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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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Nucleosome dynamics: Sequence matters.

Behrouz Eslami-Mossallam1, Helmut Schiessel2, John van Noort3

  • 1Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, Leiden 2333 CA, The Netherlands; Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, Leiden 2333 CA, The Netherlands; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, Delft 2628 CJ, The Netherlands.

Advances in Colloid and Interface Science
|February 21, 2016
PubMed
Summary
This summary is machine-generated.

DNA sequence significantly impacts nucleosome physical and dynamic properties. This review highlights how base pair sequence influences nucleosome positioning, stability, and higher-order structures.

Keywords:
ChromatinDNA sequenceNucleosome

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genomics

Background:

  • Eukaryotic DNA is largely organized into nucleosomes, with histone proteins forming the core.
  • Nucleosomes exhibit diversity due to histone post-translational modifications and, crucially, DNA sequence variations.

Purpose of the Study:

  • To review experimental and theoretical advances emphasizing the role of DNA base pair sequence in nucleosome function.
  • To explore how DNA sequence influences key nucleosome behaviors and higher-order structures.

Main Methods:

  • Literature review of experimental studies on nucleosome dynamics and DNA mechanics.
  • Theoretical modeling and computational analyses of DNA sequence-nucleosome interactions.

Main Results:

  • Nucleosomal base pair sequence is a critical determinant of nucleosome positioning and stability.
  • DNA sequence dictates mechanical properties influencing nucleosome sliding, breathing, unwrapping, and dissociation.
  • Sequence-dependent DNA mechanics significantly affect nucleosome dynamics and higher-order chromatin organization.

Conclusions:

  • The mechanical properties of DNA, dictated by its sequence, are fundamental to nucleosome physical and dynamic characteristics.
  • A comprehensive understanding of nucleosome function requires considering the impact of DNA sequence alongside histone modifications.