Nucleosome spacing controls chromatin spatial structure and accessibility

Abstract

Recent research highlights the significance of the three-dimensional structure of chromatin in regulating various cellular processes, particularly transcription. This is achieved through dynamic chromatin structures that facilitate long-range contacts and control spatial accessibility. Chromatin consists of DNA and a variety of proteins, of which histones play an essential structural role by forming nucleosomes. Extensive experimental and theoretical research in recent decades has yielded conflicting results about key factors that regulate the spatial structure of chromatin, which remains enigmatic. By using a computer model that allows us to simulate chromatin volumes containing physiological nucleosome concentrations, we investigated whether nucleosome spacing or nucleosome density is fundamental for three-dimensional chromatin accessibility. Unexpectedly, the regularity of the nucleosome spacing is crucial for determining the accessibility of the chromatin network to diffusive processes, whereas variation in nucleosome concentrations has only minor effects. Using only the basic physical properties of DNA and nucleosomes was sufficient to generate chromatin structures consistent with published electron microscopy data. Contrary to other work, we found that nucleosome density did not substantially alter the properties of chromatin fibers or contact probabilities of genomic loci. No breakup of fiber-like structures was observed at high molar density. These findings challenge previous assumptions and highlight the importance of nucleosome spacing as a key driver of chromatin organization. These results identified changes in nucleosome spacing as a tentative mechanism for altering the spatial chromatin structure and thus genomic functions.

Figure 1

Model of a nucleosome chain. (A) $i$ represents the number of beads in the chain, yellow circles indicate nucleosome bead positions, and blue circles indicate DNA bead positions. The nucleosome is represented by a red cylinder. The segment vector $\overrightarrow{s_i}$ points from one bead to the next bead. A local coordination system ($\widehat{u_i},\widehat{v_i},\widehat{f_i}$) ($\widehat{v_i}=\widehat{u_i}\times \widehat{f_i}$ not shown) describes the orientation of a bead. Vector $\overrightarrow{a_i}$ describes the direction from the center of the segment to the nucleosome center $\overrightarrow{m_i}$, c is its length, and vector $\overrightarrow{o_i}$ describes the orientation of the nucleosome. Vector $\overrightarrow{a_i}$ is defined by two rotations of vector $\widehat{v_i}$ around $\overrightarrow{u_i}$ by the angle $\epsilon$ and around vector $\widehat{f_i}$ by the angle $\phi$ (for $\epsilon$ and $\phi$, see B). (B) The relative orientation of the nucleosome is described by the angle $\alpha ,\delta ,\epsilon ,\gamma ,\phi$ (modified from (24)). $\beta$ is the torsional orientation of subsequent nucleosomes. $l$ is the length of the DNA used to model the linker DNA, d is the distance between the entry and the exit point of the linker DNA at the nucleosome, and c is the distance between the center of the nucleosome segment and the center of the oblate spherocylinder used to model the nucleosome. To see this figure in color, go online.

Figure 2

Visualization of simulated configurations at different density concentrations. (A) True-to-scale sketch of DNA length and the volumes into which it is compressed. (B and C) Visualizations for an increasing (left to right) nucleosome concentration (scale bar: 40 nm). (B) Equidistantly spaced nucleosome chains. (C) Randomly spaced nucleosome chains. (a) Three-dimensional visualizations of typical configurations; (b) examples for 25-nm-thick slices; (c) simulated ChromEMT slices; and (d) sample of experimental ChromEMT slice with a thickness of 1.28 nm from Ou et al. for comparison (8). See also Videos S1, S2, and S3. To see this figure in color, go online.

Figure 3

Comparison of a genomic region based on data from K562 cells and synthetic nucleosome spacing. Nucleosome concentration: 145 μM. Equidistant: equidistant nucleosome spaced synthetic fiber; K562: nucleosomes spaced as in a region of K562 cells; and random: randomly spaced nucleosomes. (A) Slices with a thickness of 25 nm. (B) Three-dimensional visualization of systems. The horizontal axis (in red) displays the standard deviation of the distribution of the linker length. See also Videos S1, S3, and S4. (C−F) Simulation of the mean-squared displacement of different spheres in chromatin. Mean-squared distance as a function of time for (C) equidistantly spaced nucleosomes (145 μM), (D) equidistantly spaced nucleosomes (304 μM), (E) randomly spaced nucleosomes (145 μM), and (F) nucleosomes spaced as in a region of K562 cells (145 μM). (G) Sketch of spheres with different radii showing random diffusion from a random start point up to half of the container size, avoiding collisions with DNA or nucleosomes. (H) Diffusion coefficients for different sphere radii for free diffusion (squares) and equidistantly spaced nucleosomes at different densities. (I) Diffusion coefficients for different sphere radii for free diffusion (black squares), randomly spaced nucleosomes (crosses), equidistantly spaced nucleosomes (diamonds), and nucleosomes spaced as in a region of K562 cells (triangles). To see this figure in color, go online.

Figure 4

Radial distribution function. Probability density of finding another nucleosome $g\left(r\right)$ (left) and the average density of nucleosomes $\rho g\left(r\right)$ (right) in radius r from a reference nucleosome for different nucleosome concentrations of systems with (A and B) equidistantly spaced nucleosomes, (C and D) randomly spaced nucleosomes, and (E and F) nucleosomes spaced as in an inactive region of K562 cells. The peak between 7 and 10 nm is a result of the adjacent nucleosomes in the chain. In (A) and (C), the second peaks at 17 and 13 nm, respectively, reflect the more regular spatial structure of the chains. To see this figure in color, go online.

Figure 5

Contact maps. The maps show the probability of contacts within a section of chains with (A) equidistantly spaced nucleosomes (35 nucleosomes, 6111 bp) and (B) randomly spaced nucleosomes (20 nucleosomes, 6351 bp). Resolution = 30 bp. Black bars below maps mark the positions of nucleosomes on DNA. Below the bars a snapshot of a typical configuration of the section is shown in a color gradient from red to green (left) and a snapshot of the whole system (right). To see this figure in color, go online.