Chromosome Research

, Volume 9, Issue 7, pp 541–567 | Cite as

Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells

  • Marion Cremer
  • Johann von Hase
  • Tanja Volm
  • Alessandro Brero
  • Gregor Kreth
  • Joachim Walter
  • Christine Fischer
  • Irina Solovei
  • Christoph Cremer
  • Thomas Cremer


A quantitative comparison of higher-order chromatin arrangements was performed in human cell types with three-dimensionally (3D) preserved, differently shaped nuclei. These cell types included flat-ellipsoid nuclei of diploid amniotic fluid cells and fibroblasts and spherical nuclei of B and T lymphocytes from peripheral human blood. Fluorescence in-situ hybridization (FISH) was performed with chromosome paint probes for large (#1–5) and small (#17–20) autosomes, and for the two sex chromosomes. Other probes delineated heterochromatin blocks of numerous larger and smaller human chromosomes. Shape differences correlated with distinct differences in higher order chromatin arrangements: in the spherically shaped lymphocyte nuclei we noted the preferential positioning of the small, gene dense #17, 19 and 20 chromosome territories (CTs) in the 3D nuclear interior – typically without any apparent connection to the nuclear envelope. In contrast, CTs of the gene-poor small chromosomes #18 and Y were apparently attached at the nuclear envelope. CTs of large chromosomes were also preferentially located towards the nuclear periphery. In the ellipsoid nuclei of amniotic fluid cells and fibroblasts, all tested CTs showed attachments to the upper and/or lower part of the nuclear envelope: CTs of small chromosomes, including #18 and Y, were located towards the centre of the nuclear projection (CNP), while the large chromosomes were positioned towards the 2D nuclear rim. In contrast to these highly reproducible radial arrangements, 2D distances measured between heterochromatin blocks of homologous and heterologous CTs were strikingly variable. These results as well as CT painting let us conclude that nuclear functions in the studied cell types may not require reproducible side-by-side arrangements of specific homologous or non-homologous CTs. 3D-modelling of statistical arrangements of 46 human CTs in spherical nuclei was performed under the assumption of a linear correlation between DNA content of each chromosome and its CT volume. In a set of modelled nuclei, we noted the preferential localization of smaller CTs towards the 3D periphery and of larger CTs towards the 3D centre. This distribution is in clear contrast to the experimentally observed distribution in lymphocyte nuclei. We conclude that presently unknown factors (other than topological constraints) may play a decisive role to enforce the different radial arrangements of large and small CTs observed in ellipsoid and spherical human cell nuclei.

chromosome territory chromosome topology 3D FISH human interphase nuclei nuclear architecture 


