Developmental regulation of DNA replication: Replication fork barriers and programmed gene amplification in Tetrahymena thermophila

Molecular and Cellular Biology

Volumn 17, Issue 10, 1997, Pages 6147-6156

  Zhang, Zhi ^a   Macalpine, David M ^a,b   Kapler, Geoffrey M ^a  

^a TEXAS A M COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA;

ARTICLE; CELL CYCLE; CONTROLLED STUDY; GENE AMPLIFICATION; NONHUMAN; PRIORITY JOURNAL; RNA REPLICATION; TETRAHYMENA THERMOPHILA; TWO DIMENSIONAL GEL ELECTROPHORESIS;

EUKARYOTA; TETRAHYMENA; TETRAHYMENA THERMOPHILA; XENOPUS LAEVIS;

EID: 0030863327     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.17.10.6147     Document Type: Article

References (63)

1. Aladjem, M. I., M. Groudine, L. L. Brody, E. S. Dieken, R. E. Fournier, G. M. Wahl, and E. M. Epner. 1995. Participation of the human beta-globin locus control region in initiation of DNA replication. Science 270:815-819.
2. Allis, C. D., M. Colavito-Shepanski, and M. A. Gorovsky. 1987. Scheduled and unscheduled DNA synthesis during development in conjugating Tetrahymena. Dev. Biol. 124:469-480.
3. Bell, S. P., and B. Stillman. 1992. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357:128-134.
4. Brewer, B. J., and W. L. Fangman. 1987. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51:463-471.
5. Brewer, B. J., and W. L. Fangman. 1988. A replication fork harrier at the 3′ end of yeast ribosomal RNA genes. Cell 55:637-643.
6. Butler, D. K., L. E. Yasuda, and M.-C. Yao. 1995. An intramolecular recombination mechanism for the formation of the rRNA gene palindrome of Tetrahymena thermophila. Mol. Cell. Biol. 15:7117-7126.
7. Caddle, M. S., and M. P. Calos. 1994. Specific initiation at an origin of replication in Schizosaccharomyces pombe. Mol. Cell. Biol. 14:1796-1805.
8. Cech, T. R., and S. L. Brehm. 1981. Replication of the extrachromosomal ribosomal RNA genes of Tetrahymena thermophila. Nucleic Acids Res. 9: 3531-3543.
9. Challoner, P. B., A. A. Amin, R. E. Pearlman, and E. H. Blackburn. 1985. Conserved arrangement of repeated DNA sequences in non-transcribed spacers of ciliated ribosomal RNA genes: evidence for molecular coevolution. Nucleic Acids Res. 13:2661-2680.
10. Coverley, D., and R. A. Laskey. 1994. Regulation of eukaryotic DNA replication. Annu. Rev. Biochem. 63:745-776.
11. Delidakis, C., and F. C. Kafatos. 1989. Amplification enhancers and replication origins in the autosomal chorion gene cluster of Drosophila. EMBO J. 8:891-901.
12. Deshpande, A. M., and C. S. Newlon. 1996. DNA replication fork pause sites dependent on transcription. Science 272:1030-1033.
13. Engberg, J., D. Mowat, and R. E. Pearlman. 1972. Preferential replication of the ribosomal RNA gene during nutritional shift-up in Tetrahymena pyriformis. Biochim. Biophys. Acta 272:312-320.
14. Epner, E., W. C. Forrester, and M. Groudine. 1988. Asynchronous DNA replication within the human β-globin locus. Proc. Natl. Acad. Sci. USA 85:8081-8085.
15. Ferguson, B. M., B. J. Brewer, A. E. Reynolds, and W. L. Fangman. 1991. A yeast origin of replication is activated late in S phase. Cell 65:507-515.
16. Forrester, W. C., S. Takegawa, T. Papayannopoulou, G. Stamatoyannopoulos, and M. Groudine. 1987. Evidence for a locus activation region: the formation of developmentally stable hypersensitive sites in globin-expressing hybrids. Nucleic Acids Res. 15:10159-10177.
17. Forrester, W. C., E. Epner, M. C. Driscoll, T. Enver, M. Brice, T. Papayannopoulou, and M. Groudine. 1990. A deletion of the human β-globin locus activation region causes a major alteration in chromatin structure and replication across the entire β-globin locus. Genes Dev. 4:1637-1659.
