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

Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

9.9K
The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
9.9K
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

7.6K
The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
7.6K
Euchromatin01:01

Euchromatin

9.2K
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
9.2K
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

12.8K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
12.8K
Chromatin Packaging02:21

Chromatin Packaging

23.0K
Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
23.0K
Chromatin Packaging02:21

Chromatin Packaging

10.2K
10.2K

You might also read

Related Articles

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

Sort by
Same author

MDNA : a software module for DNA structure generation and analysis.

Nucleic acids research·2026
Same author

A kinetic proofreading argument to understand the role of H3K9 trimethylation in phase-separated chromatin states.

Biophysical journal·2026
Same author

A Self-Organized Liquid Reaction Container for Cellular Memory.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

The effects of DMSO on DNA conformations and mechanics.

Biophysical journal·2025
Same author

Coalescence of liquid or gel-like DNA-encapsulating microdroplets.

The Journal of chemical physics·2024
Same author

Chromatin remodelers: a concise introduction for biophysicists.

Biophysical reviews·2024

Related Experiment Video

Updated: Mar 24, 2026

Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells
06:48

Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells

Published on: January 5, 2024

5.7K

Transcription Driven Phase Separation in Chromatin Brush.

Tetsuya Yamamoto1, Helmut Schiessel2

  • 1National Composite Center, Nagoya University Furo-cho , Chikusa-ku, Nagoya 464-8603, Japan.

Langmuir : the ACS Journal of Surfaces and Colloids
|March 15, 2016
PubMed
Summary

We predict DNA brushes exhibit phase separation in confined spaces, leading to distinct regions of high and low nucleosome density. This phenomenon is driven by transcription-influenced nucleosome dynamics and excluded volume interactions.

More Related Videos

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision
09:27

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

Published on: December 23, 2016

17.5K
Chromatin Isolation by RNA Purification ChIRP
11:09

Chromatin Isolation by RNA Purification ChIRP

Published on: March 25, 2012

89.1K

Related Experiment Videos

Last Updated: Mar 24, 2026

Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells
06:48

Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells

Published on: January 5, 2024

5.7K
The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision
09:27

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

Published on: December 23, 2016

17.5K
Chromatin Isolation by RNA Purification ChIRP
11:09

Chromatin Isolation by RNA Purification ChIRP

Published on: March 25, 2012

89.1K

Area of Science:

  • Biophysics
  • Molecular Biology
  • Polymer Science

Background:

  • Nucleosomes regulate DNA accessibility for processes like transcription.
  • DNA brushes are model systems for studying polymer behavior and biological interactions.
  • Understanding nucleosome organization is crucial for gene regulation.

Purpose of the Study:

  • To theoretically predict the local density of nucleosomes on DNA brushes.
  • To investigate the phenomenon of phase separation in confined DNA brush systems.
  • To identify factors influencing nucleosome distribution and phase behavior.

Main Methods:

  • Theoretical modeling of nucleosome-DNA brush interactions.
  • Analysis of phase separation dynamics driven by transcription and excluded volume effects.
  • Construction of miscibility phase diagrams to map critical points.

Main Results:

  • DNA brushes in confined solutions exhibit phase separation into high and low nucleosome occupancy regions.
  • Phase separation is driven by transcription rate increases with decreased nucleosome occupancy and RNA polymerase-nucleosome collisions.
  • Critical points in the phase diagram are sensitive to transcription rate constants, DNA-nucleosome interactions, and applied pressure.

Conclusions:

  • Confined DNA brushes can undergo nucleosome-driven phase separation.
  • Transcription-related molecular collisions and excluded volume interactions are key drivers of this instability.
  • The phase behavior is tunable via physical and biochemical parameters, offering insights into gene regulation in crowded environments.