Physical Modeling of Dynamic Coupling between Chromosomal Loci Thomas J. Lampo, Andrew S. Kennard, Andrew J. Spakowitz  Biophysical Journal  Volume 110, Issue 2, Pages 338-347 (January 2016) DOI: 10.1016/j.bpj.2015.11.3520 Copyright © 2016 Biophysical Society Terms and Conditions

Figure 1 A Rouse polymer model for chromosome locus dynamics. (A) Schematic of the viscoelastic Rouse polymer model with two tagged monomers labeled red and green. (B) Schematic of chromosome loci labeled by the fluorescent repressor operator system (FROS) indicated by the green and red stars. Example images show false-color fluorescent (left) and bright-field (right) microscopy of a budding yeast (Saccharomyces cerevisiae) for in vivo locus tracking using a model No. IX70 fluorescence microscope (Olympus, Melville, NY). To see this figure in color, go online. Biophysical Journal 2016 110, 338-347DOI: (10.1016/j.bpj.2015.11.3520) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 2 Velocity autocorrelation function for the 84′ chromosome locus in E. coli. (A) Normalized velocity autocorrelation function for δ ranging from 1 s to 50 s in 1 s intervals indicated by the color bar. (B) Normalized velocity autocorrelation function with time rescaled by δ. (Dark gray line) Theoretical prediction from Eq. 5 for β = 0.39. Figure reproduced from results previously reported in Weber et al. (24). To see this figure in color, go online. Biophysical Journal 2016 110, 338-347DOI: (10.1016/j.bpj.2015.11.3520) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 3 VVC function for a viscoelastic Rouse polymer (α = 0.7). (A–E) Heat maps of the normalized VVC function Cvv(δ)(t,N/2,n2)/Cvv(δ)(0,N/2,N/2) for values of δ/tR ranging from 1.0×10−6 to 1.0×100. The VVC color scale is indicated by the color bar for all heat maps. (F) The three limiting behaviors for the VVC function: autocorrelated motion of the Rouse monomer before terminal relaxation (dotted line), autocorrelated motion of an effective particle or any Rouse monomer beyond the Rouse time (solid line), and uncorrelated motion (dashed line). To see this figure in color, go online. Biophysical Journal 2016 110, 338-347DOI: (10.1016/j.bpj.2015.11.3520) Copyright © 2016 Biophysical Society Terms and Conditions

Figure 4 VVC function for δ≪tR and |Δn|≪N with α=0.7. (A) Normalized VVC function heat map. The VVC scale is indicated by the color bar normalized to the autocorrelation result at t=0. (B) Colored curves are slices taken from (A) for varying values of δ/tΔn. To see this figure in color, go online. Biophysical Journal 2016 110, 338-347DOI: (10.1016/j.bpj.2015.11.3520) Copyright © 2016 Biophysical Society Terms and Conditions