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Title of Journal: J Stat Phys

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Abbravation: Journal of Statistical Physics

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Springer US

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DOI

10.1007/s00441-004-0963-x

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1572-9613

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Statistical Mechanics of Nucleosomes Constrained b

Authors: Răzvan V Chereji Alexandre V Morozov
Publish Date: 2011/05/15
Volume: 144, Issue: 2, Pages: 379-404
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Abstract

Eukaryotic DNA is packaged into chromatin onedimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30nm chromatin fibers which in turn form higherorder structures Felsenfeld and Groudine in Nature 421448 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 423145 2003 In order to describe how chromatin fiber formation affects nucleosome positioning and energetics we have developed a thermodynamic model of finitesize particles with effective nearestneighbor interactions and arbitrary DNAbinding energies We show that both one and twobody interactions can be extracted from oneparticle density profiles based on highthroughput maps of in vitro or in vivo nucleosome positions Although a simpler approach that neglects twobody 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 twobody effects Finally we construct a minimal model in which nucleosomes are positioned primarily by steric exclusion and twobody interactions rather than intrinsic histoneDNA sequence preferences The model reproduces nucleosome occupancy patterns observed over transcribed regions in living cells

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