caa a22 4500 445391472 CHVBK 20180317143048.0 cr unu---uuuuu 170323e20110701xx s 000 0 eng 10.1007/s10955-011-0214-y doi (NATIONALLICENCE)springer-10.1007/s10955-011-0214-y Statistical Mechanics of Nucleosomes Constrained by Higher-Order Chromatin Structure [Elektronische Daten] [Răzvan Chereji, Alexandre Morozov] Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures (Felsenfeld and Groudine in Nature 421:448, 2003). Each nucleosome, the fundamental unit of chromatin, has 147 base pairs (bp) of DNA wrapped around a histone octamer (Richmond and Davey in Nature 423:145, 2003). In order to describe how chromatin fiber formation affects nucleosome positioning and energetics, we have developed a thermodynamic model of finite-size particles with effective nearest-neighbor interactions and arbitrary DNA-binding energies. We show that both one- and two-body interactions can be extracted from one-particle density profiles based on high-throughput maps of in vitro or in vivo nucleosome positions. Although a simpler approach that neglects two-body interactions (even if they are in fact present in the system) can be used to predict sequence determinants of nucleosome positions, the full theory is required to disentangle one- and two-body effects. Finally, we construct a minimal model in which nucleosomes are positioned primarily by steric exclusion and two-body interactions rather than intrinsic histone-DNA sequence preferences. The model reproduces nucleosome occupancy patterns observed over transcribed regions in living cells. Springer Science+Business Media, LLC, 2011 Chromatin structure nationallicence Nucleosome positioning nationallicence One-dimensional classical fluid of interacting particles nationallicence Chereji Răzvan Department of Physics and Astronomy, Rutgers University, 08854-8019, Piscataway, NJ, USA aut Morozov Alexandre Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, 08854-8019, Piscataway, NJ, USA aut Journal of Statistical Physics Springer US; http://www.springer-ny.com 144/2(2011-07-01), 379-404 0022-4715 144:2<379 2011 144 10955 https://doi.org/10.1007/s10955-011-0214-y text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s10955-011-0214-y text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Chereji Răzvan Department of Physics and Astronomy, Rutgers University, 08854-8019, Piscataway, NJ, USA aut NATIONALLICENCE 700 1- Morozov Alexandre Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, 08854-8019, Piscataway, NJ, USA aut NATIONALLICENCE 773 0- Journal of Statistical Physics Springer US; http://www.springer-ny.com 144/2(2011-07-01), 379-404 0022-4715 144:2<379 2011 144 10955 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer