Exploiting nuclear duality of ciliates to analyse topological requirements for DNA replication and transcription

Journal of Cell Science

Volumn 118, Issue 17, 2005, Pages 3973-3983

  Postberg, Jan ^a,b   Alexandrova, Olga ^b   Cremer, Thomas ^b   Lipps, Hans J ^a  

^a UNIVERSITY OF WITTEN HERDECKE   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

Macronucleus; Micronucleus; Nuclear architecture; Replication foci; Stylonychia lemnae

Indexed keywords

CYCLINE; TELOMERASE;

ARTICLE; CELL NUCLEUS; CELL STRUCTURE; CELLULAR DISTRIBUTION; CHROMATIN; CHROMOSOME REPLICATION; CHROMOSOME STRUCTURE; CILIATE; CONTROLLED STUDY; DIFFERENTIATION; DNA REPLICATION; DNA TRANSCRIPTION; EUKARYOTE; GENETIC CONSERVATION; GENETIC EPIGENESIS; MACRONUCLEUS; MICRONUCLEUS; MOLECULAR EVOLUTION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN LOCALIZATION; SIGNAL TRANSDUCTION; SPECIES COMPARISON; STYLONYCHIA LEMNAE; TRANSCRIPTION REGULATION;

ANIMALS; CELL NUCLEUS; CILIOPHORA; DNA REPLICATION; FLUORESCENT DYES; IN SITU HYBRIDIZATION, FLUORESCENCE; NUCLEAR PROTEINS; NUCLEIC ACID CONFORMATION; PROTOZOAN PROTEINS; TRANSCRIPTION, GENETIC;

CILIOPHORA; EUKARYOTA; MAMMALIA; METAZOA; STYLONYCHIA LEMNAE;

EID: 26244452986     PISSN: 00219533     EISSN: None     Source Type: Journal    
DOI: 10.1242/jcs.02497     Document Type: Article

References (60)

