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Related Concept Videos

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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Chromatin Packaging01:32

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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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Nucleosome Remodeling02:54

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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 process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
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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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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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Polymer model with long-range interactions: analysis and applications to the chromatin structure.

A Amitai1, D Holcman1

  • 1Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|December 17, 2013
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Summary

We developed a new polymer model for chromatin dynamics, accounting for long-range interactions. This model helps interpret experimental data like chromosome capture, revealing local monomer interactions from diffusion exponents.

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Area of Science:

  • Molecular Biology
  • Polymer Physics
  • Genomics

Background:

  • Chromatin, the complex of DNA and proteins, forms a hierarchical structure within the cell nucleus.
  • Existing polymer models like the Rouse model often overlook long-range interactions crucial for chromatin dynamics.

Purpose of the Study:

  • To develop and analyze a novel polymer model for chromatin dynamics.
  • To incorporate long-range interactions beyond nearest-neighbor contacts.
  • To provide a framework for interpreting experimental chromatin data.

Main Methods:

  • Development of a new polymer model for chromatin structure.
  • Analysis of the model to account for long-range interactions.
  • Calculation of anomalous diffusion exponents, cross-correlation functions, and loop formation times.

Main Results:

  • The model successfully recovers local monomer interactions from the anomalous diffusion exponent.
  • Asymptotic computations for cross-correlation functions and mean loop formation times were performed.
  • The model provides a theoretical basis for understanding chromatin polymer behavior.

Conclusions:

  • The developed polymer model offers a more realistic representation of chromatin dynamics.
  • It enables the interpretation of experimental data, particularly chromosome capture data.
  • This approach advances our understanding of nuclear organization and genome regulation.