Common themes and cell type specific variations of higher order chromatin arrangements in the mouse

BMC Cell Biology

Volumn 6, Issue , 2005, Pages

  Mayer, Robert ^a   Brero, Alessandro ^a   von Hase, Johann ^b   Schroeder, Timm ^c   Cremer, Thomas ^a   Dietzel, Steffen ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; CELL DIFFERENTIATION; CELL TYPE; CENTROMERE; CHROMATIN; CHROMOSOME SIZE; CONFOCAL LASER MICROSCOPY; CORRELATION ANALYSIS; EMBRYONIC STEM CELL; FIBROBLAST; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC CONSERVATION; GENOME ANALYSIS; HETEROCHROMATIN; HUMAN; HUMAN CELL; KARYOTYPE; LYMPHOCYTE; MACROPHAGE; MOLECULAR EVOLUTION; MOUSE; MYOBLAST; MYOTUBE; NONHUMAN; SPECIES DIFFERENCE; ANIMAL; CELL CULTURE; CELL NUCLEUS; CHROMOSOME; COMPARATIVE STUDY; CONFOCAL MICROSCOPY; SKELETAL MUSCLE; STEM CELL; ULTRASTRUCTURE;

ANIMALIA; MAMMALIA;

ANIMALS; CELL NUCLEUS; CELLS, CULTURED; CHROMATIN; CHROMOSOMES; FIBROBLASTS; IN SITU HYBRIDIZATION, FLUORESCENCE; LYMPHOCYTES; MACROPHAGES; MICE; MICROSCOPY, CONFOCAL; MUSCLE FIBERS, SKELETAL; MYOBLASTS; STEM CELLS;

EID: 29244451509     PISSN: 14712121     EISSN: 14712121     Source Type: Journal    
DOI: 10.1186/1471-2121-6-44     Document Type: Article

References (77)

