Histone dynamics mediate DNA unwrapping and sliding in nucleosomes

Abstract

Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly wrap ∼147 DNA base pairs around an octamer of histone proteins. How nucleosome structural dynamics affect genome functioning is not completely clear. Here we report all-atom molecular dynamics simulations of nucleosome core particles at a timescale of 15 microseconds. At this timescale, functional modes of nucleosome dynamics such as spontaneous nucleosomal DNA breathing, unwrapping, twisting, and sliding were observed. We identified atomistic mechanisms of these processes by analyzing the accompanying structural rearrangements of the histone octamer and histone-DNA contacts. Octamer dynamics and plasticity were found to enable DNA unwrapping and sliding. Through multi-scale modeling, we showed that nucleosomal DNA dynamics contribute to significant conformational variability of the chromatin fiber at the supranucleosomal level. Our study further supports mechanistic coupling between fine details of histone dynamics and chromatin functioning, provides a framework for understanding the effects of various chromatin modifications.

Fig. 1. Overview of NCP structure and dynamics.

a NCP and its reference axes (z - superhelical, y - dyad). White arrows on DNA strands show 5′-3″ direction. Spheres highlight the proximal and distal ends of the double helix. Superhelical locations (SHL) are shown for the proximal half of the DNA (SHL < 0). Proximal H3-H4/H2A-H2B dimers are in the front (z > 0). Key arginines inserted in DNA minor grooves are shown in dark blue. b NCP in a simulation box with solvent. c, d Dynamics of NCP with truncated and with full-length histone tails (NCP^tt₁₄₅ and NCP₁₄₇ systems, respectively). Overlay of MD snapshots spaced 0.1 µs apart. e Sequences of the core histones and their secondary structure features: α-helices, β-strands, loops, flexible histone tails, etc. For simulations with truncated histone tails, the respective positions are marked with black triangle. Positively and negatively charged residues are highlighted in blue and red, respectively. Key arginines are highlighted with dark blue frames. Black asterisk - H2B residues absent in the recombinant protein.

Fig. 2. DNA-histone interactions in the nucleosome (based on NCP₁₄₇ simulation).

a Profile of stable amino acid residue-nucleotide contacts during the first microsecond of simulations plotted for the left half of the nucleosomal DNA. Individual histone residues are labeled on top of each bar. Residues that formed stable contacts for the entire 15 µs trajectory are shown in black frames. b Changes in the number of DNA-histone atom-atom contacts along MD trajectory. c The average number of histone-DNA atom-atom contacts classified by interacting entities: histone core or tail parts, DNA phosphates, sugars or bases.

Fig. 3. Mechanisms of DNA unwrapping in nucleosomes with truncated histone tails based on NCP^tt₁₄₅ simulation.

Top panel: different DNA unwrapping states. Middle panel: substates within each state showing different conformations of the H3-latch residues interacting with the nucleosomal DNA end and the neighboring DNA gyre. Bottom panel: profile of the extent of DNA unwrapping during MD simulations. Thin semitransparent lines are used to plot instantaneous unwrapping values; thick lines depict smoothed signal with Savitzky-Golay filter using 100 ns window and first-degree polynomial.

Fig. 4. Mechanisms of DNA unwrapping in nucleosomes with full-length histone tails based on NCP₁₄₇ simulation.

Figure follows the design of Fig. 3. The middle panel shows typical conformations of histone tails and H3-latch residues for selected unwrapping states/substates.

Fig. 5. Characteristics of DNA unwrapping in nucleosomes.

a–d 2D projections of DNA paths in nucleosome reference frame for NCP₁₄₇ and NCP^tt₁₄₅ systems; e Scatter plot of DNA end fluctuations along the Z and X-axis of the nucleosomal reference frame relative to its initial position in NCP^tt₁₄₅ simulation; f Average DNA rewrapping times as a function of DNA unwrapping extent estimated from MD trajectories. States with up to three unwrapped base pairs are considered as a wrapped state for this analysis.

Fig. 6. Effects of DNA unwrapping on chromatin fiber elasticity and bendability.

a End-to-end distance distribution in a simulated conformational ensemble of six NCPs connected by straight 15 bp linker DNA segments. Odd and even NCPs are colored in yellow and red, respectively, to highlight the fiber’s “two-start” structure. b Decay of orientational correlations along the nucleosome fibers due to DNA unwrapping. Persistence length estimates are shown on the plot. Below the plot, two different conformations of the fiber are shown.

Fig. 7. Formation/relaxation of twist-defects in NCP^tt₁₄₅ simulation.

a Plots of DNA relative twist profile along the DNA. The DNA sequence for the top strand of NCPtt145 is given along the X-axis. b A heatplot of changes in nucleotide positions for the proximal half of the top DNA strand during simulations. Starting from ~4 µs the half twist-defect relaxation causes the shift on the top DNA strand nucleotides in the region ~−50 to −72 by one step toward the dyad. c–e Successive stages of twist-defect relaxation at SHL -5 resulting in DNA sliding by 1 bp from SHL −7 to SHL −5. Snapshots are overlaid on the X-ray structure shown in cyan. Three base pairs (positions −59, −54, −49, and −44) around the SHL −5 region are highlighted in orange (X-ray positions) and magenta (MD positions). L1L2 binding sites are the DNA binding sites formed by L1 and L2 loops of histone folds. SHL stands for superhelix location.

Fig. 8. Plasticity of the histone octamer in NCP and its effects on the nucleosomal DNA dynamics.

a–d Present data for NCP^tt₁₄₅ simulations. a 2D projections of histone α2-helices’ Cα-atoms (α2-Cα-atoms) on the plane perpendicular to the superhelical axis for MD snapshots vs. X-ray structure. b Same as (a), but for the two MD snapshots with the maximum RMSD as measured by positions of α2-Cα-atoms. c Variation of RMSD with simulation time measured for α2-Cα-atoms positions with respect to the initial X-ray structure and a cryo-EM structure of a “squeezed” NCP (PDB ID 6FQ6). d RMSD calculated for Cα-atoms of the H2A α2-helices as a function of simulation time. Insets show inward bending of the helix associated with higher average RMSD. e Average DNA fluctuations for one half of the nucleosomal DNA compared for NCP147 simulations (<8 µs) and NCPfixed147 simulations with restrained histone folds. f Distance between Cα-atoms of H3L82 and H3V81 residues. Thick lines in (d) and (f) show signal smoothed with Savitzky-Golay filter.

Fig. 9. Coupling between DNA unwrapping and DNA loosening near the dyad through H3-latch interactions.

a DNA unwrapping as a function of simulation time of the distal DNA end in NCP^tt₁₄₇. b DNA distortions of the proximal half of the nucleosomal DNA visualized through the position register shift plot for the bottom DNA strand. c An MD snapshot showing the simultaneous DNA unwrapping, DNA distortion near the dyad, and detachment of the H3-latch from the inner DNA gyre near the dyad. Initial X-ray state is shown in cyan.