Nucleosome Switches

We present a statistical-mechanical model for the positioning of nucleosomes along genomic DNA molecules as a function of the strength of the binding potential and the chemical potential of the nucleosomes. We show that a significant section of the DNA is composed of two-level nucleosome switching regions where the nucleosome distribution undergoes a localized, first-order transition. The location of the nucleosome switches shows a strong correlation with the location of gene-regulation regions.

Figure 1

Temperature dependence of the overlap parameter $\Psi$ with temperature in units of the reference temperature. Short dashed line: $\mu =62$ with zero temperature occupancy of 89.6%. Solid line: $\mu =24$ with zero temperature occupancy of 83.3%. Long dashed line: $\mu =0$ with zero temperature occupancy of 51.5%. Insets: Plot of site occupancy probability between sites 9000 and 10 000 at $\mu =24$ for $T/T_0=0.1$ (bottom left) and $T/T_0=8.0$ (top right).

Figure 2

Site occupancy of an unstable section (bp 6500–9500) at $T/T_0=0.5$ for different values of the chemical potential. The mean occupancies are 88.8%, 89.3%, and 90%. For higher, respectively, lower, chemical potentials, the occupation pattern is stable with, respectively, 12 and 11 nucleosomes. The unstable sequence for intermediate chemical potential is the superposition of the two stable patterns.

Figure 3

Average number of nucleosomes between sites 6970 and 8730 of yeast chromosome II as a function of chemical potential. Solid line: $T/T_0=0.1$ Short dashed line: $T/T_0=0.5$. Long dashed line: $T/T_0=1$. Inset: Histogram of the distribution of the overlap parameter $\Psi$ for the same stretch of DNA obtained from Monte Carlo simulations at $\mu \approx 47.9$ where the 11 and 12 nucleosome configurations are energetically nearly degenerate for $T/T_0=2$.