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

9.1K
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...
9.1K
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

5.5K
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...
5.5K
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

6.2K
Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
6.2K
The Nucleosome Core Particle02:10

The Nucleosome Core Particle

12.1K
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...
12.1K
The Nucleosome01:19

The Nucleosome

1.5K
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...
1.5K
Chromosome Replication02:31

Chromosome Replication

8.7K
Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone proteins.  This process begins at numerous origins of replication during the S phase of the cell cycle in each of a cell’s chromosomes simultaneously. Certain nucleotides can act as origins of replication, but these sequences are not well defined - especially in complex, multi-cellular, eukaryotic species. The length of DNA that spans an origin...
8.7K

You might also read

Related Articles

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

Sort by
Same author

DNA Sequence and Histone Variant H2A.Z Jointly Govern Nucleosome Unwrapping Pathways.

bioRxiv : the preprint server for biology·2026
Same author

Structural dynamics in the CENP-A nucleosome impacted by protein-protein interactions with centromere protein N.

Nanoscale·2026
Same author

H2A.Z facilitates Sox2-nucleosome interaction by promoting DNA and histone H3 tail mobility.

Nucleic acids research·2026
Same author

Mapping Allosteric Communication in the Nucleosome with Conditional Activity.

Journal of chemical information and modeling·2026
Same author

From Molecules to Mechanisms: Integrating MD and Stochastic Modeling to Decipher RXR-RAR Gene Regulation.

The journal of physical chemistry. B·2025
Same author

Mapping Allosteric Communication in the Nucleosome with Conditional Activity.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: Jun 29, 2025

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

1.1K

Sequence Dependence in Nucleosome Dynamics.

Prabir Khatua1, Phu K Tang1,2, Abhik Ghosh Moulick1

  • 1Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States.

The Journal of Physical Chemistry. B
|March 26, 2024
PubMed
Summary
This summary is machine-generated.

DNA sequence influences nucleosome positioning and dynamics. Molecular dynamics simulations reveal sequence-specific DNA unwrapping pathways and histone tail interactions, impacting chromatin structure.

More Related Videos

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
09:52

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Published on: January 31, 2019

11.6K
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

1.8K

Related Experiment Videos

Last Updated: Jun 29, 2025

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

1.1K
Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
09:52

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Published on: January 31, 2019

11.6K
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

1.8K

Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • The nucleosome is the fundamental unit of eukaryotic chromatin, consisting of DNA wrapped around histone proteins.
  • DNA sequence is known to influence nucleosome positioning, but the molecular mechanisms governing this interaction and nucleosome dynamics are not fully understood.

Purpose of the Study:

  • To investigate the interplay between DNA sequence and nucleosome dynamics at the molecular level.
  • To elucidate sequence-dependent DNA unwrapping pathways using all-atom molecular dynamics simulations.

Main Methods:

  • Performed all-atom molecular dynamics simulations of nucleosomes with human α-satellite palindromic (ASP) and Widom-601 DNA sequences.
  • Simulated nucleosomes at high salt concentrations (10-20x physiological) to screen electrostatic interactions and promote DNA unwrapping.
  • Analyzed microsecond-timescale simulations to understand sequence-dependent DNA unwrapping events.

Main Results:

  • The ASP DNA sequence promoted loop formation around superhelical location ±5, associated with increased histone tail contacts and counterion release.
  • The Widom-601 DNA sequence exhibited significant breathing motions at the DNA ends, linked to N-terminal H3 tail collapse and alpha-helix formation.
  • Observed distinct sequence-dependent behaviors in DNA unwrapping and histone tail interactions.

Conclusions:

  • DNA sequence critically dictates nucleosome dynamics and DNA unwrapping pathways.
  • Histone tail dynamics and potential post-translational modifications (PTMs) are likely key regulators of nucleosome dynamics.
  • These findings provide molecular insights into sequence-specific chromatin organization and regulation.