Architecture of the replication fork stalled at the 3' end of yeast ribosomal genes

Molecular and Cellular Biology

Volumn 20, Issue 15, 2000, Pages 5777-5787

  Gruber, Markus ^a   Wellinger, Ralf Erik ^a   Sogo, José M ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; RIBOSOME RNA;

ARTICLE; DNA REPLICATION; ENZYME ACTIVITY; GENE EXPRESSION; GENE STRUCTURE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ISOLATION; PROTEIN SYNTHESIS; SACCHAROMYCES CEREVISIAE;

BASE SEQUENCE; DEOXYRIBONUCLEASE HINDIII; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA REPLICATION; ENDODEOXYRIBONUCLEASES; MOLECULAR SEQUENCE DATA; RNA, RIBOSOMAL; YEASTS;

SACCHAROMYCES CEREVISIAE;

EID: 0033925785     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.20.15.5777-5787.2000     Document Type: Article

References (46)

1. Aparicio, O. M., D. M. Weinstein, and S. P. Bell. 1997. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell 91:59-69.
2. Bambara, R. A., R. S. Murante, and L. A. Henricksen. 1997. Enzymes and reactions at the eukaryotic DNA replication fork. J. Biol. Chem. 272:4647-4650.
3. Bielinsky, A. K., and S. A. Gerbi. 1998. Discrete start sites for DNA synthesis in the yeast ARS1 origin. Science 279:95-98.
4. Brewer, B. J., and W. L. Fangman. 1993. Initiation at closely spaced replication origins in a yeast chromosome. Science 262:1728-1731.
5. Brewer, B. J., and W. L. Fangman. 1988. A replication fork barrier at the 3′ end of yeast ribosomal RNA genes. Cell 55:637-643.
6. Brewer, B. J., D. Lockshon, and W. L. Fangman. 1992. The arrest of replication forks in the rDNA of yeast occurs independently of transcription. Cell 71:267-276.
7. Burhans, W. C., L. T. Vassilev, J. Wu, J. M. Sogo, F. S. Nallaseth, and M. L. DePamphilis. 1991. Emetine allows identification of origins of mammalian DNA replication by imbalanced DNA synthesis, not through conservative nucleosome segregation. EMBO J. 10:4351-4360.
8. Cordeiro-Stone, M., L. S. Zaritskaya, L. K. Price, and W. K. Kaufmann. 1997. Replication fork bypass of a pyrimidine dimer blocking leading strand DNA synthesis. J. Biol. Chem. 272:13945-13954.
9. Dammann, R., R. Lucchini, T. Koller, and J. M. Sogo. 1995. Transcription in the yeast rRNA gene locus: distribution of the active gene copies and chromatin structure of their flanking regulatory sequences. Mol. Cell. Biol. 15: 5294-5303.
10. Defossez, P. A., R. Prusty, M. Kaeberlein, S. J. Lin, P. Ferrigno, P. A. Silver, R. L. Keil, and L. Guarente. 1999. Elimination of replication block protein Fob1 extends the life span of yeast mother cells. Mol. Cell 3:447-455.
11. DePamphilis, M. L., and P. M. Wassarman. 1980. Replication of eukaryotic chromosomes: a close-up of the replication fork. Annu. Rev. Biochem. 49:627-666.
12. Gerber, J. K., E. Gogel, C. Berger, M. Wallisch, F. Muller, I. Grummt, and F. Grummt. 1997. Termination of mammalian rDNA replication: polar arrest of replication fork movement by transcription termination factor TTF-I. Cell 90:559-567.
13. Hernandez, P., L. Martin-Parras, M. L. Martinez-Robles, and J. B. Schvartzman. 1993. Conserved features in the mode of replication of eukaryotic ribosomal RNA genes. EMBO J. 12:1475-1485.
14. Ishimi, Y., Y. Komamura, Z. You, and H. Kimura. 1998. Biochemical function of mouse minichromosome maintenance 2 protein. J. Biol. Chem. 273: 8369-8375.
15. Jensch, F., and B. Kemper. 1986. Endonuclease VII resolves Y-junctions in branched DNA in vitro. EMBO J. 5:181-189.
16. Kemper, B. 1997. Branched DNA resolving enzymes, p. 179-204. In J. A. Nickoloff and M. Hoekstra (ed.), DNA damage and repair. Humana Press, Totowa, N.J.
17. Khatri, G. S., T. MacAllister, P. R. Sista, and D. Bastia. 1989. The replication terminator protein of E. coli is a DNA sequence-specific contra-helicase. Cell 59:667-674.
18. Kobayashi, T., D. J. Heck, M. Nomura, and T. Horiuchi. 1998. Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev. 12:3821-3830.
19. Kobayashi, T., M. Hidaka, M. Nishizawa, and T. Horiuchi. 1992 Identification of a site required for DNA replication fork blocking activity in the rRNA gene cluster in Saccharomyces cerevisiae. Mol. Gen. Genet. 233:355-362.