1. Schardin M, Cremer T, Hager HD, Lang M: Specific staining of human chromosomes in Chinese hamster x man hybrid cell lines demonstrates interphase chromosome territories. Hum Genet 1985, 71(4):281-287.
2. Manuelidis L: Individual interphase chromosome domains revealed by in situ hybridization. Hum Genet 1985, 71(4):288-293.
3. Lucas JN, Cervantes E: Significant large-scale chromosome territory movement occurs as a result of mitosis, but not during interphase. Int J Radiat Biol 2002, 78(6):449-455.
4. Walter J, Schermelleh L, Cremer M, Tashiro S, Cremer T: Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages. J Cell Biol 2003, 160(5):685-697.
5. Postberg J, Alexandrova O, Cremer T, Lipps HJ: Exploiting nuclear duality of ciliates to analyze topological requirements for DNA replication and transcription. J Cell Sci 2005, 118:3973-3983.
6. Alexandrova O, Solovei I, Cremer T, David CN: Replication labeling patterns and chromosome territories typical of mammalian nuclei are conserved in the early metazoan Hydra. Chromosoma 2003, 112(4):190-200.
7. Habermann FA, Cremer M, Walter J, Kreth G, von Hase J, Bauer K, Wienberg J, Cremer C, Cremer T, Solovei I: Arrangements of macro- and microchromosomes in chicken cells. Chromosome Res 2001, 9(7):569-584.
8. O'Keefe RT, Henderson SC, Spector DL: Dynamic organization of DNA replication in mammalian cell nuclei: spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences. J Cell Biol 1992, 116(5):1095-1110.
9. Sadoni N, Langer S, Fauth C, Bernardi G, Cremer T, Turner BM, Zink D: Nuclear organization of mammalian genomes. Polar chromosome territories build up functionally distinct higher order compartments. J Cell Biol 1999, 146(6):1211-1226.
10. Mayr C, Jasencakova Z, Meister A, Schubert I, Zink D: Comparative analysis of the functional genome architecture of animal and plant cell nuclei. Chromosome Res 2003, 11(5):471-484.
11. Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA: Differences in the Localization and Morphology of Chromosomes in the Human Nucleus. J Cell Biol 1999, 145(6):1119-1131.
12. Cremer M, von Hase J, Volm T, Brero A, Kreth G, Walter J, Fischer C, Solovei I, Cremer C, Cremer T: Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res 2001, 9(7):541-567.
13. Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA: The spatial organization of human chromosomes within the nuclei of normal and emerinmutant cells. Hum Mol Genet 2001, 10(3):211-219.
14. Tanabe H, Müller S, Neusser M, von Hase J, Calcagno E, Cremer M, Solovei I, Cremer C, Cremer T: Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci U S A 2002, 99(7):4424-4429.
15. Bridger JM, Boyle S, Kill IR, Bickmore WA: Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts. Curr Biol 2000, 10(3):149-152.
16. Sun HB, Shen J, Yokota H: Size-dependent positioning of human chromosomes in interphase nuclei. Biophys J 2000, 79(1):184-190.
17. Bolzer A, Kreth G, Solovei I, Köhler D, Saracoglu K, Fauth C, Müller S, Eils R, Cremer C, Speicher MR, Cremer T: Three-dimensional maps of all chromosome positions demonstrate a probabilistic order in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 2005, 3(5):e157.
18. Parada L, McQueen P, Misteli T: Tissue-specific spatial organization of genomes. Genome Biology 2004, 5(7):R44.
19. Stadler S, Schnapp V, Mayer R, Stein S, Cremer C, Bonifer C, Cremer T, Dietzel S: The architecture of chicken chromosome territories changes during differentiation. BMC Cell Biol 2004, 5(1):44.
20. Manuelidis L: Different central nervous system cell types display distinct and nonrandom arrangements of satellite DNA sequences. Proc-Natl-Acad-Sci-U-S-A 1984, 81(10):3123-3127.
21. van Dekken H, Hulspas R: Spatial analysis of intranuclear human repetitive DNA regions by in situ hybridization and digital fluorescence microscopy. Histochem-J 1993, 25(3):173-182.
22. Dietzel S, Weilandt E, Eils R, Münkel C, Cremer C, Cremer T: Three-dimensional distribution of centromeric or paracentromeric heterochromatin of chromosomes 1, 7, 15 and 17 in human lymphocyte nuclei studied with light microscopic axial tomography. Bioimaging 1995, 3:121-133.
23. Manuelidis L: Indications of centromere movement during interphase and differentiation. Ann N Y Acad Sci 1985, 450:205-221.
24. Martou G, de Boni U: Nuclear topology of murine, cerebellar Purkinje neurons: changes as a function of development. Exp Cell Res 2000, 256(1):131-139.
25. Solovei I, Grandi N, Knoth R, Volk B, Cremer T: Postnatal changes of pericentromeric heterochromatin and nucleoli in postmitotic Purkinje cells during murine cerebellum development. Cytogenetics and Genome Research 2004, 105(2-4):142-150.
26. Kim SH, McQueen PG, Lichtman MK, Shevach EM, Parada LA, Misteli T: Spatial genome organization during T-cell differentiation. Cytogenet Genome Res 2004, 105(2-4):292-301.
