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).
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
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 18:1084–1093
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 173:1407–1419
Baumann P, Benson FE, West SC (1996) Human Rad51 protein promotes ATP-dependent homologous pairing and strand transfer reactions in vitro. Cell 87:757–766
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 47:217–225
Belmont A (2003) Dynamics of chromatin, proteins, and bodies within the cell nucleus. Curr Opin Cell Biol 15:304–310
Berezney R, Coffey DS (1974) Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60:1410–1417
Berezney R, Wei X (1998) The new paradigm: integrating genomic function and nuclear architecture. J Cell Biochem Suppl 30–31:238–242
Berezney R, Mortillaro MJ, Ma H, Wei X, Samarabandu J (1995) The nuclear matrix: a structural milieu for genomic function. Int Rev Cytol 162A: 1–65
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 153:367–380
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 273:21482–21488
Boisvert FM, Hendzel MJ, Bazett-Jones DP (2000) Promyelocytic leukemia (PML) nuclear bodies are protein structures that do not accumulate RNA. J Cell Biol 148:283–292
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: 0826–0842
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 10:2297–2307
Boveri T (1909) Die Blastomerenkerne von Ascaris megalocephala und die Theorie der Chromosomenindividualität. Arch Zellforsch 3:181–268
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.
Brede G, Solheim J, Prydz H (2002) PSKH1, a novel splice factor compartment-associated serine kinase. Nucleic Acids Res 30:5301–5309
Buchhop S, Gibson MK, Wang XW, Wagner P, Sturzbecher HW, Harris CC (1997) Interaction of p53 with the human Rad51 protein. Nucleic Acids Res 25:3868–3874
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 93:477–486
Cerda MC, Berrios S, Fernandez-Donoso R, Garagna S, Redi C (1999) Organisation of complex nuclear domains in somatic mouse cells. Biol Cell 91:55–65
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 290:1962–1965
Cheutin T, McNairn AJ, Jenuwein T, Gilbert DM, Singh PB, Misteli T (2003) Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299:721–725
Chubb JR, Bickmore WA (2003) Considering nuclear compartmentalization in the light of nuclear dynamics. Cell 112:403–406
Chubb JR, Boyle S, Perry P, Bickmore WA (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12:439–145
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 10:211–223
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 116:335–343
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 15:265–275
Comings DE (1968) The rationale for an ordered arrangement of chromatin in the interphase nucleus. Am J Hum Genet 20:440–460
Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2:292–301.
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 62:201–209
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 80:235–246
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 58:777–792
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 12:179–212
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 9:541–567
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 162:809–820
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 48:15–28
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
D’Amours D, Jackson SP (2002) The Mrel 1 complex: at the crossroads of DNA repair and checkpoint signalling. Nat Rev Mol Cell Biol 3:317–327
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 273:951–953
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 252:363–375
Dostie J, Lejbkowicz F, Sonenberg N (2000) Nuclear eukaryotic initiation factor 4E (eIF4E) colocalizes with splicing factors in speckles. J Cell Biol 148:239–247
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 21:2030–2037
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 78:1903–1917
Failla AV, Cavallo A, Cremer C (2002) Subwavelength size determination by spatially modulated illumination virtual microscopy. Appl Opt 41:6651–6659
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 92:5915–5919
Frey MR, Matera AG (2001) RNA-mediated interaction of Cajal bodies, U2 snRNA genes. J Cell Biol 154:499–509
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 1400–1403
Geiman TM, Robertson KD (2002) Chromatin remodeling, histone modifications, DNA methylation-how does it all fit together? J Cell Biochem 87:117–125
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 26:5388–5393
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 2:730–736
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 92:2298–2302
Handwerger KE, Murphy C, Gall JG (2003) Steady-state dynamics of Cajal body components in the Xenopus germinal vesicle. J Cell Biol 160:495–504
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 105:473–485
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.
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 22:1878–1888
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):4651–4661
Kojima T, Zama T, Wada K, Onogi H, Hagiwara M (2001) Cloning of human PRP4 reveals interaction with Clkl. J Biol Chem 276:32247–32256
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 86:1–10
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 150:41–51
Lamond Al, Spector DL (2003) Nuclear speckles: a model for nuclear organelles. Nat Rev Mol Cell Biol 4:605–612
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 11:871–876
Le XF, Yang P, Chang KS (1996) Analysis of the growth and transformation suppressor domains of promyelocytic leukemia gene, PML. J Biol Chem 271:130–135
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 95:335–341
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
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 80:224–234
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 143:1415–1425
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 159:753–763
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 157:579–589
Manuelidis L (1985) Individual interphase chromosome domains revealed by in situ hybridization. Hum Genet 71:288–293
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 17:6087–6096
Matera AG (1998) Of coiled bodies, gems, and salmon. J Cell Biochem 70:181–192
Matera AG (1999) Nuclear bodies: multifaceted subdomains of the interchromatin space. Trends Cell Biol 9:302–309
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 19:179–181
Mirzoeva OK, Petrini JH (2001) DNA damage-dependent nuclear dynamics of the Mrel 1 complex. Mol Cell Biol 21:281–288
Misteli T, Caceres JF, Spector DL (1997) The dynamics of a pre-mRNA splicing factor in living cells. Nature 387:523–527
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 15:197–206
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 22:6631–6641
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.
