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...

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

Master Transcription Regulators

Master Transcription Regulators

Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...

Master Transcription Regulators

Master Transcription Regulators

RNA Polymerase II Accessory Proteins

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...

Co-activators and Co-repressors

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...

You might also read

Related Articles

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

Sort by

Same author

One chromatin, many structures: From ensemble contact maps to single-cell 3D organization.

Biophysical journal·2026

Same author

Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2025

Same author

Geometrically encoded positioning of introns, intergenic segments, and exons in the human genome.

bioRxiv : the preprint server for biology·2025

Same author

Mature chromatin packing domains persist after RAD21 depletion in 3D.

Science advances·2025

Same author

Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system.

Science advances·2025

Same author

The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle.

The Journal of chemical physics·2024

Same journal

Kinesin-5/Cut7 C-terminal tail phosphorylation influence on motor regulation through multi-scale molecular modeling.

Biophysical journal·2026

Same journal

Dynamic conformations of fluorophores on self-labeling protein tags.

Biophysical journal·2026

Same journal

Different actions of RyR2 open and closed channel block explained by a multiscale Ca<sup>2+</sup> release model.

Biophysical journal·2026

Same journal

Membrane Environment Sets the Functional pK<sub>a</sub> of Ionizable Lipids.

Biophysical journal·2026

Same journal

Distinguishable spreading dynamics in microbial communities.

Biophysical journal·2026

Same journal

Phylogeny of SK channels and functional characterization of the conserved Phe in the S3-S4 loop.

Biophysical journal·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 2, 2026

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Dynamic Crowding Regulates Transcription.

Anne R Shim¹, Rikkert J Nap¹, Kai Huang¹

¹Department of Biomedical Engineering, Northwestern University, Evanston, Illinois; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois.

Biophysical Journal

|December 11, 2019

Summary

This summary is machine-generated.

Dynamic crowding, or changing macromolecular density in the nucleus, significantly impacts gene expression. This study reveals dynamic crowding as a novel regulatory mechanism, altering transcription kinetics and expression levels differently than steady-state conditions.

More Related Videos

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Related Experiment Videos

Last Updated: Jan 2, 2026

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Area of Science:

Nuclear biology
Molecular biophysics
Systems biology

Background:

The cell nucleus is crowded with macromolecules like chromatin and proteins.
Existing models often assume steady-state crowding, neglecting dynamic changes.
Dynamic changes in nuclear crowding affect molecular interactions and processes.

Purpose of the Study:

To investigate the influence of dynamic crowding on gene transcription.
To develop a framework integrating dynamic crowding with gene expression.
To explore the regulatory potential of dynamic crowding in the nuclear environment.

Main Methods:

A systems-molecular approach combining chemical reaction systems with molecular simulations.
Brownian dynamics and Monte Carlo simulations to model protein diffusion and DNA-protein binding.
Quantification of macromolecular density effects on transcription rates.

Main Results:

Transcription is critically dependent on dynamic crowding, differing significantly from steady-state crowding.
Dynamic crowding can lead to both amplification and suppression of gene expression.
Expression levels vary based on gene properties and are influenced by dynamic crowding.

Conclusions:

Dynamic crowding represents a novel regulatory framework for gene expression in the nuclear nanoenvironment.
This framework can explain gene expression under conditions like biomechanical stress or for circadian rhythms.
Understanding dynamic crowding is crucial for comprehending nuclear biological processes.