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

Chua EY, Vasudevan D, Davey GE, Wu B, Davey CA - Nucleic Acids Res. (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.

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.

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KMnO4 footprinting reveals DNA context-dependent distortions. (A and B) DNA samples, comprising six different constructs, correspond to purine sequencing standard (m) or naked DNA (D) and NCP (N) that were subjected to permanganate reactivity analysis. Minor groove-inward-facing nucleotides (highlighted in orange), regions of DNA stretching (magenta arrows; dashed for mixed stretched and non-stretched configurations) and the central nucleotide (blue dot) are based on the crystal structure assignments (Figure 1B).
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gks261-F7: KMnO4 footprinting reveals DNA context-dependent distortions. (A and B) DNA samples, comprising six different constructs, correspond to purine sequencing standard (m) or naked DNA (D) and NCP (N) that were subjected to permanganate reactivity analysis. Minor groove-inward-facing nucleotides (highlighted in orange), regions of DNA stretching (magenta arrows; dashed for mixed stretched and non-stretched configurations) and the central nucleotide (blue dot) are based on the crystal structure assignments (Figure 1B).

Mentions: The Quantity One program (Bio-Rad Laboratories) was used for intensity quantification of gel bands (Table 3). The reactivity hotspot intensities for the nucleosomal state (Figure 7B, lanes 3 and 9), and the corresponding locations in the naked DNA state (lanes 2 and 8), were placed on a relative scale by normalizing with respect to the band intensity associated with nucleotide 5 (SHL ±0.5) of NCP-601L (lane 3). For SHL sites containing more than one reactive nucleotide, normalized intensities were summed to yield the values given in Table 3.Table 3.


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

Chua EY, Vasudevan D, Davey GE, Wu B, Davey CA - Nucleic Acids Res. (2012)

KMnO4 footprinting reveals DNA context-dependent distortions. (A and B) DNA samples, comprising six different constructs, correspond to purine sequencing standard (m) or naked DNA (D) and NCP (N) that were subjected to permanganate reactivity analysis. Minor groove-inward-facing nucleotides (highlighted in orange), regions of DNA stretching (magenta arrows; dashed for mixed stretched and non-stretched configurations) and the central nucleotide (blue dot) are based on the crystal structure assignments (Figure 1B).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3401446&req=5

gks261-F7: KMnO4 footprinting reveals DNA context-dependent distortions. (A and B) DNA samples, comprising six different constructs, correspond to purine sequencing standard (m) or naked DNA (D) and NCP (N) that were subjected to permanganate reactivity analysis. Minor groove-inward-facing nucleotides (highlighted in orange), regions of DNA stretching (magenta arrows; dashed for mixed stretched and non-stretched configurations) and the central nucleotide (blue dot) are based on the crystal structure assignments (Figure 1B).
Mentions: The Quantity One program (Bio-Rad Laboratories) was used for intensity quantification of gel bands (Table 3). The reactivity hotspot intensities for the nucleosomal state (Figure 7B, lanes 3 and 9), and the corresponding locations in the naked DNA state (lanes 2 and 8), were placed on a relative scale by normalizing with respect to the band intensity associated with nucleotide 5 (SHL ±0.5) of NCP-601L (lane 3). For SHL sites containing more than one reactive nucleotide, normalized intensities were summed to yield the values given in Table 3.Table 3.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.

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.

Show MeSH
Related in: MedlinePlus