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Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22257-62. doi: 10.1073/pnas.0909511106. Epub 2009 Dec 14.

Nucleosome positioning by genomic excluding-energy barriers.

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  • 1Universitè Claude Bernard Lyon 1, Université de Lyon, F-69000 Lyon, France.

Abstract

Recent genome-wide nucleosome mappings along with bioinformatics studies have confirmed that the DNA sequence plays a more important role in the collective organization of nucleosomes in vivo than previously thought. Yet in living cells, this organization also results from the action of various external factors like DNA-binding proteins and chromatin remodelers. To decipher the code for intrinsic chromatin organization, there is thus a need for in vitro experiments to bridge the gap between computational models of nucleosome sequence preferences and in vivo nucleosome occupancy data. Here we combine atomic force microscopy in liquid and theoretical modeling to demonstrate that a major sequence signaling in vivo are high-energy barriers that locally inhibit nucleosome formation rather than favorable positioning motifs. We show that these genomic excluding-energy barriers condition the collective assembly of neighboring nucleosomes consistently with equilibrium statistical ordering principles. The analysis of two gene promoter regions in Saccharomyces cerevisiae and the human genome indicates that these genomic barriers direct the intrinsic nucleosome occupancy of regulatory sites, thereby contributing to gene expression regulation.

PMID:
20018700
[PubMed - indexed for MEDLINE]
PMCID:
PMC2799728
Free PMC Article

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