Experimental FISH data for spatial distances <i>R</i>²(|<i>N</i>₂−<i>N</i>₁|) between targeted chromosome sites compared to the estimates based on the WLC model (A) and results from our simulations (B–F).

<p><i>Brown ○</i>: <i>Saccharomyces cerevisiae</i> Chr6 and Chr14 <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000153#pcbi.1000153-Bystricky1" target="_blank">[16]</a>. <i>Blue ○ and ◊</i>: <i>Homo Sapiens</i> Chr4, |<i>N</i>₂−<i>N</i>₁|<4.5 Mbp and |<i>N</i>₂−<i>N</i>₁|>4.5 Mbp, respectively <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000153#pcbi.1000153-Sachs1" target="_blank">[17]</a>. <i>Orange and green ○</i>: <i>Drosophila melanogaster</i> Chr2L, DS5 and DS1 embryos respectively <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000153#pcbi.1000153-Lowenstein1" target="_blank">[18]</a>. DS5 and DS1 are two phases of cell cycle. DS1 appears later. <i>Black continuous line</i>: Mean-square internal distances predicted by the WLC model, Equation 1. (A) <i>Black dashed line</i>: Mean-square internal distances of an ideal polymer chain inside a spherical nucleus of 5 µm radius <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000153#pcbi.1000153-Doi1" target="_blank">[7]</a>. (The exact probability distribution function of the square internal distances <i>R</i>²(|<i>N</i>₂−<i>N</i>₁|) of a polymer without self-interactions obeys diffusion equation <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000153#pcbi.1000153-Doi1" target="_blank">[7]</a> with null boundary conditions (in our case the boundary is the sphere which models the nucleus).)While data for Chr4 and Chr2L show a reasonable agreement at short-length scales, the apparent large-length scale Chr4 behavior <i>L</i>^2/3<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000153#pcbi.1000153-Mnkel2" target="_blank">[29]</a> contrasts with the observed <i>L</i>² for Chr2L. The insets show two schematic drawings of the Chr4 territory in a human nucleus (blue) and of Chr2L in Rabl phase in a <i>Drosophila</i> nucleus (orange). (B–E) Gray lines represent internal distances in the initial, “metaphase-like” chromosome configuration (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000153#s4" target="_blank">Materials and Methods</a>). Internal distances in simulated chromosomes have been averaged over 3 time windows of exponentially growing size: 240 s<<i>t</i><2,400 s (dark red line), 2,400 s<<i>t</i><24,000 s (magenta line) and 24,000 s<<i>t</i><240,000 s (cyan line). Since yeast chromosomes rapidly equilibrate only averages over the first 24,000 s are here reported (panel C). In panel E, <i>N</i>₁ = 0, i.e., has been fixed at the origin of the chain to make equilibration of the chain ends evident. (F) Data from simulations of three ring polymers of decreasing half-size <i>L</i>_c = 97.2, 48.6, and 2.7 Mbp (green, magenta and red lines respectively). Mean distances seem to extrapolate to an effective power law ∼<i>L</i>^2/3. <i>Inset</i>: Initial (left) and final (right) conformation of a (randomly chosen) half of the largest (2×97.2 Mbp) simulated ring chromosome.