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  1. Alcobia I, Dilao R, Parreira L (2000) Spatial associations of centromeres in the nuclei of hematopoietic cells: evidence for cell-type-specific organizational patterns. Blood 95: 1608-1615.Google Scholar
  2. Allison DC, Nestor AL (1999) Evidence for a relatively random array of human chromosomes on the mitotic ring. J Cell Biol 145: 1-14.Google Scholar
  3. Bolzer A, Craig JM, Cremer T, Speicher MR (1999) A complete set of repeat-depleted, PCR-amplifiable, human chromosome-specific painting probes. Cytogenet Cell Genet 84: 233-240.Google Scholar
  4. Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA (2001) The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 10: 211-219.Google Scholar
  5. Bridger JM, Boyle S, Kill IR, Bickmore WA (2000) Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts. Curr Biol 10: 149-152.Google Scholar
  6. Chandley AC, Speed RM, Leitch AR (1996) Different distributions of homologous chromosomes in adult human Sertoli cells and in lymphocytes signify nuclear differentiation. J Cell Sci 109: 773-776.Google Scholar
  7. Comings DE (1968) The rationale for an ordered arrangement of chromatin in the interphase nucleus. Am J Hum Genet 20: 440-460.Google Scholar
  8. Comings DE (1980) Arrangement of chromatin in the nucleus. Hum Genet 53: 131-143.Google Scholar
  9. Cooke HJ, Hindley J (1979) Cloning of human satellite III DNA: different components are on different chromosomes. Nucleic Acids Res 6: 3177-3197.Google Scholar
  10. Cooke HJ, Schmidtke J, Gosden JR (1982) Characterisation of a human Y chromosome repeated sequence and related sequences in higher primates. Chromosoma 87: 491-502.Google Scholar
  11. Craig JM, Bickmore WA (1994) The distribution of CpG islands in mammalian chromosomes [see comments]. [Published erratum appears in Nat Genet 1994 Aug;7(4):551.] Nat Genet 7: 376-382.Google Scholar
  12. Craig JM, Kraus J, Cremer T (1997) Removal of repetitive sequences from FISH probes using PCR-assisted affinity chromatography. Hum Genet 100: 472-476.Google Scholar
  13. Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2: 292-301.Google Scholar
  14. Cremer T, Baumann H, Nakanishi K, Cremer C (1984) Correlation between interphase and metaphase chromosome arrangements as studied by laser-uv-microbeam experiments. Chromosomes Today 8: 203-212.Google Scholar
  15. Cremer C, Cremer T, Gray JW (1982a) Induction of chromosome damage by ultraviolet light and caffeine: correlation of cytogenetic evaluation and flow karyotype. Cytometry 2: 287-290.Google Scholar
  16. Cremer T, Cremer C, Schneider T, Baumann H, Hens L, Kirsch-Volders M (1982b) Analysis of chromosome positions in the interphase nucleus of Chinese hamster cells by laser-UV-microirradiation experiments. Hum Genet 62: 201-209.Google Scholar
  17. Cremer T, Landegent J, Bruckner A et al. (1986) Detection of chromosome aberrations in the human interphase nucleus by visualization of specific target DNAs with radioactive and non-radioactive in situ hybridization techniques: diagnosis of trisomy 18 with probe L1.84. Hum Genet 74: 346-352.Google Scholar
  18. Cremer T, Kurz A, Zirbel R et al. (1993) Role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harb Symp Quant Biol 58: 777-792.Google Scholar
  19. Cremer T, Kreth G, Koester H et al. (2000) Chromosome territories, interchromatin domain compartment, and nuclear matrix: An integrated view of the functional nuclear architecture. Crit Rev Eukaryotic Gene Expression 12: 179-212.Google Scholar
  20. Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA (1999) Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 145: 1119-1131.Google Scholar
  21. Deloukas P, Schuler GD, Gyapay G et al. (1998) A physical map of 30,000 human genes. Science 282: 744-746.Google Scholar
  22. Devilee P, Cremer T, Slagboom P et al. (1986) Two subsets of human alphoid repetitive DNA show distinct preferential localization in the pericentric regions of chromosomes 13, 18, and 21. Cytogenet Cell Genet 41: 193-201.Google Scholar
  23. Dunham I, Lengauer C, Cremer T, Featherstone T (1992) Rapid generation of chromosome-specific alphoid DNA probes using the polymerase chain reaction. Hum Genet 88: 457-462.Google Scholar
  24. Emmerich P, Loos P, Jauch A et al. (1989) Double in situ hybridization in combination with digital image analysis: a new approach to study interphase chromosome topography. Exp Cell Res 181: 126-140.Google Scholar
  25. Ferguson M, Ward DC (1992) Cell cycle dependent chromosomal movement in pre-mitotic human T-lymphocyte nuclei. Chromosoma 101: 557-565.Google Scholar
  26. Habermann F, Cremer M, Walter J et al. (2001) Territories of macro-and microchromosomes in chicken cell nuclei. Chromosome Res 9: 569-584.Google Scholar