18. Gaertig, J., L. Gu, B. Hai, and M. A. Gorovsky. 1994. Gene replacement and high frequency vector-mediated electrotransformation on Tetrahymena. Nucleic Acids Res. 22:5391-5398.
19. Godiska, R., and M.-C. Yao. 1990. A programmed site-specific DNA rearrangement in Tetrahymena thermophila requires flanking polypurine tracts. Cell 61:1237-1246.
20. Greenfelder, S. A., and C. S. Newlon. 1992. Replication forks pause at yeast centromeres. Mol. Cell. Biol. 12:4056-4066.
21. Handeli, S., A. Klar, M. Meuth, and H. Cedar. 1989. Mapping replication units in animal cells. Cell 57:909-920.
22. Heck, M. M. S., and A. C. Spradling. 1990. Multiple replication origins are used during Drosophila chorion gene amplification. J. Cell Biol. 110:903-914.
23. Hyrien, O., C. Maric, and M. Mechali. 1996. Transition in specification of embryonic metazoan DNA replication origins. Science 270:994-997.
24. Hyrien, O., and M. Mechali. 1993. Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. EMBO J. 12:4511-4520.
25. Jacob, F., S. Brenner, and F. Cuzin. 1963. On the regulation of DNA replication in bacteria. Cold Spring Harbor Symp. Quant. Biol. 28:329-348.
26. Kapler, G. M., and E. H. Blackburn. 1994. A weak germline excision mutation blocks developmentally controlled amplification of the rDNA minichromosome of Tetrahymena thermophila. Genes Dev. 8:84-95.
27. Kapler, G. M., E. Orias, and E. H. Blackburn. 1994. Tetrahymena thermophila mutants defective in the developmentally programmed maturation and maintenance of the rDNA minichromosome. Genetics 137:455-466.
28. Kapler, G. M., D. L. Dobbs, and E. H. Blackburn. 1996. DNA replication in Tetrahymena, p. 915-932. In M. L. DePamphilis (ed.), DNA replication in eukaryotic cells. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
29. Karrer, K. M. 1986. The nuclear DNA of holotrichous cilliates, p. 85-110. In J. G. Gall (ed.), The molecular biology of ciliated protozoa. Academic Press, Orlando, Fla.
30. Kearsey, S. E., K. Labib, and D. Maiorano. 1996. Cell cycle control of eukaryotic DNA replication. Curr. Opin. Genet. Dev. 6:208-214.
31. Kelly, R. E., M. L. DeRose, B. W. Draper, and G. M. Wahl. 1995. Identification of an origin of bidirectional DNA replication in the ubiquitously expressed mammalian CAD gene. Mol. Cell. Biol. 15:4136-4148.
32. Kitsberg, D., S. Selig, and H. Cedar. 1993. Replication structure of the human β-globin gene domain. Nature 366:588-590.
33. Larson, D. D., E. H. Blackburn, P. C. Yaeger, and E. Orias. 1986. Control of rDNA replication in Tetrahymena involves a cis-acting upstream repeat of a promoter element. Cell 47:229-240.
34. Levine, A., S. Autret, and S. Serore. 1995. A check point involving RTP, the replication terminator protein, arrests replication downstream of the origin during stringent response in Bacillus subtilis. Mol. Microbiol. 15:287-295.
35. Liang, C., J. D. Spitzer, H. S. Smith, and S. A. Gerbi. 1993. Replication initiates at a confined region during DNA amplification in Sciara DNA puff II/9A. Genes Dev. 7:1072-1084.
36. Liang, C., M. Weinreich, and B. Stillman. 1995. ORC and Cdc6p interact and determine the frequency of initiation of DNA replication in the genome. Cell 81:667-676.
37. Linskens, M. H. K., and J. A. Huberman. 1988. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:4927-4935.
38. Little, R. D., T. H. Platt, and C. L. Schildkraut. 1993. Initiation and termination of DNA replication in human rRNA genes. Mol. Cell. Biol. 13:6600-6613.
39. MacAlpine, D. M., Z. Zhang, and G. M. Kapler. 1997. Type I elements mediate replication fork pausing at conserved upstream sites in the Tetrahymena thermophila ribosomal DNA minichromosome. Mol. Cell. Biol. 17:4517-4525.
40. Marahrens, Y., and B. Stillman. 1992. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255:817-823.
