Skip to main content
SpringerLink
Log in

Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries

  • Published:
Chromosome Research Aims and scope Submit manuscript

Abstract

The nuclear topography of splicing snRNPs, mRNA transcripts and chromosome domains in various mammalian cell types are described. The visualization of splicing snRNPs, defined by the Sm antigen, and coiled bodies, revealed distinctly different distribution patterns in these cell types. Heat shock experiments confirmed that the distribution patterns also depend on physiological parameters. Using a combination of fluorescencein situ hybridization and immunodetection protocols, individual chromosome domains were visualized simultaneously with the Sm antigen or the transcript of an integrated human papilloma virus genome. Three-dimensional analysis of fluorescence-stained target regions was performed by confocal laser scanning microscopy. RNA transcripts and components of the splicing machinery were found to be generally excluded from the interior of the territories occupied by the individual chromosomes. Based on these findings we present a model for the functional compartmentalization of the cell nucleus. According to this model the space between chromosome domains, including the surface areas of these domains, defines a three-dimensional network-like compartment, termed the interchromosome domain (ICD) compartment, in which transcription and splicing of mRNA occurs.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Andrade LEC, Tan EM, Chan EKL (1993) Immunocytochemical analysis of the coiled body in the cell cycle and during cell proliferation.Proc Natl Acad Sci USA 90: 1947–1951.

    Google Scholar 

  • Arndt-Jovin DJ, Robert-Nicoud M, Kaufman SJ, Jovin TM (1985) Fluorescence digital imaging microscopy in cell biology.Science 230: 247–256.

    Google Scholar 

  • Ascoli CA, Maul GG (1991) Identification of a novel nuclear domain.J Cell Biol 112: 785–795.

    Google Scholar 

  • Bachmann M, Mayet WJ, Schröder HC, Pfeifer K, Meyer zum Büschenfelde K-H, Müller WEG (1986) Association of La and Ro antigens with intracellular structures in HEp-2 carcinoma cells.Proc Natl Acad Sci USA 83: 7770–7774.

    Google Scholar 

  • Benyajati C, Worcel A (1976) Isolation, characterization, and structure of the folded interphase genome ofDrosophila melanogaster.Cell 9: 393–407.

    Google Scholar 

  • Berezney R (1991) The nuclear matrix: A heuristic model for investigating genomic organization and function in the cell nucleus.J Cell Biochem 47: 109–123.

    Google Scholar 

  • Berman SA, Bursztajn S, Bowen B, Gilbert W (1990) Localization of an acetylcholine receptor intron to the nuclear membrane.Science 247: 212–214.

    Google Scholar 

  • Blobel G (1985) Gene gating: a hypothesis.Proc Natl Acad Sci USA 82: 8527–8529.

    Google Scholar 

  • Bond U (1988) Heat shock but not other stress inducers leads to the disruption of a sub-set of sn-RNPs and inhibition ofin vitro splicing in HeLa cells.EMBO J 7: 3509–3518.

    Google Scholar 

  • Bouteille M, Laval M, Dupuy-Coin AM (1974) Localization of nuclear functions as revealed by ultrastructural autoradiography and cytochemistry. In: Busch H, ed.The Cell Nucleus. New York: Academic Press.

    Google Scholar 

  • Bradl J, Hausmann M, Ehemann V, Komitowski D, Cremer C (1992) A tilting device for three-dimensional microscopy: application toin situ imaging of interphase cell nuclei.J Microsc 168: 47–57.

    Google Scholar 

  • Brakenhoff GJ, Blom P, Barends P (1979) Confocal scanning light microscopy with high aperture lenses.J Microsc 117: 219–232.

    Google Scholar 

  • Carmo-Fonseca M, Tollervey D, Pepperkok R,et al. (1991a) Mammalian nuclei contain foci which are highly enriched in components of the pre-mRNA splicing machinery.EMBO J 10: 196–206.

