Fig. 2:

Nucleosome spacing pattern, not just mean spacing, impact long-range DNA contact probability. DNA contact probability of different nucleosome spacing (i.e., linker length) models, defined as the proportion of configurations with the two loci within 10nm, shown as heatmaps (A-C) and families of curves (D-F). A,D Evenly-spaced nucleosomes with no variation result in a repeated pattern of high contact (red ridges), consistent with the model assumption that the twist repeat of DNA is 10.5 bp. B,E Introducing variation into the uniform model results in the loss of the spaced ridges, and reveals larger regions of increased and decreased contact probability. C,F Exponentially-distributed nucleosome spacings (i.e., a spatial Poisson process or lattice gas) result in a smoother contact probability profile. Contact probabilities are highly sensitive to changes in nucleosome spacing, for example changing from 30 bp to 90 bp results in a 88% decrease in contact probability 1kbp away from the locus-of-interest in the Poisson process contact probability model (F, dashed black arrows). The magenta dashed vertical line in C and curve in F indicate the best-fit estimate from our analysis of electron microscopy data (Figure 3).