title: Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization.
abstract: Bacterial chromosome has a compact structure that dynamically changes its shape in response to bacterial growth rate and growth phase. Determining how chromatin remains accessible to DNA binding proteins, and transcription machinery is crucial to understand the link between genetic regulation, DNA structure, and topology. Here, we study very large supercoiled dsDNA using high-resolution characterization, theoretical modeling, and molecular dynamics calculations. We unveil a new type of highly ordered DNA organization forming in the presence of attractive DNA-DNA interactions, which we call hyperplectonemes. We demonstrate that their formation depends on DNA size, supercoiling, and bacterial physiology. We compare structural, nanomechanic, and dynamic properties of hyperplectonemes bound by three highly abundant nucleoid-associated proteins (FIS, H-NS, and HU). In all these cases, the negative supercoiling of DNA determines molecular dynamics, modulating their 3D shape. Overall, our findings provide a mechanistic insight into the critical role of DNA topology in genetic regulation.
authors.affiliation: Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland.
authors.forename: Aleksandre
authors.initials: A
authors.lastname: Japaridze
authors.affiliation: Jacobs University , D-28759 Bremen, Germany.|Agricultural University of Georgia , 0159 Tbilisi, Georgia.
authors.forename: Georgi
authors.initials: G
authors.lastname: Muskhelishvili
authors.affiliation: Center for Integrative Genomics, University of Lausanne , 1015 Lausanne, Switzerland.|Vital-IT, SIB Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Benedetti
authors.affiliation: Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland.
authors.forename: Agni F M
authors.initials: AF
authors.lastname: Gavriilidou
authors.affiliation: Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland.
authors.forename: Renato
authors.initials: R
authors.lastname: Zenobi
authors.affiliation: Vital-IT, SIB Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland.|Laboratoire de Biophysique Statistique, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland.
authors.forename: Paolo
authors.initials: P
authors.lastname: De Los Rios
authors.affiliation: Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland.|Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche , Rome, Italy.
authors.forename: Giovanni
authors.identifier: 0000-0003-2434-2155
authors.initials: G
authors.lastname: Longo
authors.affiliation: Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Dietler
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry / Q000648:ultrastructure*; D004278:DNA, Superhelical / Q000737:chemistry / Q000648:ultrastructure*; D004926:Escherichia coli / Q000737:chemistry / Q000648:ultrastructure*; D018625:Microscopy, Atomic Force; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation
chemical_list: D004269:DNA, Bacterial; D004278:DNA, Superhelical
keywords: DNA; FIS; H-NS; HU; nucleoid associated proteins; plectonemes; self-organization; supercoiling