DNA Shape Dominates Sequence Affinity in Nucleosome Formation

Gordon S. Freeman, Joshua P. Lequieu, Daniel M. Hinckley, Jonathan K. Whitmer, and Juan J. de Pablo

Phys. Rev. Lett. 113, 168101 – Published 14 October 2014

Abstract

Nucleosomes provide the basic unit of compaction in eukaryotic genomes, and the mechanisms that dictate their position at specific locations along a DNA sequence are of central importance to genetics. In this Letter, we employ molecular models of DNA and proteins to elucidate various aspects of nucleosome positioning. In particular, we show how DNA’s histone affinity is encoded in its sequence-dependent shape, including subtle deviations from the ideal straight B-DNA form and local variations of minor groove width. By relying on high-precision simulations of the free energy of nucleosome complexes, we also demonstrate that, depending on DNA’s intrinsic curvature, histone binding can be dominated by bending interactions or electrostatic interactions. More generally, the results presented here explain how sequence, manifested as the shape of the DNA molecule, dominates molecular recognition in the problem of nucleosome positioning.

Received 3 December 2013

DOI:https://doi.org/10.1103/PhysRevLett.113.168101

Authors & Affiliations

Gordon S. Freeman¹, Joshua P. Lequieu², Daniel M. Hinckley¹, Jonathan K. Whitmer^1,2,3, and Juan J. de Pablo^2,3,*

¹Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
²Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
³Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA

^*depablo@uchicago.edu

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Vol. 113, Iss. 16 — 17 October 2014

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Figure 1
DNA sequence plays a crucial role in determining nucleosome affinity. (a) Coarse-graining scheme and representative nucleosome configuration. DNA is modeled using three sites per nucleotide [20]; the histone is represented with one site per amino acid, located at the center-of-mass of the side chain [21]. Nucleosomal configurations are obtained by mapping our coarse model onto the 1KX5 crystal structure [23] and then performing molecular dynamics. Note that 1KX5 is only used to provide an initial condition; no information from 1KX5 is encoded into our model. (b) Minimum-energy structure of c1, c2, c3, d1, d2, and d3 DNA sequences used in study. Differences in DNA sequence result in large variations of intrinsic curvature. A sequence with no curvature is shown for reference. (c) Sequences used in study (as represented in Ref. [7]). Red blocks denote TA nucleotides which are known to enhance DNA orientational preference.
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Figure 2
(a) Predicted and experimental binding free energy. The trends predicted for nucleosome binding affinity in simulations are consistent with experiments from Refs. [7, 9], and [24]. The dashed line is a guide to the eye corresponding to exact agreement. (b) Binding free energy as a function of DNA orientation around the histone core. Increasing the number of favorable dinucleotide binding motifs enhances DNA orientational preference. Sequences ranked by number of favorable motifs are $c 2 > c 3 > c 1$ . The location of the free energy minima is consistent with the narrow minor groove at TA-rich motifs pointing inward toward the protein core.
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Figure 3
The role of intrinsic curvature and minor groove width. (a) Free energies of nucleosome formation, relative to sequence TG, decrease with increasing intrinsic curvature, $⟨ A_{f}^{0} ⟩$ , in both simulation (black circles) and experiment (red triangles) [9]. To compare all sequences, $Δ Δ A$ values were calculated for both c1 and d1 relative to TG; sequences c1–c3 and d1–d3 are omitted from the experimental points due a lack of analogous experimental data. (b) Affinity may be understood through the minor groove width profile, shown for sequences TG (black lines, $Δ Δ A = 0 kJ / mol$ ), TG-T (blue lines, $Δ Δ A = 17.4 kJ / mol$ ) and TRGC (red lines, $Δ Δ A = 12.1 kJ / mol$ ). The top panel shows relative minor groove widths ( ${MGW}_{rel} = MGW − {MGW}_{TG}$ ), and the bottom panel shows the corresponding Fourier transformed intensity, $| F (q) |$ .
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Figure 4
Identification of the dominant mechanism in nucleosome formation. (a) Schematic Description of Models “A,” “H,” and “S” for sequence c1. The shape corresponds to the minimum energy configuration. Colors represent local base step flexibility (blue: flexible, red: stiff), as measured by a local, base-step dependent bending constant $k_{bend}$ [22]. (b) Predicted and experimental binding free energy for each model. Correlation coefficients for best fit lines are $r_{A} = 0.89$ , $r_{H} = 0.98$ , $r_{S} = - 0.74$ . The dashed line is a guide to the eye corresponding to exact agreement. (c) Relative importance of DNA-deformation and DNA-protein energy contributions. The mechanism of nucleosomal assembly is a strong function of sequence.
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