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Related Concept Videos

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.
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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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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 Nucleosome02:33

The Nucleosome

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DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to 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.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
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The Nucleosome01:19

The Nucleosome

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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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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? 
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Related Experiment Video

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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

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Interactions Between Nucleosomes: From Atomistic Simulation to Polymer Model.

Chengwei Zhang1,2,3,4, Jing Huang2,3,4

  • 1College of Life Sciences, Zhejiang University, Hangzhou, China.

Frontiers in Molecular Biosciences
|April 29, 2021
PubMed
Summary
This summary is machine-generated.

This study details nucleosome interactions using all-atom simulations, revealing atomistic details crucial for understanding chromatin organization and gene regulation.

Keywords:
chromatincoarse-grainmolecular dynamics simulationnucleosomepotential of mean forceumbrella sampling

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • Genome organization in space and time is critical for gene expression and regulation.
  • Chromatin folding follows biophysical rules and biological processes.
  • Nucleosomes are the fundamental units of chromatin structure.

Purpose of the Study:

  • To investigate the effective interactions between two nucleosomes under physiological conditions.
  • To provide atomistic details of nucleosome interactions in solution.
  • To inform the development of bottom-up coarse-grained models of chromatin.

Main Methods:

  • Explicit-solvent all-atom molecular dynamics simulations were employed.
  • Umbrella sampling simulations were used to derive free energy landscapes.
  • Simulations were conducted under physiological conditions.

Main Results:

  • The derived free energy landscapes align with existing experimental and simulation data.
  • Atomistic insights into the interactions between two nucleosomes were obtained.
  • The study provides a foundation for detailed chromatin modeling.

Conclusions:

  • Explicit-solvent all-atom simulations effectively capture nucleosome interactions.
  • Understanding these interactions is key to deciphering chromatin dynamics.
  • The findings facilitate the creation of more accurate chromatin models.