  27. Hager HD, Schroeder-Kurth TM, Vogel F (1982) Position of chromosomes in the human interphase nucleus. An analysis of nonhomologous chromatid translocations in lymphocyte cultures after Trenimon treatment and from patients with Fanconi's anemia and Bloom's syndrome. Hum Genet 61: 342-356.Google Scholar
  28. Hartung J (1991) Statistik. München: Wien.Google Scholar
  29. Hens L, Kirsch-Volders M, Verschaeve L, Susanne C (1982) The central localization of the small and early replicating chromosomes in human diploid metaphase figures. Hum Genet 60: 249-256.Google Scholar
  30. Higgins MJ, Wang HS, Shtromas I et al. (1985) Organization of a repetitive human 1.8 kb KpnI sequence localized in the heterochromatin of chromosome 15. Chromosoma 93: 77-86.Google Scholar
  31. Höfers C, Baumann P, Hummer G, Jovin T, Arndt-Jovin D (1993) The localization of chromosome domains in human interphase nuclei. Three-dimensional distance determinations of fluorescence in situ hybridization signals from confocal laser scanning microscopy. Bioimaging 1: 96-106.Google Scholar
  32. Hulsebos T, Schonk D, van Dalen I et al. (1988) Isolation and characterization of alphoid DNA sequences specific for the pericentric regions of chromosomes 4, 5, 9, and 19. Cytogenet Cell Genet 47: 144-148.Google Scholar
  33. Knuth DE. (1981) The Art of Computer Programming. Reading UK: Addison.Google Scholar
  34. Koutna I, Kozubek S, Zaloudik J et al. (2000) Topography of genetic loci in tissue samples: towards new diagnostic tool using interphase FISH and high-resolution image analysis techniques. Anal Cell Pathol 20: 173-185.Google Scholar
  35. Kreth G, Edelmann P, Münkel C, Langowski J, Cremer C (2001) Translocation frequencies for X and Y chromosomes predicted by computer simulations of nuclear structure. In: Sobit RC, Obe G, eds. Some Aspects of Chromosome Structures.Google Scholar
  36. Lander ES, Linton LM, Birren B et al. (2001) Initial sequencing and analysis of the human genome. International Human Genome Sequencing Consortium. Nature 409: 860-921.Google Scholar
  37. Leitch AR (2000) Higher levels of organization in the interphase nucleus of cycling and differentiated cells. Microbiol Mol Biol Rev 64: 138-152.Google Scholar
  38. Leitch AR, Brown JK, Mosgoller W, Schwarzacher T, Heslop-Harrison JS (1994) The spatial localization of homologous chromosomes in human fibroblasts at mitosis. Hum Genet 93: 275-280.Google Scholar
  39. Lesko SA, Callahan DE, LaVilla ME, Wang ZP, Ts'o PO (1995) The experimental homologous and heterologous separation distance histograms for the centromeres of chromosomes 7, 11, and 17 in interphase human T-lymphocytes. Exp Cell Res 219: 499-506.Google Scholar
  40. Manuelidis L (1985) Individual interphase chromosome domains revealed by in situ hybridization. Hum Genet 71: 288-293.Google Scholar
  41. Manuelidis L (1990) A view of interphase chromosomes. Science 250: 1533-1540.Google Scholar
  42. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21: 1087-1092.Google Scholar
  43. Morton NE (1991) Parameters of the human genome. Proc Natl Acad Sci USA 88: 7474-7476.Google Scholar
  44. Mosgöller W, Leitch AR, Brown JK, Heslop-Harrison JS (1991) Chromosome arrangements in human fibroblasts at mitosis. Hum Genet 88: 27-33.Google Scholar
  45. Moyzis RK, Albright KL, Bartholdi MF et al. (1987) Human chromosome-specific repetitive DNA sequences: novel markers for genetic analysis. Chromosoma 95: 375-386.Google Scholar
  46. Münkel C, Eils R, Imhoff J, Dietzel S, Cremer C, Cremer T (1995) Simulation of the distribution of chromosome targets in cell nuclei under topological constraints. Bioimaging 3: 108-120.Google Scholar
  47. Nagele R, Freeman T, McMorrow L, Lee HY (1995) Precise spatial positioning of chromosomes during prometaphase: evidence for chromosomal order. Science 270: 1831-1835.Google Scholar
  48. Nagele RG, Freeman T, Fazekas J, Lee KM, Thomson Z, Lee HY (1998) Chromosome spatial order in human cells: evidence for early origin and faithful propagation. Chromosoma 107: 330-338.Google Scholar
  49. Nagele RG, Freeman T, McMorrow L, Thomson Z, Kitson-Wind K, Lee H (1999) Chromosomes exhibit preferential positioning in nuclei of quiescent human cells. J Cell Sci 112: 525-535.Google Scholar
  50. Nikiforova MN, Stringer JR, Blough R, Medvedovic M, Fagin JA, Nikiforov YE (2000) Proximity of chromosomal loci that participate in radiation-induced rearrangements in human cells [In Process Citation]. Science 290: 138-141.Google Scholar
  51. O'Brien SJ, Menotti-Raymond M, Murphy WJ et al. (1999) The promise of comparative genomics in mammals. Science 286: 458-462, 479–481.Google Scholar
  52. Ochs BA, Franke WW, Moll R, Grund C, Cremer M, Cremer T (1983) Epithelial character and morphologic diversity of cell cultures from human amniotic fluids examined by immunofluorescence microscopy and gel electrophoresis of cytoskeletal proteins. Differentiation 24: 153-173.Google Scholar
