Advertisement

Nuclear Architecture: Topology and Function of Chromatin- and Non-Chromatin Nuclear Domains

  • Satoshi Tashiro
  • Marion Cremer
  • Irina Solovei
  • Thomas Cremer

Abstract

The driving force behind studies on nuclear architecture is based on the assumption that nuclear architecture is an integrated part of the complex epigenetic regulatory mechanisms which control cell type specific gene expression patterns. Epigenetic mechanisms comprise the chromatin level, including DNA methylation, histone modifications and chromatin remodeling factors, and the nuclear level, which includes the dynamics and three-dimensional (3D) spatial higher-order organization of the genome inside the cell nucleus. There is increasing evidence that such a higher-order organization of chromatin arrangement contributes essentially to the regulation of gene expression and other nuclear functions (for review see Spector 2003; van Driel et al. 2003).

Keywords

Fluorescence Recovery After Photobleaching Chromatin Domain Chromosome Territory Cajal Body Nijmegen Breakage Syndrome 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Alcalay M, Tomassoni L, Colombo E, Stoldt S, Grignani F, Fagioli M, Szekely L, Helin K, Pelicci PG (1998) The promyelocytic leukemia gene product (PML) forms stable complexes with the retinoblastoma protein. Mol Cell Biol 18:1084–1093PubMedGoogle Scholar
  2. Andrade LE, Chan EK, Raska I, Peebles CL, Roos G, Tan EM (1991) Human autoantibody to a novel protein of the nuclear coiled body: immunological characterization and cDNA cloning of p80-coilin. J Exp Med 173:1407–1419PubMedGoogle Scholar
  3. Baumann P, Benson FE, West SC (1996) Human Rad51 protein promotes ATP-dependent homologous pairing and strand transfer reactions in vitro. Cell 87:757–766PubMedGoogle Scholar
  4. Beil M, Durschmied D, Paschke S, Schreiner B, Nolte U, Bruel A, Irinopoulou T (2002) Spatial distribution patterns of interphase centromeres during retinoic acid-induced differentiation of promyelocytic leukemia cells. Cytometry 47:217–225PubMedGoogle Scholar
  5. Belmont A (2003) Dynamics of chromatin, proteins, and bodies within the cell nucleus. Curr Opin Cell Biol 15:304–310PubMedGoogle Scholar
  6. Berezney R, Coffey DS (1974) Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60:1410–1417PubMedGoogle Scholar
  7. Berezney R, Wei X (1998) The new paradigm: integrating genomic function and nuclear architecture. J Cell Biochem Suppl 30–31:238–242PubMedGoogle Scholar
  8. Berezney R, Mortillaro MJ, Ma H, Wei X, Samarabandu J (1995) The nuclear matrix: a structural milieu for genomic function. Int Rev Cytol 162A: 1–65PubMedGoogle Scholar
  9. Bischof O, Kim SH, Irving J, Beresten S, Ellis NA, Campisi J (2001) Regulation and localization of the Bloom syndrome protein in response to DNA damage. J Cell Biol 153:367–380PubMedGoogle Scholar
  10. Bishop DK, Ear U, Bhattacharyya A, Calderone C, Beckett M, Weichselbaum RR, Shinohara A (1998) Xrcc3 is required for assembly of Rad51 complexes in vivo. J Biol Chem 273:21482–21488PubMedGoogle Scholar
  11. Boisvert FM, Hendzel MJ, Bazett-Jones DP (2000) Promyelocytic leukemia (PML) nuclear bodies are protein structures that do not accumulate RNA. J Cell Biol 148:283–292PubMedGoogle Scholar
  12. Bolzer, A. Kreth, G,. Solovei, I., Koehler, D., Saracoglu, K., Fauth, C, Muller, S., Eils, R., Cremer, C., Speicher, M.R., Cremer, T. (2005) Twenty-four color chromosome painting in three-dimensionally preserved human fibroblast nuclei and prometaphase rosettes demonstrates the probabilistic nature of non-random chromosome arrangements. PLoS Biology 3: 0826–0842Google Scholar
