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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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Double helix association, conformation and positioning on the histone octamer. (A and B) Minor and major groove-inward-facing regions are orange and black, respectively, with ‘pressure points’ at minor groove-inward centres highlighted gold. Histone proteins are blue, H3, green, H4, yellow, H2A and red, H2B (DNA-binding motifs: L, loop, A, α-helix). (A) Section of the NCP-601L crystal structure with phosphorous atoms of the ‘binding platforms’ shown as spheres. Bound single-strand regions act as a ‘hinge’, allowing conformational variation between different DNA sequences. (B) NCP constructs are arranged in order of increasing salt stability. Severe kinks at locations of DNA stretching around SHL ±2 or ±5 (magenta underlines), associated with a single base pair shift in histone-nucleotide register, are depicted as gaps in the sequence. DNA-permanganate reactivity hotspots in the nucleosomal state from footprinting analysis (six constructs) are indicated with green asterisks. Sites where the nucleosomal DNA shows reduced permanganate reactivity relative to the naked state are indicated with blue arrowheads. Capitalized bases in the Widom consensus sequence represent the most highly conserved nucleotides (17). The histone–DNA register assignments for NCP-601R and the Widom consensus sequence, for which crystal structures are not available, were inferred from the structures of NCP-601 and NCP-601L.
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gks261-F1: Double helix association, conformation and positioning on the histone octamer. (A and B) Minor and major groove-inward-facing regions are orange and black, respectively, with ‘pressure points’ at minor groove-inward centres highlighted gold. Histone proteins are blue, H3, green, H4, yellow, H2A and red, H2B (DNA-binding motifs: L, loop, A, α-helix). (A) Section of the NCP-601L crystal structure with phosphorous atoms of the ‘binding platforms’ shown as spheres. Bound single-strand regions act as a ‘hinge’, allowing conformational variation between different DNA sequences. (B) NCP constructs are arranged in order of increasing salt stability. Severe kinks at locations of DNA stretching around SHL ±2 or ±5 (magenta underlines), associated with a single base pair shift in histone-nucleotide register, are depicted as gaps in the sequence. DNA-permanganate reactivity hotspots in the nucleosomal state from footprinting analysis (six constructs) are indicated with green asterisks. Sites where the nucleosomal DNA shows reduced permanganate reactivity relative to the naked state are indicated with blue arrowheads. Capitalized bases in the Widom consensus sequence represent the most highly conserved nucleotides (17). The histone–DNA register assignments for NCP-601R and the Widom consensus sequence, for which crystal structures are not available, were inferred from the structures of NCP-601 and NCP-601L.

Mentions: The phosphate groups comprising the binding platforms correspond to those from the nucleotide pairs on the inside of the superhelix that span the major-to-minor groove-inward transitions (black and orange phosphate pairs in Figure 1). The nucleotide numbers of the binding platform phosphate groups can be derived from the histone–DNA register assignments in Figure 1B: NCP145, chains I and J, −54, −53, −43, −42, −33, −32, −23, −22, −13, −12, −3, −2, 7, 8, 17, 18, 27, 28, 37, 38, 47, 48, 58, 59; NCP-601L, chains I and J, −54, −53, −44, −43, −34, −33, −24, −23, −13, −12, −3, −2, 7, 8, 17, 18, 28, 29, 38, 39, 48, 49, 58, 59; NCP146b, chain I, −54, −53, −44, −43, −34, −33, −24, −23, −13, −12, −3, −2, 7, 8, 17, 18, 28, 29, 38, 39, 48, 49, 59, 60, chain J, −55, −54, −44, −43, −34, −33, −24, −23, −13, −12, −3, −2, 7, 8, 17, 18, 28, 29, 38, 39, 48, 49, 58, 59; NCP147, chains I and J, −55, −54, −44, −43, −34, −33, −24, −23, −13, −12, −3, −2, 7, 8, 17, 18, 28, 29, 38, 39, 48, 49, 59, 60. For the double helix binding variability between NCP constructs analysis (Table 2), the positional deviation comparison sets entailed the 24 phosphorous atoms of the binding platforms from each H3–H4 tetramer and H2A–H2B dimer pair.Figure 1.