    Google Scholar 

  • Carmo-Fonseca M, Pepperkok R, Sproat BS, Ansorge W, Swanson MS, Lamond AI (1991b)In vivo detection of snRNP-rich organelles in the nuclei of mammalian cells.EMBO J 10: 1863–1873.

    Google Scholar 

  • Carmo-Fonseca M, Pepperkok R, Carvalho MT, Lamond AI (1992) Transcription-dependent colocalization of the U1, U2, U4/U6, and U5 snRNPs in coiled bodies.J Cell Biol 117: 1–14.

    Google Scholar 

  • Carmo-Fonseca M, Ferreira J, Lamond AI (1993) Assembly of snRNP-containing coiled bodies is regulated in interphase and mitosis—evidence that the coiled body is a kinetic nuclear structure.J Cell Biol 120: 841–852.

    Google Scholar 

  • Carter KC, Taneja KL, Lawrence JB (1991) Discrete nuclear domains of poly(A)RNA and their relationship to the functional organization of the nucleus.J Cell Biol 115: 1191–1202.

    Google Scholar 

  • Collins C, Kuo WL, Segraves R, Fuscoe J, Pinkel D, Gray J (1991) Construction and characterization of plasmid libraries enriched in sequences from single human chromosomes.Genomics 11: 997–1006.

    Google Scholar 

  • Comings DE (1980) Arrangement of chromatin in the nucleus.Hum Genet 53: 131–143.

    Google Scholar 

  • Cremer C, Cremer T (1978) Considerations on a laser-scanning-microscope with high resolution and depth of field.Microsc Acta 81: 31–44.

    Google Scholar 

  • Cremer T, Cremer C, Baumann H,et al. (1982) Rabl's model of the interphase chromosome arrangement tested in Chinese hamster cells by premature chromosome condensation and laser UV-microbeam experiments.Hum Genet 60: 46–56.

    Google Scholar 

  • Cremer T, Lichter P, Borden J, Ward DC, Manuelidis L (1988) Detection of chromosome aberrations in metaphase and interphase tumor cells byin situ hybridization using chro- mosome specific library probes.Hum Genet 80: 235–246.

    Google Scholar 

  • Fakan S, Leser G, Martin TE (1984) Ultrastructural distribution of nuclear ribonucleoproteins as visualized by immunocytochemistry on thin sections.J Cell Biol 98: 358–363.

    Google Scholar 

  • Fakan S, Leser G, Martin TE (1986) Immunoelectron microscope visualisation of nuclear ribonucleoprotein antigens within spread transcription complexes.J Cell Biol 103: 1153–1157.

    Google Scholar 

  • Gall JG (1991) Spliceosomes and snurposomes.Science 252: 1499–1500.

    Google Scholar 

  • Hiraoka Y, Sedat JW, Agard DA (1987) The use of a chargecoupled device for quantitative optical microscopy of biological structures.Science 238: 36–41.

    Google Scholar 

  • Hochstrasser M, Sedat JW (1987) Three-dimensional organization ofDrosophila melanogaster interphase nuclei. II. Chromosome spatial organization and gene expression.J Cell Biol 104: 1471–1482.

    Google Scholar 

  • Huang S, Spector DL (1992) U1 and U2 small nuclear RNAs are present in nuclear speckles.Proc Natl Acad Sci USA 89: 305–308.

    Google Scholar 

  • Hutchison N, Weintraub H (1985) Localization of DNAse I-sensitive sequences to specific regions of interphase nuclei.Cell 43: 471–482.

    Google Scholar 

  • Jovin TM, Arndt-Jovin DJ (1989) Luminescence digital imaging microscopy.Annu Rev Biophys & Biophys Chem 18: 271–308.

    Google Scholar 

  • Lamond AI, Carmo-Fonseca M (1993) The coiled body.Trends Cell Biol.

  • Lawrence JB, Singer RH, Marselle LM (1989) Highly localized tracts of specific transcripts within interphase nuclei visualized byin situ hybridization.Cell 57: 493–502.

