Flexible histone tails in a new mesoscopic oligonucleosome model

Abstract

We describe a new mesoscopic model of oligonucleosomes that incorporates flexible histone tails. The nucleosome cores are modeled using the discrete surface-charge optimization model, which treats the nucleosome as an electrostatic surface represented by hundreds of point charges; the linker DNAs are treated using a discrete elastic chain model; and the histone tails are modeled using a bead/chain hydrodynamic approach as chains of connected beads where each bead represents five protein residues. Appropriate charges and force fields are assigned to each histone chain so as to reproduce the electrostatic potential, structure, and dynamics of the corresponding atomistic histone tails at different salt conditions. The dynamics of resulting oligonucleosomes at different sizes and varying salt concentrations are simulated by Brownian dynamics with complete hydrodynamic interactions. The analyses demonstrate that the new mesoscopic model reproduces experimental results better than its predecessors, which modeled histone tails as rigid entities. In particular, our model with flexible histone tails: correctly accounts for salt-dependent conformational changes in the histone tails; yields the experimentally obtained values of histone-tail mediated core/core attraction energies; and considers the partial shielding of electrostatic repulsion between DNA linkers as a result of the spatial distribution of histone tails. These effects are crucial for regulating chromatin structure but are absent or improperly treated in models with rigid histone tails. The development of this model of oligonucleosomes thus opens new avenues for studying the role of histone tails and their variants in mediating gene expression through modulation of chromatin structure.

FIGURE 1

Nucleosome core modeling using DiSCO. The top figure shows the crystal structure of the nucleosome without the histone tail residues (nucleosome core). The bottom figure shows our model nucleosome core with discretized charges. The charges on the nucleosome core are deliberately shown smaller than their excluded volume for clarity, and they are color-coded according to their magnitude relative to the electronic charge (e), as shown in the color chart. The surface of the nucleosome core has been displaced inwards by 2 Å to allow visibility of the charges.

FIGURE 2

Discrete elastic bead model for linker DNA. The top figure shows the atomistic linker DNA while the bottom figure shows our model.

FIGURE 3

(a) Schematic representation of our model nucleosomal arrays with a total of N nucleosome cores and linker DNA beads. Each linker DNA is represented by six beads in red for this illustration. For clarity, nucleosome cores are drawn as gray cylinders while only one out of 10 histone tails with five beads is shown in blue. Missing portions between the second nucleosome and the last are shown as thick dots. (b) Schematic representation of the nucleosome core without histone tails showing the wound DNA supercoil and the relative positions of the entering and leaving linker DNA. (c) Model geometry showing the coordinate systems adopted for modeling linker DNA-nucleosome mechanics.

FIGURE 4

Two-step modeling of histone tails. The top figure shows the atomistic description of the H3 histone tail. The middle figure portrays the subunit model corresponding to that tail. The bottom figure shows the protein-bead model developed in this study derived from the subunit model.

FIGURE 5

Repeating motif of an oligonucleosome containing 51-bp linker DNA. The top figure shows its atomistic representation, while the bottom figure shows its coarse-grained representation via flexible-tail model. The histone tails are color-coded as follows: H3 (blue), H4 (green), H2A (yellow), and H2B (red); the nucleosome cores and linker beads are colored gray and red, respectively.

FIGURE 6

Variation of the maximum nucleosome extension (top) and the radius of gyration (bottom) versus the monovalent salt concentration. Simulation results are represented by circles and experimental data from Bertin et al. (56) as squares. The dashed line for the simulation results serves as a guide to the eye.

FIGURE 7

Positional distribution of histone tail beads projected onto the a-b plane of the nucleosome. Top and bottom figures correspond to monovalent salt concentrations of 0.01 M and 0.2 M, respectively. Color-coding for the histone tails is as follows: H3 (blue), H4 (green), H2A (yellow), and H2B (red). The nucleosome core in the background is colored black.

FIGURE 8

Dependence of the diffusion constant of mononucleosome (solid symbols), dinucleosomes (gray symbols), and trinucleosomes (open symbols) on the salt concentration. Circular symbols represent experimental values from Yao et al. (57) (mononucleosomes), Yao et al. (58) (dinucleosomes), and Bednar et al. (59) (trinucleosomes). Square and triangular symbols represent results from Brownian dynamics simulations of flexible-tail and fixed-tail model of oligonucleosomes, respectively. The dashed lines, which represent the mean experimental diffusion values for the three array sizes, serve to guide the eye.

FIGURE 9

Two starting configurations for the 12-unit nucleosomal array simulations corresponding to a solenoidlike (solenoid with straight linkers) configuration (left) and zigzag (right). Insets show corresponding stacking patterns without histone tails. In the main figures, the histone tails are color-coded according to: H3 (blue), H4 (green), H2A (yellow), and H2B (red); the nucleosome cores and linker beads are shaded gray and red, respectively. In the insets, the nucleosome core is white and the wrapped + linker DNA is red.

FIGURE 10

Configuration of the 12-unit nucleosomal array at the end of 5-μs runs at 0.2 M (left) and 0.01 M (right) salt concentration. Insets show corresponding stacking patterns without histone tails. In the main figures, the histone tails are color-coded according to: H3 (blue), H4 (green), H2A (yellow), and H2B (red); the nucleosome cores and linker beads are shaded gray and red, respectively. In the insets, the nucleosome core is white and the wrapped + linker DNA is red.

FIGURE 11

Sedimentation coefficients versus salt concentration obtained using Brownian dynamics of the oligonucleosome model developed in this study (open circles). Also shown are sedimentation coefficients obtained experimentally by Hansen et al. (60) (open triangles), and those obtained theoretically using the fixed-tail model (open squares and diamonds). The open squares represent results obtained by Sun et al. (30) via Monte Carlo simulations and the open diamonds represent results obtained via Brownian dynamics simulations in the current study.