  53. Pearson PL, Bobrow M, Vosa CG (1970) Technique for identifying Y chromosomes in human interphase nuclei. Nature 226: 78-80.Google Scholar
  54. Popp S, Scholl HP, Loos P et al. (1990) Distribution of chromosome 18 and X centric heterochromatin in the interphase nucleus of cultured human cells. Exp Cell Res 189: 1-12.Google Scholar
  55. Rappold GA, Cremer T, Hager HD, Davies KE, Muller CR, Yang T (1984) Sex chromosome positions in human interphase nuclei as studied by in situ hybridization with chromosome specific DNA probes. Hum Genet 67: 317-325.Google Scholar
  56. Rocchi M, Miller DA, Miller OJ, Baldini A (1989) Human alpha-DNA clone specific for chromosome 12. Cytogenet Cell Genet 51: 1067.Google Scholar
  57. Sadoni N, Langer S, Fauth C et al. (1999) Nuclear organization of mammalian genomes. Polar chromosome territories build up functionally distinct higher order compartments. J Cell Biol. 146: 1211-1226.Google Scholar
  58. Schardin M, Cremer T, Hager HD, Lang M (1985) Specific staining of human chromosomes in Chinese hamster × man hybrid cell lines demonstrates interphase chromosome territories. Hum Genet 71: 281-287.Google Scholar
  59. Schermelleh L, Thalhammer S, Heckl W et al. (1999) Laser microdissection and laser pressure catapulting for the generation of chromosome-specific paint probes. Biotechniques 27: 362-267.Google Scholar
  60. Schwarzacher H. (1976) Chromosomes in Mitosis and Interphase. Berlin, Heidelberg, New York: Springer.Google Scholar
  61. Skalnikova M, Kozubek S, Lukasova E et al. (2000) Spatial arrangement of genes, centromeres and chromosomes in human blood cell nuclei and its changes during the cell cycle, differentiation and after irradiation. Chromosome Res 8: 487-499.Google Scholar
  62. Solovei I, Walter J, Cremer M, Habermann F, Schermelleh L, Cremer T (2001) FISH on three-dimensionally preserved nuclei. In: Squire J, Beatty B, Mai S, Eds. FISH: A Practical Approach. Oxford: Oxford University Press.Google Scholar
  63. Spaeter M (1975) [Non-random position of homologous chromosomes (no. 9 and YY) in interphase nuclei of human fibroblasts (author's transl)]. Humangenetik 27: 111-118.Google Scholar
  64. Sun HB, Shen J, Yokota H (2000) Size-dependent positioning of human chromosomes in interphase nuclei. Biophys J 79: 184-190.Google Scholar
  65. Vogel F, Schroeder TM (1974) The internal order of the interphase nucleus. Humangenetik 25: 265-297.Google Scholar
  66. Vourc'h C, Taruscio D, Boyle AL, Ward DC (1993) Cell cycle-dependent distribution of telomeres, centromeres, and chromosome-specific subsatellite domains in the interphase nucleus of mouse lymphocytes. Exp Cell Res 205: 142-151.Google Scholar
  67. Waye JS, England SB, Willard HF (1987) Genomic organization of alpha satellite DNA on human chromosome 7: evidence for two distinct alphoid domains on a single chromosome. Mol Cell Biol 7: 349-356.Google Scholar
  68. Willard HF, Waye JS (1987) Chromosome-specific subsets of human alpha satellite DNA: Analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat. J Mol Evol 25: 207-214.Google Scholar
  69. Willard HF, Waye JS, Skolnick MH, Schwartz CE, Powers VE, England SB (1986) Restriction length polymorphisms at the centromeres of human chromosomes using chromosome specific alpha satellite DNA. Proc Natl Acad Sci USA 83: 5611-5615.Google Scholar
  70. Wollenberg C, Kiefaber MP, Zang KD (1982) Quantitative studies on the arrangement of human metaphase chromosomes. IX. Arrangement of chromosomes with and without spindle apparatus. Hum Genet 62: 310-315.Google Scholar
  71. Zorn C, Cremer T, Cremer C, Zimmer J (1976) Laser UV microirradiation of interphase nuclei and post-treatment with caffeine. A new approach to establish the arrangement of interphase chromosomes. Hum Genet 35: 83-89.Google Scholar
  72. Zorn C, Cremer C, Cremer T, Zimmer J (1979) Unscheduled DNA synthesis after partial UV irradiation of the cell nucleus. Distribution in interphase and metaphase. Exp Cell Res 124: 111-119.Google Scholar

Copyright information

© Kluwer Academic Publishers 2001

Authors and Affiliations

  • Marion Cremer
    • 1
  • Johann von Hase
    • 2
  • Tanja Volm
    • 3
  • Alessandro Brero
    • 1
  • Gregor Kreth
    • 2
  • Joachim Walter
    • 1
  • Christine Fischer
    • 3
  • Irina Solovei
    • 1
  • Christoph Cremer
    • 2
  • Thomas Cremer
    • 1
  1. 1.Institute of Anthropology and Human GeneticsUniversity of Munich (LMU)MunichGermany
  2. 2.Kirchhoff-Institute of PhysicsUniversity of HeidelbergHeidelbergGermany
  3. 3.Institute of Human GeneticsUniversity of HeidelbergHeidelbergGermany

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