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    Keywords: IN-VIVO ; ATOMIC-FORCE MICROSCOPY ; LIGAND-BINDING ; GENE-REGULATION ; COOPERATIVE BINDING ; TARGET SITES ; TRANSCRIPTION-FACTOR-BINDING ; ONE-DIMENSIONAL LATTICES ; NUCLEOSOME POSITIONS ; LINEAR LATTICE
    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.
    Type of Publication: Journal article published
    PubMed ID: 21386588
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