Dresden 2009 – scientific programme
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BP: Fachverband Biologische Physik
BP 20: DNA, RNA and Chromatin
BP 20.11: Talk
Thursday, March 26, 2009, 17:00–17:15, HÜL 186
Physical Analysis of Statistical Nucleosome Positioning in the Yeast Genome — •Wolfram Möbius1,2 and Ulrich Gerland1,2 — 1Institute for Theoretical Physics, Universität zu Köln — 2Arnold Sommerfeld Center and Center for NanoScience, LMU München
Recent experiments determined nucleosome positions in the yeast genome [1-3] and identified two salient features in the spatial organization: (i) nucleosome-free regions upstream of many transcription start sites (TSS), and (ii) an oscillatory nucleosome density downstream. The mechanisms underlying these patterns are less clear. One possible scenario is that the majority of nucleosome positions near the TSS are directly determined by DNA sequence [4], binding competition with other proteins [5], or by active remodelling. An alternative scenario is that only a minority of these nucleosomes is directly positioned by the DNA sequence, forming barriers which strongly constrain the positions of closeby nucleosomes, purely on statistical grounds [3]. Specifically, the nucleosomes might be seen as a one-dimensional gas of rods (Tonks gas) with a few barriers in between. To quantitatively test this scenario, we assess whether the experimentally observed oscillations in nucleosome occupancy are indeed compatible with Tonks gas statistics. Furthermore, we estimate whether biologically reasonable binding specificity suffices to form barriers able to create nucleosome free regions as observed. [1] G.-C. Yuan et al., Science 309, 626 (2005) [2] W. Lee et al., Nature Genetics 39, 1235 (2007) [3] T. Mavrich et al., Genome Research 18, 1073 (2008) [4] E. Segal et al., Nature 442, 772 (2006) [5] A.V. Morozov et al., arxiv.org:0805.4017v1 (2008)