Daniele Zink ¹, Margarida D. Amaral ^{2, 3}, Andreas Englmann ¹, Susanne Lang ¹, Luka A. Clarke ², Carsten Rudolph ⁴, Felix Alt ¹, Kathrin Luther ¹, Carla Braz ², Nicolas Sadoni ¹, Joseph Rosenecker ⁴, and Dirk Schindelhauer ^{5, 6}

¹ Ludwig Maximilians University Munich, Department of Biology II, 80336 Munich, Germany
² Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
³ Center of Human Genetics, National Institute of Health, 1649-016 Lisboa, Portugal
⁴ Ludwig Maximilians University Munich, Division of Molecular Pulmonology, Department of Pediatrics, 80337 Munich, Germany
⁵ Technical University of Munich, Institute of Human Genetics, 81675 Munich, Germany
⁶ Life Science Center Weihenstephan, 85354 Freising, Germany

Address correspondence to: D. Zink, Ludwig Maximilians University Munich,
Department of Biology II, Grosshaderner Str. 2, 82152 Planegg-Martinstried, Germany.
Tel.: (49) 89-2180-74133. Fax: (49) 89-2180-75618. email: Dani.Zink@lrz.uni-muenchen.de

We investigated in different human cell types nuclear positioning and transcriptional regulation of the functionally unrelated genes GASZ, CFTR, and CORTBP2, mapping to adjacent loci on human chromosome 7q31. When inactive, GASZ, CFTR, and CORTBP2 preferentially associated with the nuclear periphery and with perinuclear heterochromatin, whereas in their actively transcribed states the gene loci preferentially associated with euchromatin in the nuclear interior. Adjacent genes associated simultaneously with these distinct chromatin fractions localizing at different nuclear regions, in accordance with their individual transcriptional regulation.
Although the nuclear localization of CFTR changed after altering its transcription levels, the transcriptional status of CFTR was not changed by driving this gene into a different nuclear environment. This implied that the transcriptional activity affected the nuclear positioning, and not vice versa. Together, the results show that small chromosomal subregions can display highly flexible nuclear organizations that are regulated at the level of individual genes in a transcription-dependent manner. 

Figure 8. Positioning of GASZ, CFTR, and CORTBP2 with respect to the chromosome 7 territory.

T-lymphocytes, 293 cells, and Calu-3 cells were hybridized with the gene-specific probes (CF1 used for CFTR) and in addition with a painting probe specific for human chromosome 7. The localization of the gene-specific FISH signals was determined with regard to the chromosome 7 territory, as defined by the FISH signal of the painting probe.

Gene-specific signals were assigned to three different categories: (1) localization within; (2) at the periphery; or (3) outside of the chromosome 7 territory.

(a) Panels show examples (gene-specific signals, red; chromosome 7 territory, green; DAPI counterstain, blue; bars, 5 µm). The arrows in the left-hand panel point to CORTBP2-specific signals positioned within the
territories, whereas the arrowhead points to a signal located at the periphery of the chromosome territory. This panel shows a Calu-3 nucleus containing three chromosome 7 territories. Both CORTBP2-specific signals (arrows) shown on the right-hand panel (T-lymphocyte nucleus) were classified as positioned outside of the corresponding chromosome territories.

(b) The diagrams summarize the results obtained for the different probes and cell types indicated. Bars indicate the fractions of FISH signals (averages ± SD) located outside (left bars in the diagrams), at the periphery (bars in the middle), or within (right-hand bars) the chromosome 7 territories.

Key Words: CFTR; nuclear architecture; gene positioning; chromatin organization; chromosome territory

S. Lang's present address is Max Planck Institute for Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany.

K. Luther's present address is Max von Pettenkofer Institute, 80336 Munich, Germany.

Abbreviations used in this paper: 3D, three-dimensional; CFTR, cystic fibrosis transmembrane conductance regulator; CORTBP2, cortactin-binding protein 2; DRB, 5,6-dichlorobenzimidazole riboside; GASZ, germ cell–specific expression, presence of ANK, SAM, and basic leucine zipper domains; H4Ac8, H4 acetylated at lysine 8; LAP2ß, lamina-associated polypeptide 2ß; TSA, trichostatin A.

Supplementary Material:

http://www.jcb.org:80/cgi/content/full/jcb.200404107/DC1

Additional References:

1. Gilbert N, Boyle S, Fiegler H, Woodfine K, Carter NP, and Bickmore WA, "Chromatin Architecture of the Human Genome: Gene-Rich Domains Are Enriched in Open Chromatin Fibers".

2. Frenster JH, and Hovsepian JA, "Ultrastructure  of Closed Loops within Euchromatin of Isolated Lymphocyte Nuclei".

3. Parada LA, McQueen PG,  and Misteli T, "Tissue-specific spatial organization of genomes".

4. Chambeyron S,  and Bickmore WA, "Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription".

5. Kreth G, Finsterle J, von Hase J, Cremer M, and Cremer C, "Radial Arrangement of Chromosome Territories in Human Cell Nuclei: A Computer Model Approach Based on Gene Density Indicates a Probabilistic Global Positioning Code".

6. Frenster JH, and Hovsepian JA, "Activator RNA Exchange during Interphase Chromatin Reprogramming".

7. Hovsepian JA, and Frenster JH, "Euchromatin as an Extensile Force within Mammalian Cell Nuclei".

8. Hovsepian JA, and Frenster JH, "Bioassays of Isolated Nuclear RNA Species as Activators of DNA Transcription".

Links to RNA and Biological Causality:

Further Topics in:  Euchromatin,  active DNA, and  RNA  ribo-regulators:

Links to Euchromatin Activator RNA Reviews:
Links to Euchromatin Activator RNA Research:
Links to Ultrastructural Probes of DNase I-Sensitive Sites:
Links to RNA as a Therapeutic Agent:
Links to Hodgkin Lymphoma Immuno-Pathology:
Links to Activated T-Lymphocyte Immunotherapy:
Links to Medical Systems Biology:
Links to Selective Gene Transcription:
Links to RNA-Induced Epigenetics:
Links to RNA-Induced Embryogenesis:
Links to RNA and Biological Causality:
Links to Reprogramming and Neoplasia:

"Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".

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