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J Phys Condens Matter. 2010 Oct 20;22(41):414105. doi: 10.1088/0953-8984/22/41/414105. Epub 2010 Sep 30.

Statistical-mechanical lattice models for protein-DNA binding in chromatin.

Author information

1
Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Vladimir.Teif@bioquant.uni-heidelberg.de

Abstract

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibria measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical-mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quantitative models for the regulation of gene expression.

PMID:
21386588
DOI:
10.1088/0953-8984/22/41/414105
[Indexed for MEDLINE]

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