27. Brown KE, Guest SS, Smale ST, Hahm K, Merkenschlager M, Fisher AG: Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 1997, 91(6):845-854.
28. Brown KE, Amoils S, Horn JM, Buckle VJ, Higgs DR, Merkenschlager M, Fisher AG: Expression of alpha- and beta-globin genes occurs within different nuclear domains in haemopoietic cells. Nat Cell Biol 2001, 3(6):602-606.
29. Brero A, Easwaran HP, Nowak D, Grunewald I, Cremer T, Leonhardt H, Cardoso 0MC: MeCP2 induces large-scale chromatin reorganization during terminal differentiation. J Cell Biol 2005, 169(5):733-743.
30. Ensembl Genome Browser [http://www.ensembl.org/], Mouse data based on NCBI assembly m34, May 2005, Genebuild: Ensembl, Sep 2005. Human data based on NCBI assembly 35, July 2004, Genebuild: Ensembl, Sep 2005.
31. Dev VG, Tantravahi R, Miller DA, Miller OJ: Nucleolus organizers in Mus musculus subspecies and in the RAG mouse cell line. Genetics 1977, 86(2 Pt. 1):389-398.
32. Winking H, Nielsen K, Gropp A: Variable positions of NORs in Mus musculus. Cytogenet Cell Genet 1980, 26(2-4):158-164.
33. Weimer R, Haaf T, Krüger J, Poot M, Schmid M: Characterization of centromere arrangements and test for random distribution in G0, G1, S, G2, G1, and early S′ phase in human lymphocytes. Hum Genet 1992, 88(6):673-682.
34. Ferguson M, Ward DC: Cell cycle dependent chromosomal movement in premitotic human T-lymphocyte nuclei. Chromosoma 1992, 101(9):557-565.
35. Vourc'h C, Taruscio D, Boyle AL, Ward DC: Cell cycle-dependent distribution of telomeres, centromeres, and chromosome-specific subsatellite domains in the interphase nucleus of mouse lymphocytes. Exp Cell Res 1993, 205(1):142-151.
36. Nagele R, Freeman T, McMorrow L, Lee HY: Precise spatial positioning of chromosomes during prometaphase: evidence for chromosomal order. Science 1995, 270(5243):1831-1835.
37. Hsu TC, Cooper JE, Mace ML, Jr., Brinkley BR: Arrangement of centromeres in mouse cells. Chromosoma 1971, 34(1):73-87.
38. Pardue ML, Gall JG: Chromosomal localization of mouse satellite DNA. Science 1970, 168(937):1356-1358.
39. Weierich C, Brero A, Stein S, von Hase J, Cremer C, Cremer T, Solovei I: Three-dimensional arrangements of centromeres and telomeres in nuclei of human and murine lymphocytes. Chromosome Res 2003, 11(5):485-502.
40. Cremer M, Küpper K, Wagler B, Wizelman L, von Hase J, Weiland Y, Kreja L, Diebold J, Speicher MR, Cremer T: Inheritance of gene density-related higher order chromatin arrangements in normal and tumor cell nuclei. J Cell Biol 2003, 162(5):809-820.
41. Springer MS, Murphy WJ, Eizirik E, O'Brien SJ: Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc Natl Acad Sci U S A 2003, 100(3):1056-1061.
42. Tumbar T, Belmont AS: Interphase movements of a DNA chromosome region modulated by VP16 transcriptional activator. Nat Cell Biol 2001, 3:134-139.
43. Dietzel S, Zolghadr K, Hepperger C, Belmont AS: Differential large-scale chromatin compaction and intranuclear positioning of transcribed versus non-transcribed transgene arrays containing beta-globin regulatory sequences. J Cell Sci 2004, 117(Pt 19):4603-4614.
44. Wiblin AE, Cui W, Clark AJ, Bickmore WA: Distinctive nuclear organisation of centromeres and regions involved in pluripotency in human embryonic stem cells. J Cell Sci 2005, 118(Pt 17):3861-3868.
45. Tanabe H, Habermann FA, Solovei I, Cremer M, Cremer T: Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications. Mutat Res 2002, 504(1-2):37-45.
46. Manuelidis L: A view of interphase chromosomes. Science 1990, 250(4987):1533-1540.
47. Nagele RG, Freeman T, Fazekas J, Lee KM, Thomson Z, Lee HY: Chromosome spatial order in human cells: evidence for early origin and faithful propagation. Chromosoma 1998, 107(5):330-338.
48. Koss LG: Characteristics of chromosomes in polarized normal human bronchial cells provide a blueprint for nuclear organization. Cytogenet Cell Genet 1998, 82(3-4):230-237.
49. Nagele RG, Freeman T, McMorrow L, Thomson Z, Kitson-Wind K, Lee H: Chromosomes exhibit preferential positioning in nuclei of quiescent human cells. J Cell Sci 1999, 112(Pt 4):525-535.
50. Allison DC, Nestor AL: Evidence for a relatively random array of human chromosomes on the mitotic ring. J Cell Biol 1999, 145(1):1-14.
51. Cornforth MN, Greulich-Bode KM, Loucas BD, Arsuaga J, Vázquez M, Sachs RK, Brückner M, Molls M, Hahnfeldt P, Hlatky L, Brenner DJ: Chromosomes are predominantly located randomly with respect to each other in interphase human cells. J Cell Biol 2002, 159(2):237-244.
52. Parada LA, McQueen PG, Munson PJ, Misteli T: Conservation of relative chromosome positioning in normal and cancer cells. Curr Biol 2002, 12(19):1692-1697.
53. Alcobia I, Dilão R, Parreira. L: Spatial associations of centromeres in the nuclei of hematopoietic cells: evidence for cell-type-specific organizational patterns. Blood 2000, 95(5):1608-1615.
