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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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Chromatin Packaging02:21

Chromatin Packaging

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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...
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The Nucleosome02:33

The Nucleosome

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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...
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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. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
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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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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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Updated: Jul 2, 2025

Author Spotlight: Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates
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Author Spotlight: Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates

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Nucleosome spacing controls chromatin spatial structure and accessibility.

Tilo Zülske1, Aymen Attou2, Laurens Groß1

  • 1Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.

Biophysical Journal
|February 29, 2024
PubMed
Summary
This summary is machine-generated.

Nucleosome spacing, not density, is key for 3D chromatin structure and accessibility. Regular spacing ensures proper DNA accessibility for cellular functions, challenging prior assumptions in chromatin research.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biophysics

Background:

  • The three-dimensional (3D) structure of chromatin is critical for regulating cellular processes like transcription.
  • Chromatin's dynamic structure involves DNA, histones, and nucleosomes, enabling long-range contacts and spatial accessibility.
  • Key factors governing chromatin's 3D organization remain incompletely understood, with conflicting prior research findings.

Purpose of the Study:

  • To investigate whether nucleosome spacing or nucleosome density is more fundamental for 3D chromatin accessibility.
  • To explore the role of basic physical properties in generating realistic chromatin structures.

Main Methods:

  • Utilized a computer model to simulate chromatin volumes at physiological nucleosome concentrations.
  • Focused on analyzing the impact of nucleosome spacing regularity versus nucleosome concentration on chromatin accessibility.
  • Compared simulation results with established electron microscopy data.

Main Results:

  • Regularity of nucleosome spacing was found to be crucial for chromatin network accessibility to diffusive processes.
  • Variations in nucleosome concentration had minimal impact on chromatin accessibility and fiber properties.
  • Simulated chromatin structures using basic physical properties matched published electron microscopy observations.
  • High nucleosome density did not disrupt fiber-like structures or alter contact probabilities of genomic loci.

Conclusions:

  • Nucleosome spacing regularity, rather than density, is a primary determinant of 3D chromatin organization and accessibility.
  • Findings challenge previous assumptions regarding the role of nucleosome density in chromatin structure.
  • Changes in nucleosome spacing represent a potential mechanism for modulating spatial chromatin structure and genomic functions.