  13. Boudonck K, Dolan L, Shaw PJ (1999) The movement of coiled bodies visualized in living plant cells by the green fluorescent protein. Mol Biol Cell 10:2297–2307PubMedGoogle Scholar
  14. Boveri T (1909) Die Blastomerenkerne von Ascaris megalocephala und die Theorie der Chromosomenindividualität. Arch Zellforsch 3:181–268Google Scholar
  15. 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.PubMedGoogle Scholar
  16. Brede G, Solheim J, Prydz H (2002) PSKH1, a novel splice factor compartment-associated serine kinase. Nucleic Acids Res 30:5301–5309PubMedGoogle Scholar
  17. Buchhop S, Gibson MK, Wang XW, Wagner P, Sturzbecher HW, Harris CC (1997) Interaction of p53 with the human Rad51 protein. Nucleic Acids Res 25:3868–3874PubMedGoogle Scholar
  18. Carney JP, Maser RS, Olivares H, Davis EM, Le Beau M, Yates JR, 3rd, Hays L, Morgan WF, Petrini JH (1998) The hMrell/hRad50 protein complex, Nijmegen breakage syndrome: linkage of double-strand break repair to the cellular DNA damage response. Cell 93:477–486PubMedGoogle Scholar
  19. Cerda MC, Berrios S, Fernandez-Donoso R, Garagna S, Redi C (1999) Organisation of complex nuclear domains in somatic mouse cells. Biol Cell 91:55–65PubMedGoogle Scholar
  20. Chen HT, Bhandoola A, Difilippantonio MJ, Zhu J, Brown MJ, Tai X, Rogakou EP, Brotz TM, Bonner WM, Ried T, Nussenzweig A (2000) Response to RAG-mediated VDJ cleavage by NBS1 and gamma-H2AX. Science 290:1962–1965PubMedGoogle Scholar
  21. Cheutin T, McNairn AJ, Jenuwein T, Gilbert DM, Singh PB, Misteli T (2003) Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299:721–725PubMedGoogle Scholar
  22. Chubb JR, Bickmore WA (2003) Considering nuclear compartmentalization in the light of nuclear dynamics. Cell 112:403–406PubMedGoogle Scholar
  23. Chubb JR, Boyle S, Perry P, Bickmore WA (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12:439–145PubMedGoogle Scholar
  24. Cmarko D, Verschure PJ, Martin TE, Dahmus ME, Krause S, Fu XD, van Driel R, Fakan S (1999) Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection. Mol Biol Cell 10:211–223PubMedGoogle Scholar
  25. Cmarko D, Verschure PJ, Otte AP, van Driel R, Fakan S (2003) Polycomb group gene silencing proteins are concentrated in the perichromatin compartment of the mammalian nucleus. J Cell Sci 116:335–343PubMedGoogle Scholar
  26. Colwill K, Pawson T, Andrews B, Prasad J, Manley JL, Bell JC, Duncan PI (1996) The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. EMBO J 15:265–275PubMedGoogle Scholar
  27. Comings DE (1968) The rationale for an ordered arrangement of chromatin in the interphase nucleus. Am J Hum Genet 20:440–460PubMedGoogle Scholar
  28. Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2:292–301.PubMedGoogle Scholar
  29. Cremer T, Cremer C, Schneider T, Baumann H, Hens L, Kirsch-Volders M (1982) Analysis of chromosome positions in the interphase nucleus of Chinese hamster cells by laser-UV-microirradiation experiments. Hum Genet 62:201–209PubMedGoogle Scholar
  30. Cremer T, Lichter P, Borden J, Ward DC, Manuelidis L (1988) Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes. Hum Genet 80:235–246PubMedGoogle Scholar
  31. Cremer T, Kurz A, Zirbel R, Dietzel S, Rinke B, Schrock E, Speicher MR, Mathieu U, Jauch A, Emmerich P, et al (1993) Role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harbor Symp Quant Biol 58:777–792PubMedGoogle Scholar
