High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes

Nanoscale. 2021 Mar 18;13(10):5435-5447. doi: 10.1039/d0nr08564b.

Abstract

Nucleosomes, the fundamental units of chromatin, regulate readout and expression of eukaryotic genomes. Single-molecule experiments have revealed force-induced nucleosome accessibility, but a high-resolution unwrapping landscape in the absence of external forces is currently lacking. Here, we introduce a high-throughput pipeline for the analysis of nucleosome conformations based on atomic force microscopy and automated, multi-parameter image analysis. Our data set of ∼10 000 nucleosomes reveals multiple unwrapping states corresponding to steps of 5 bp DNA. For canonical H3 nucleosomes, we observe that dissociation from one side impedes unwrapping from the other side, but in contrast to force-induced unwrapping, we find only a weak sequence-dependent asymmetry. Notably, centromeric CENP-A nucleosomes do not unwrap anti-cooperatively, in stark contrast to H3 nucleosomes. Finally, our results reconcile previous conflicting findings about the differences in height between H3 and CENP-A nucleosomes. We expect our approach to enable critical insights into epigenetic regulation of nucleosome structure and stability and to facilitate future high-throughput AFM studies that involve heterogeneous nucleoprotein complexes.

MeSH terms

  • Centromere / metabolism
  • Centromere Protein A / genetics
  • Epigenesis, Genetic
  • Histones* / metabolism
  • Nucleosomes*

Substances

  • Centromere Protein A
  • Histones
  • Nucleosomes