    Google Scholar 

  • Lerner EA, Lerner MR, Janeway JCA, Steitz JA (1981) Monoclonal antibodies to nucleic acid-containing cellular constituents: Probes for molecular biology and auto- immune disease.Proc Nat Acad Sci USA,78: 2737–2741.

    Google Scholar 

  • Lichter P, Cremer T (1992) Chromosome analysis by nonisotopicin situ hybridization. In: Rooney DE, Czepulkowski BH, eds.Human Cytogenetics. New York: Oxford University Press.

    Google Scholar 

  • Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC (1988) Delineation of individual human chromosomes in metaphase and interphase cells byin situ suppression hybridization using recombinant DNA libraries.Hum Genet 80: 224–234.

    Google Scholar 

  • Lichter P, Tang CC, Call K,et al. (1990) High resolution mapping of human chromosome 11 byin situ hybridization with cosmid clones.Science 247: 64–69.

    Google Scholar 

  • Lichter P, Boyle AL, Cremer T, Ward DC (1991) Analysis of genes and chromosomes by non-isotopicin situ hybridization.Genet Anal Tech Appl 8: 24–35.

    Google Scholar 

  • Manuelidis L (1985) Individual interphase chromosome domains revealed byin situ hybridization.Hum Genet 71: 288–293.

    Google Scholar 

  • Manuelidis L (1985a)In situ detection of DNA sequences using biotinylated probes.Focus 7: 4–8.

    Google Scholar 

  • Manuelidis L (1990) A view of interphase chromosomes.Science 250: 1533–1540.

    Google Scholar 

  • Manuelidis L, Borden J (1988) Reproducible compartmentalization of individual chromosome domains in human CNS cells revealed byin situ hybridization and three-dimensional reconstruction.Chromosoma 96: 397–410.

    Google Scholar 

  • Mattioli M, Reichlin M (1971) Characterization of a soluble nuclear ribonucleoprotein antigen reactive with SLE sera.J Immunol 107: 1281–1290.

    Google Scholar 

  • Monneron A, Bernhard W (1969) Fine structural organization of the interphase nucleus in some mammalian cells.J Ultrastructural Res 27: 266–288.

    Google Scholar 

  • Northway JD, Tan EM (1972) Differentiation of antinclear antibodies giving speckled staining pattern in immunofluorescence.Clin Immunol Immunopathol 1: 140–154

    Google Scholar 

  • Nyman U, Hallman H, Hadlaczky G, Pettersson I, Sharp G, Ringertz NR (1986) Intranuclear localization of snRNP antigens.Cell Biol 102: 137–144.

    Google Scholar 

  • Paulson JR, Laemmli UK (1977) The structure of histone-depleted metaphase chromosomes.Cell 12: 817–828.

    Google Scholar 

  • Pinkel D, Straume T, Gray JW (1986) Cytogenetic analysis using quantitative, high sensitivity, fluorescence hybridization.Proc Natl Acad Sci USA 83: 2934–2938.

    Google Scholar 

  • Pinkel D, Landegent J, Collins C,et al. (1988) Fluorescencein situ hybridization with human chromosome-specific libraries: detection of trisomy 21 and translocations of chromosome 4.Proc Natl Acad Sci USA 85: 9138–9142.

    Google Scholar 

  • Raap AK, van de Rijke FM, Dirks RW, Sol CJ, Boom R, van der Ploeg M (1991) Bicolor fluorescencein situ hybridization to intron and exon mRNA sequences.Exp Cell Res 197: 319–322.

    Google Scholar 

  • Reuter R, Appel B, Bringmann P, Rinke J, Lührmann R (1984) 5′-terminal caps of snRNAs are reactive with antibodies specific for 2,2,7-trimethylguanosine in whole cells and nuclear matrices.Exp Cell Res 154: 548–560.

