Data from: New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts

The nuclei of higher eukaryotic cells display compartmentalization and
certain nuclear compartments have been shown to follow a degree of spatial
organization. To date, the study of nuclear organization has often
involved simple quantitative procedures that struggle with both the
irregularity of the nuclear boundary and the problem of handling replicate
images. Such studies typically focus on inter-object distance, rather than
spatial location within the nucleus. The concern of this paper is the
spatial preference of nuclear compartments, for which we have developed
statistical tools to quantitatively study and explore nuclear
organization. These tools combine replicate images to generate ‘aggregate
maps' which represent the spatial preferences of nuclear
compartments. We present two examples of different compartments in
mammalian fibroblasts (WI-38 and MRC-5) that demonstrate new knowledge of
spatial preference within the cell nucleus. Specifically, the spatial
preference of RNA polymerase II is preserved across normal and
immortalized cells, whereas PML nuclear bodies exhibit a change in spatial
preference from avoiding the centre in normal cells to exhibiting a
preference for the centre in immortalized cells. In addition, we show that
SC35 splicing speckles are excluded from the nuclear boundary and localize
throughout the nucleoplasm and in the interchromatin space in
non-transformed WI-38 cells. This new methodology is thus able to reveal
the effect of large-scale perturbation on spatial architecture and
preferences that would not be obvious from single cell imaging.