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Nucleic Acids Res July 1, 2012; 40 (13): 6338-52.

The mechanics behind DNA sequence-dependent properties of the nucleosome.

Chua EY , Vasudevan D , Davey GE , Wu B , Davey CA .

Chromatin organization and composition impart sophisticated regulatory features critical to eukaryotic genomic function. Although DNA sequence-dependent histone octamer binding is important for nucleosome activity, many aspects of this phenomenon have remained elusive. We studied nucleosome structure and stability with diverse DNA sequences, including Widom 601 derivatives with the highest known octamer affinities, to establish a simple model behind the mechanics of sequence dependency. This uncovers the unique but unexpected role of TA dinucleotides and a propensity for G|C-rich sequence elements to conform energetically favourably at most locations around the histone octamer, which rationalizes G|C% as the most predictive factor for nucleosome occupancy in vivo. In addition, our findings reveal dominant constraints on double helix conformation by H3-H4 relative to H2A-H2B binding and DNA sequence context-dependency underlying nucleosome structure, positioning and stability. This provides a basis for improved prediction of nucleosomal properties and the design of tailored DNA constructs for chromatin investigations.

PubMed ID: 22453276
PMC ID: PMC3401446
Article link: Nucleic Acids Res
Grant support: [+]

Species referenced: Xenopus
Genes referenced: h2ac21 h2bc21 taar2

Article Images: [+] show captions
References [+] :
, The CCP4 suite: programs for protein crystallography. 2004, Pubmed