  32. Cremer T, Kreth G, Koester H, Fink RHA, Heintzmann R, Cremer M, Solovei I, Zink D, Creer C (2000) Chromosome territories, interchromatin domain compartment, and nuclear matrix: An integrated view of the functional nuclear architecture. Crit Rev Eukaryotic Gene Expr 12:179–212Google Scholar
  33. Cremer M, von Hase J, Volm T, Brero A, Kreth G, Walter J, Fischer C, Solovei I, Cremer C, Cremer T (2001) Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res 9:541–567PubMedGoogle Scholar
  34. Cremer M, Kupper K, Wagler B, Wizelman L, von Hase J, Weiland Y, Kreja L, Diebold J, Speicher MR, Cremer T (2003) Inheritance of gene density-related higher order chromatin arrangements in normal and tumor cell nuclei. J Cell Biol 162:809–820PubMedGoogle Scholar
  35. Cremer M, Zinner R, Stein S, Albiez H, Wagler B, Cremer C, Cremer T (2004) Three dimensional analysis of histone methylation patterns in normal and tumor cell nuclei. Eur J Histochem 48:15–28PubMedGoogle Scholar
  36. 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 145:1119–1131PubMedGoogle Scholar
  37. D’Amours D, Jackson SP (2002) The Mrel 1 complex: at the crossroads of DNA repair and checkpoint signalling. Nat Rev Mol Cell Biol 3:317–327Google Scholar
  38. Desbois C, Rousset R, Bantignies F, Jalinot P (1996) Exclusion of Int-6 from PML nuclear bodies by binding to the HTLV-I Tax oncoprotein. Science 273:951–953PubMedGoogle Scholar
  39. Dietzel S, Schiebel K, Little G, Edelmann P, Rappold GA, Eils R, Cremer C, Cremer T (1999) The 3D positioning of ANT2, ANT3 genes within female X chromosome territories correlates with gene activity. Exp Cell Res 252:363–375PubMedGoogle Scholar
  40. Dostie J, Lejbkowicz F, Sonenberg N (2000) Nuclear eukaryotic initiation factor 4E (eIF4E) colocalizes with splicing factors in speckles. J Cell Biol 148:239–247PubMedGoogle Scholar
  41. Essers J, Houtsmuller AB, van Veelen L, Paulusma C, Nigg AL, Pastink A, Vermeulen W, Hoeijmakers JH, Kanaar R (2002) Nuclear dynamics of RAD52 group homologous recombination proteins in response to DNA damage. EMBOJ 21:2030–2037Google Scholar
  42. Everett RD, Sourvinos G, Leiper C, Clements JB, Orr A (2004) Formation of nuclear foci of the herpes simplex virus type 1 regulatory protein ICP4 at early times of infection: localization, dynamics, recruitment of ICP27, and evidence for the de novo induction of NDlO-like complexes. J Virol 78:1903–1917PubMedGoogle Scholar
  43. Failla AV, Cavallo A, Cremer C (2002) Subwavelength size determination by spatially modulated illumination virtual microscopy. Appl Opt 41:6651–6659PubMedGoogle Scholar
  44. Frey MR, Matera AG (1995) Coiled bodies contain U7 small nuclear RNA and associate with specific DNA sequences in interphase human cells. Proc Natl Acad Sci USA 92:5915–5919PubMedGoogle Scholar
  45. Frey MR, Matera AG (2001) RNA-mediated interaction of Cajal bodies, U2 snRNA genes. J Cell Biol 154:499–509PubMedGoogle Scholar
  46. Gao J, Köhler D, Solovei I, Cremer T, Eils R, Mattes J (2004) Assessing the similarity of spatial configurations using distance differences and bending energy: Application to chromosomal interphase arrangements in HeLa cell clones. In: ISBI2004, Arlington, VA, USA, pp 1400–1403Google Scholar
  47. Geiman TM, Robertson KD (2002) Chromatin remodeling, histone modifications, DNA methylation-how does it all fit together? J Cell Biochem 87:117–125PubMedGoogle Scholar
  48. Golub EI, Gupta RC, Haaf T, Wold MS, Radding CM (1998) Interaction of human rad51 recombination protein with single-stranded DNA binding protein, RPA. Nucleic Acids Res 26:5388–5393PubMedGoogle Scholar
