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Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding.

Jan Huertas1, Caitlin M MacCarthy2, Hans R Schöler3

  • 1In Silico Biomolecular Structure and Dynamics Group, Hubrecht Institute, Utrecht, the Netherlands; Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany; and.

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Pioneer transcription factors (TFs) like Oct4 can bind to DNA within nucleosomes, a key step in cell fate changes. This study reveals how nucleosome structure and dynamics facilitate this crucial pioneer TF binding.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Genetics

Background:

  • Transcription factors (TFs) regulate gene expression by binding to DNA.
  • Chromatin, composed of DNA wrapped around histones, often restricts TF access.
  • Pioneer TFs are hypothesized to initiate gene activation by accessing DNA within nucleosomes.

Purpose of the Study:

  • To elucidate the structural dynamics of nucleosomes that enable binding by the pioneer transcription factor Oct4.
  • To understand how Oct4 interacts with DNA in the context of a nucleosome.

Main Methods:

  • Utilizing molecular dynamics simulations to model Oct4-nucleosome interactions.
  • Analyzing nucleosome flexibility, motion, and structural configurations during TF binding.

Main Results:

  • Nucleosome flexibility and motions (breathing, twisting) increase with multiple TF binding sites.
  • Regions near TF binding sites exhibit heightened local structural flexibility.
  • Oct4 can form stable interactions with partial nucleosomal binding sites, accommodating DNA curvature and histone interactions.

Conclusions:

  • A structural mechanism for pioneer TF (Oct4) recognition of nucleosomal DNA is proposed.
  • This mechanism provides insight into how chromatin is opened for gene regulation during cell fate transitions.