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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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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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Histone Modification02:32

Histone Modification

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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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The Nucleosome Core Particle02:10

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.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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.
Writers
The writer...
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Related Experiment Video

Updated: Feb 26, 2026

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
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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, Rutika Patel1,2

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

Journal of Chemical Information and Modeling
|February 24, 2026
PubMed
Summary
This summary is machine-generated.

We developed CONDACT, a Python library, to analyze nucleosome dynamics and map communication pathways. This reveals how histone-DNA interactions influence genome accessibility and offers therapeutic targets.

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Area of Science:

  • Structural biology
  • Computational biophysics
  • Genomics

Background:

  • Nucleosome core particles (NCPs) regulate genome accessibility via allosteric communication between histones and DNA.
  • Understanding these dynamics is crucial for deciphering gene regulation and disease mechanisms.

Purpose of the Study:

  • To quantify time-resolved kinetic correlations in nucleosome systems using molecular dynamics simulations.
  • To develop an open-source Python library, CONDACT, for analyzing nucleosome dynamics.
  • To identify long-range allosteric communication pathways within NCPs.

Main Methods:

  • Utilized long-time molecular dynamics simulations of NCPs with Widom-601 and ASP DNA sequences.
  • Developed and applied the CONDACT (CONDitional ACTivity) Python library.
  • Tracked dihedral angle transitions to identify residues with high dynamical memory and map communication pathways.

Main Results:

  • Identified kinetically connected domains within NCPs, including histone subunits and DNA.
  • Mapped inter-residue communication pathways, revealing dynamic coupling up to 7.5 nm.
  • Highlighted the involvement of post-translational modification sites and oncogenic mutation sites in these pathways.

Conclusions:

  • The study provides new insights into the long-range allosteric behavior of nucleosomes and its role in chromatin accessibility.
  • CONDACT enables quantitative analysis of nucleosome dynamics, revealing functionally important communication networks.
  • Findings suggest potential therapeutic targets within nucleosome domains for intervention.