  49. Guo A, Salomoni P, Luo J, Shih A, Zhong S, Gu W, Paolo Pandolfi P (2000) The function of PML in p53-dependent apoptosis. Nat Cell Biol 2:730–736PubMedGoogle Scholar
  50. Haaf T, Golub El, Reddy G, Radding CM, Ward DC (1995) Nuclear foci of mammalian Rad51 recombination protein in somatic cells after DNA damage and its localization in synaptonemal complexes. Proc Natl Acad Sci USA 92:2298–2302PubMedGoogle Scholar
  51. Handwerger KE, Murphy C, Gall JG (2003) Steady-state dynamics of Cajal body components in the Xenopus germinal vesicle. J Cell Biol 160:495–504PubMedGoogle Scholar
  52. Hoprher KP, Karcher A, Craig L, Woo TT, Carney JP, Tainer JA (2001) Structural biochemistry and interaction architecture of the DNA double-strand break repair Mrel 1 nuclease, Rad50-ATPase. Cell 105:473–485Google Scholar
  53. Ishov AM, Sotnikov AG, Negorev D, Vladimirova OV, Neff N, Kamitani T, Yeh ET, Strauss JF 3rd, Maul GG (1999) PML is critical for ND10 formation and recruits the PML-interacting protein daxx to this nuclear structure when modified by SUMO-1. J Cell Biol 147:221–234.PubMedGoogle Scholar
  54. Jady BE, Darzacq X, Tucker KE, Matera AG, Bertrand E, Kiss T (2003) Modification of Sm small nuclear RNAs occurs in the nucleoplasmic Cajal body following import from the cytoplasm. EMBO J 22:1878–1888PubMedGoogle Scholar
  55. Jagatheesan G, Thanumalayan S, Muralikrishna B, Rangaraj N, Karande AA, Parnaik VK (1999) Co localization of intranuclear lamin foci with RNA splicing factors. J Cell Sci 112 (Pt 24):4651–4661PubMedGoogle Scholar
  56. Kojima T, Zama T, Wada K, Onogi H, Hagiwara M (2001) Cloning of human PRP4 reveals interaction with Clkl. J Biol Chem 276:32247–32256PubMedGoogle Scholar
  57. Kreth G, Finsterle J, von Hase J, Cremer M, Cremer C (2004) Radial arrangement of chromosome territories in human cell nuclei: a computer model approach based on gene density indicates a probabilistic global positioning code. Biophys J 86:1–10Google Scholar
  58. Kruhlak MJ, Lever MA, Fischle W, Verdin E, Bazett-Jones DP, Hendzel MJ (2000) Reduced mobility of the alternate splicing factor (ASF) through the nucleoplasm and steady state speckle compartments. J Cell Biol 150:41–51PubMedGoogle Scholar
  59. Lamond Al, Spector DL (2003) Nuclear speckles: a model for nuclear organelles. Nat Rev Mol Cell Biol 4:605–612PubMedGoogle Scholar
  60. Lavau C, Marchio A, Fagioli M, Jansen J, Falini B, Lebon P, Grosveld F, Pandolfi PP, Pelicci PG, Dejean A (1995) The acute promyelocytic leukaemia-associated PML gene is induced by interferon. Oncogene 11:871–876PubMedGoogle Scholar
  61. Le XF, Yang P, Chang KS (1996) Analysis of the growth and transformation suppressor domains of promyelocytic leukemia gene, PML. J Biol Chem 271:130–135PubMedGoogle Scholar
  62. Leitch AR, Mosgoller W, Schwarzacher T, Bennett MD, Heslop-Harrison JS (1990) Genomic in situ hybridization to sectioned nuclei shows chromosome domains in grass hybrids. J Cell Sci 95:335–341PubMedGoogle Scholar
  63. 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 219:499–506PubMedGoogle Scholar
  64. Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC (1988) Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet 80:224–234PubMedGoogle Scholar
  65. Ma H, Samarabandu J, Devdhar RS, Acharya R, Cheng PC, Meng C, Berezney R (1998) Spatial and temporal dynamics of DNA replication sites in mammalian cells. J Cell Biol 143:1415–1425PubMedGoogle Scholar
  66. Mahy NL, Perry PE, Bickmore WA (2002a) Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol 159:753–763PubMedGoogle Scholar
