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Nucleosome flipping drives kinetic proofreading and processivity by SWR1.

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  • 1Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.

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The SWR1 complex facilitates histone dimer exchange in yeast nucleosomes. This study reveals a processive, two-step mechanism where nucleosomes flip, allowing efficient double exchange without dissociation.

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Area of Science:

  • Chromatin biology
  • Molecular mechanisms of DNA repair and replication
  • Epigenetics

Background:

  • The SWR1 complex is crucial for replacing canonical histone H2A-H2B dimers with Htz1-H2B dimers in nucleosomes.
  • Understanding the mechanism of SWR1-mediated exchange is key to comprehending nucleosome dynamics and epigenetic regulation.

Purpose of the Study:

  • To elucidate the step-by-step mechanism of double histone dimer exchange by the SWR1 complex.
  • To investigate whether nucleosome release is required for processive double exchange.
  • To determine the role of nucleosome flipping and the Swc2 subunit in the SWR1 complex's function.

Main Methods:

  • Single-molecule analysis to observe real-time histone dimer exchange.
  • Cryo-electron microscopy to visualize structural intermediates and conformational states.
  • Biochemical assays to measure binding dwell times and reaction intermediates.

Main Results:

  • Demonstrated a two-step, processive double exchange mechanism for H2A-H2B dimers by SWR1, occurring without nucleosome release.
  • Observed nucleosomes flipping between distinct states, presenting different faces and histone dimers to SWR1.
  • Identified a hexasome intermediate bound in a fixed orientation and highlighted the Swc2 subunit's role in facilitating conformational changes.

Conclusions:

  • The SWR1 complex employs a processive mechanism for double dimer exchange, involving nucleosome flipping and specific subunit interactions.
  • This mechanism allows SWR1 to efficiently 'proofread' histone dimer identities within nucleosomes.
  • The findings provide a detailed molecular understanding of SWR1's role in chromatin remodeling and epigenetic regulation.