DNA replication origin plasticity and perturbed fork progression in human inverted repeats

Molecular and Cellular Biology

Volumn 25, Issue 15, 2005, Pages 6789-6797

  Lebofsky, Ronald ^a   Bensimon, Aaron ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RIBOSOME RNA;

ARTICLE; DNA REPLICATION; GENE STRUCTURE; GENETIC TRANSCRIPTION; HELA CELL; HUMAN; HUMAN CELL; HUMAN GENOME; INVERTED REPEAT; PRIORITY JOURNAL; TRANSCRIPTION TERMINATION;

DNA REPLICATION; DNA, INTERGENIC; GENE REARRANGEMENT; HELA CELLS; HUMANS; REPETITIVE SEQUENCES, NUCLEIC ACID; REPLICATION ORIGIN; RNA, RIBOSOMAL;

METAZOA;

EID: 22544454138     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.25.15.6789-6797.2005     Document Type: Article

References (48)

1. Akgun, E., J. Zahn, S. Baumes, G. Brown, F. Liang, P. J. Romanicnko, S. Lewis, and M. Jasin. 1997. Palindrome resolution and recombination in the mammalian germ line. Mol. Cell. Biol. 17:5559-5570.
2. Anglana, M., F. Apiou, A. Bensimon, and M. Debatisse. 2003. Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing. Cell 114:385-394.
3. Bensimon, A., A. Simon, A. Chiffaudel, V. Croquette, F. Heslot, and D. Bensimon. 1994. Alignment and sensitive detection of DNA by a moving interface. Science 265:2096-2098.
4. 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.
5. 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.
6. Caburet, S., C. Conti, C. Schurra, R. Lebofsky, S. J. Edelstein, and A. Bensimon. A new paradigm for ribosomal DNA arrays incorporating a broad range of palindromic pseudogenes. Genome Res., in press.
7. Cheung, S. W., L. Sun, and T. Featherstone. 1990. Molecular cytogenetic evidence to characterize breakpoint regions in Robertsonian translocations. Cytogenet. Cell Genet. 54:97-102.
8. Conconi, A., R. M. Widmer, T. Koller, and J. M. Sogo. 1989. Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell 57:753-761.
9. Coverley, D., and R. A. Laskey. 1994, Regulation of eukaryotic DNA replication. Annu. Rev. Biochem. 63:745-776.
10. Cromie, G. A., C. B. Millar, K. H. Schmidt, and D. R. Leach. 2000. Palindromes as substrates for multiple pathways of recombination in Escherichia coli. Genetics 154:513-522.
11. Demeret, C., Y. Vassetzky, and M. Mechali. 2001. Chromatin remodelling and DNA replication: from nucleosomes to loop domains. Oncogene 20: 3086-3093.
12. DePamphilis, M. L. 1999. Replication origins in metazoan chromosomes: fact or fiction? Bioessays 21:5-16.
13. Edenberg, H. J., and J. A. Huberman. 1975. Eukaryotic chromosome replication. Annu. Rev. Genet. 9:245-284.
14. Flores, M. J., H. Bierne, S. D. Ehrlich, and B. Michel. 2001. Impairment of lagging strand synthesis triggers the formation of a RuvABC substrate at replication forks. EMBO J. 20:619-629.
15. Gencheva, M., B. Anachkova, and G. Russev. 1996. Mapping the sites of initiation of DNA replication in rat and human rRNA genes. J. Biol. Chem. 271:2608-2614.
16. Gerbi, S. A., and A. K. Bielinsky. 2002. DNA replication and chromatin. Curr. Opin. Genet. Dev. 12:243-248.
17. Gonzalez, I. L., and J. E. Sylvester. 1995. Complete sequence of the 43-kb human ribosomal DNA repeat: analysis of the intergenic spacer. Genomics 27:320-328.
18. Gordenin, D. A., K. S. Lobachev, N. P. Degtyareva, A. L. Malkova, E. Perkins, and M. A. Resnick. 1993. Inverted DNA repeats-a source of eukaryotic genomic instability. Mol. Cell. Biol. 13:5315-5322.
19. Herrick, J., P. Stanislawski, O. Hyrien, and A. Bensimon. 2000. Replication fork density increases during DNA synthesis in X. laevis egg extracts. J. Mol. Biol. 300:1133-1142.
20. Ivessa, A. S., J. Q. Zhou, and V. A. Zakian. 2000. The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA. Cell 100:479-489.
21. Jackson, D. A., and A. Pombo. 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.
22. Johnson, R. D., and M. Jasin. 2000. Sister chromatid gene conversion is a prominent double-strand break repair pathway in mammalian cells. EMBO J. 19:3398-3407.
23. Linskens, M. H. K., and J. A. Huberman. 1988. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:4927-4935.
24. 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.
