Gao1, Ann Yang2, Elena Rivas2

  • 1Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

IUBMB Life
|December 10, 2022
PubMed
Summary

Inferring conserved RNA structure from sequence alignments is challenging. New methods help distinguish true structural covariation from artifacts and identify long non-coding RNAs with biologically relevant structures.

More Related Videos

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

12.3K
RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
09:36

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

Published on: April 10, 2018

25.5K

Related Experiment Videos

Last Updated: Aug 18, 2025

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
07:24

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Published on: July 9, 2021

2.5K
Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

12.3K
RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
09:36

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

Published on: April 10, 2018

25.5K

Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Computational Biology

Background:

  • Covariation in RNA alignments can reveal conserved RNA structure.
  • However, accurately inferring structure is complicated by homologous sequence evolution and artifacts.
  • Distinguishing true structural covariation from other sources is crucial.

Purpose of the Study:

  • To critically discuss methods for inferring conserved RNA structure using comparative sequence analysis.
  • To address challenges like extraneous covariation and data limitations.
  • To provide new approaches for identifying long non-coding RNAs (lncRNAs) with biologically relevant structures.

Main Methods:

  • Investigating and critically discussing existing practices in comparative sequence analysis for RNA structure inference.
  • Developing and presenting new methods to differentiate structural covariation from other signals.
  • Applying these methods to identify functional lncRNAs.

Main Results:

  • Identified significant challenges in RNA structure inference due to non-structural covariation and artifacts.
  • Proposed methods to improve the accuracy of distinguishing true structural covariation.
  • Provided a framework for selecting lncRNAs with biologically relevant structures.

Conclusions:

  • Comparative sequence analysis is a powerful tool for RNA structure inference, but requires careful methodological consideration.
  • New methods are needed to overcome limitations and accurately identify conserved RNA structures, particularly in lncRNAs.
  • This work offers a pathway to better understand the structural biology of lncRNAs.