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

You might also read

Related Articles

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

Sort by

Same author

Neutrophil Transcriptomic Changes in Severe Sterile Vasoplegic Syndrome Resemble a Distinct Molecular Subtype of Septic Shock.

Shock (Augusta, Ga.)·2026

Same author

Relationship among Toll-like receptors, β2 adrenergic receptor, and mitogen-activated protein kinases in regulating Il1b transcription.

Journal of immunology (Baltimore, Md. : 1950)·2025

Same author

Stepwise neofunctionalization of the NF-κB family member Rel during vertebrate evolution.

Nature immunology·2025

Same author

NF-κB RelB suppresses the inflammatory gene expression programs of dendritic cells by competing with RelA for binding to target gene promoters.

Cell discovery·2025

Same author

Examining NF-κB genomic interactions by ChIP-seq and CUT&Tag.

bioRxiv : the preprint server for biology·2024

Same author

Selective regulation of a defined subset of inflammatory and immunoregulatory genes by an NF-κB p50-IκBζ pathway.

Genes & development·2024

Same journal

High-Throughput Microbial Assay for Amino Acid Measurement in Ground Maize Seed Samples Utilizing Auxotrophic <i>E. coli</i>.

Cold Spring Harbor protocols·2025

Same journal

Grain Quality in Maize.

Cold Spring Harbor protocols·2025

Same journal

High-Throughput Assay for Measuring Phytate and Available Phosphorus in Ground Maize Seed Samples.

Cold Spring Harbor protocols·2025

Same journal

Functional Genomic Analysis of Transposon Insertion Mutant Maize Plants from the UniformMu National Public Resource.

Cold Spring Harbor protocols·2025

Same journal

The UniformMu National Public Resource: Transposon<i>-</i>Induced Mutant Seeds for Functional Genomics Studies in Maize.

Cold Spring Harbor protocols·2025

Same journal

Insights from the Study of B<i>-</i>Cell Epitopes of a Microbial Pathogen by Phage Display.

Cold Spring Harbor protocols·2025

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 16, 2026

A Fluorescence-based Exonuclease Assay to Characterize DmWRNexo, Orthologue of Human Progeroid WRN Exonuclease, and Its Application to Other Nucleases

A Fluorescence-based Exonuclease Assay to Characterize DmWRNexo, Orthologue of Human Progeroid WRN Exonuclease, and Its Application to Other Nucleases

Published on: December 23, 2013

Nuclear run-on assay.

Stephen T Smale

Cold Spring Harbor Protocols

|February 13, 2010

Summary

This summary is machine-generated.

The nuclear run-on assay measures transcription initiation rates in mammalian genes, offering insights into gene regulation independent of RNA stability. This method helps determine if polymerase pausing or attenuation controls gene expression.

More Related Videos

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

Published on: August 31, 2013

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Published on: February 27, 2026

Related Experiment Videos

Last Updated: Jun 16, 2026

A Fluorescence-based Exonuclease Assay to Characterize DmWRNexo, Orthologue of Human Progeroid WRN Exonuclease, and Its Application to Other Nucleases

A Fluorescence-based Exonuclease Assay to Characterize DmWRNexo, Orthologue of Human Progeroid WRN Exonuclease, and Its Application to Other Nucleases

Published on: December 23, 2013

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

Published on: August 31, 2013

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Published on: February 27, 2026

Area of Science:

Molecular Biology
Gene Regulation
Biochemistry

Background:

Gene expression regulation in mammals is complex.
Assessing transcription initiation rates is crucial for understanding gene control.
Existing methods often conflate initiation rates with RNA stability.

Purpose of the Study:

To introduce and validate the nuclear run-on assay.
To demonstrate its utility in measuring transcription initiation rates.
To differentiate the role of initiation from RNA stability in gene expression.

Main Methods:

Cells are chilled to pause RNA polymerase.
Nuclei are permeabilized and incubated with radiolabeled UTP.
Nascent RNA transcripts are purified and hybridized to gene-specific DNA.

Main Results:

The assay quantifies nascent RNA synthesis.
The amount of incorporated radioactivity correlates with transcription initiation frequency.
This method is largely independent of RNA degradation rates.

Conclusions:

The nuclear run-on assay accurately measures transcription initiation rates.
It provides a valuable tool for studying gene regulation mechanisms.
The assay can distinguish between transcriptional control and post-transcriptional effects like RNA stability.