41. Martin-Parras, L., P. Hernandez, M. L. Martinez-Robles, and J. B. Schvartzman. 1991. Unidirectional replication as visualized by two-dimensional agarose gel electrophoresis. J. Mol. Biol. 220:843-853.
42. Maundrell, K., A. Hutchison, and S. Shall. 1988. Sequence analysis of ARS elements in fission yeast. EMBO J. 7:2203-2209.
43. Orias, E., and A. D. Bradshaw. 1992. Stochastic developmental variation in the ratio of allelic rDNAs among newly differentiated, heterozygous macronuclei of Tetrahymena thermophila. Dev. Genet. 13:87-93.
44. Orias, E., and E. P. Hamilton. 1979. Cytogamy: an inducible alternate pathway of conjugation in Tetrahymena thermophila. Genetics 91:657-671.
45. Orias, E. O., and P. J. Bruns. 1975. Induction and isolation of mutants in Tetrahymena. Methods Cell Biol. 5:247-282.
46. Osheim, Y. N., O. L. Miller, and A. L. Beyer. 1988. Visualization of Drosophila chorion genes undergoing amplification. Mol. Cell. Biol. 8:2811-2821.
47. Palen, T. E., and T. R. Cech. 1984. Chromatin structure at the replication origins and transcription-initiation regions of the ribosomal RNA genes of Tetrahymena. Cell 36:933-942.
48. Pan, W.-J., R. C. Gallagher, and E. H. Blackburn. 1995. Replication of an rRNA gene origin plasmid in the Tetrahymena thermophila macronucleus is prevented by transcription through the origin from an RNA polymerase I promoter. Mol. Cell. Biol. 15:3372-3381.
49. Reischmann, K. P., Z. Zhang, and G. M. Kapler. Unpublished results.
50. Shinomiya, T., and S. Ina. 1993. DNA replication of histone gene repeats in Drosophila melanogaster tissue culture cells: multiple initiation sites and replication pause sites. Mol. Cell. Biol. 13:4098-4106.
51. Spangler, E. A., T. Ryan, and E. H. Blackburn. 1988. Developmentally regulated telomere addition in Tetrahymena thermophila. Nucleic Acids Res. 16:5569-5585.
52. Stark, G. R., M. DeBatisse, E. Giulotto, and G. M. Wahl. 1989. Recent progress in understanding mechanisms of mammalian gene amplification. Cell 57:901-908.
53. Stark, G. R., and G. M. Wahl. 1984. Gene amplifications. Annu. Rev. Biochem. 53:447-491.
54. Stillman, B. 1993. Replication renaissance. Nature 366:506-507.
55. Vaughn, J. P., P. A. Dijkwel, and J. L. Hamlin. 1990. Replication initiates in a broad zone in the amplified CHO dihydrofolate reductase domain. Cell 61:1075-1087.
56. Ward, J. G., P. Blomberg, N. Hoffman, and M.-C. Yao. The intranuclear organization of normal, hemizygous and excision-deficient rRNA genes during developmental amplification in Tetrahymena thermophila. Chromosoma, in press.
57. Yaeger, P. C., E. Orias, W.-L. Shaiu, D. D. Larson, and E. H. Blackburn. 1989. The replication advantage of a free linear rRNA gene is restored by somatic recombination in Tetrahymena thermophila. Mol. Cell. Biol. 9:452-460.
58. Yao, M.-C., A. R. Kimmel, and M. A. Gorovsky. 1974. A small number of cistrons for ribosomal RNA in the germline nucleus of a eukaryote, Tetrahymena pyriformis. Proc. Natl. Acad. Sci. USA 71:3082-3086.
59. Yao, M.-C., C.-H. Yao, and B. Monks. 1990. The controlling sequence for site-specific chromosome breakage in Tetrahymena. Cell 63:763-772.
60. Yao, M.-C., K. Zheng, and C.-H. Yao. 1987. A conserved nucleotide sequence at the site of developmentally regulated chromosomal breakage in Tetrahymena. Cell 48:779-788.
61. Yasuda, L. F., and M.-C. Yao. 1991. Short inverted repeats at a free end signal large palindromic DNA formation in Tetrahymena. Cell 67:505-516.
62. Zhang, Z., and G. M. Kapler. Unpublished results.
63. Zhu, J., C. Brun, H. Kurooka, M. Yanagida, and J. A. Huberman. 1992. Identification and characterization of a complex chromosomal replication origin in Schizosaccharomyces pombe. Chromosoma 102:S7-S16.