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备区室化特征，已有研究证实部分细胞核区室呈现一定程度的空间组织特性。截至目前，细胞核组织相关研究多采用简单定量手段，但这类方法难以同时应对细胞核边界不规则性与重复成像样本处理的双重难题。此类研究通常聚焦于目标间的距离，而非细胞核内部的空间位置分布。本文聚焦于细胞核区室的空间偏好性问题，为此我们开发了一套可用于定量研究与解析细胞核组织的统计工具。该工具可整合重复成像数据，生成用以表征细胞核区室空间偏好性的“整合图谱（aggregate maps）”。我们以哺乳动物成纤维细胞（WI-38与MRC-5）中的两种不同区室为例，展示了细胞核内空间偏好性的全新研究发现。具体而言，RNA聚合酶II（RNA polymerase II）的空间偏好性在正常细胞与永生化细胞中保持稳定；而PML核体（PML nuclear bodies）的空间偏好性则发生了显著变化：在正常细胞中其倾向于避开细胞核中心，而在永生化细胞中则表现出对细胞核中心的偏好性。此外，我们还发现，在非转化型WI-38细胞中，SC35剪接斑点（SC35 splicing speckles）会被排除在细胞核边界之外，广泛定位于核质与染色质间间隙内。综上，这套全新方法能够揭示大规模扰动对空间结构与偏好性的影响，而这类效应仅凭单细胞成像难以观测到。