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, 117:535

First Online: 03 July 2008Received: 13 December 2007Revised: 13 May 2008Accepted: 13 May 2008


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.

Electronic supplementary materialThe online version of this article doi:10.1007-s00412-008-0168-2 contains supplementary material, which is available to authorized users.

Communicated by E. A. Nigg

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Autor: Claudia Hepperger - Alexander Mannes - Julia Merz - Jürgen Peters - Steffen Dietzel


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