title: Three-dimensional positioning of genes in mouse cell nuclei.
abstract: 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 beta-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.
authors.affiliation: Department Biologie II, Ludwig-Maximilians-Universität München, Grosshaderner Stasse 2, 82152 Planegg-Martinsried, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Hepperger
authors.forename: Alexander
authors.initials: A
authors.lastname: Mannes
authors.forename: Julia
authors.initials: J
authors.lastname: Merz
authors.forename: Jürgen
authors.initials: J
authors.lastname: Peters
authors.forename: Steffen
authors.initials: S
authors.lastname: Dietzel
mesh_terms: D000818:Animals; D001482:Base Composition; D002460:Cell Line; D002467:Cell Nucleus / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics; D053595:Embryonic Stem Cells / Q000378:metabolism; D018628:Gene Dosage; D005786:Gene Expression Regulation; D005796:Genes / Q000235:genetics*; D016678:Genome; D017404:In Situ Hybridization, Fluorescence; D008264:Macrophages / Q000378:metabolism; D051379:Mice; D012091:Repetitive Sequences, Nucleic Acid; D055544:beta-Globins / Q000378:metabolism
chemical_list: D055544:beta-Globins