1. Alexandrova, O., Solovei, L, Crerner, T. and David, C. N. (2003). Replication labeling patterns and chromosome territories typical of mammalian nuclei are conserved in the early metazoan Hydra. Chromosoma 112, 190-200.
2. Allen, R. L., Olins, A. L., Harp, J. M. and Olins, D. E. (1985). Isolation and characterization of chromatin replication bands and macronuclei from Euplotes eurystomus. Eur. J. Cell Biol. 39, 217-223.
3. Ammermann, D. (1970). The micronucleus of the ciliate Stylonychia mytilus; its nucleic acid synthesis and its function. Exp. Cell Res. 61, 6-12.
4. Ammermann, D. (1971). Morphology and development of the macronuclei of the ciliates Stylonychia mytilus and Euplotes aediculatus. Chromosoma 33, 209-238.
5. Ammermann, D., Steinbruck, G., Berger, L. V. and Hennig, W. (1974). The development of the macronucleus in the ciliated protozoan Stylonychia mytilus. Chromosoma 45, 401-429.
6. Blackburn, E. H. (1991a). Structure and function of telomeres. Nature 350, 569-573.
7. Blackburn, E. H. (1991b). Telomeres. Trends Biochem. Sci. 16, 378-381.
8. Boisvert, F. M., Hendzel, M. J. and Bazett-Jones, D. P. (2000). Promyelocytic leukemia (PML) nuclear bodies are protein structures that do not accumulate RNA. J. Cell Biol. 148, 283-292.
9. Bolzer, A., Kreth, G., Solovei, I., Koehler, D., Saracoglu, K., Fauth, C., Muller, S., Eils, R., Cremer, C., Speicher, M. R. et al. (2005). Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 3, e157.
10. Cavalcanti, A. R., Stover, N. A., Orecchia, L., Doak, T. G. and Landweber, L. F. (2004). Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma 113, 69-76.
11. Cook, P. R. (1999). The organization of replication and transcription. Science 284, 1790-1795.
12. Cremer, T. and Cremer, C. (2001). Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2, 292-301.
13. Cremer, T., Kopper, K., Dietzel, S. and Fakan, S. (2004). Higher order chromatin architecture in the cell nucleus: on the way from structure to function. Biol. Cell 96, 555-567.
14. Erwin, D. H. and Davidson, E. H. (2002). The last common bilaterian ancestor. Development 129, 3021-3032.
15. Evenson, D. P. and Prescott, D. M. (1970). Disruption of DNA synthesis in Euplotes by heat shock. Exp. Cell Res. 63, 245-252.
16. Fakan, S. and Van Driel, R. (2004). Where do we go in the nucleus? Biol. Cell 96, 553-554.
17. Gasser, S. M. (2002). Visualizing chromatin dynamics in interphase nuclei. Science 296, 1412-1416.
18. Grivell, A. R. and Jackson, J. F. (1968). Thymidine kinase: evidence for its absence from Neurospora crassa and some other micro-organisms, and the relevance of this to the specific labelling of deoxyribonucleic acid. J. Gen. Microbiol. 54, 307-317.
19. Gulbis, J. M., Kelman, Z., Hurwitz, J., O'Donnell, M. and Kuriyan, J. (1996). Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA. Cell 87, 297-306.
20. Habermann, F. A., Cremer, M., Walter, J., Kreth, G., von Huse, J., Bauer, K., Wienberg, J., Cremer, C., Cremer, T. and Solovei, I. (2001). Arrangements of macro- and microchromosomes in chicken cells. Chromosome Res. 9, 569-584.
21. Hodson, J. A., Bailis, J. M. and Forsburg, S. L. (2003). Efficient labeling of fission yeast Schizosaccharomyces pombe with thymidine and BUDr Nucleic Acids Res. 31, e134.
22. Hozak, P., Jackson, D. A. and Cook, P. R. (1994). Replication factories and nuclear bodies: the ultrastructural characterization of replication sites during the cell cycle. J. Cell Sci. 107, 2191-2202.
23. Jaunin, F. and Fakan, S. (2002). DNA replication and nuclear architecture. J. Cell Biochem. 85, 1-9.
24. Jaunin, F., Visser, A. E., Cmarko, D., Aten, J. A. and Fakan, S. (2000). Fine structural in situ analysis of nascent DNA movement following DNA replication. Exp. Cell Res. 260, 313-323.
25. Javaux, E. J., Knoll, A. H. and Walter, M. (2003). Recognizing and interpreting the fossils of early eukaryotes. Origins Life Evol. B 33, 75-94.
26. Jonsson, F. A. L. H. J. (2002). The Biology of Telomeres in Hypotrichous Ciliates. In Telomerases, Telomeres and Cancer (ed. G. K. A. R. Parwaresch), pp. 205-222. Georgetown: Landes Bioscience, Kluwer Academic/Plenum Publishers.
27. Jonsson, F., Postberg, J., Schaffitzel, C. and Lipps, H. J. (2002). Organization of the macronuclear gene-sized pieces of stichotrichous ciliates into a higher order structure via telomere-matrix interactions. Chromosome Res. 10, 445-453.
28. Juranek, S., Jönsson, F., Maercker, C. and Lipps, H. J. (2000). The telomeres of replicating macronuclear DNA molecules of the ciliate Stylonychia lemnae. Protistology 1, 148-151.
29. Kloetzel, J. A. (1970). Compartmentalization of the developing macronuclei following conjugation in Stylonychia and Euplotes. J. Cell Biol. 47, 395-407.
30. Kraut, H., Lipps, H. J. and Prescott, D. M. (1986). The genome of hypotrichous ciliates. Int. Rev. Cytol. 99, 1-28.
31. Krishna, T. S., Kong, X. P., Gary, S., Burgers, P. M. and Kuriyan, J. (1994). Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79, 1233-1243.
32. Leonhardt, H., Rahn, H. P., Weinzierl, P., Sporbert, A., Cremer, T., Zink, D. and Cardoso, M. C. (2000). Dynamics of DNA replication factories in living cells. J. Cell Biol. 149, 271-280.
