Fig 1.
Schematic illustration of our polymer model for CDs.
(A) A nucleosome fiber is represented as a polymer bead chain and forms a CD. The size scaling of CDs is expressed as , where the fractal dimension represents the effective conformational state of CDs: df = 1, 2, and 3 correspond to a straight line, the ideal chain, and the fractal globule, respectively. (B) The viscoelasticity of the medium, where the movement of particles shows the subdiffusive FBM 〈Δr(t)2〉∼tα, is described using the friction coefficient with memory, γ(t)∼t−α. When a nucleosome with coordinates Rn(t) dynamically fluctuates in the viscoelastic medium, the movement of nucleosomes in CDs shows subdiffusion: 〈ΔRn(t)2〉∼tβ.
Fig 2.
Single-nucleosome imaging and analysis.
(A) Single-nucleosome image of a human HeLa cell nucleus expressing H2B-PA-mCherry. Each dot represents single nucleosome. (B) Evidence that each dot represents single-nucleosome molecule. Each H2B-PA-mCherry dot shows single-step photobleaching. The vertical axis represents the fluorescence intensity of each H2B-PA-mCherry dot. The horizontal axis is the tracking time series (each photobleaching point is set as time 0; the average and the standard deviation at each time point were calculated for 50 dots.). Due to the clear single-step photobleaching profile of the H2B-PA-mCherry dots, each dot shows a single H2B-PA-mCherry molecule in a single nucleosome. (C) A scheme for nuclear interior (Top) and periphery (Bottom) imaging. Focal plane (red) in the living cells is shown. See also S1 Fig. (D) Representative trajectories of fluorescently labeled single nucleosome (50 ms per frame). (E) Plots of the MSD at the interior and periphery regions. These fit well with the MSD curves using Eq 1.
Fig 3.
Structural information of CDs provided by single-nucleosome dynamics.
(A) The fractal dimension df within the nuclear interior region (β = 0.44) and the periphery region (β = 0.39) for α, according to Eq 16. (B) df and the size 〈R〉CD of CDs, and (C) df and the relaxation time τdf,α of nucleosomes in CDs within the nuclear interior region (colored circle) and the periphery region (colored square) calculated for various α values, according to Eqs 16, 17 and 18. (D) 〈R〉CD and the τdf,α within the nuclear interior region (colored circle) and the periphery region (colored square) calculated for α = 0.9 and various 〈N〉CD values, corresponding to the range of 200 kb to 4 Mb, according to Eqs 17 and 18.
Table 1.
Estimated values of the fractal dimension df, the size 〈R〉CD, and the relaxation time τdf,α for α = 0.8 and α = 0.9.