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.

高等真核细胞的细胞核具有区室化特征，且已有研究表明部分细胞核区室具备一定程度的空间组织特性。迄今为止，细胞核组织研究多采用简易定量方法，但这类方法难以同时应对核边界不规则性与重复图像处理的双重难题。此类研究通常聚焦于对象间的距离，而非细胞核内部的空间定位。本研究的核心关注点为细胞核区室的空间偏好，为此我们开发了可用于定量研究与解析细胞核组织的统计工具。这些工具可整合重复图像，生成能够反映细胞核区室空间偏好的“聚合图谱”。我们以哺乳动物成纤维细胞（WI-38与MRC-5）中的两类不同区室为例，揭示了细胞核内空间偏好的全新认知。具体而言，RNA聚合酶II（RNA polymerase II）的空间偏好于正常细胞与永生细胞中均保持一致；而PML核体（PML nuclear bodies）的空间偏好则发生改变：在正常细胞中其倾向于避开细胞核中心，而在永生细胞中则偏好定位于细胞核中心。此外，我们发现，在未转化的WI-38细胞中，SC35剪接斑点（SC35 splicing speckles）会被排除在核边界之外，均匀分布于核质与染色质间间隙中。因此，这套全新方法能够揭示单细胞成像难以察觉的大规模扰动对细胞核空间架构与偏好性的影响。