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.
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.
Nagele R, Freeman T, McMorrow L, Lee HY (1995) Precise spatial positioning of chromosomes during prometaphase: evidence for chromosomal order. Science 270:1831–1835
Nelms BE, Maser RS, MacKay JF, Lagally MG, Petrini JH (1998) In situ visualization of DNA double-strand break repair in human fibroblasts. Science 280:590–592
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 94:4446–4450
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 276:22148–22153
Ogawa T, Yu X, Shinohara A, Egelman EH (1993) Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science 259:1896–1899
Okada TA, Comings DE (1979) Higher order structure of chromosomes. Chromosoma 72:1–14
Parada LA, Sotiriou S, Misteli T (2004) Spatial genome organization. Exp Cell Res 296:64–70
Paull TT, Gellert M (1999) Nbs1 potentiates ATP-driven DNA unwinding and endonuclease cleavage by the Mrel l/Rad50 complex. Genes Dev 13:1276–1288
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 10:886–895
Pederson T (2004) The spatial organization of the genome in mammalian cells. Curr Opin Genet Dev 14:203–209
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 414:660–665
Petrini JH, Stracker TH (2003) The cellular response to DNA double-strand breaks: defining the sensors and mediators. Trends Cell Biol 13:458–462
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 151:1561–1574
Platani M, Goldberg I, Lamond AI, Swedlow JR (2002) Cajal body dynamics and association with chromatin are ATP-dependent. Nat Cell Biol 4:502–508
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 93:5920–5924
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.
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 96:1921–1926
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.
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 71:281–287
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 9:77–80
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 88:265–275
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 386:804–810
Shinohara A, Ogawa H, Ogawa T (1992) Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein. Cell 69:457–470
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 4:239–243
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 162:981–990
Singer RH, Green MR (1997) Compartmentalization of eukaryotic gene expression: causes and effects. Cell 91:291–294
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 151:653–662
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 276:10–23
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: 410–423
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: 302–310
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 17:598–608
Spector DL (2003) The dynamics of chromosome organization and gene regulation. Annu Rev Biochem 72:573–608
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.
Swedlow JR (2003) Quantitative fluorescence microscopy and image deconvolution. Methods Cell Biol 72:349–367
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 9:325–328
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 12:2165–2170
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 150:283–291
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): 157–168
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 18:7147–7156
van den Bosch M, Bree RT, Lowndes NF (2003) The MRN complex: coordinating and mediating the response to broken chromosomes. EMBO Rep 4:844–849
van Driel R, Fransz PF, Verschure PJ (2003) The eukaryotic genome: a system regulated at different hierarchical levels. J Cell Sci 116:4067–4075
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 93:467–476
Vazquez J, Belmont AS, Sedat JW (2001) Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Curr Biol 11:1227–1239
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 4:861–866
Visser AE, Jaunin F, Fakan S, Aten JA (2000) High resolution analysis of interphase chromosome domains. J Cell Sci 113:2585–2593
Vogel F, Schroeder TM (1974) The internal order of the interphase nucleus. Humangenetik 25:265–297
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): 1565–1576
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 150:265–273
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 160:685–697
Wang ZG, Ruggero D, Ronchetti S, Zhong S, Gaboli M, Rivi R, Pandolfi PP (1998) PML is essential for multiple apoptotic pathways. Nat Genet 20:266–272
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 140:180–188
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 272:163–175
Wischnitzer S (1973) The submicroscopic morphology of the interphase nucleus. Int Rev Cytol 34:1–48
Xu ZX, Timanova-Atanasova A, Zhao RX, Chang KS (2003) PML colocalizes with and stabilizes the DNA damage response protein TopBPl. Mol Cell Biol 23:4247–4256
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 18:7941–7947
Zhong S, Muller S, Ronchetti S, Freemont PS, Dejean A, Pandolfi PP (2000a) Role of SUMO-1-modified PML in nuclear body formation. Blood 95:2748–2752
Zhong S, Salomoni P, Pandolfi PP (2000b) The transcriptional role of PML and the nuclear body. Nat Cell Biol 2:E85–90
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 191:631–640
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 25:347–352
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
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Springer
About this chapter
Cite this chapter
Tashiro, S., Cremer, M., Solovei, I., Cremer, T. (2007). Nuclear Architecture: Topology and Function of Chromatin- and Non-Chromatin Nuclear Domains. In: Nagata, K., Takeyasu, K. (eds) Nuclear Dynamics. Springer, Tokyo. https://doi.org/10.1007/978-4-431-30130-1_9
Download citation
DOI: https://doi.org/10.1007/978-4-431-30130-1_9
Publisher Name: Springer, Tokyo
Print ISBN: 978-4-431-30054-0
Online ISBN: 978-4-431-30130-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)