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

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
What is Gene Expression?01:42

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
What is Gene Expression?01:42

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
What is Gene Expression?01:36

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...

You might also read

Related Articles

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

Sort by
Same author

Author Correction: An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA.

Nature·2025
Same author

Analysis of Functional cis-Regulatory Elements Reveals Novel Transcriptional Regulatory Mechanisms in Gonadal Development.

Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation·2025
Same author

Fast and accurate short-read alignment with hybrid hash-tree data structure.

Genomics & informatics·2024
Same author

An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases.

Science (New York, N.Y.)·2024
Same author

CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing.

Nature communications·2024
Same author

CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing.

bioRxiv : the preprint server for biology·2023

Related Experiment Video

Updated: Jun 7, 2026

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

Deep cap analysis of gene expression.

Junpei Kurosawa1, Hiromi Nishiyori, Yoshihide Hayashizaki

  • 1RIKEN Omics Science Center, Yokohama City, Kanagawa, Japan.

Methods in Molecular Biology (Clifton, N.J.)
|October 23, 2010
PubMed
Summary

Cap Analysis of Gene Expression (CAGE) detects transcriptional start sites and expression levels. DeepCAGE enhances this technique for deeper transcriptome analysis and regulatory network insights using next-generation sequencing.

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Cap Analysis of Gene Gene Expression (CAGE) is a method for identifying transcription start sites (TSSs) and quantifying gene expression.
  • CAGE utilizes 5' cDNA tags and PCR amplification, where template amount influences PCR efficiency.
  • It's a key technique for analyzing promoter activity and discovering novel transcripts, including alternative spliced and noncoding RNAs.

Purpose of the Study:

  • To introduce deepCAGE, a powerful advancement of CAGE technology.
  • To leverage high-throughput next-generation sequencing for enhanced transcriptome analysis.
  • To provide deeper insights into gene regulatory networks.

Main Methods:

  • Utilizing Cap Analysis of Gene Expression (CAGE) technology.

More Related Videos

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

Related Experiment Videos

Last Updated: Jun 7, 2026

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

  • Implementing deepCAGE for high-throughput sequencing.
  • Generating deep transcriptome datasets.

    • Main Results:

    • DeepCAGE enables significantly deeper transcriptome profiling compared to standard CAGE.
    • The enhanced depth reveals more intricate details of gene regulatory networks.
    • Identification of a larger number of transcriptional starting sites and transcripts.

    Conclusions:

    • DeepCAGE represents a significant improvement in transcriptome analysis capabilities.
    • This technology facilitates a more comprehensive understanding of gene regulation.
    • DeepCAGE is poised to advance research in genomics and molecular biology.