Fig. 5: A biophysical model predicts chromatin density class dependent nucleosome motion.
A Schematic of biophysical model of fractal polymer domain structure in a viscoelastic medium. Nucleosome anomalous exponent (αnuc) can be modeled as a function of the HaloTag-NLS anomalous exponent (αhalo) and the estimated fractal dimension of the nucleosomes (fd). The nucleosome diffusion coefficient (Dnuc) can be modeled as a function of the HaloTag-NLS anomalous exponent (αhalo), the estimated fractal dimension of the nucleosomes (fd), the size of a chromatin domain (Rd), the diffusion coefficient of the HaloTag-NLS (Dhalo) and the nucleosome density (ρ). B Outline of empirical measurements and associated figures used to parameterize the biophysical model. C The comparison between the model-predicted and the experimentally measured (Fig. 2B) nucleosome diffusion coefficients across different chromatin density classes. Open circles indicate mean model predicted results and closed squares indicate mean experimentally measured results. The error bars for the experimental measured results represent the standard deviation of the experimental data. The error bars for the model predicted results are computed by propagating the error from the experimentally measured terms to the model output. D The comparison between model-predicted and experimentally measured (Fig. 2C) nucleosome anomalous alpha exponent across different chromatin density classes. The plot follows the same convention as (C). Experimental data from (C) and (D) are from n = 88 cells across 8 independent biological replicates.