  67. Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA (2002b) Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J Cell Biol 157:579–589PubMedGoogle Scholar
  68. Manuelidis L (1985) Individual interphase chromosome domains revealed by in situ hybridization. Hum Genet 71:288–293PubMedGoogle Scholar
  69. Maser RS, Monsen KJ, Nelms BE, Petrini JH (1997) hMrel 1 and hRad50 nuclear foci are induced during the normal cellular response to DNA double-strand breaks. Mol Cell Biol 17:6087–6096PubMedGoogle Scholar
  70. Matera AG (1998) Of coiled bodies, gems, and salmon. J Cell Biochem 70:181–192PubMedGoogle Scholar
  71. Matera AG (1999) Nuclear bodies: multifaceted subdomains of the interchromatin space. Trends Cell Biol 9:302–309PubMedGoogle Scholar
  72. Matsuura S, Tauchi H, Nakamura A, Kondo N, Sakamoto S, Endo S, Smeets D, Solder B, Belohradsky BH, Der Kaloustian VM, Oshimura M, Isomura M, Nakamura Y, Komatsu K (1998) Positional cloning of the gene for Nijmegen breakage syndrome. Nat Genet 19:179–181PubMedGoogle Scholar
  73. Mirzoeva OK, Petrini JH (2001) DNA damage-dependent nuclear dynamics of the Mrel 1 complex. Mol Cell Biol 21:281–288PubMedGoogle Scholar
  74. Misteli T, Caceres JF, Spector DL (1997) The dynamics of a pre-mRNA splicing factor in living cells. Nature 387:523–527PubMedGoogle Scholar
  75. Moen PT Jr, Johnson CV, Byron M, Shopland LS, de la Serna IL, Imbalzano AN, Lawrence JB (2004) Repositioning of muscle-specific genes relative to the periphery of SC-35 domains during skeletal myogenesis. Mol Biol Cell 15:197–206PubMedGoogle Scholar
  76. Molenaar C, Wiesmeijer K, Verwoerd NP, Khazen S, Eils R, Tanke HJ, Dirks RW (2003) Visualizing telomere dynamics in living mammalian cells using PNA probes. EMBO J 22:6631–6641PubMedGoogle Scholar
  77. Muller S, Matunis MJ, Dejean A (1998) Conjugation with the ubiquitin-related modifier SUMO-1 regulates the partitioning of PML within the nucleus. EMBOJ 17:61–70.Google Scholar
  78. Muratani M, Gerlich D, Janicki SM, Gebhard M, Eils R, Spector DL (2002) Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nat Cell Biol 4:106–110.PubMedGoogle Scholar
  79. Munkel C, Eils R, Dietzel S, Zink D, Mehring C, Wedemann G, Cremer T, Langowski J (1999) Compartmentalization of interphase chromosomes observed in simulation and experiment. J Mol Biol 285:1053–1065.PubMedGoogle Scholar
  80. Nagele R, Freeman T, McMorrow L, Lee HY (1995) Precise spatial positioning of chromosomes during prometaphase: evidence for chromosomal order. Science 270:1831–1835PubMedGoogle Scholar
  81. Nelms BE, Maser RS, MacKay JF, Lagally MG, Petrini JH (1998) In situ visualization of DNA double-strand break repair in human fibroblasts. Science 280:590–592PubMedGoogle Scholar
  82. Nickerson JA, Krockmalnic G, Wan KM, Penman S (1997) The nuclear matrix revealed by eluting chromatin from a cross-linked nucleus. Proc Natl Acad Sci USA 94:4446–4450PubMedGoogle Scholar
  83. O’Regan P, Wilson C, Townsend S, Thacker J (2001) XRCC2 is a nuclear RAD51-like protein required for damage-dependent RAD51 focus formation without the need for ATP binding. J Biol Chem 276:22148–22153PubMedGoogle Scholar
  84. Ogawa T, Yu X, Shinohara A, Egelman EH (1993) Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science 259:1896–1899PubMedGoogle Scholar
  85. Okada TA, Comings DE (1979) Higher order structure of chromosomes. Chromosoma 72:1–14PubMedGoogle Scholar
  86. Parada LA, Sotiriou S, Misteli T (2004) Spatial genome organization. Exp Cell Res 296:64–70PubMedGoogle Scholar
