title: Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes.
abstract: Studies of higher-order chromatin arrangements are an essential part of ongoing attempts to explore changes in epigenome structure and their functional implications during development and cell differentiation. However, the extent and cell-type-specificity of three-dimensional (3D) chromosome arrangements has remained controversial. In order to overcome technical limitations of previous studies, we have developed tools that allow the quantitative 3D positional mapping of all chromosomes simultaneously. We present unequivocal evidence for a probabilistic 3D order of prometaphase chromosomes, as well as of chromosome territories (CTs) in nuclei of quiescent (G0) and cycling (early S-phase) human diploid fibroblasts (46, XY). Radial distance measurements showed a probabilistic, highly nonrandom correlation with chromosome size: small chromosomes-independently of their gene density-were distributed significantly closer to the center of the nucleus or prometaphase rosette, while large chromosomes were located closer to the nuclear or rosette rim. This arrangement was independently confirmed in both human fibroblast and amniotic fluid cell nuclei. Notably, these cell types exhibit flat-ellipsoidal cell nuclei, in contrast to the spherical nuclei of lymphocytes and several other human cell types, for which we and others previously demonstrated gene-density-correlated radial 3D CT arrangements. Modeling of 3D CT arrangements suggests that cell-type-specific differences in radial CT arrangements are not solely due to geometrical constraints that result from nuclear shape differences. We also found gene-density-correlated arrangements of higher-order chromatin shared by all human cell types studied so far. Chromatin domains, which are gene-poor, form a layer beneath the nuclear envelope, while gene-dense chromatin is enriched in the nuclear interior. We discuss the possible functional implications of this finding.
authors.affiliation: Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Bolzer
authors.forename: Gregor
authors.initials: G
authors.lastname: Kreth
authors.forename: Irina
authors.initials: I
authors.lastname: Solovei
authors.forename: Daniela
authors.initials: D
authors.lastname: Koehler
authors.forename: Kaan
authors.initials: K
authors.lastname: Saracoglu
authors.forename: Christine
authors.initials: C
authors.lastname: Fauth
authors.forename: Stefan
authors.initials: S
authors.lastname: Müller
authors.forename: Roland
authors.initials: R
authors.lastname: Eils
authors.forename: Christoph
authors.initials: C
authors.lastname: Cremer
authors.forename: Michael R
authors.initials: MR
authors.lastname: Speicher
authors.forename: Thomas
authors.initials: T
authors.lastname: Cremer
mesh_terms: D018929:Cell Culture Techniques; D002467:Cell Nucleus / Q000648:ultrastructure*; D002675:Child, Preschool; D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000648:ultrastructure*; D004171:Diploidy; D005347:Fibroblasts / Q000166:cytology*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D011336:Probability; D049468:Prometaphase / Q000235:genetics*; D012867:Skin / Q000166:cytology