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BP: Fachverband Biologische Physik

BP 9: Posters: DNA \& DNA Enzymes

BP 9.9: Poster

Monday, March 14, 2011, 17:15–20:00, P3

A unified model for statistical nucleosome positioning — •Brendan Osberg, Wolfram Moebius, and Ulrich Gerland — Ludwig Maximilians Universitaet, Munich, Germany

Recent genome-wide maps of nucleosome positions in different eukaryotes have revealed a common pattern around transcription start sites, involving a nucleosome-free region flanked by a pronounced periodic pattern in the average nucleosome density. For the yeast S. cerevisiae, a description of the periodic pattern has been established based on the statistical positioning mechanism of Kornberg and Stryer. This description derives from the physics of a dense one dimensional gas consisting of fixed-size particles. Here, we consider 12 Hemiascomycota yeast species, each of which displays a distinct nucleosome pattern. Since the chromatin constituents are highly conserved between species, and thus the mechanism underlying the formation of the patterns is expected to be related, we present a unified quantitative description.We extend the simple one-dimensional gas model account for transient unwrapping of short segments of nucleosomal DNA. Chromatin behavior in the majority of species is well described by this generalized gas model -only the average nucleosome density is a species-dependent variable. An exception is K. lactis, where we find an increased effective nucleosome width (potentially due to an increased use of linker histone H1 in this species). Together, our results provide a biochemically plausible role for nucleosome unwrapping in global chromatin behavior and establish a unified nucleosome gas model, providing a basis for quantitative analysis of chromatin effects on cis-regulatory transcription control.