  87. Paull TT, Gellert M (1999) Nbs1 potentiates ATP-driven DNA unwinding and endonuclease cleavage by the Mrel l/Rad50 complex. Genes Dev 13:1276–1288PubMedGoogle Scholar
  88. Paull TT, Rogakou EP, Yamazaki V, Kirchgessner CU, Gellert M, Bonner WM (2000) A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage. Curr Biol 10:886–895PubMedGoogle Scholar
  89. Pederson T (2004) The spatial organization of the genome in mammalian cells. Curr Opin Genet Dev 14:203–209PubMedGoogle Scholar
  90. Petersen S, Casellas R, Reina-San-Martin B, Chen HT, Difilippantonio MJ, Wilson PC, Hanitsch L, Celeste A, Muramatsu M, Pilch DR, Redon C, Ried T, Bonner WM, Honjo T, Nussenzweig MC, Nussenzweig A (2001) AID is required to initiate Nbsl/gamma-H2AX focus formation and mutations at sites of class switching. Nature 414:660–665PubMedGoogle Scholar
  91. Petrini JH, Stracker TH (2003) The cellular response to DNA double-strand breaks: defining the sensors and mediators. Trends Cell Biol 13:458–462PubMedGoogle Scholar
  92. Platani M, Goldberg I, Swedlow JR, Lamond AI (2000) In vivo analysis of Cajal body movement, separation, and joining in live human cells. J Cell Biol 151:1561–1574PubMedGoogle Scholar
  93. Platani M, Goldberg I, Lamond AI, Swedlow JR (2002) Cajal body dynamics and association with chromatin are ATP-dependent. Nat Cell Biol 4:502–508PubMedGoogle Scholar
  94. Plug AW, Xu J, Reddy G, Golub EI, Ashley T (1996) Presynaptic association of Rad51 protein with selected sites in meiotic chromatin. Proc Natl Acad Sci U S A 93:5920–5924PubMedGoogle Scholar
  95. Quignon F, De Bels F, Koken M, Feunteun J, Ameisen JC, de The H (1998) PML induces a novel caspase-independent death process. Nat Genet 20:259–265.PubMedGoogle Scholar
  96. Raderschall E, Golub El, Haaf T (1999) Nuclear foci of mammalian recombination proteins are located at single-stranded DNA regions formed after DNA damage. Proc Natl Acad Sci USA 96:1921–1926PubMedGoogle Scholar
  97. Regad T, Saib A, Lallemand-Breitenbach V, Pandolfi PP, de The H, Chelbi-Alix MK (2001) PML mediates the interferon-induced antiviral state against a complex retrovirus via its association with the viral transactivator. EMBO J 20:3495–3505.PubMedGoogle Scholar
  98. Schardin M, Cremer T, Hager HD, Lang M (1985) Specific staining of human chromosomes in Chinese Hamster x man hybrid cell lines demonstrates interphase chromosome territories. Hum Genet 71:281–287PubMedGoogle Scholar
  99. Schermelleh L, Solovei I, Zink D, Cremer T (2001) Two-color fluorescence labeling of early and mid-to-late replicating chromatin in living cells. Chromosome Res 9:77–80PubMedGoogle Scholar
  100. Scully R, Chen J, Plug A, Xiao Y, Weaver D, Feunteun J, Ashley T, Livingston DM (1997) Association of BRCA1 with Rad51 in mitotic and meiotic cells. Cell 88:265–275PubMedGoogle Scholar
  101. Sharan SK, Morimatsu M, Albrecht U, Lim DS, Regel E, Dinh C, Sands A, Eichele G, Hasty P, Bradley A (1997) Embryonic lethality and radiation hypersensitivity mediated by Rad51 in mice lacking Brca2. Nature 386:804–810PubMedGoogle Scholar
  102. Shinohara A, Ogawa H, Ogawa T (1992) Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein. Cell 69:457–470PubMedGoogle Scholar
  103. Shinohara A, Ogawa H, Matsuda Y, Ushio N, Ikeo K, Ogawa T (1993) Cloning of human, mouse and fission yeast recombination genes homologous to RAD51 and recA. Nat Genet 4:239–243PubMedGoogle Scholar
  104. Shopland LS, Johnson CV, Byron M, McNeil J, Lawrence JB (2003) Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods. J Cell Biol 162:981–990PubMedGoogle Scholar
