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

Nucleosome Remodeling02:54

Nucleosome Remodeling

10.6K
Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
10.6K
The Nucleosome Core Particle02:10

The Nucleosome Core Particle

13.9K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
13.9K
The Nucleosome Core Particle01:12

The Nucleosome Core Particle

2.0K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
2.0K
The Nucleolus02:55

The Nucleolus

10.1K
The nucleolus is the most prominent substructure of the nucleus. When it was first discovered, it was considered to be an isolated organelle that forms fibrils and granules. In 1931, the relationship between the nucleolus and chromosomes was first described by Heitz. He observed that the appearance and size of nucleolus varies depending on the stage of the cell cycle. He also noticed constricted regions on different chromosomes clustered together at definite cell cycle stages. These regions,...
10.1K
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

24.5K
Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
24.5K
The Nucleosome01:19

The Nucleosome

3.5K
Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
3.5K

You might also read

Related Articles

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

Sort by
Same author

Performing SELEX experiments in silico.

The Journal of chemical physics·2017
Same author

Colloidal Spherocylinders at an Interface: Flipper Dynamics and Bilayer Formation.

Physical review letters·2017
Same author

Designing nucleosomal force sensors.

Physical review. E·2017
Same author

Kinetic proofreading of gene activation by chromatin remodeling.

HFSP journal·2009
Same author

Stochastic model for nucleosome sliding under an external force.

Physical review. E, Statistical, nonlinear, and soft matter physics·2009
Same author

Rayleigh instability of charged aggregates: Role of the dimensionality, ionic strength, and dielectric contrast.

Physical review. E, Statistical, nonlinear, and soft matter physics·2006
Same journal

Erratum: Low-dimensional model for adaptive networks of spiking neurons [Phys. Rev. E 111, 014422 (2025)].

Physical review. E·2026
Same journal

Disentangling the effects of many-body forces on depletion interactions.

Physical review. E·2026
Same journal

Charge transport and mode transition in dual-energy electron beam diodes.

Physical review. E·2026
Same journal

Optimization of multisite reactions in complex compartmentalized media.

Physical review. E·2026
Same journal

Origin of geometric cohesion in nonconvex granular materials: Interplay between interdigitation and rotational constraints enhancing frictional stability.

Physical review. E·2026
Same journal

Interaction of walkers with a standing Faraday wave.

Physical review. E·2026
See all related articles

Related Experiment Video

Updated: Dec 26, 2025

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
06:32

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

2.1K

Translational nucleosome positioning: A computational study.

J Neipel1,2,3, G Brandani4, H Schiessel3

  • 1Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.

Physical Review. E
|March 15, 2020
PubMed
Summary
This summary is machine-generated.

This study shows that predicting DNA translational positioning within nucleosomes requires considering guanine-cytosine content and entropy, not just energy. A refined DNA model accurately predicts nucleosome positioning maps.

More Related Videos

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

22.8K
Author Spotlight: Efficient Nucleosome Reconstitution for Single-Molecule Techniques
05:58

Author Spotlight: Efficient Nucleosome Reconstitution for Single-Molecule Techniques

Published on: September 6, 2024

1.5K

Related Experiment Videos

Last Updated: Dec 26, 2025

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
06:32

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

2.1K
Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

22.8K
Author Spotlight: Efficient Nucleosome Reconstitution for Single-Molecule Techniques
05:58

Author Spotlight: Efficient Nucleosome Reconstitution for Single-Molecule Techniques

Published on: September 6, 2024

1.5K

Area of Science:

  • Genomics
  • Biophysics
  • Molecular Biology

Background:

  • Nucleosomes, composed of DNA spooled around proteins, are fundamental to eukaryotic DNA organization.
  • DNA sequence influences nucleosome incorporation through geometry and elasticity, affecting rotational and translational positioning.

Purpose of the Study:

  • To evaluate the predictive power of a coarse-grained DNA model (rigid base-pair model) for nucleosome translational positioning.
  • To investigate the roles of DNA sequence-dependent elasticity, entropy, and energy in nucleosome positioning.

Main Methods:

  • Utilized a coarse-grained DNA model incorporating sequence-dependent elasticity (rigid base-pair model).
  • Assessed the model's ability to predict translational nucleosome positioning.
  • Incorporated assumptions regarding changes in DNA elasticity upon nucleosome complexation and local equilibration of nucleosome positions.

Main Results:

  • The rigid base-pair model, while good for rotational positioning, struggles with translational positioning.
  • Translational positioning is primarily driven by guanine-cytosine content-dependent entropy, rather than energy.
  • An enhanced model, accounting for altered DNA elasticity and local equilibration, achieves excellent quantitative agreement with experimental nucleosome maps.

Conclusions:

  • Predicting nucleosome translational positioning necessitates incorporating entropic effects related to base composition.
  • A modified rigid base-pair model, with specific assumptions, provides a powerful tool for quantitative prediction of in vitro nucleosome organization.