caa a22 4500 463209524 CHVBK 20180405153136.0 cr unu---uuuuu 170326e20070601xx s 000 0 eng 10.1007/s00412-007-0098-4 doi (NATIONALLICENCE)springer-10.1007/s00412-007-0098-4 Radial chromatin positioning is shaped by local gene density, not by gene expression [Elektronische Daten] [Katrin Küpper, Alexandra Kölbl, Dorothee Biener, Sandra Dittrich, Johann von Hase, Tobias Thormeyer, Heike Fiegler, Nigel Carter, Michael Speicher, Thomas Cremer, Marion Cremer] G- and R-bands of metaphase chromosomes are characterized by profound differences in gene density, CG content, replication timing, and chromatin compaction. The preferential localization of gene-dense, transcriptionally active, and early replicating chromatin in the nuclear interior and of gene-poor, later replicating chromatin at the nuclear envelope has been demonstrated to be evolutionary-conserved in various cell types. Yet, the impact of different local chromatin features on the radial nuclear arrangement of chromatin is still not well understood. In particular, it is not known whether radial chromatin positioning is preferentially shaped by local gene density per se or by other related parameters such as replication timing or transcriptional activity. The interdependence of these distinct chromatin features on the linear deoxyribonucleic acid (DNA) sequence precludes a simple dissection of these parameters with respect to their importance for the reorganization of the linear DNA organization into the distinct radial chromatin arrangements observed in the nuclear space. To analyze this problem, we generated probe sets of pooled bacterial artificial chromosome (BAC) clones from HSA 11, 12, 18, and 19 representing R/G-band-assigned chromatin, segments with different gene density and gene loci with different expression levels. Using multicolor 3D flourescent in situ hybridization (FISH) and 3D image analysis, we determined their localization in the nucleus and their positions within or outside the corresponding chromosome territory (CT). For each BAC data on local gene density within 2- and 10-Mb windows, as well as GC (guanine and cytosine) content, replication timing and expression levels were determined. A correlation analysis of these parameters with nuclear positioning revealed regional gene density as the decisive parameter determining the radial positioning of chromatin in the nucleus in contrast to band assignment, replication timing, and transcriptional activity. We demonstrate a polarized distribution of gene-dense vs gene-poor chromatin within CTs with respect to the nuclear border. Whereas we confirm previous reports that a particular gene-dense and transcriptionally highly active region of about 2Mb on 11p15.5 often loops out from the territory surface, gene-dense and highly expressed sequences were not generally found preferentially at the CT surface as previously suggested. Springer-Verlag, 2007 Küpper Katrin Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut Kölbl Alexandra Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut Biener Dorothee Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut Dittrich Sandra Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut von Hase Johann Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany aut Thormeyer Tobias Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut Fiegler Heike The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK aut Carter Nigel The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK aut Speicher Michael Institute of Medical Biology and Human Genetics, Medical University of Graz, Graz, Austria aut Cremer Thomas Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut Cremer Marion Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut Chromosoma Springer-Verlag 116/3(2007-06-01), 285-306 0009-5915 116:3<285 2007 116 412 https://doi.org/10.1007/s00412-007-0098-4 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s00412-007-0098-4 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Küpper Katrin Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut NATIONALLICENCE 700 1- Kölbl Alexandra Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut NATIONALLICENCE 700 1- Biener Dorothee Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut NATIONALLICENCE 700 1- Dittrich Sandra Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut NATIONALLICENCE 700 1- von Hase Johann Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany aut NATIONALLICENCE 700 1- Thormeyer Tobias Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut NATIONALLICENCE 700 1- Fiegler Heike The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK aut NATIONALLICENCE 700 1- Carter Nigel The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK aut NATIONALLICENCE 700 1- Speicher Michael Institute of Medical Biology and Human Genetics, Medical University of Graz, Graz, Austria aut NATIONALLICENCE 700 1- Cremer Thomas Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut NATIONALLICENCE 700 1- Cremer Marion Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany aut NATIONALLICENCE 773 0- Chromosoma Springer-Verlag 116/3(2007-06-01), 285-306 0009-5915 116:3<285 2007 116 412 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer