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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...
12.9K
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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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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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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Related Experiment Video

Updated: May 17, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.

Rutika Patel1,2, Sharon M Loverde1,2,3,4

  • 1Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.

Journal of Chemical Theory and Computation
|April 28, 2025
PubMed
Summary

Histone tails in nucleosomes, the building blocks of chromatin, adopt distinct conformations. Acetylation of the H2B tail promotes secondary structure, impacting gene regulation.

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Area of Science:

  • Structural biology
  • Molecular dynamics
  • Biophysics

Background:

  • Nucleosome core particles (NCPs) are fundamental chromatin units, essential for DNA packaging and regulation.
  • Histone N-terminal tails undergo epigenetic modifications influencing chromatin structure and biological processes like transcription.
  • Understanding histone tail dynamics is crucial for deciphering gene regulation mechanisms.

Purpose of the Study:

  • To elucidate distinct conformations and dynamics of histone tails using advanced computational methods.
  • To characterize the kinetics and conformational landscape of histone tails within the nucleosome.
  • To investigate the specific effects of acetylation on the H2B tail's structure and dynamics.

Main Methods:

  • All-atom molecular dynamics (MD) simulations of nucleosomes at microsecond timescales.
  • Construction of Markov state models (MSMs) to analyze conformational dynamics.
  • Time-lagged independent component analysis (tICA) and k-means clustering to identify slow dynamics and conformational states.

Main Results:

  • MSMs successfully identified distinct conformational states and transition probabilities for histone tails.
  • Analysis revealed the essential slow dynamics governing tail conformations.
  • Acetylation of the H2B tail was shown to increase secondary structure formation and transition rates.

Conclusions:

  • The study provides insights into the conformational dynamics and kinetics of histone tails.
  • Findings highlight the role of H2B tail acetylation in modulating nucleosome stability and gene regulation.
  • This work lays the foundation for understanding the functional significance of histone tail conformations.