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Related Concept Videos

Nucleosome Remodeling02:54

Nucleosome Remodeling

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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...
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The Nucleosome Core Particle01:12

The Nucleosome Core Particle

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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...
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Histone Modification02:32

Histone Modification

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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
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The Nucleosome01:19

The Nucleosome

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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...
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Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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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...
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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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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. 
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Related Experiment Video

Updated: Jul 14, 2025

Reconstitution of Nucleosomes with Differentially Isotope-labeled Sister Histones
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Reconstitution of Nucleosomes with Differentially Isotope-labeled Sister Histones

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Structural and Dynamic Changes of Nucleosome upon GATA3 Binding.

Hisashi Ishida1, Atsushi Matsumoto1, Hiroki Tanaka2

  • 1Institute for Quantum Life Science, Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba city, Chiba 263-8555, Japan.

Journal of Molecular Biology
|October 7, 2023
PubMed
Summary

Pioneer factor GATA3 binding to nucleosomes alters DNA accessibility. Its N- and C-fingers promote DNA dissociation from histones, initiating chromatin conformational changes crucial for gene regulation.

Keywords:
GATA3SAXSdynamicsnucleosomepioneer factor

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

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Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells
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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
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Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells
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Area of Science:

  • Molecular Biology
  • Chromatin Dynamics
  • Epigenetics

Background:

  • Pioneer factors bind nucleosomes and influence chromatin structure.
  • The precise impact of pioneer factor binding on nucleosome conformation and dynamics remains largely unknown.

Purpose of the Study:

  • To elucidate the binding mechanism of the pioneer factor GATA3 to nucleosomal DNA.
  • To investigate how GATA3 binding affects nucleosome conformation and dynamics.

Main Methods:

  • Small-angle X-ray scattering (SAXS) for structural data.
  • Molecular modeling to generate structural hypotheses.
  • Molecular dynamics (MD) simulations to analyze conformational changes and DNA dynamics.

Main Results:

  • Structural models and SAXS data indicate GATA3's N- and C-fingers bind distinct sites on nucleosomal DNA.
  • MD simulations reveal GATA3's N-finger binding enhances DNA fluctuation and dissociation at the unbound DNA end.
  • GATA3's C-finger binding promotes DNA dissociation at the bound DNA end, differing from N-finger binding.

Conclusions:

  • GATA3 binding, via its N- and C-fingers, facilitates DNA dissociation from the histone core at specific DNA ends.
  • This differential DNA dissociation triggers significant conformational changes in chromatin, impacting gene accessibility.