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Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding.

Stefjord Todolli1, Robert T Young1, Abigail S Watkins1

  • 1Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.

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Summary

Nucleosomes exhibit varied DNA twisting, challenging the static model. Undertwisted DNA structures impact nucleosome function and higher-order chromatin organization.

Keywords:
DNA minicircleMonte Carlo DNA simulationnucleosomal twist uptakenucleosome gapingoligonucleosome arrayundertwisted nucleosome

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Area of Science:

  • Structural biology
  • Chromatin dynamics
  • Molecular biophysics

Background:

  • Nucleosomes, the basic units of DNA packaging, are often viewed as static despite their dynamic functions.
  • Existing high-resolution structures suggest DNA within nucleosomes is generally overtwisted.
  • However, documented twist defects indicate a more complex reality.

Purpose of the Study:

  • To analyze the distribution of DNA twist in nucleosomal structures.
  • To investigate the implications of DNA folding variations on nucleosome function and chromatin organization.
  • To compare the behavior of chromatin models based on overtwisted versus undertwisted nucleosomes.

Main Methods:

  • Analysis of high-resolution nucleosome structures from the Protein Data Bank.
  • Computational simulations of oligonucleosome arrays using different DNA twist models.
  • Assessment of DNA pathway differences in nucleosome-decorated minicircles.

Main Results:

  • Nucleosomal DNA exhibits a heterogeneous twist distribution, with a significant fraction of undertwisted structures.
  • Differences in DNA folding, beyond twist, influence nucleosome disassembly and higher-order structures.
  • Simulations show undertwisted models lead to distinct chromatin compaction and inter-nucleosome interactions compared to overtwisted models.

Conclusions:

  • The prevailing view of uniformly overtwisted nucleosomal DNA is an oversimplification.
  • Variations in DNA twist and pathway are critical for nucleosome dynamics and higher-order chromatin structure.
  • Understanding these subtle structural differences is key to deciphering nucleosome function and chromatin regulation.