title: Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays.
abstract: The first level of genome packaging in eukaryotic cells involves the formation of dense nucleosome arrays, with DNA coverage near 90% in yeasts. How cells achieve such high coverage within a short time, e.g. after DNA replication, remains poorly understood. It is known that random sequential adsorption of impenetrable particles on a line reaches high density extremely slowly, due to a jamming phenomenon. The nucleosome-shifting action of remodeling enzymes has been proposed as a mechanism to resolve such jams. Here, we suggest two biophysical mechanisms which assist rapid filling of DNA with nucleosomes, and we quantitatively characterize these mechanisms within mathematical models. First, we show that the 'softness' of nucleosomes, due to nucleosome breathing and stepwise nucleosome assembly, significantly alters the filling behavior, speeding up the process relative to 'hard' particles with fixed, mutually exclusive DNA footprints. Second, we explore model scenarios in which the progression of the replication fork could eliminate nucleosome jamming, either by rapid filling in its wake or via memory of the parental nucleosome positions. Taken together, our results suggest that biophysical effects promote rapid nucleosome filling, making the reassembly of densely packed nucleosomes after DNA replication a simpler task for cells than was previously thought.
authors.affiliation: Theory of Complex Biosystems, Physik-Department, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany.
authors.forename: Brendan
authors.initials: B
authors.lastname: Osberg
authors.affiliation: Theory of Complex Biosystems, Physik-Department, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Nuebler
authors.affiliation: Adolf-Butenandt-Institut, University of Munich, Schillerstrasse 44, 80336 Munich, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Korber
authors.affiliation: Theory of Complex Biosystems, Physik-Department, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany gerland@tum.de.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Gerland
mesh_terms: D004261:DNA Replication; D007700:Kinetics; D008957:Models, Genetic; D009707:Nucleosomes / Q000378:metabolism*
chemical_list: D009707:Nucleosomes