Nascent RNA synthesis in the context of chromatin architecture (original) (raw)

• 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.
  Article PubMed CAS Google Scholar
• Cheutin T, McNairn AJ, Jenuwein T et al. (2003) Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299: 721–725.
  Article PubMed CAS Google Scholar
• Cmarko D, Verschure P, Martin TE et al. (1999) Ultrstructural analysis of transcription and splicing in the cell nucleus after Bromo-UTP microinjection. Mol Biol Cell 10: 211–223.
  PubMed CAS Google Scholar
• Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2: 292–301.
  Article PubMed CAS Google Scholar
• Cremer T, Kurz A, Zirbel R et al. (1993) The role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harb Symp Quant Biol 58: 777–792.
  PubMed CAS Google Scholar
• Cremer T, Dietzel S, Eils R, Lichter P, Cremer C (1995) Chromosome Territories, Nuclear Matrix Filaments and Inter-chromatin Channels: A Topological View on Nuclear Architecture and Function. Kew: Royal Botanic Gardens, pp. 63–81.
  Google Scholar
• Crissman HA, Hirons GT (1994) Staining of DNA in live and fixed cells. In Methods in Cell Biology, Vol. 41. New york: Academic Press Inc., pp.195–209.
  Google Scholar
• Eils R, Dietzel S, Bertin E et al. (1996) Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure. J Cell Biol 135: 1427–1440.
  Article PubMed CAS Google Scholar
• Fakan S (1994) Perichromatin fibrils are in situ forms of nascent transcripts. Trends Cell Biol 4: 86–90.
  Article PubMed CAS Google Scholar
• Fakan S, Bernhard W (1971) Localization of rapidly and slowly labeled nuclear RNA as visualized by high resolution autoradiography. Exp Cell Res 67: 129–141.
  Article PubMed CAS Google Scholar
• Fay FS, Taneja KL, Shenoy S, Lifshitz L, Singer RH (1997) Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, SC35 and Poly(A). Exp Cell Res 231: 27–37.
  Article PubMed CAS Google Scholar
• Iborra FJ, Pombo A, Jackson DA, Cook PR (1996) Active RNA polymerases are localized within discrete transcription 'factories' in human nuclei. J Cell Sci 109: 1427–1436.
  PubMed CAS Google Scholar
• Jackson DA, Pombo A (1998) Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells. J Cell Biol 140: 1285–1295.
  Article PubMed CAS Google Scholar
• Jackson DA, Hassan AB, Errington RJ, Cook PR (1993) Visualization of focal sites of transcription within human nuclei. EMBO J 12: 1059–1065.
  PubMed CAS Google Scholar
• Jackson DA, Iborra FJ, Manders EMM, Cook PR (1998) Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol Biol Cell 9: 1523–1536.
  PubMed CAS Google Scholar
• Kanda T, Sullivan KF, Wahl GM (1998) Histone-GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells. Curr Biol 8: 377–385.
  Article PubMed CAS Google Scholar
• Kriete A, Naim M, Schafer L (2001) Quality measures in applications of image restoration. Scanning 23: 313–9.
  Article PubMed CAS Google Scholar
• Längst G, Becker PB, Grummt I (1998) TTF-I determines the chromatin architecture of the active rDNA promoter. EMBO J 17: 3135–3145.
  Article PubMed Google Scholar
• Ma H, Samarabandu J, Devdhar RS et al. (1998) Spatial and temporal dynamics of DNA replication sites in mammalian cells. J Cell Biol 143: 1415–1425.
  Article PubMed CAS Google Scholar
• Markham J, Conchello JA (2001) Artefacts in restored images due to intensity loss in three-dimensional fluorescence microscopy. J Microsc 204: 93–8.
  Article PubMed CAS Google Scholar
• Martin S, Pombo A (2003) Transcription factories: quantitative studies of nanostructures in the mammlian nucleus. Chromosome Res 11: 461–470.
  Article PubMed CAS Google Scholar
• Mükel C, Eils R, Dietzel S et al. (1999) Compartmentalization of interphase chromosomes observed in simulation and experiment. J Mol Biol 285: 1053–1065.
  Article Google Scholar
• Nickerson JA (2001) Experimental observations of a nuclear matrix. J Cell Sci 114: 463–474.
  PubMed CAS Google Scholar
• Pawley JB (1995). Handbook of Biological Confocal Microscopy. New York: Plenum Press.
  Google Scholar
• Politz JC, Tuft RA, Pederson T, Singer RH (1999) Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr Biol 9: 285–291.
  Article PubMed CAS Google Scholar
• Pombo A, Hollinshead M, Cook PR (1999) Bridging the resolution gap: Imaging the same transcription factories in cryosections by light and electron microscopy. J Histochem Cytochem 47: 471–480.
  PubMed CAS Google Scholar
• 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.
  Article PubMed CAS Google Scholar
• Sadoni N, Sullivan KF, Weinzierl P, Stelzer E, Zink D (2001) Large-scale chromatin fibers of living cells display a discontinous functional organization. Chromosoma 110: 39–51.
  PubMed CAS Google Scholar
• 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.
  Article PubMed CAS Google Scholar
• Sparvoli E, Levi M, Rossi E (1994) Replication clusters may form structurally stable complexes of chromatin and chromosomes. J Cell Sci 107: 3097–3103.
  PubMed CAS Google Scholar
• Verschure PJ, van der Kraan I, Manders EMM, van Driel R (1999) Spatial relationship between transcription sites and chromosome territories. J Cell Biol 147: 13–24.
  Article PubMed CAS Google Scholar
• Verschure P, van der Kraan I, Manders EMM et al. (2003) Condensed chromatin domains in the mammalian nucleus are accessible to large macromolecules. EMBO Rep 4: 861–866.
  Article PubMed CAS Google Scholar
• Wallace W, Schaefer LH, Swedlow JR (2001) Workingperson's Guide to Deconvolution in Light Microscopy. BioTechniques 31: 1076–1097.
  PubMed CAS Google Scholar
• Wansink DG, Schul W, van der Kraan I et al. (1993) Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II domains scattered throughout the nucleus. J Cell Biol 122: 283–293.
  Article PubMed CAS Google Scholar
• Wansink DG, Sibon OC, Cremers FF, van Driel R, de Jong L (1996) Ultrasructural localization of active genes in nuclei of A431 cells. J Cell Biochem 62: 10–18.
  Article PubMed CAS Google Scholar
• Wei X, Somanathan S, Samarabandu J, Berezney R (1999) Three-dimensional visualization of transcription sites and their association with splicing factor-rich nuclear speckles. J Cell Biol 146: 543–558.
  Article PubMed CAS Google Scholar
• Zink D, Cremer T, Saffrich R et al. (1998) Structure and dynamics of human interphase chromosome territories in vivo. Hum. Genet. 102: 241–251.
  Article PubMed CAS Google Scholar
• Zink D, Bornfleth H, Visser A, Cremer C, Cremer T (1999) Organization of early and late replicating DNA in human chromosome territories. Exp Cell Res 247: 176–188.
  Article PubMed CAS Google Scholar
• Zink D, Sadoni N, Stelzer E (2003) Visualizing chromatin and chromosomes in living cells. Methods 29: 42–50.
  Article PubMed CAS Google Scholar