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

Nucleosome Remodeling

Nucleosome Remodeling

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...

Chromatin Packaging

Chromatin Packaging

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 structures.

Chromatin Packaging

Chromatin Packaging

Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...

The Nucleosome

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to 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.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...

The Nucleosome

The Nucleosome

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...

Spreading of Chromatin Modifications

Spreading of Chromatin Modifications

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 is an enzyme that can...

You might also read

Related Articles

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

Sort by

Same author

Chromatin architecture sets origin licensing capacity.

bioRxiv : the preprint server for biology·2026

Same author

cGAS bends unpaired DNA to form an unconventional structure that hyperactivates the innate immune response.

bioRxiv : the preprint server for biology·2026

Same author

Native nucleosome-positioning elements as alternatives to the 601 sequence for nucleosome repositioning studies.

Nucleic acids research·2025

Same author

GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion.

Nature structural & molecular biology·2025

Same author

A competitive regulatory mechanism of the Chd1 remodeler is integral to distorting nucleosomal DNA.

Nature structural & molecular biology·2025

Same author

Androgens mediate sexual dimorphism in Pilarowski-Bjornsson Syndrome.

medRxiv : the preprint server for health sciences·2025

Search research articles

Related Experiment Video

Updated: May 28, 2026

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

Extranucleosomal DNA binding directs nucleosome sliding by Chd1.

Jeffrey N McKnight¹, Katherine R Jenkins, Ilana M Nodelman

¹TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218-2685, USA.

Molecular and Cellular Biology

|October 5, 2011

Summary

Chromatin remodelers like Chd1 use DNA-binding domains to sense DNA and direct nucleosome sliding. Replacing Chd1's domain with foreign ones redirected sliding, showing DNA-binding affinity dictates movement direction.

More Related Videos

In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy

In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy

Published on: September 6, 2024

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

Published on: September 10, 2013

Related Experiment Videos

Last Updated: May 28, 2026

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy

In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy

Published on: September 6, 2024

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

Published on: September 10, 2013

Area of Science:

Molecular Biology
Epigenetics
Chromatin Dynamics

Background:

Chd1 and ISWI chromatin remodelers sense extranucleosomal DNA, influencing nucleosome positioning.
DNA-binding domains are thought crucial for sensing DNA and enabling robust nucleosome sliding.
The precise role of these domains in directing nucleosome movement remains unclear.

Purpose of the Study:

To investigate the role of the Chd1 DNA-binding domain in nucleosome sliding and centering.
To determine if foreign DNA-binding domains can confer directionality to Chd1-mediated nucleosome sliding.
To elucidate the mechanism by which DNA-binding domains influence the directionality of chromatin remodeling.

Main Methods:

Utilized Chd1 chromatin remodeler with its native DNA-binding domain and with substituted foreign DNA-binding domains (E. coli AraC, D. melanogaster engrailed).
Assessed nucleosome sliding and centering on short DNA fragments using the modified Chd1 remodelers.
Introduced specific target DNA sequences to evaluate their influence on remodeler binding and nucleosome positioning.

Main Results:

The DNA-binding domain of Chd1 is not essential for nucleosome sliding itself but is critical for centering mononucleosomes.
Replacing the native domain with foreign DNA-binding domains enabled directed nucleosome sliding towards specific target DNA sequences.
The affinity of the DNA-binding domain for extranucleosomal DNA was identified as the primary determinant for the direction of Chd1-mediated nucleosome shifting.

Conclusions:

The DNA-binding domain's interaction with extranucleosomal DNA dictates the direction of Chd1 nucleosome sliding.
Foreign DNA-binding domains can be engineered to control the directionality of chromatin remodeling.
Nucleosome centering is a key function mediated by the Chd1 DNA-binding domain, influenced by DNA sequence proximity.