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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.
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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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The Nucleosome Core Particle01:12

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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 Nucleosome Core Particle02:10

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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 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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Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
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Mapping Allosteric Communication in the Nucleosome with Conditional Activity.

Augustine C Onyema1,2, Chukwuebuka Dikeocha3, Jonathan Moussa4

  • 1Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States.

Biorxiv : the Preprint Server for Biology
|September 26, 2025
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Summary
This summary is machine-generated.

This study introduces CONDACT, a Python tool to analyze nucleosome dynamics. It reveals long-range communication within the nucleosome core particle, impacting genome accessibility.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • The nucleosome core particle (NCP) is crucial for genome accessibility, regulated by allosteric communication between histones and DNA.
  • Understanding these dynamic interactions is key to deciphering gene regulation and disease mechanisms.

Purpose of the Study:

  • To develop and apply a computational method for quantifying time-resolved kinetic correlations in nucleosome systems.
  • To investigate long-range allosteric communication within the NCP across different DNA sequences.

Main Methods:

  • Utilized molecular dynamics simulations of NCP systems.
  • Developed the open-source Python library CONDACT (CONDitional ACTivity) to analyze kinetic correlations.
  • Tracked dihedral angle transitions in histone proteins and DNA.

Main Results:

  • Identified residues with significant dynamical memory and mapped inter-residue communication pathways.
  • Revealed kinetically connected domains involving key functional sites (PTMs, mutations, DNA contacts).
  • Observed dynamic coupling spanning distances up to 7.5 nm within the NCP.

Conclusions:

  • The study provides novel insights into the long-range allosteric behavior of the nucleosome.
  • Findings highlight the role of dynamic communication in regulating chromatin accessibility.
  • Quantification of allosteric behavior may identify therapeutic targets for chromatin-related diseases.