Chromosome territories

Meaburn, Karen J.; Misteli, Tom

doi:10.1038/445379a

Cited by 342 publications

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“…Apart from molecular factors binding directly to DNA and changes in the local chromatin environment, the nuclear organization of chromatin has come into focus as a potential level of genome regulation (for reviews see Kosak and Groudine 2004;Foster and Bridger 2005;Cremer et al 2006;Fraser and Bickmore 2007;Lanctôt et al 2007;Meaburn and Misteli 2007;Misteli 2007). To understand this level of genome organization, it is essential to know the three-dimensional distribution of the genome.…”

Section: Introductionmentioning

confidence: 99%

“…To understand this level of genome organization, it is essential to know the three-dimensional distribution of the genome. During interphase, chromosomes occupy a restricted space in the cell nucleus, the chromosome territory Meaburn and Misteli 2007). A nonrandom distribution of chromosome territories was described in nuclei of human origin (Croft et al 1999;Cremer et al 2001;Bolzer et al 2005;Wiblin et al 2005) from other primates (Tanabe et al 2002;Neusser et al 2007), mice (Parada et al 2004;Mayer et al 2005), and chicken (Habermann et al 2001;Stadler et al 2004).…”

Section: Introductionmentioning

confidence: 99%

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Three-dimensional positioning of genes in mouse cell nuclei

et al. 2008

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To understand the regulation of the genome, it is necessary to understand its three-dimensional organization in the nucleus. We investigated the positioning of eight gene loci on four different chromosomes, including the β-globin gene, in mouse embryonic stem cells and in in vitro differentiated macrophages by fluorescence in situ hybridization on structurally preserved nuclei, confocal microscopy, and 3D quantitative image analysis. We found that gene loci on the same chromosome can significantly differ from each other and from their chromosome territory in their average radial nuclear position. Radial distribution of a given gene locus can change significantly between cell types, excluding the possibility that positioning is determined solely by the DNA sequence. For the set of investigated gene loci, we found no relationship between radial distribution and local gene density, as it was described for human cell nuclei. We did find, however, correlation with other genomic properties such as GC content and certain repetitive elements such as long terminal repeats or long interspersed nuclear elements. Our results suggest that gene density itself is not a driving force in nuclear positioning. Instead, we propose that other genomic properties play a role in determining nuclear chromatin distribution.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Three-dimensional positioning of genes in mouse cell nuclei

et al. 2008

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“…Concurrently, due to improvements in optical microscopy and fluorescent labeling, it has been shown that the cell nucleus is compartmentalized into well-defined subregions and that the spatial position of genes in the nucleus correlates with their expression and cellular activities (3)(4)(5). Furthermore, the positioning of certain genes, such as HES5 and FRA2, has been shown to differ between normal and cancer cells in a cell culture model of cancer (6) and in patient tissue sections (7).…”

Section: Introductionmentioning

confidence: 99%

Automatic segmentation and supervised learning‐based selection of nuclei in cancer tissue images

et al. 2012

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Analysis of preferential localization of certain genes within the cell nuclei is emerging as a new technique for the diagnosis of breast cancer. Quantitation requires accurate segmentation of 100-200 cell nuclei in each tissue section to draw a statistically significant result. Thus, for large-scale analysis, manual processing is too time consuming and subjective. Fortuitously, acquired images generally contain many more nuclei than are needed for analysis. Therefore, we developed an integrated workflow that selects, following automatic segmentation, a subpopulation of accurately delineated nuclei for positioning of fluorescence in situ hybridization-labeled genes of interest. Segmentation was performed by a multistage watershed-based algorithm and screening by an artificial neural network-based pattern recognition engine. The performance of the workflow was quantified in terms of the fraction of automatically selected nuclei that were visually confirmed as well segmented and by the boundary accuracy of the well-segmented nuclei relative to a 2D dynamic programming-based reference segmentation method. Application of the method was demonstrated for discriminating normal and cancerous breast tissue sections based on the differential positioning of the HES5 gene. Automatic results agreed with manual analysis in 11 out of 14 cancers, all four normal cases, and all five noncancerous breast disease cases, thus showing the accuracy and robustness of the proposed approach. Published 2012 Wiley-Periodicals, Inc. y

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“…It has become evident that the genomic architecture and thus the three-dimensional organization of genes in the genome are far from random [1][2][3][4] . It is well-established that genomes tend to have specific conformations, typical organization during different steps of the cell cycle and specific regions that are more efficiently transcribed [5][6][7][8] .…”

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confidence: 99%

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

2014

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It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of threedimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture.

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Chromosome territories

Cited by 342 publications

References 0 publications

Three-dimensional positioning of genes in mouse cell nuclei

Three-dimensional positioning of genes in mouse cell nuclei

Automatic segmentation and supervised learning‐based selection of nuclei in cancer tissue images

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

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