title: The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes.
abstract: Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness of the DNA wrapping around the nucleosome core is intrinsically ambidextrous, and depends on the pre-assembly supercoiling state of the DNA, i.e., it is not uniquely determined by the octameric histone core. Nucleosomes assembled onto negatively supercoiled DNA are found to exhibit a left-handed conformation, whereas assembly onto positively supercoiled DNA results in right-handed nucleosomes. This intrinsic flexibility to adopt both chiralities is observed both for canonical H3 nucleosomes, and for centromere-specific variant CENP-A nucleosomes. These data support recent advances suggesting an intrinsic adaptability of the nucleosome, and provide insights into how nucleosomes might rapidly re-assemble after cellular processes that generate positive supercoiling in vivo.
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands.
authors.forename: R
authors.identifier: http://orcid.org/0000-0001-8909-9518
authors.initials: R
authors.lastname: Vlijm
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands.
authors.forename: S H
authors.initials: SH
authors.lastname: Kim
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands.
authors.forename: P L
authors.identifier: http://orcid.org/0000-0003-2718-3882
authors.initials: PL
authors.lastname: De Zwart
authors.affiliation: Chromatin Structure and Epigenetic Mechanisms Unit, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA. dalaly@mail.nih.gov C.Dekker@tudelft.nl.
authors.forename: Y
authors.initials: Y
authors.lastname: Dalal
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands.
authors.forename: C
authors.initials: C
authors.lastname: Dekker
mesh_terms: D002503:Centromere; D000076247:Centromere Protein A / Q000737:chemistry*; D004278:DNA, Superhelical / Q000737:chemistry*; D006657:Histones / Q000737:chemistry*; D009707:Nucleosomes / Q000737:chemistry*
chemical_list: D000076247:Centromere Protein A; D004278:DNA, Superhelical; D006657:Histones; D009707:Nucleosomes