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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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Dinucleotide step parameters. (A) Illustration of the six degrees of freedom for DNA structure at the base pair step level. (B) Dinucleotide step values for NCP-601L (blue) and NCP147 (green) averaged over one particle half and for the two particle halves of NCP146b (red and yellow; NCP146b displays a distinct DNA–histone register in each half). Dinucleotide steps in major groove-inward sections in addition to the flanking major-to-minor groove-inward interface steps have a grey shaded background. The four dinucleotide steps in each minor groove-inward section have a white background with a gold shading indicating the step located at the pressure point.
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gks261-F3: Dinucleotide step parameters. (A) Illustration of the six degrees of freedom for DNA structure at the base pair step level. (B) Dinucleotide step values for NCP-601L (blue) and NCP147 (green) averaged over one particle half and for the two particle halves of NCP146b (red and yellow; NCP146b displays a distinct DNA–histone register in each half). Dinucleotide steps in major groove-inward sections in addition to the flanking major-to-minor groove-inward interface steps have a grey shaded background. The four dinucleotide steps in each minor groove-inward section have a white background with a gold shading indicating the step located at the pressure point.

Mentions: The general attributes that appear to endow the 601L (like the consensus) sequence with exceptional histone octamer affinity have been previously outlined (12). These include the presence of the most flexible dinucleotide type, TA (29), at minor groove-inward positions where DNA distortion is energetically most challenging (30,31) and G/C-rich elements, which are predisposed to major groove bending/compression, at major groove-inward positions. Moreover, 601L and the other 601 sequences contain TTTAA elements at minor groove-inward locations situated 1.5 double helix turns from the nucleosome centre (SHL ±1.5). This coincides with the most stringent singular positioning signal in the nucleosome (9), whereby extreme narrowing of the minor groove is required (10), and α-satellite derivatives engineered with TTTAA elements at SHL ±1.5 (NCP-TA and NCP-TA2) also display increased stability over their parent constructs (Figure 2 and Supplementary Figure S2). Nonetheless, the reason why TA steps in the highest affinity sequences occupy such uniquely defined positions within the different minor groove-inward locations (Figure 1B) is not clear. Moreover, as apparent from the crystal structure of NCP-601L, the TA elements do not take up the strongly kinked conformations expected based on the behaviour of highly flexible CA = TG dinucleotides in the earlier α-satellite structures (Figures 3 and 4). Additionally, the high stability of NCP-601R in spite of having GGG(G) elements over six of the eight minor groove-inward locations around the nucleosome centre (Figure 1B) blatantly conflicts with the general preference of G/C sequences to take up the opposite orientation of major groove-inward (3,6,17).Figure 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)

Dinucleotide step parameters. (A) Illustration of the six degrees of freedom for DNA structure at the base pair step level. (B) Dinucleotide step values for NCP-601L (blue) and NCP147 (green) averaged over one particle half and for the two particle halves of NCP146b (red and yellow; NCP146b displays a distinct DNA–histone register in each half). Dinucleotide steps in major groove-inward sections in addition to the flanking major-to-minor groove-inward interface steps have a grey shaded background. The four dinucleotide steps in each minor groove-inward section have a white background with a gold shading indicating the step located at the pressure point.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gks261-F3: Dinucleotide step parameters. (A) Illustration of the six degrees of freedom for DNA structure at the base pair step level. (B) Dinucleotide step values for NCP-601L (blue) and NCP147 (green) averaged over one particle half and for the two particle halves of NCP146b (red and yellow; NCP146b displays a distinct DNA–histone register in each half). Dinucleotide steps in major groove-inward sections in addition to the flanking major-to-minor groove-inward interface steps have a grey shaded background. The four dinucleotide steps in each minor groove-inward section have a white background with a gold shading indicating the step located at the pressure point.
Mentions: The general attributes that appear to endow the 601L (like the consensus) sequence with exceptional histone octamer affinity have been previously outlined (12). These include the presence of the most flexible dinucleotide type, TA (29), at minor groove-inward positions where DNA distortion is energetically most challenging (30,31) and G/C-rich elements, which are predisposed to major groove bending/compression, at major groove-inward positions. Moreover, 601L and the other 601 sequences contain TTTAA elements at minor groove-inward locations situated 1.5 double helix turns from the nucleosome centre (SHL ±1.5). This coincides with the most stringent singular positioning signal in the nucleosome (9), whereby extreme narrowing of the minor groove is required (10), and α-satellite derivatives engineered with TTTAA elements at SHL ±1.5 (NCP-TA and NCP-TA2) also display increased stability over their parent constructs (Figure 2 and Supplementary Figure S2). Nonetheless, the reason why TA steps in the highest affinity sequences occupy such uniquely defined positions within the different minor groove-inward locations (Figure 1B) is not clear. Moreover, as apparent from the crystal structure of NCP-601L, the TA elements do not take up the strongly kinked conformations expected based on the behaviour of highly flexible CA = TG dinucleotides in the earlier α-satellite structures (Figures 3 and 4). Additionally, the high stability of NCP-601R in spite of having GGG(G) elements over six of the eight minor groove-inward locations around the nucleosome centre (Figure 1B) blatantly conflicts with the general preference of G/C sequences to take up the opposite orientation of major groove-inward (3,6,17).Figure 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