  105. Singer RH, Green MR (1997) Compartmentalization of eukaryotic gene expression: causes and effects. Cell 91:291–294PubMedGoogle Scholar
  106. Snaar S, Wiesmeijer K, Jochemsen AG, Tanke HJ, Dirks RW (2000) Mutational analysis of fibrillarin and its mobility in living human cells. J Cell Biol 151:653–662PubMedGoogle Scholar
  107. Solovei I, Cavallo A, Schermelleh L, Jaunin F, Scasselati C, Cmarko D, Cremer C, Fakan S, Cremer T (2002) Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). Exp Cell Res 276:10–23PubMedGoogle Scholar
  108. Solovei I, Schermelleh L, Düring K, Engelhardt A, Stein S, von Hase J, Cremer C, Cremer T (2004a) Differences in centromere positioning of cycling and post-mitotic human cell types. Chromosoma 112: 410–423PubMedGoogle Scholar
  109. Solovei I, Grandi N, Knoth R, Volk B, Cremer T (2004b) Positional changes of pericentromeric heterochromatin and nucleoli in postmitotic Purkinje cells during murine cerebellum development. Cytogenet Genome Res 105: 302–310Google Scholar
  110. Sonoda E, Sasaki MS, Buerstedde JM, Bezzubova O, Shinohara A, Ogawa H, Takata M, Yamaguchi-Iwai Y, Takeda S (1998) Rad51-deficient vertebrate cells accumulate chromosomal breaks prior to cell death. EMBO J 17:598–608PubMedGoogle Scholar
  111. Spector DL (2003) The dynamics of chromosome organization and gene regulation. Annu Rev Biochem 72:573–608PubMedGoogle Scholar
  112. Sternsdorf T, Jensen K, Will H (1997) Evidence for covalent modification of the nuclear dot-associated proteins PML, Sp100 by PIC1/SUMO-1. J Cell Biol 139:1621–1634.PubMedGoogle Scholar
  113. Swedlow JR (2003) Quantitative fluorescence microscopy and image deconvolution. Methods Cell Biol 72:349–367PubMedGoogle Scholar
  114. Tan TL, Essers J, Citterio E, Swagemakers SM, de Wit J, Benson FE, Hoeijmakers JH, Kanaar R (1999) Mouse Rad54 affects DNA conformation, DNA-damage-induced Rad51 foci formation. Curr Biol 9:325–328PubMedGoogle Scholar
  115. Tashiro S, Kotomura N, Shinohara A, Tanaka K, Ueda K, Kamada N (1996) S phase specific formation of the human Rad51 protein nuclear foci in lymphocytes. Oncogene 12:2165–2170PubMedGoogle Scholar
  116. Tashiro S, Walter J, Shinohara A, Kamada N, Cremer T (2000) Rad51 accumulation at sites of DNA damage and in postreplicative chromatin. J Cell Biol 150:283–291PubMedGoogle Scholar
  117. Trinkle-Mulcahy L, Ajuh P, Prescott A, Claverie-Martin F, Cohen S, Lamond AI, Cohen P (1999) Nuclear organisation of NIPP1, a regulatory subunit of protein phosphatase 1 that associates with pre-mRNA splicing factors. J Cell Sci 112 (Pt 2): 157–168PubMedGoogle Scholar
  118. Vallian S, Chin KV, Chang KS (1998) The promyelocytic leukemia protein interacts with Sp1 and inhibits its transactivation of the epidermal growth factor receptor promoter. Mol Cell Biol 18:7147–7156PubMedGoogle Scholar
  119. van den Bosch M, Bree RT, Lowndes NF (2003) The MRN complex: coordinating and mediating the response to broken chromosomes. EMBO Rep 4:844–849PubMedGoogle Scholar
  120. van Driel R, Fransz PF, Verschure PJ (2003) The eukaryotic genome: a system regulated at different hierarchical levels. J Cell Sci 116:4067–4075PubMedGoogle Scholar
  121. Varon R, Vissinga C, Platzer M, Cerosaletti KM, Chrzanowska KH, Saar K, Beckmann G, Seemanova E, Cooper PR, Nowak NJ, Stumm M, Weemaes CM, Gatti RA, Wilson RK, Digweed M, Rosenthal A, Sperling K, Concannon P, Reis A (1998) Nibrin, a novel DNA double-strand break repair protein, is mutated in Nijmegen breakage syndrome. Cell 93:467–476PubMedGoogle Scholar
