Figure 2.

Comparisons between the “Clamping and Sliding” Model and the ParB_F DNA Binding Pattern

High-resolution ChIP-sequencing data from a previous study (Sanchez et al., 2015) display the average number of reads per 100-bp windows as a function of the genomic coordinates (red circles). Note that the signal at parS_F (coordinate 0) is normalized to 1 by averaging the number of reads over the 550-bp centromere locus.

(A) The model from Equation (2) contains the three kinetic parameters D = 4.3$\times$10⁵ bp² s⁻¹ (Guilhas et al., 2020), R = 0.1 s⁻¹, and U = 0.017 s⁻¹ (Figures S1B–S1D). The exact solution (black line) and the Monte Carlo (MC; blue dots) simulation data are plotted on the right side of parS_F. The theoretical prediction is compared to the ChIP-seq data (Sanchez et al., 2015). The large discrepancy between the model and the ChIP-seq data is essentially due to the amplitude (value of R).

(B) Simulation in the absence (black diamonds) and in the presence (blue circles) of a roadblock compared to the ChIP-seq data with the optimized parameters (R = 1.91 s⁻¹ and U = 0.0047 s⁻¹). The two strong roadblocks (green bars), present at ∼3-kb and 4.5-kb on the left of parS_F, are due to the binding of RepE to incC and ori2 iterons, respectively (Rodionov et al., 1999; Sanchez et al., 2015). Note that the two MC simulations overlap on the right side of parS_F.

See also Figure S2.