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Related Concept Videos

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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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.
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The Nucleosome01:19

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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.
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Histone Modification02:32

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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.
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Histone Variants at the Centromere02:30

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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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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, 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...
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Author Spotlight: Efficient Nucleosome Reconstitution for Single-Molecule Techniques
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Competitive Chemical Reaction Kinetic Model of Nucleosome Assembly Using the Histone Variant H2A.Z and H2A In Vitro.

Hongyu Zhao1,2, Xueqin Shao1, Mingxin Guo1

  • 1School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China.

International Journal of Molecular Sciences
|November 14, 2023
PubMed
Summary

This study extends a chemical kinetic model to understand H2A.Z nucleosome assembly, revealing histone H2A outcompetes H2A.Z in vitro. These findings clarify H2A.Z-containing nucleosome dynamics.

Keywords:
competitive chemical reaction kineticshistone variantnucleosome dynamicsnucleosome positioningnucleosome reconstitution in vitro

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Nucleosomes are fundamental to eukaryotic chromatin structure and gene regulation.
  • Histone variant H2A.Z dynamically modulates gene expression.
  • The assembly dynamics of H2A.Z nucleosomes are not well understood.

Purpose of the Study:

  • To extend a chemical kinetic model for nucleosome assembly to include H2A.Z.
  • To investigate the competitive assembly dynamics between H2A and H2A.Z.
  • To provide a method for assessing histone competitive assembly abilities.

Main Methods:

  • Utilized a previously established chemical kinetic model.
  • Extended the model to incorporate H2A.Z and canonical H2A competition.
  • Performed in vitro experiments to validate kinetic model predictions.

Main Results:

  • Nucleosome assembly efficiency correlates positively with histone octamer concentration, rate constant, and time.
  • Histone H2A demonstrates higher in vitro competitive ability than H2A.Z.
  • The model accurately describes H2A.Z-containing nucleosome assembly governed by chemical kinetics.

Conclusions:

  • The chemical kinetic model is adaptable for studying H2A.Z nucleosome assembly.
  • Histone H2A is more competitive than H2A.Z in nucleosome formation in vitro.
  • Chemical kinetics principles govern in vitro H2A.Z nucleosome assembly.