25. Lobachev, K. S., B. M. Shor, H. T. Tran, W. Taylor, J. D. Keen, M. A. Resnick, and D. A. Gordenin. 1998. Factors affecting inverted repeat stimulation of recombination and deletion in Saccharomyces cerevisiae. Genetics 148:1507-1524.
26. McGlynn, P., and R. G. Lloyd. 2002. Recombinational repair and restart of damaged replication forks. Nat. Rev. Mol. Cell Biol. 3:859-870.
27. Michalet, X., R. Ekong, F. Fougerousse, S. Rousseaux, C. Schurra, N. Hornigold, M. van Slegtenhorst, J. Wolfe, S. Povey, J. S. Beckmann, and A. Bensimon. 1997. Dynamic molecular combing: stretching the whole human genome for high-resolution studies. Science 277:1518-1523.
28. Michel, B., S. D. Ehrlich, and M. Uzest. 1997. DNA double-strand breaks caused by replication arrest. EMBO J. 16:430-438.
29. Michel, B., M. J. Flores, E. Viguera, G. Grompone, M. Seigneur, and V. Bidnenko. 2001. Rescue of arrested replication forks by homologous recombination. Proc. Natl. Acad. Sci. USA 98:8181-8188.
30. Mizuuchi, K., M. Mizuuchi, and M. Gellert. 1982. Cruciform structures in palindromic DNA are favored by DNA supercoiling. J. Mol. Biol. 156:229-243.
31. Norio, P., and C. L. Schildkraut. 2001. Visualization of DNA replication on individual Epstein-Barr virus episomes. Science 294:2361-2364.
32. Pasero, P., A. Bensimon, and E. Schwob. 2002. Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus. Genes Dev. 16:2479-2484.
33. Pliss, A., K. Koberna, J. Vecerova, J. Malinsky, M. Masata, M. Fialova, I. Raska, and R. Berezney. 2005. Spatio-temporal dynamics at rDNA foci: global switching between DNA replication and transcription. J. Cell. Biochem. 94:554-565.
34. Postow, L., N. J. Crisona, B. J. Peter, C. D. Hardy, and N. R. Cozzarelli. 2001. Topological challenges to DNA replication: conformations at the fork. Proc. Natl. Acad. Sci. USA 98:8219-8226.
35. Richardson, C., M. E. Moynahan, and M. Jasin. 1998. Double-strand break repair by interchromosomal recombination: suppression of chromosomal translocations. Genes Dev. 12:3831-3842.
36. Rothstein, R., and S. Gangloff. 1999. The shuffling of a mortal coil. Nat. Genet. 22:4-6.
37. Rothstein, R., B. Michel, and S. Gangloff. 2000. Replication fork pausing and recombination or "gimme a break". Genes Dev. 14:1-10.
38. Saffer, L. D., and O. L. Miller. 1986. Electron-microscopic study of Saccharomyces cerevisiae rDNA chromatin replication. Mol. Cell. Biol. 6:1148-1157.
39. 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.
40. Schvartzman, J. B., and A. Stasiak. 2004. A topological view of the replicon. EMBO Rep. 5:256-261.
41. Scott, R. S., K. Y. Truong, and J. M. Vos. 1997. Replication initiation and elongation fork rates within a differentially expressed human multicopy locus in early S phase. Nucleic Acids Res. 25:4505-4512.
42. Shaffer, L. G., and J. R. Lupski. 2000. Molecular mechanisms for constitutional chromosomal rearrangements in humans. Annu. Rev. Genet. 34:297-329.
43. Torres, J. Z., J. B. Bessler, and V. A. Zakian. 2004. Local chromatin structure at the ribosomal DNA causes replication fork pausing and genome instability in the absence of the S-cerevisiae DNA helicase Rrm3p. Genes Dev. 18: 498-503.
44. Tran, H., N. Degtyareva, D. Gordenin, and M. A. Resnick. 1997. Altered replication and inverted repeats induce mismatch repair-independent recombination between highly diverged DNAs in yeast. Mol. Cell. Biol. 17: 1027-1036.
45. Weaver, D. T., and M. L. DePamphilis. 1984. The role of palindromic and non-palindromic sequences in arresting DNA synthesis in vitro and in vivo. J. Mol. Biol. 180:961-986.
46. Weitao, T., M. Budd, L. L. Hoopes, and J. L. Campbell. 2003. Dna2 helicase/nuclease causes replicative fork stalling and double-strand breaks in the ribosomal DNA of Saccharomyces cerevisiae. J. Biol. Chem. 278:22513-22522.
47. Yoon, Y., J. A. Sanchez, C. Brun, and J. A. Huberman. 1995. Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis. Mol. Cell. Biol. 15:2482-2489.
48. Zhang, Z., D. M. Macalpine, and G. M. Kapler. 1997. Developmental regulation of DNA replication: replication fork barriers and programmed gene amplification in Tetrahymena thermophila. Mol. Cell. Biol. 17:6147-6156.