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

9.1K
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...
9.1K
RNA Structure01:23

RNA Structure

68.5K
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
68.5K

You might also read

Related Articles

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

Sort by
Same author

Transcriptomic responses to endurance exercise training in rats.

BMC genomic data·2026
Same author

Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.

bioRxiv : the preprint server for biology·2026
Same author

Systems genetics reveals ITIH5 as a key mediator of adipocyte-Endothelial crosstalk.

Molecular metabolism·2026
Same author

RNA Folding Nearest Neighbor Parameters Including the Modification 1-Methyl-Pseudouridine.

bioRxiv : the preprint server for biology·2026
Same author

The Rayleigh Quotient and Contrastive Principal Component Analysis II.

bioRxiv : the preprint server for biology·2026
Same author

Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation.

bioRxiv : the preprint server for biology·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

Related Experiment Video

Updated: Apr 21, 2026

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

4.7K

Rational experiment design for sequencing-based RNA structure mapping.

Sharon Aviran1, Lior Pachter2

  • 1Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, California 95616, USA saviran@ucdavis.edu.

RNA (New York, N.Y.)
|October 22, 2014
PubMed
Summary
This summary is machine-generated.

We developed a new computational method to optimize RNA structure mapping experiments using next-generation sequencing (NGS). This approach improves the precision of mapping measurements and guides the design of large-scale, in vivo transcriptome studies.

Keywords:
RNA structuregenomic big datahigh-throughput genomicsnext-generation sequencingstructure mapping

More Related Videos

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
05:41

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

1.9K
Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms
05:12

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

1.5K

Related Experiment Videos

Last Updated: Apr 21, 2026

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

4.7K
2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
05:41

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

1.9K
Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms
05:12

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

1.5K

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Structure mapping is crucial for understanding nucleic acid function.
  • Advances in chemistry, genomics, and informatics have revitalized structure mapping techniques.
  • Next-generation sequencing (NGS) has significantly enhanced the throughput and scope of these assays.

Purpose of the Study:

  • To introduce a novel computational approach for the quantitative design of multiplexed NGS structure mapping assays.
  • To characterize the relationship between experimental parameters and mapping measurement precision.
  • To provide insights into the design of genome-wide transcriptome probing methods.

Main Methods:

  • Development of a model-based in silico approach for assay design.
  • Utilizing direct, digital NGS readouts for quantitative analysis.
  • Assessing experimental parameter dependencies and tradeoffs.
  • Quantitative evaluation of SHAPE-Seq (selective 2'-hydroxyl acylation analyzed by primer extension) robustness.

Main Results:

  • The computational approach effectively characterizes the complex interplay between experimental parameters and mapping precision.
  • Identified critical tradeoffs and potential pitfalls in assay design.
  • Demonstrated the robustness of SHAPE-Seq measurements through quantitative assessment.
  • Provided design considerations for advanced in vivo transcriptome analysis.

Conclusions:

  • The novel in silico approach enables quantitative design of large-scale multiplexed NGS structure mapping assays.
  • This method aids in optimizing experimental parameters for enhanced precision and robustness.
  • Facilitates the development of advanced genome-wide methods for probing RNA structure in vivo.