54. Alcobia I, Quina AS, Neves H, Clode N, Parreira L: The spatial organization of centromeric heterochromatin during normal human lymphopoiesis: evidence for ontogenically determined spatial patterns. Exp Cell Res 2003, 290(2):358-369.
55. Lukasova E, Kozubek S, Kozubek M, Kjeronska J, Ryznar L, Horakova J, Krahulcova E, Horneck G: Localisation and distance between ABL and BCR genes in interphase nuclei of bone marrow cells of control donors and patients with chronic myeloid leukaemia. Hum Genet 1997, 100(5-6):525-535.
56. Neves H, Ramos C, da Silva MG, Parreira. A, Parreira L: The nuclear topography of ABL, BCR, PML, and RARalpha genes: evidence for gene proximity in specific phases of the cell cycle and stages of hematopoietic differentiation. Blood 1999, 93(4):1197-1207.
57. Nikiforova MN, Stringer JR, Blough R, Medvedovic M, Fagin JA, Nikiforov YE: Proximity of chromosomal loci that participate in radiation-induced rearrangements in human cells. Science 2000, 290(5489):138-141.
58. Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T: Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet 2003, 34(3):287-291.
59. Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA: Interchromosomal associations between alternatively expressed loci. Nature 2005, 435(7042):637-645.
60. Arnoldus EPJ, Peters ACB, Bots GTAM, Raap AK, van der Ploeg M: Somatic pairing of chromosome 1 centromeres in interphase nuclei of human cerebellum. Hum-Genet 1989, 83(3):231-234.
61. Arnoldus EP, Noordermeer IA, Peters AC, Raap AK, Van der Ploeg M: Interphase cytogenetics reveals somatic pairing of chromosome 17 centromeres in normal human brain tissue, but no trisomy 7 or sex-chromosome loss. Cytogenet Cell Genet 1991, 56(3-4):214-216.
62. Chandley AC, Speed RM, Leitch AR: Different distributions of homologous chromosomes in adult human Sertoli cells and in lymphocytes signify nuclear differentiation. J Cell Sci 1996, 109(Pt 4):773-776.
63. Choh V, De Boni U: Spatial repositioning of centromeric domains during regrowth of axons in nuclei of murine dorsal root ganglion neurons in vitro. J Neurobiol 1996, 31(3):325-332.
64. Cerda MC, Berríos S, Fernández-Donoso R, Garagna S, Redi C: Organisation of complex nuclear domains in somatic mouse cells. Biol Cell 1999, 91(1):55-65.
65. Chaly N, Munro SB: Centromeres reposition to the nuclear periphery during L6E9 myogenesis in vitro. Exp Cell Res 1996, 223(2):274-278.
66. Beil M, Durschmied D, Paschke S, Schreiner B, Nolte U, Bruel A, Irinopoulou T: Spatial distribution patterns of interphase centromeres during retinoic acid-induced differentiation of promyelocytic leukemia cells. Cytometry 2002, 47(4):217-225.
67. Solovei I, Schermelleh L, Düring K, Engelhardt A, Stein S, Cremer C, Cremer T: Differences in centromere positioning of cycling and postmitotic human cell types. Chromosoma 2004, 112(8):410-423.
68. Faust N, Huber MC, Sippel AE, Bonifer C: Different macrophage populations develop from embryonic/fetal and adult hematopoietic tissues. Exp Hematol 1997, 25(5):432-444.
69. Nakano T, Kodama H, Honjo T: Generation of lymphohematopoietic cells from embryonic stem cells in culture. Science 1994, 265(5175):1098-1101.
70. Schroeder T, Fraser ST, Ogawa M, Nishikawa S, Oka C, Bornkamm GW, Honjo T, Just U: Recombination signal sequence-binding protein Jkappa alters mesodermal cell fate decisions by suppressing cardiomyogenesis. Proc Natl Acad Sci U S A 2003, 100(7):4018-4023.
71. Faust N, Bonifer C, Wiles MV, Sippel AE: An in vitro differentiation system for the examination of transgene activation in mouse macrophages. DNA Cell Biol 1994, 13(9):901-907.
72. Kaufmann U, Kirsch J, Irintchev A, Wernig A, Starzinski-Powitz A: The M-cadherin catenin complex interacts with microtubules in skeletal muscle cells: implications for the fusion of myoblasts. J Cell Sci 1999, 112((Pt 1)):55-68.
73. Cardoso MC, Joseph C, Rahn HP, Reusch R, Nadal-Ginard B, Leonhardt H: Mapping and use of a sequence that targets DNA ligase I to sites of DNA replication in vivo. J Cell Biol 1997, 139(3):579-587.
74. Dernburg AF, Sedat JW: Mapping three-dimensional chromosome architecture in situ. In: Methods in Cell Biology: Nuclear structure and function. Edited by Berrios M, vol. 53: Academic Press; 1998: 187-233.
75. Telenius H, Pelmear AH, Tunnacliffe A, Carter NP, Behmel A, Ferguson-Smith MA, Nordenskjold M, Pfragner R, Ponder BA: Cytogenetic analysis by chromosome painting using DOP-PCR amplified flow-sorted chromosomes. Genes Chromosomes Cancer 1992, 4(3):257-263.
76. Rabbitts P, Impey H, Heppell-Parton A, Langford C, Tease C, Lowe N, Bailey D, Ferguson-Smith M, Carter N: Chromosome specific paints from a high resolution flow karyotype of the mouse. Nat Genet 1995, 9(4):369-375.
77. ImageJ [http://rsb.info.nih.gov/ij/]