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

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

Double helix association, conformation and positioning on the histone octamer. (A and B) Minor and major groove-inward-facing regions are orange and black, respectively, with ‘pressure points’ at minor groove-inward centres highlighted gold. Histone proteins are blue, H3, green, H4, yellow, H2A and red, H2B (DNA-binding motifs: L, loop, A, α-helix). (A) Section of the NCP-601L crystal structure with phosphorous atoms of the ‘binding platforms’ shown as spheres. Bound single-strand regions act as a ‘hinge’, allowing conformational variation between different DNA sequences. (B) NCP constructs are arranged in order of increasing salt stability. Severe kinks at locations of DNA stretching around SHL ±2 or ±5 (magenta underlines), associated with a single base pair shift in histone-nucleotide register, are depicted as gaps in the sequence. DNA-permanganate reactivity hotspots in the nucleosomal state from footprinting analysis (six constructs) are indicated with green asterisks. Sites where the nucleosomal DNA shows reduced permanganate reactivity relative to the naked state are indicated with blue arrowheads. Capitalized bases in the Widom consensus sequence represent the most highly conserved nucleotides (17). The histone–DNA register assignments for NCP-601R and the Widom consensus sequence, for which crystal structures are not available, were inferred from the structures of NCP-601 and NCP-601L.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gks261-F1: Double helix association, conformation and positioning on the histone octamer. (A and B) Minor and major groove-inward-facing regions are orange and black, respectively, with ‘pressure points’ at minor groove-inward centres highlighted gold. Histone proteins are blue, H3, green, H4, yellow, H2A and red, H2B (DNA-binding motifs: L, loop, A, α-helix). (A) Section of the NCP-601L crystal structure with phosphorous atoms of the ‘binding platforms’ shown as spheres. Bound single-strand regions act as a ‘hinge’, allowing conformational variation between different DNA sequences. (B) NCP constructs are arranged in order of increasing salt stability. Severe kinks at locations of DNA stretching around SHL ±2 or ±5 (magenta underlines), associated with a single base pair shift in histone-nucleotide register, are depicted as gaps in the sequence. DNA-permanganate reactivity hotspots in the nucleosomal state from footprinting analysis (six constructs) are indicated with green asterisks. Sites where the nucleosomal DNA shows reduced permanganate reactivity relative to the naked state are indicated with blue arrowheads. Capitalized bases in the Widom consensus sequence represent the most highly conserved nucleotides (17). The histone–DNA register assignments for NCP-601R and the Widom consensus sequence, for which crystal structures are not available, were inferred from the structures of NCP-601 and NCP-601L.
Mentions: The phosphate groups comprising the binding platforms correspond to those from the nucleotide pairs on the inside of the superhelix that span the major-to-minor groove-inward transitions (black and orange phosphate pairs in Figure 1). The nucleotide numbers of the binding platform phosphate groups can be derived from the histone–DNA register assignments in Figure 1B: NCP145, chains I and J, −54, −53, −43, −42, −33, −32, −23, −22, −13, −12, −3, −2, 7, 8, 17, 18, 27, 28, 37, 38, 47, 48, 58, 59; NCP-601L, chains I and J, −54, −53, −44, −43, −34, −33, −24, −23, −13, −12, −3, −2, 7, 8, 17, 18, 28, 29, 38, 39, 48, 49, 58, 59; NCP146b, chain I, −54, −53, −44, −43, −34, −33, −24, −23, −13, −12, −3, −2, 7, 8, 17, 18, 28, 29, 38, 39, 48, 49, 59, 60, chain J, −55, −54, −44, −43, −34, −33, −24, −23, −13, −12, −3, −2, 7, 8, 17, 18, 28, 29, 38, 39, 48, 49, 58, 59; NCP147, chains I and J, −55, −54, −44, −43, −34, −33, −24, −23, −13, −12, −3, −2, 7, 8, 17, 18, 28, 29, 38, 39, 48, 49, 59, 60. For the double helix binding variability between NCP constructs analysis (Table 2), the positional deviation comparison sets entailed the 24 phosphorous atoms of the binding platforms from each H3–H4 tetramer and H2A–H2B dimer pair.Figure 1.

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