title: Uncovering the forces between nucleosomes using DNA origami.
abstract: Revealing the energy landscape for nucleosome association may contribute to the understanding of higher-order chromatin structures and their impact on genome regulation. We accomplish this in a direct measurement by integrating two nucleosomes into a DNA origami-based force spectrometer, which enabled subnanometer-resolution measurements of nucleosome-nucleosome distance frequencies via single-particle electron microscopy imaging. From the data, we derived the Boltzmann-weighted distance-dependent energy landscape for nucleosome pair interactions. We find a shallow but long-range (~6 nm) attractive nucleosome pair potential with a minimum of -1.6 kcal/mol close to direct contact distances. The relative nucleosome orientation had little influence, but histone H4 acetylation or removal of histone tails drastically decreased the interaction strength. Because of the weak and shallow pair potential, higher-order nucleosome assemblies will be compliant and experience dynamic shape fluctuations in the absence of additional cofactors. Our results contribute to a more accurate description of chromatin and our force spectrometer provides a powerful tool for the direct and high-resolution study of molecular interactions using imaging techniques.
authors.affiliation: Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, Germany.
authors.forename: Jonas J
authors.initials: JJ
authors.lastname: Funke
authors.affiliation: Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, Germany.
authors.forename: Philip
authors.initials: P
authors.lastname: Ketterer
authors.affiliation: Biomedical Center, Molecular Biology, Ludwig-Maximilians-Universität München, Martinsried near Munich, Germany.
authors.forename: Corinna
authors.initials: C
authors.lastname: Lieleg
authors.affiliation: Biomedical Center, Molecular Biology, Ludwig-Maximilians-Universität München, Martinsried near Munich, Germany.
authors.forename: Sarah
authors.initials: S
authors.lastname: Schunter
authors.affiliation: Biomedical Center, Molecular Biology, Ludwig-Maximilians-Universität München, Martinsried near Munich, Germany.
authors.forename: Philipp
authors.identifier: 0000-0001-7526-6549
authors.initials: P
authors.lastname: Korber
authors.affiliation: Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, Germany.
authors.forename: Hendrik
authors.initials: H
authors.lastname: Dietz
mesh_terms: D000107:Acetylation; D000818:Animals; D004247:DNA / Q000737:chemistry*; D004331:Drosophila melanogaster; D006657:Histones / Q000737:chemistry*; D009707:Nucleosomes / Q000737:chemistry*
chemical_list: D006657:Histones; D009707:Nucleosomes; D004247:DNA
keywords: Cryo EM; DNA; DNA Origami; Nucleosome; TEM; biophysical; chromatin; molecular biology; nanotechnology; self-assembly