Nucleic Acids Research Advance Access originally published online on July 22, 2009
Nucleic Acids Research 2009 37(17):5641-5655; doi:10.1093/nar/gkp610
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Nucleic Acids Research, 2009, Vol. 37, No. 17 5641-5655
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Gene Regulation, Chromatin and Epigenetics |
Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities
1Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and 2Institute of Bioorganic Chemistry, Belarus National Academy of Sciences, Kuprevich 5/2, 220141, Minsk, Belarus
*To whom correspondence should be addressed. Tel: +49 6221 54 51378; Email: Vladimir.Teif{at}bioquant.uni-heidelberg.de Correspondence may also be addressed to Karsten Rippe. Tel: +49 6221 54 51376; Email: Karsten.Rippe{at}bioquant.uni-heidelberg.de
Received March 9, 2009. Revised July 3, 2009. Accepted July 6, 2009.
Nucleosome positions on the DNA are determined by the intrinsic affinities of histone proteins to a given DNA sequence and by the ATP-dependent activities of chromatin remodeling complexes that can translocate nucleosomes with respect to the DNA. Here, we report a theoretical approach that takes into account both contributions. In the theoretical analysis two types of experiments have been considered: in vitro experiments with a single reconstituted nucleosome and in vivo genome-scale mapping of nucleosome positions. The effect of chromatin remodelers was described by iteratively redistributing the nucleosomes according to certain rules until a new steady state was reached. Three major classes of remodeler activities were identified: (i) the establishment of a regular nucleosome spacing in the vicinity of a strong positioning signal acting as a boundary, (ii) the enrichment/depletion of nucleosomes through amplification of intrinsic DNA-sequence-encoded signals and (iii) the removal of nucleosomes from high-affinity binding sites. From an analysis of data for nucleosome positions in resting and activated human CD4+ T cells [Schones et al., Cell 132, p. 887] it was concluded that the redistribution of a nucleosome map to a new state is greatly facilitated if the remodeler complex translocates the nucleosome with a preferred directionality.