Radial chromatin positioning is shaped by local gene density, not by gene expression

Küpper, Katrin; Kölbl, Alexandra C.; Biener, Dorothee; Dittrich, Sandra; Hase, Johann von; Thormeyer, Tobias; Fiegler, Heike; Carter, Nigel P.; Speicher, Michael R.; Cremer, Marion

doi:10.1007/s00412-007-0098-4

Cited by 172 publications

(167 citation statements)

References 80 publications

(127 reference statements)

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“…Our results thus indicate a preference of gene loci for a particular subregion of the chromosome territory while the territory has itself a preferred radial nuclear position. This argues for a polar radial organization of chromosome territories, as has been suggested by others (Ferreira et al 1997;Croft et al 1999;Sadoni et al 1999;Saccone et al 2002;Scheuermann et al 2004;Küpper et al 2007).…”

Section: Experimental Designsupporting

confidence: 73%

“…In most cases, the average nuclear radial position of a locus was significantly different from the average radial position of the harboring chromosome territory, indicating a preference of the gene locus for specific subregions of the territory. Our dataset did not show a correlation of radial nuclear gene locus positioning with local gene density as it was described in human cells (Murmann et al 2005;Küpper et al 2007). Instead, we found a correlation with GC content and with interspersed repetitive elements.…”

Section: Introductioncontrasting

confidence: 44%

“…When subsets of data were reevaluated by another person or the same person on a different day, similar results were obtained. Absolute 3D distance measurements from signal voxels to the nearest surface of the nucleus or chromosome territory was performed with the software eADS, developed by J. von Hase and T. Thormeyer (Albiez et al 2006;Küpper et al 2007). Briefly, at the determined threshold, a surface around the reference object (nucleus or territory) is generated.…”

Section: Dna Probes and Fishmentioning

confidence: 99%

“…However, expression has also been reported for genes at the nuclear periphery (Nielsen et al 2002;Ragoczy et al 2006) and a study using a transgene tethered to the nuclear lamina could show that this transgene maintains transcriptional activity (Kumaran and Spector 2008). Two studies on a number of endogenous human genes could not find a relationship between expression state and radial nuclear positioning (Murmann et al 2005;Küpper et al 2007). It therefore appears that a positioning of transcribed regions towards the nuclear center is not a requirement for all genes.…”

Section: Introductionmentioning

confidence: 99%

“…These two studies instead described a correlation of the radial position of a gene locus and the local gene density within a 2-or 10-Mbp genomic window around the locus. In addition, one of these studies compared radial distribution of pools of gene loci with GC content and found a correlation of high GC percentages and internal positioning (Küpper et al 2007). …”

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: Experimental Designsupporting

confidence: 73%

Section: Introductioncontrasting

confidence: 44%

Section: Dna Probes and Fishmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Three-dimensional positioning of genes in mouse cell nuclei

et al. 2008

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Transcriptome activity of isochores during preimplantation process in human and mouse

et al. 2016

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This work investigates the role of isochores during preimplantation process. Using RNA-seq data from human and mouse preimplantation stages, we created the spatio-temporal transcriptional profiles of the isochores during preimplantation. We found that from early to late stages, GC-rich isochores increase their expression while GC-poor ones decrease it. Network analysis revealed that modules with few coexpressed isochores are GC-poorer than medium-large ones, characterized by an opposite expression as preimplantation advances, decreasing and increasing respectively. Our results reveal a functional contribution of the isochores, supporting the presence of structuralfunctional interactions during maturation and early-embryonic development.

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