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Electrostatic mechanism of nucleosomal array folding revealed by computer simulation.

Jian Sun1, Qing Zhang, Tamar Schlick

  • 1Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA.

Proceedings of the National Academy of Sciences of the United States of America
|May 28, 2005
PubMed
Summary

Chromatin fiber structure changes with salt concentration. Histone tails are crucial for folding, with H3 tails stabilizing the fiber at physiological salt levels.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • Chromatin fiber conformation is known to be salt-dependent.
  • The precise molecular mechanisms driving these salt-dependent changes remain poorly understood.

Purpose of the Study:

  • To elucidate the molecular mechanism behind salt-dependent chromatin fiber rearrangements.
  • To investigate the role of histone tails in nucleosomal array condensation.

Main Methods:

  • Utilized an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome.
  • Performed Monte Carlo simulations on a 12-nucleosome array.
  • Analyzed energy contributions to internucleosome and DNA-nucleosome interactions.

Main Results:

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  • Nucleosomal arrays exhibit salt-dependent condensation, aligning with hydrodynamic measurements.
  • At high salt, arrays form irregular 3D zig-zag structures; at low salt, they adopt an extended 'beads-on-a-string' form.
  • Histone tails, especially H3 tails, are essential for internucleosome and linker DNA-nucleosome attractions, stabilizing the fiber at physiological salt.

Conclusions:

  • Linker DNA repulsion drives the extended conformation at low salt.
  • Internucleosome attraction, mediated by histone tails, drives folding at high salt.
  • The balance of these forces dictates salt-dependent chromatin condensation, with H3 tails playing a key stabilizing role.