33. Lin, M. and Prescott, D. M. (1985). Electron microscope autoradiography of DNA synthesis in the replication band of two hypotrichous ciliates. J. Protozool. 32, 144-149.
34. Lipps, H. J. (1980). In vitro aggregation of the gene-sized DNA molecules of the ciliate Stylonychia mytilus. Proc. Natl. Acad. Sci. USA 77, 4104-4107.
35. Lipps, H. J., Nock, A., Riewe, M. and Steinbruck, G. (1978). Chromatin structure in the macronucleus of the ciliate Stylonychia mytilus. Nucleic Acids Res. 5, 4699-4709.
36. Lipps, H. J., Gruissem, W. and Prescott, D. M. (1982). Higher order DNA structure in macronuclear chromatin of the hypotrichous ciliate Oxytricha nova. Proc. Natl. Acad. Sci. USA 79, 2495-2499.
37. Mayr, C., Jasencakova, Z., Meister, A., Schubert, I. and Zink, D. (2003). Comparative analysis of the functional genome architecture of animal and plant cell nuclei. Chromosome Res. 11, 471-484.
38. Meyer, G. F. and Lipps, H. J. (1981). The formation of polytene chromosomes during macronuclear development of the hypotrichous ciliate Stylonychia mytilus. Chromosoma 82, 309-314.
39. Mollenbeck, M., Postberg, J., Paeschke, K., Rossbach, M., Jonsson, F. and Lipps, H. J. (2003). The telomerase-associated protein p43 is involved in anchoring telomerase in the nucleus. J. Cell Sci. 116, 1757-1761.
40. Murti, K. G. (1973). Electron-microscopic observations on the macronuclear development of Stylonychia mytilus and Tetrahymena pyriformis (Ciliophora-Protozoa). J. Cell Sci. 13, 479-509.
41. Murti, K. G. and Prescott, D. M. (1983). Replication forms of the gene-sized DNA molecules of hypotrichous ciliates. Mol. Cell Biol. 3, 1562-1566.
42. Murti, K. G. and Prescott, D. M. (2002). Topological organization of DNA molecules in the macronucleus of hypotrichous ciliated protozoa. Chromosome Res. 10, 165-173.
43. Nakamura, H., Morita, T. and Sato, C. (1986). Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. Exp. Cell Res. 165, 291-297.
44. O'Keefe, R. T., Henderson, S. C. and Spector, D. L. (1992). Dynamic organization of DNA replication in mammalian cell nuclei: spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences. J. Cell Biol. 116, 1095-1110.
45. Olins, A. L., Olins, D. E., Franke, W. W., Lipps, H. J. and Prescott, D. M. (1981). Stereo-electron microscopy of nuclear structure and replication in ciliated protozoa (Hypotricha). Eur. J. Cell Biol. 25, 120-130.
46. Olins, D. E. and Olins, A. L. (1994). The replication band of ciliated protozoa. Int. Rev. Cytol. 153, 137-170.
47. Olins, D. E., Olins, A. L., Cacheiro, L. H. and Tan, E. M. (1989). Proliferating cell nuclear antigen/cyclin in the ciliate Euplotes eurystomus: localization in the replication band and in micronuclei. J. Cell Biol. 109, 1399-1410.
48. Pasero, P., Duncker, B. P. and Gasser, S. M. (1999). In vitro DNA replication in yeast nuclear extracts. Methods 18, 323, 368-376.
49. Postberg, J., Juranek, S. A., Feiler, S., Kortwig, H., Jönsson, F. and Lipps, H. J. (2001). Association of the telomere-telomere binding protein-complex of hypotrichous ciliates with the nuclear matrix and dissociation during replication. J. Cell Sci. 114, 1861-1866.
50. Prescott, D. M. (1994). The DNA of ciliated protozoa. Microbiol. Rev. 58, 233-267.
51. Prescott, D. M. and Kimball, R. F. (1961). Relation between RNA, DNA, and protein syntheses in the replicating nucleus of Euplotes. Proc. Natl. Acad. Sci. USA 47, 686-693.
52. Roth, L. E. (1957). An electron microscope study of the cytology of the protozoan Euplotes patella. J. Biophys. Biochem. Cytol. 3, 985-1000.
53. Sadoni, N., Langer, S., Fauth, C., Bernardi, G., Cremer, T., Turner, B. M. and Zink, D. (1999). Nuclear organization of mammalian genomes. Polar chromosome territories build up functionally distinct higher order compartments. J. Cell Biol. 146, 1211-1226.
54. Sadoni, N., Cardoso, M. C., Stelzer, E. H., Leonharft H. and Zink, D. (2004). Stable chromosomal units determine the spatial and temporal organization of DNA replication. J. Cell Sci. 117, 5353-5365.
55. Schaffitzel, C., Berger, I., Postberg, J., Hanes, J., Lipps, H. J. and Pluckthun, A. (2001). In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc. Natl. Acad. Sci. USA 98, 8572-8577.
56. Schurtenberger, P., Egelhaaf, S. U., Hindges, R., Maga, G., Jonsson, Z. O., May, R. P., Glatter, O. and Hubscher, U. (1998). The solution structure of functionally active human proliferating cell nuclear antigen determined by small-angle neutron scattering. J. Mol. Biol. 275, 123-132.
57. Sporbert, A., Gahl, A., Ankerhold, R., Leonhardt, H. and Cardoso, M. C. (2002). DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters. Mol. Cell 10, 1355-1365.
58. Stambrook, P. J. and Flickinger, R. A. (1970). Changes in chromosomal DNA replication patterns in developing frog embryos. J. Exp. Zool. 174, 101-113.
59. Stein, F. (1859). Der Organismus der Infusionsthiere nach eigenen Forschungen in systematischer Reihenfolge bearbeitet. Leipzig: Engelmann.
60. Wray, C. G., Langer, M. R., DeSalle, R., Lee, J. J. and Lipps, J. H. (1995). Origin of the foraminifera. Proc. Natl. Acad. Sci. USA 92, 3075.