Quantitative Analysis of Cell Nucleus Organisation

Shiels, Carol; Adams, Niall M.; Islam, Suhail A.; Stephens, David A.; Freemont, Paul S.

doi:10.1371/journal.pcbi.0030138

Cited by 23 publications

(29 citation statements)

References 82 publications

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“…The use of automated analysis of subnuclear structures enables the objective and unbiased detection of the object studied [30], [33]. The developed software allows for the quantification of transcription sites from the identification of local peaks of intensity (curvature) in the BrRNA signal in 3D confocal series.…”

Section: Resultsmentioning

confidence: 99%

Transcription Sites Are Developmentally Regulated during the Asexual Cycle of Plasmodium falciparum

et al. 2013

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Increasing evidence shows that the spatial organization of transcription is an important epigenetic factor in eukaryotic gene regulation. The malaria parasite Plasmodium falciparum shows a remarkably complex pattern of gene expression during the erythrocytic cycle, paradoxically contrasting with the relatively low number of putative transcription factors encoded by its genome. The spatial organization of nuclear subcompartments has been correlated with the regulation of virulence genes. Here, we investigate the nuclear architecture of transcription during the asexual cycle of malaria parasites. As in mammals, transcription is organized into discrete nucleoplasmic sites in P. falciparum, but in a strikingly lower number of foci. An automated analysis of 3D images shows that the number and intensity of transcription sites vary significantly between rings and trophozoites, although the nuclear volume remains constant. Transcription sites are spatially reorganized during the asexual cycle, with a higher proportion of foci located in the outermost nuclear region in rings, whereas in trophozoites, foci are evenly distributed throughout the nucleoplasm. As in higher eukaryotes, transcription sites are predominantly found in areas of low chromatin density. Immunofluorescence analysis shows that transcription sites form an exclusive nuclear compartment, different from the compartments defined by the silenced or active chromatin markers. In conclusion, these data suggest that transcription is spatially contained in discrete foci that are developmentally regulated during the asexual cycle of malaria parasites and located in areas of low chromatin density.

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Section: Resultsmentioning

confidence: 99%

Transcription Sites Are Developmentally Regulated during the Asexual Cycle of Plasmodium falciparum

et al. 2013

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“…Although fluorescent MeC- and DNA-specific staining produces measurable signals in nuclei that can be extracted from individual 2-D optical sections or projections of 3-D image data, the signals do not usually generate quantitative and reproducible patterns of exact geometrical positions that are shared by all the cells. Also, due to the high variability and limitations of current imaging modalities it is challenging to precisely localize DNA signals and other similar nuclear structures [26]. Based on the dynamic self-organization of the genome, the spatial distribution of different classes of DNA (referred to as chromatin texture) is a descriptive feature in the differential characterization of cells and tissues in diverse states, as experienced in basic science [27–28] and translational medicine [29–30].…”

Section: Discussionmentioning

confidence: 99%

Measuring topology of low-intensity DNA methylation sites for high-throughput assessment of epigenetic drug-induced effects in cancer cells

Gertych

Farkas

Tajbakhsh

2010

Experimental Cell Research

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Epigenetic anti-cancer drugs with demethylating effects have shown to alter genome organization in mammalian cell nuclei. The interest in the development of novel epigenetic drugs has increased the demand for cell-based assays to evaluate drug performance in pre-clinical studies. An imaging-based cytometrical approach that can measure demethylation effects as changes in the spatial nuclear distributions of methylated cytosine and global DNA in cancer cells is introduced in this paper. The cells were studied by immunofluorescence with a specific antibody against 5-methylcytosine (MeC), and 4,6-diamidino-2-phenylindole (DAPI) for delineation of methylated sites and global DNA in nuclei. In the preprocessing step the segmentation of nuclei in three-dimensional images (3-D) is followed by an automated assessment of nuclear DAPI/MeC patterns to exclude dissimilar entities. Next, low-intensity MeC (LIM) and low-intensity DNA (LID) sites of similar nuclei are localized and processed to obtain specific nuclear density profiles. These profiles sampled at half of the total nuclear volume yielded two parameters: LIM0.5 and LID0.5. The analysis shows that zebularine and 5-azacytidine - the two tested epigenetic drugs introduce changes in the spatial distribution of low-intensity DNA and MeC signals. LIM0.5 and LID0.5 were significantly different (p<0.001) in 5-azacytidine treated (n=660) and zebularine treated (n=496) vs. untreated (n=649) DU145 human prostate cancer cells. In the latter case the LIM sites were predominantly found at the nuclear border, whereas treated populations showed different degrees of increase in LIMs towards the interior nuclear space, in which a large portion of heterochromatin is located. The cell-by-cell evaluation of changes in the spatial reorganization of MeC/DAPI signals revealed that zebularine is a more gentle demethylating agent than 5-azacytidine. Measuring changes in the topology of low-intensity sites can potentially be a valuable component in the high throughput assessment of demethylation and risk of chromatin reorganization in epigenetic-drug screening tasks.

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“…In plants, distance analysis was used to demonstrate the preferential localization of A. thaliana centromeres at the nuclear periphery of diploid cells [Fang and Spector, 2005]. The popularity of radial distance analysis in nuclear organisation studies [Shiels et al, 2007] is probably due to the simple spherical shape of cultured animal cell nuclei. The diversity of plant nuclear shapes ( fig.…”

Section: Modeling Approaches To Uncover Plant Nuclear Architecturementioning

confidence: 99%

Nuclear Architecture and Chromatin Dynamics in Interphase Nuclei of <b><i>Arabidopsis thaliana</i></b>

Prete

Arpòn

Sakai

et al. 2014

Cytogenet Genome Res

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The interphase cell nucleus is extraordinarily complex, ordered, and dynamic. In the last decade, remarkable progress has been made in deciphering the functional organisation of the cell nucleus, and intricate relationships between genome functions (transcription, DNA repair, or replication) and various nuclear compartments have been revealed. In this review, we describe the architecture of the Arabidopsis thaliana interphase cell nucleus and discuss the dynamic nature of its organisation. We underline the need for further developments in quantitative and modelling approaches to nuclear organization.

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Quantitative Analysis of Cell Nucleus Organisation

Cited by 23 publications

References 82 publications

Transcription Sites Are Developmentally Regulated during the Asexual Cycle of Plasmodium falciparum

Transcription Sites Are Developmentally Regulated during the Asexual Cycle of Plasmodium falciparum

Measuring topology of low-intensity DNA methylation sites for high-throughput assessment of epigenetic drug-induced effects in cancer cells

Nuclear Architecture and Chromatin Dynamics in Interphase Nuclei of <b><i>Arabidopsis thaliana</i></b>

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