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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.
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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
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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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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.
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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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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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Correlating histone acetylation with nucleosome core particle dynamics and function.

Tae Hun Kim1,2,3,4, Michael L Nosella2,4, Nicolas Bolik-Coulon1,2,3

  • 1Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.

Proceedings of the National Academy of Sciences of the United States of America
|April 3, 2023
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Summary
This summary is machine-generated.

Histone acetylation, an epigenetic mark, alters nucleosome dynamics. Acetylation of H2A significantly increases its structural dynamics, impacting protein factor accessibility and biological output.

Keywords:
conformational heterogeneitymethyl-TROSY NMRnucleosomal DNA ligation and degradationnucleosome structural dynamics

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Area of Science:

  • Biochemistry
  • Epigenetics
  • Structural Biology

Background:

  • Histone lysine acetylation is a key epigenetic modification regulating gene expression.
  • Previous studies suggest acetylation increases histone tail dynamics, but its effect on the nucleosome core is less understood.
  • A systematic experimental investigation is needed to understand how histone acetylation influences nucleosome structural dynamics and protein factor accessibility.

Purpose of the Study:

  • To experimentally evaluate the effects of individual histone acetylation on nucleosome core particle (NCP) dynamics.
  • To investigate how histone acetylation impacts the accessibility of protein factors like ligases and nucleases.
  • To develop a thermodynamic model for nucleosome-core particle stacking.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy of nucleosome core particles (NCPs).
  • Evaluation of acetylation effects on individual histone tails and core dynamics.
  • Dynamic Light Scattering (DLS) experiments to assess inter-NCP interactions.

Main Results:

  • Acetylation of histones H2B, H3, and H4 minimally affected histone core particle dynamics, despite increased tail motions.
  • Acetylation of histone H2A significantly increased its structural dynamics, particularly the docking domain and L1 loop.
  • Increased H2A dynamics correlated with enhanced NCP susceptibility to nuclease digestion and DNA ligation.
  • Acetylation decreased inter-NCP interactions in a histone-dependent manner.

Conclusions:

  • Histone acetylation induces nuanced changes in NCP structural dynamics, varying by histone.
  • Acetylation, especially of H2A, modulates protein factor interactions and accessibility.
  • These dynamic changes influence biological output by altering nucleosome interactions and accessibility.