    Google Scholar 

  • Ramon y Cajal SR (1903) Un sencillo metodo de coloracion seletiva del reticulo protoplasmico y sus efectos en los diversos organos nerviosos de vertebrados y invertebrados.Trab Lab Invest Biol 2: 129–221.

    Google Scholar 

  • Raska I, Andrade LEC, Ochs RL,et al. (1991) Immunological and ultrastructural studies of the nuclear coiled body with autoimmune antibodies.Exp Cell Res 195: 27–37.

    Google Scholar 

  • Roggenbuck B, Larsen PM, Fey SJ, Bartsch D, Gissman L, Schwarz E (1991) Human papilloma virus type 18 E6*, E6, and E7 protein synthesis in cell-free translation systems and comparison of E6 and E7in vitro translation products to proteins immunoprecipitated from human epithelial cells.J Virol 65: 5068–5072.

    Google Scholar 

  • 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 

  • Schneider-Gädicke A, Schwarz E (1986) Different human cervical carcinoma cell show similar transcription patterns of human papilloma virus type 18 early genes.EMBO J 5: 2285–2292.

    Google Scholar 

  • Shotton DM (1989) Confocal scanning optical microscopy and its applications for biological specimens.J Cell Sci 94: 175–206.

    Google Scholar 

  • Spector DL (1984) Colocalization of U1 and U2 small nuclear RNPs by immunocytochemistry.Biol Cell 51: 109–111.

    Google Scholar 

  • Spector DL (1990) Higher order nuclear organization: three-dimensional distribution of small nuclear ribonucleoprotein particles.Proc Natl Acad Sci USA 87: 147–151.

    Google Scholar 

  • Spector DL, Lark G, Huang S (1992) Differences in snRNP localization between transformed and nontransformed cells.Mol Biol Cell 3: 555–569.

    Google Scholar 

  • Spector DL, Fu X-D, Maniatis T (1991) Associations between distinct pre-mRNA splicing components and the cell nucleus.EMBO J 10: 3467–3481.

    Google Scholar 

  • Spector DL, Schrier WH, Busch H (1983) Immunoelectron microscopic localization of snRNPs.Biol Cell 49: 1–10.

    Google Scholar 

  • Van der Voort HTM, Brakenhoff GJ (1990) 3-D image formation in high-aperture fluorescence confocal microscopy: a numerical analysis.J Microsc 158: 43–54.

    Google Scholar 

  • Verheijen R, Kuijpers H, Vooijs P, Van Venrooij W, Ramaekers F (1986) Distribution of the 70K RNA-associated protein during interphase and mitosis.J Cell Sci 86: 173–190.

    Google Scholar 

  • Xing Y, Lawrence JB (1991) Preservation of specific RNA distribution within the chromatin-depleted nuclear substructure demonstrated byin situ hybridization coupled with biochemical fractionation.J Cell Biol 112: 1055–1063.

    Google Scholar 

  • Xing Y, Johnson CV, Dobner PR, Lawrence JB (1993) Higher level organization of individual gene transcription and RNA splicing.Science 259: 1326–1330.

    Google Scholar 

  • Zorn C, Cremer C, Cremer T, Zimmer J (1979) Unscheduled DNA synthesis after partial UV irradiation of the cell nucleus.Exp Cell Res 124: 111–119.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. the Abt. Organisation komplexer Genome, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, W-6900, Heidelberg, Germany

    R. M. Zirbel, U. R. Mathieu, A. Kurz & P. Lichter

  2. the Institut fúr Humangenetik und Anthropologie der Universität, W-6900, Heidelberg, Germany

    T. Cremer

Authors
  1. R. M. Zirbel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. U. R. Mathieu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. A. Kurz
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. T. Cremer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. P. Lichter
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zirbel, R.M., Mathieu, U.R., Kurz, A. et al. Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries. Chromosome Res 1, 93–106 (1993). https://doi.org/10.1007/BF00710032

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00710032

Key words

Search

Navigation