  122. Vazquez J, Belmont AS, Sedat JW (2001) Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Curr Biol 11:1227–1239PubMedGoogle Scholar
  123. Verschure PJ, van der Kraan I, Manders EM, Hoogstraten D, Houtsmuller AB, van Driel R (2003) Condensed chromatin domains in the mammalian nucleus are accessible to large macromolecules. EMBO Rep 4:861–866PubMedGoogle Scholar
  124. Visser AE, Jaunin F, Fakan S, Aten JA (2000) High resolution analysis of interphase chromosome domains. J Cell Sci 113:2585–2593PubMedGoogle Scholar
  125. Vogel F, Schroeder TM (1974) The internal order of the interphase nucleus. Humangenetik 25:265–297PubMedGoogle Scholar
  126. Volpi EV, Chevret E, Jones T, Vatcheva R, Williamson J, Beck S, Campbell RD, Goldsworthy M, Powis SH, Ragoussis J, Trowsdale J, Sheer D (2000) Largescale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J Cell Sci 113 (Pt 9): 1565–1576PubMedGoogle Scholar
  127. von Mikecz A, Zhang S, Montminy M, Tan EM, Hemmerich P (2000) CREB-binding protein (CBP)/p300, RNA polymerase II colocalize in transcriptionally active domains in the nucleus. J Cell Biol 150:265–273Google Scholar
  128. Walter J, Schermelleh L, Cremer M, Tashiro S, Cremer T (2003) Chromosome order in HeLa cells changes during mitosis and early Gl, but is stably maintained during subsequent interphase stages. J Cell Biol 160:685–697PubMedGoogle Scholar
  129. Wang ZG, Ruggero D, Ronchetti S, Zhong S, Gaboli M, Rivi R, Pandolfi PP (1998) PML is essential for multiple apoptotic pathways. Nat Genet 20:266–272PubMedGoogle Scholar
  130. Wiesmeijer K, Molenaar C, Bekeer IM, Tanke HJ, Dirks RW (2002) Mobile foci of Sp100 do not contain PML: PML bodies are immobile but PML, Sp100 proteins are not. J Struct Biol 140:180–188PubMedGoogle Scholar
  131. Williams RR, Broad S, Sheer D, Ragoussis J (2002) Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei. Exp Cell Res 272:163–175PubMedGoogle Scholar
  132. Wischnitzer S (1973) The submicroscopic morphology of the interphase nucleus. Int Rev Cytol 34:1–48PubMedGoogle Scholar
  133. Xu ZX, Timanova-Atanasova A, Zhao RX, Chang KS (2003) PML colocalizes with and stabilizes the DNA damage response protein TopBPl. Mol Cell Biol 23:4247–4256PubMedGoogle Scholar
  134. Zhong S, Hu P, Ye TZ, Stan R, Ellis NA, Pandolfi PP (1999) A role for PML and the nuclear body in genomic stability. Oncogene 18:7941–7947PubMedGoogle Scholar
  135. Zhong S, Muller S, Ronchetti S, Freemont PS, Dejean A, Pandolfi PP (2000a) Role of SUMO-1-modified PML in nuclear body formation. Blood 95:2748–2752PubMedGoogle Scholar
  136. Zhong S, Salomoni P, Pandolfi PP (2000b) The transcriptional role of PML and the nuclear body. Nat Cell Biol 2:E85–90PubMedGoogle Scholar
  137. Zhong S, Salomoni P, Ronchetti S, Guo A, Ruggero D, Pandolfi PP (2000c) Promyelocytic leukemia protein (PML), Daxx participate in a novel nuclear pathway for apoptosis. J Exp Med 191:631–640PubMedGoogle Scholar
  138. Zhu XD, Kuster B, Mann M, Petrini JH and de Lange T (2000) Cell-cycle-regulated association of RAD50/MRE11/NBS1 with TRF2 and human telomeres. Nat Genet 25:347–352PubMedGoogle Scholar
  139. 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. 35:83–89PubMedGoogle Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • Satoshi Tashiro
    • 1
  • Marion Cremer
    • 2
  • Irina Solovei
    • 2
  • Thomas Cremer
    • 2
  1. 1.Department of Cellular Biology, Research Institute for Radiation Biology and medicineHiroshima UniversityHiroshimaJapan
  2. 2.Department of Biology IILudwig Maximilians University (LMU)MartinsriedGermany

Personalised recommendations