Fig. 4

Heterochromatin and nucleolus positions. a Left panel: Localization probability density (LPD) plots of the nucleolus and all pericentromeric heterochromatin regions in the model. On average, the nucleolus occupies an intermediate position between the center and the periphery and is surrounded by pericentromeric heterochromatin. Right panel: LPD plots for pericentromeric heterochromatin of different chromosome arms. They all exhibit different preferred locations. Those of chr4 and chrX are significantly more peripheral than those of the other chromosomes. b Clustering of pericentromeric heterochromatin regions based on their averaged surface-to-surface distances. Heterochromatin domains of arms from the same chromosome naturally show preferred clustering. Heterochromatin domains from chr4 and chrX are usually closer to each other than to those from other chromosomes. c Left panel: FISH signals in larval brain cells. The image shows the middle Z-stack of a representative nucleus. Scale bar = 1 μm. Right panel: The position of FISH probes used for this study, relative to the pericentromeric regions of each chromosome (chrX, chr2, chr4). Note that the 359bp probe signal (orange in the scheme) is rendered in white in the FISH image. d Top panel: The positions (center-to-center distance normalized by the diameter of the nucleus) of heterochromatic satellites from different chromosomes relative to each other, measured in FISH experiments on larval brains; ****p value <0.0001 by paired t-test, N = 55 cells. Bottom panel: Pairwise distances (surface-to-surface distance normalized by the diameter of the nucleus) between the heterochromatin domains as measured in the model. Similar to the data in vivo, the distance between the heterochromatin domains of chrX and chr4 is significantly smaller than the distance between the other two pairs according to paired t-tests (p value <2.2e − 16). e Left panel: Positions of heterochromatic satellites from different chromosomes relative to the nuclear periphery, obtained from FISH experiments on larval brain cells. The heterochromatic satellites on chrX and chr4 are closer to the NE than those of chr2. Right panel: The distance from the center of heterochromatin to the NE normalized by the nuclear diameter as measured in the model. The models show a very good agreement with the experiment when considering the main trends, mainly: chrX and chr4 have higher histogram peaks located closer to the NE in comparison to chr2, and show a more focused localization probability towards the nuclear envelope. Note that the physical volume of the satellite repeats (imaged by FISH) is much smaller than the physical volume of the entire heterochromatin domain represented by a relatively large sphere in the model. This difference explains the offset observed at small distance values (i.e., starting at larger values) for the histograms, which corresponds to the radii of the corresponding spheres (i.e., 0.09, 0.05, and 0.08 normalized by nuclear diameter for chrX, chr4, and chr2R, respectively). For example, if a heterochromatin sphere is touching the NE, by definition the center distance to the NE is its radius. However, the satellite repeats that would be located inside the sphere could still be close to the NE