The mechanics behind DNA sequence-dependent properties of the nucleosome
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 structur...
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sg-ntu-dr.10356-971792023-02-28T16:55:59Z The mechanics behind DNA sequence-dependent properties of the nucleosome Chua, Eugene Yue Dao Vasudevan, Dileep Davey, Gabriela Elzbieta Wu, Bin Davey, Curtis Alexander School of Biological Sciences DRNTU::Science::Biological sciences::Genetics 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. Published version 2013-05-27T02:40:48Z 2019-12-06T19:39:53Z 2013-05-27T02:40:48Z 2019-12-06T19:39:53Z 2012 2012 Journal Article 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. https://hdl.handle.net/10356/97179 http://hdl.handle.net/10220/9991 10.1093/nar/gks261 22453276 en Nucleic acids research © 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: [http://dx.doi.org/10.1093/nar/gks261]. 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. application/pdf |
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DRNTU::Science::Biological sciences::Genetics Chua, Eugene Yue Dao Vasudevan, Dileep Davey, Gabriela Elzbieta Wu, Bin Davey, Curtis Alexander The mechanics behind DNA sequence-dependent properties of the nucleosome |
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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. |
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School of Biological Sciences |
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School of Biological Sciences Chua, Eugene Yue Dao Vasudevan, Dileep Davey, Gabriela Elzbieta Wu, Bin Davey, Curtis Alexander |
format |
Article |
author |
Chua, Eugene Yue Dao Vasudevan, Dileep Davey, Gabriela Elzbieta Wu, Bin Davey, Curtis Alexander |
author_sort |
Chua, Eugene Yue Dao |
title |
The mechanics behind DNA sequence-dependent properties of the nucleosome |
title_short |
The mechanics behind DNA sequence-dependent properties of the nucleosome |
title_full |
The mechanics behind DNA sequence-dependent properties of the nucleosome |
title_fullStr |
The mechanics behind DNA sequence-dependent properties of the nucleosome |
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The mechanics behind DNA sequence-dependent properties of the nucleosome |
title_sort |
mechanics behind dna sequence-dependent properties of the nucleosome |
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2013 |
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https://hdl.handle.net/10356/97179 http://hdl.handle.net/10220/9991 |
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