20. Kobayashi, T., and T. Horiuchi. 1996. A yeast gene product. Fob1 protein, required for both replication fork blocking and recombinational hotspot activities. Genes Cells 1:465-74.
21. Lilley, D. M., and B. Kemper. 1984. Cruciform-resolvase interactions in supercoiled DNA. Cell 36:413-422.
22. Linskens, M. H., and J. A. Huberman. 1988. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:4927-4935.
23. 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.
24. Lopez-Estrano, C., J. B. Schvartzman, D. B. Krimer, and P. Hernandez. 1998. Co-localization of polar replication fork barriers and rRNA transcription terminators in mouse rDNA. J. Mol. Biol. 277:249-256.
25. Lucchini, R., and J. M. Sogo. 1994. Chromatin structure and transcriptional activity around the replication forks arrested at the 3′ end of the yeast rRNA genes. Mol. Cell. Biol. 14:318-326.
26. Lucchini, R., and J. M. Sogo. 1992. Different chromatin structures along the spacers flanking active and inactive Xenopus rRNA genes. Mol. Cell. Biol. 12:4288-4296.
27. Lucchini, R., and J. M. Sogo. 1995. Replication of transcriptionally active chromatin. Nature 374:276-280.
28. Mizuuchi, K., B. Kemper, J. Hays, and R. A. Weisberg. 1982. T4 endonuclease VII cleaves Holliday structures. Cell 29:357-365.
29. Nethanel, T., T. Zlotkin, and G. Kaufmann. 1992. Assembly of simian virus 40 Okazaki pieces from DNA primers is reversibly arrested by ATP depletion. J. Virol. 66:6634-6640.
30. Newlon, C. S. 1996. Mechanisms for completing DNA replication, p. 873-924. In M. L. DePamphilis (ed.), DNA replication in eukaryotic cells. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
31. Newton, C. R., and A. Graham. 1994. PCR, p. 13. BIOS Scientific Publishers Limited, Oxford, United Kingdom.
32. Portmann, R., W. Schaffner, and M. Birnstiel. 1976. Parital denaturation mapping of cloned histone DNA from the sea urchin Psammechinus miliaris. Nature 264:31-34.
33. Pottmeyer, S., and B. Kemper. 1992. T4 endonuclease VII resolves cruciform DNA with nick and counter-nick and its activity is directed by local nucleotide sequence. J. Mol. Biol. 223:607-615.
34. Ruven, H. J., C. M. Seelen, P. H. Lobman, L. H. Mullenders, and A. A. van Zeeland. 1994. Efficient synthesis of 32P-labeled single-stranded DNA probes using linear PCR; application of the method for analysis of strand-specific DNA repair. Mutat. Res. 315:189-195.
35. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
36. Sanchez, J. A., S. M. Kim, and J. A. Huberman. 1998. Ribosomal DNA replication in the fission yeast, Schizosaccharomyces pombe. Exp. Cell Res. 238:220-230.
37. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad, Sci. USA 74:5463-5467.
38. Sherman, F., G. R. Fink, and J. B. Hicks (ed.). 1986. Methods in yeast genetics: a laboratory course manual, p. 163-164. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
39. Sinclair, D. A., and L. Guarente. 1997. Extrachromosomal rDNA circles - a cause of aging in yeast. Cell 91:1033-1042.
40. Skryabin, K. G., M. A. Eldarov, V. L. Larionov, A. A. Bayev, J. Klootwijk, V. C. de Regt, G. M. Veldman, R. J. Planta, O. I. Georgiev, and A. A. Hadjiolov. 1984. Structure and function of the nontranscribed spacer regions of yeast rDNA. Nucleic Acids Res. 12:2955-2968.
41. Waga, S., and B. Stillman. 1998. The DNA replication fork in eukaryotic cells. Annu. Rev. Biochem. 67:721-751.
42. Walmsley, R. M., L. H. Johnston, D. H. Williamson, and S. G. Oliver. 1984. Replicon size of yeast ribosomal DNA. Mol. Gen. Genet. 195:260-266.
43. Wellinger, R. E., and F. Thoma. 1997. Nucleosome structure and positioning modulate nucleotide excision repair in the non-transcribed strand of an active gene, EMBO J. 16:5046-5056.
44. White, M. F., M. J. Giraud-Panis, J. R. Pohler, and D. M. Lilley. 1997. Recognition and manipulation of branched DNA structure by junction-resolving enzymes. J. Mol. Biol. 269:647-664.
45. Wiesendanger, B., R. Lucchini, T. Koller, and J. M. Sogo. 1994. Replication fork barriers in the Xenopus rDNA. Nucleic Acids Res. 22:5038-5046.
46. Wu, J. R., and D. M. Gilbert. 1995. Rapid DNA preparation for 2D gel analysis of replication intermediates. Nucleic Acids Res. 23:3997-3998.