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Title: The mechanics behind DNA sequence-dependent properties of the nucleosome
Authors: Chua, Eugene Yue Dao
Vasudevan, Dileep
Davey, Gabriela Elzbieta
Wu, Bin
Davey, Curtis Alexander
Keywords: DRNTU::Science::Biological sciences::Genetics
Issue Date: 2012
Source: Chua, E. Y. D., Vasudevan, D., Davey, G. E., Wu, B., & Davey, C. A. (2012). The mechanics behind DNA sequence-dependent properties of the nucleosome. Nucleic Acids Research, 40(13), 6338-6352.
Series/Report no.: Nucleic acids research
Abstract: 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.
DOI: 10.1093/nar/gks261
Rights: © 2012 The Author(s). This paper was published in Nucleic Acids Research and is made available as an electronic reprint (preprint) with permission of The Author(s). The paper can be found at the following official DOI: []. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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