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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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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
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In silico evidence for sequence-dependent nucleosome sliding.

Joshua Lequieu1, David C Schwartz2,3,4, Juan J de Pablo5,6

  • 1Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637.

Proceedings of the National Academy of Sciences of the United States of America
|October 29, 2017
PubMed
Summary
This summary is machine-generated.

Nucleosome positioning is influenced by DNA sequence and protein interactions. This study reveals how DNA sequence, histone modifications, and chromatin remodelers collectively regulate nucleosome dynamics.

Keywords:
advanced sampling techniqueschromatin dynamicsmolecular simulationnucleosome repositioning

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biophysics

Background:

  • Nucleosomes are fundamental units of chromatin, controlling cellular processes through their genomic positioning.
  • Nucleosome location is determined by DNA sequence and protein interactions, crucial for cellular function.
  • The interplay between DNA sequence and nucleosome dynamics is not fully understood.

Purpose of the Study:

  • To investigate the interplay between DNA sequence and nucleosome dynamics using a molecular model.
  • To develop a comprehensive understanding of free energy surfaces and nucleosome repositioning dynamics.

Main Methods:

  • Utilized a molecular model to simulate nucleosome repositioning.
  • Analyzed free energy surfaces and associated dynamics.
  • Investigated the role of DNA sequence, binding energy, and chromatin remodelers.

Main Results:

  • Nucleosome repositioning is strongly linked to DNA sequence and histone core binding energy.
  • Chromatin remodelers can overcome DNA sequence preferences by applying torque.
  • The histone H4 tail acts as a crucial coupling point for DNA sequence, histone modifications, and remodelers.

Conclusions:

  • The study provides molecular insights into nucleosome dynamics and regulation.
  • Identified key molecular mechanisms governing chromatin organization and function.
  • Highlights the coordinated roles of DNA sequence, histone modifications, and remodelers in gene regulation.