title: New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts.
abstract: 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.
authors: Department of Computer Science and Information Systems, Birkbeck College, University of London, London, UK dweston@dcs.bbk.ac.uk.
authors: David J
authors: http://orcid.org/0000-0001-9459-3430
authors: DJ
authors: Weston
authors: Department of Optometry and Visual Science, City University London, London, UK.
authors: Richard A
authors: RA
authors: Russell
authors: Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington, London, UK.
authors: Elizabeth
authors: E
authors: Batty
authors: Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington, London, UK.
authors: Kirsten
authors: K
authors: Jensen
authors: Department of Mathematics and Statistics, McGill University, Montreal, Québec, Canada.
authors: David A
authors: DA
authors: Stephens
authors: Department of Mathematics, Imperial College London, South Kensington, London, UK Heilbronn Institute for Mathematical Research, University of Bristol, Bristol, UK n.adams@imperial.ac.uk.
authors: Niall M
authors: http://orcid.org/0000-0003-0342-0513
authors: NM
authors: Adams
authors: Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington, London, UK p.freemont@imperial.ac.uk.
authors: Paul S
authors: http://orcid.org/0000-0002-5658-8486
authors: PS
authors: Freemont
mesh_terms: D000952:Antigens, Polyomavirus Transforming / Q000737:chemistry; D002460:Cell Line; D002467:Cell Nucleus / Q000378:metabolism*; D002843:Chromatin / Q000737:chemistry; D003593:Cytoplasm / Q000378:metabolism; D005347:Fibroblasts / Q000378:metabolism / Q000473:pathology*; D006801:Humans; D008856:Microscopy, Fluorescence; D009687:Nuclear Proteins / Q000378:metabolism; D000071156:Promyelocytic Leukemia Protein; D012319:RNA Polymerase II / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D025521:Tumor Suppressor Proteins / Q000378:metabolism
chemical_list: D000952:Antigens, Polyomavirus Transforming; D002843:Chromatin; D009687:Nuclear Proteins; D000071156:Promyelocytic Leukemia Protein; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins; C070576:PML protein, human; D012319:RNA Polymerase II
keywords: intensity estimation; mammalian fibroblasts; nuclear compartments; spatial point pattern analysis; spatial preference; thin-plate spline
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