High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes

Nat Commun. 2018 Nov 6;9(1):4628. doi: 10.1038/s41467-018-06758-1.

Abstract

Nucleosomes play a dual role in compacting the genome and regulating the access to DNA. To unravel the underlying mechanism, we study fluorescently labeled mononucleosomes by multi-parameter FRET measurements and characterize their structural and dynamic heterogeneity upon NaCl-induced destabilization. Species-selective fluorescence lifetime analysis and dynamic photon distribution analysis reveal intermediates during nucleosome opening and lead to a coherent structural and kinetic model. In dynamic octasomes and hexasomes the interface between the H2A-H2B dimers and the (H3-H4)2 tetramer opens asymmetrically by an angle of ≈20° on a 50 and 15 µs time scale, respectively. This is followed by a slower stepwise release of the dimers coupled with DNA unwrapping. A mutation (H2A-R81A) at the interface between H2A and H3 facilitates initial opening, confirming the central role of the dimer:tetramer interface for nucleosome stability. Partially opened states such as those described here might serve as convenient nucleation sites for DNA-recognizing proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin Assembly and Disassembly*
  • DNA / chemistry*
  • Dimerization
  • Energy Transfer
  • Fluorescence
  • Fluorescence Resonance Energy Transfer / methods*
  • Histones / chemistry*
  • Histones / genetics
  • Kinetics
  • Models, Molecular
  • Mutation
  • Nucleosomes / chemistry*
  • Photons
  • Protein Conformation
  • Protein Multimerization
  • Sodium Chloride
  • Thermodynamics

Substances

  • Histones
  • Nucleosomes
  • Sodium Chloride
  • DNA