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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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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

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Computational study of remodeling in a nucleosomal array.

Raoul D Schram1, Henrike Klinker, Peter B Becker

  • 1Instituut-Lorentz, Leiden University, P.O. Box 9506, 2300 RA, Leiden, The Netherlands.

The European Physical Journal. E, Soft Matter
|August 8, 2015
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Summary
This summary is machine-generated.

Chromatin remodeling complexes like ACF and ISWI alter DNA accessibility. Simple models reveal distinct remodeling activities between ISWI and ACF, prompting further microscopic analysis of nucleosomal arrays.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Biochemistry

Background:

  • Chromatin remodeling complexes use ATP hydrolysis to alter chromatin structure.
  • Nucleosome sliding along DNA is a key mechanism for changing DNA accessibility.
  • The ACF and ISWI enzymes are crucial for chromatin remodeling.

Purpose of the Study:

  • To model DNA accessibility changes during chromatin remodeling by ACF and ISWI.
  • To compare the remodeling activities of the ACF enzyme and its ISWI subunit.
  • To investigate microscopic models for ACF-mediated nucleosomal array remodeling.

Main Methods:

  • Development of simple models to describe experimental data.
  • Analysis of DNA accessibility changes along synthetic nucleosomal arrays.
  • Comparative study of ACF and ISWI remodeling activities.

Main Results:

  • Significant qualitative differences observed between ISWI and ACF remodeling.
  • Models successfully describe experimental data for DNA accessibility changes.
  • Microscopic models were employed to further understand ACF behavior.

Conclusions:

  • ISWI and ACF exhibit distinct chromatin remodeling mechanisms.
  • The developed models provide insights into nucleosome sliding dynamics.
  • Further investigation into microscopic models is necessary for a complete understanding of ACF remodeling.