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

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...

You might also read

Related Articles

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

Sort by

Same author

Enhanced EBNA2-dependent activity in EBV-transformed B cells from patients with multiple sclerosis.

medRxiv : the preprint server for health sciences·2026

Same author

Systematic discovery of pathogen effector functions across human pathogens and pathways.

Cell·2026

Same author

BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes.

bioRxiv : the preprint server for biology·2026

Same author

Autoimmune non-coding variants perturb transcription factor-cofactor complex assembly linked to enhancer activity.

bioRxiv : the preprint server for biology·2026

Same author

An Updated Comprehensive Management Algorithm for Anterior and Lateral Spontaneous Cerebrospinal Fluid Leaks.

Neurosurgery·2026

Same author

Gene regulatory networks define human airway epithelial cell types and their distinct responses to type I interferon.

bioRxiv : the preprint server for biology·2026

Search research articles

Related Experiment Video

Updated: Oct 1, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants.

David Bray^1,2,3,4, Heather Hook^1,2,4, Rose Zhao^1,2

¹Department of Biology, Boston University, Boston, MA, USA.

|March 7, 2022

Summary

We developed CASCADE, a new high-throughput method to study how non-coding DNA variants affect gene regulation by changing protein complex binding. CASCADE profiles cofactor recruitment, aiding the study of genetic variations impacting gene expression.

More Related Videos

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

Published on: March 3, 2015

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Related Experiment Videos

Last Updated: Oct 1, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

Published on: March 3, 2015

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Non-coding DNA variants (NCVs) influence gene expression by modifying regulatory complex binding sites.
Characterizing the functional impact of NCVs on these interactions requires advanced high-throughput methodologies.

Purpose of the Study:

To introduce CASCADE (Customizable Approach to Survey Complex Assembly at DNA Elements), a novel array-based high-throughput method.
To profile cofactor (COF) recruitment and quantify the effects of NCVs on transcription factor-cofactor (TF-COF) complex assembly at DNA elements.

Main Methods:

Developed CASCADE for high-throughput profiling of TF-COF complex formation in nuclear extracts.
Applied CASCADE to assess condition-specific COF recruitment (p300, RBBP5) to the CXCL10 promoter in response to lipopolysaccharide (LPS) stimulation.
Utilized CASCADE to analyze TF-COF binding across ~1,700 single-nucleotide polymorphism quantitative trait loci (SNP-QTLs) in human macrophages.

Main Results:

Demonstrated CASCADE's sensitivity in detecting condition-specific COF recruitment to the CXCL10 promoter.
Quantified the impact of all possible NCVs on TF-COF binding at the CXCL10 promoter.
Identified perturbed ETS domain-containing complexes associated with SNP-QTLs in macrophages.

Conclusions:

CASCADE is a sensitive and versatile high-throughput method for profiling TF-COF complex assembly.
The method enables the characterization of NCVs' impact on regulatory complex binding.
CASCADE will accelerate the investigation of molecular mechanisms underlying NCVs in various biological contexts.