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

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

2010-04-30

arxiv.org/abs/1004.5514v1

J. Phys.: Condens. Matter 22 (2010) 414105

Physics

Biological Physics

19 pages, 7 figures, accepted author manuscript, to appear in J. Phys.: Cond. Mat.

Scientific paper

10.1088/0953-8984/22/41/414105

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums 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.

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