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

Teif, VB and Rippe, K (2010) 'Statistical-mechanical lattice models for protein-DNA binding in chromatin.' Journal of Physics: Condensed Matter, 22 (41). p. 414105. ISSN 0953-8984

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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. © 2010 IOP Publishing Ltd.

Item Type: Article
Additional Information: 19 pages, 7 figures, accepted author manuscript, to appear in J. Phys.: Cond. Mat.
Uncontrolled Keywords: Chromatin; Nucleosomes; Histones; Transcription Factors; DNA; Adenosine Triphosphate; Chromatin Assembly and Disassembly; Gene Expression Regulation; Nucleic Acid Conformation; Protein Structure, Quaternary; Protein Binding; Thermodynamics; Models, Molecular; Protein Multimerization; Mechanical Phenomena; Biomechanical Phenomena
Subjects: Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health
Faculty of Science and Health > Life Sciences, School of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 16 Oct 2017 10:47
Last Modified: 06 Jan 2022 14:49
URI: http://repository.essex.ac.uk/id/eprint/20480

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