Biology – Quantitative Biology – Genomics
Scientific paper
2010-12-26
Biology
Quantitative Biology
Genomics
22 pages, 10 figures
Scientific paper
10.1007/s10955-011-0214-y
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. Each nucleosome, the fundamental unit of chromatin, has 147 base pairs of DNA wrapped around a histone octamer. 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 accurately 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 by steric exclusion and two-body interactions rather than intrinsic histone-DNA sequence preferences. The model accurately reproduces nucleosome occupancy patterns observed over transcribed regions in living cells.
Chereji Răzvan V.
Morozov Alexandre V.
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