Figure 3

Three-dimensional relative radial nuclear distribution of mouse chromosome territories from a total of 481 nuclei with two labeled pairs of chromosomes each. Each nucleus was divided in 25 shells with equal spacing. The relative amount of the signal from a given chromosome paint probe or of the DNA counterstain (cst) in each of the shells was measured and averaged over all nuclei of the respective cell type (see Methods for details). Graphs on the left (a,d,g,j,m) show the percentage of each signal in the 25 shells. Error bars in (a-o) show the standard error of the mean. For each nucleus and territory signal, the median radius of the relative radial distribution was calculated (see additional data file 1 for complete listing). Graphs in the center (b,e,h,k,n) show the averages of these medians plotted against the gene density of the painted chromosome. In the graphs on the right (c,f,i,l,o) these averages of medians are plotted against chromosomal size. For cell types with investigated territories from six types of chromosomes, the black lines show the linear regression. The box shows the correlation coefficient R and the p-value indicating the probability that there is no correlation but that the observed relation was a chance result. Both values were calculated from individual medians from all nuclei while the regression line shown was fitted to the six average values of the medians represented by the dots. (a-c) Lymphocyte nuclei in S-phase (continuous lines in (a), circles in (b), all six investigated chromosomes) and in G0 (broken lines in (a), squares in b,c, MMU11 and MMUX only). In (b,c), data points for average medians in G0 lymphocytes fall exactly on data points in S-phase and are thus difficult to distinguish. G0 lymphocytes were not included in the linear regression analysis. (d-f) Fibroblast S-phase nuclei. (g-i) ES-cell S-phase nuclei. (j-l) Macrophage G0 nuclei. Color code shown in (a) also applies to (b-l). (m-o) Myoblast (continuous lines) and myotube nuclei (broken lines). Correlation coefficients for myoblasts (0.26, p = 0.032) and myotubes (0.68, p < 0.001) are not directly comparable since only two chromosomes were investigated. Note that in all cell types there is a correlation for gene poor as well as large chromosome territories to be more peripheral, although for some chromosome territories average medians diverge from this pattern.