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Mol Cell Biol. 1988 November; 8(11): 4927-4935

Organization of replication of ribosomal DNA in Saccharomyces cerevisiae.

Department of Molecular and Cellular Biology, Roswell Park Memorial Institute, Buffalo, New York 14263.

ABSTRACT

Using recently developed replicon mapping techniques, we have analyzed the replication of the ribosomal DNA in Saccharomyces cerevisiae. The results show that (i) the functional origin of replication colocalizes with an autonomously replicating sequence element previously mapped to the nontranscribed spacer region, (ii) only a fraction of the potential origins are utilized in a single S phase, and (iii) the replication forks moving counter to the direction of transcription of the 37S precursor RNA stop at or near the termination site of transcription. Consequently, most ribosomal DNA is replicated unidirectionally by forks moving in the direction of transcription and most replicons are larger than the repeat unit. The significance of this finding for the replication of abundantly transcribed genes is discussed.

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• Guo, Z., Qian, L., Liu, R., Dai, H., Zhou, M., Zheng, L., Shen, B. (2008). Nucleolar Localization and Dynamic Roles of Flap Endonuclease 1 in Ribosomal DNA Replication and Damage Repair. Mol. Cell. Biol. 28: 4310-4319 [Abstract] [Full Text]  
• Hershman, S. G., Chen, Q., Lee, J. Y., Kozak, M. L., Yue, P., Wang, L.-S., Johnson, F. B. (2008). Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae. Nucleic Acids Res 36: 144-156 [Abstract] [Full Text]  
• Torres-Rosell, J., De Piccoli, G., Cordon-Preciado, V., Farmer, S., Jarmuz, A., Machin, F., Pasero, P., Lisby, M., Haber, J. E., Aragon, L. (2007). Anaphase Onset Before Complete DNA Replication with Intact Checkpoint Responses. Science 315: 1411-1415 [Abstract] [Full Text]  
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• Coulon, S., Noguchi, E., Noguchi, C., Du, L.-L., Nakamura, T. M., Russell, P. (2006). Rad22Rad52-dependent Repair of Ribosomal DNA Repeats Cleaved by Slx1-Slx4 Endonuclease. Mol. Biol. Cell 17: 2081-2090 [Abstract] [Full Text]  
• Johzuka, K., Terasawa, M., Ogawa, H., Ogawa, T., Horiuchi, T. (2006). Condensin Loaded onto the Replication Fork Barrier Site in the rRNA Gene Repeats during S Phase in a FOB1-Dependent Fashion To Prevent Contraction of a Long Repetitive Array in Saccharomyces cerevisiae.. Mol. Cell. Biol. 26: 2226-2236 [Abstract] [Full Text]  
• Mohanty, B. K., Bairwa, N. K., Bastia, D. (2006). The Tof1p-Csm3p protein complex counteracts the Rrm3p helicase to control replication termination of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 103: 897-902 [Abstract] [Full Text]  
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• Calzada, A., Hodgson, B., Kanemaki, M., Bueno, A., Labib, K. (2005). Molecular anatomy and regulation of a stable replisome at a paused eukaryotic DNA replication fork. Genes Dev. 19: 1905-1919 [Abstract] [Full Text]  
• Lebofsky, R., Bensimon, A. (2005). DNA Replication Origin Plasticity and Perturbed Fork Progression in Human Inverted Repeats. Mol. Cell. Biol. 25: 6789-6797 [Abstract] [Full Text]  
• Mirkin, E. V., Mirkin, S. M. (2005). Mechanisms of Transcription-Replication Collisions in Bacteria. Mol. Cell. Biol. 25: 888-895 [Abstract] [Full Text]  
• Stedman, W., Deng, Z., Lu, F., Lieberman, P. M. (2004). ORC, MCM, and Histone Hyperacetylation at the Kaposi's Sarcoma-Associated Herpesvirus Latent Replication Origin. J. Virol. 78: 12566-12575 [Abstract] [Full Text]  
• Bessler, J. B., Zakian, V. A. (2004). The Amino Terminus of the Saccharomyces cerevisiae DNA Helicase Rrm3p Modulates Protein Function Altering Replication and Checkpoint Activity. Genetics 168: 1205-1218 [Abstract] [Full Text]  
• Torres, J. Z., Bessler, J. B., Zakian, V. A. (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 [Abstract] [Full Text]  
• Mohanty, B. K., Bastia, D. (2004). Binding of the Replication Terminator Protein Fob1p to the Ter Sites of Yeast Causes Polar Fork Arrest. J. Biol. Chem. 279: 1932-1941 [Abstract] [Full Text]  
• Sanchez-Gorostiaga, A., Lopez-Estrano, C., Krimer, D. B., Schvartzman, J. B., Hernandez, P. (2004). Transcription Termination Factor reb1p Causes Two Replication Fork Barriers at Its Cognate Sites in Fission Yeast Ribosomal DNA In Vivo. Mol. Cell. Biol. 24: 398-406 [Abstract] [Full Text]  
• Kobayashi, T. (2003). The Replication Fork Barrier Site Forms a Unique Structure with Fob1p and Inhibits the Replication Fork. Mol. Cell. Biol. 23: 9178-9188 [Abstract] [Full Text]  
• Takeuchi, Y., Horiuchi, T., Kobayashi, T. (2003). Transcription-dependent recombination and the role of fork collision in yeast rDNA. Genes Dev. 17: 1497-1506 [Abstract] [Full Text]  
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• Lunyak, V. V., Ezrokhi, M., Smith, H. S., Gerbi, S. A. (2002). Developmental Changes in the Sciara II/9A Initiation Zone for DNA Replication. Mol. Cell. Biol. 22: 8426-8437 [Abstract] [Full Text]  
• Ivessa, A. S., Zakian, V. A. (2002). To fire or not to fire: origin activation in Saccharomyces cerevisiae ribosomal DNA. Genes Dev. 16: 2459-2464 [Full Text]  
• Pasero, P., Bensimon, A., Schwob, E. (2002). Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus. Genes Dev. 16: 2479-2484 [Abstract] [Full Text]  
• Zhou, J.-Q., Qi, H., Schulz, V. P., Mateyak, M. K., Monson, E. K., Zakian, V. A. (2002). Schizosaccharomyces pombe pfh1+ Encodes an Essential 5' to 3' DNA Helicase That Is a Member of the PIF1 Subfamily of DNA Helicases. Mol. Biol. Cell 13: 2180-2191 [Abstract] [Full Text]  
• Sidorova, J. M., Breeden, L. L. (2002). Precocious S-Phase Entry in Budding Yeast Prolongs Replicative State and Increases Dependence Upon Rad53 for Viability. Genetics 160: 123-136 [Abstract] [Full Text]  
• Dalgaard, J. Z., Klar, A. J.S. (2001). A DNA replication-arrest site RTS1 regulates imprinting by determining the direction of replication at mat1 in S. pombe. Genes Dev. 15: 2060-2068 [Abstract] [Full Text]  
• Kobayashi, T., Nomura, M., Horiuchi, T. (2001). Identification of DNA cis Elements Essential for Expansion of Ribosomal DNA Repeats in Saccharomyces cerevisiae. Mol. Cell. Biol. 21: 136-147 [Abstract] [Full Text]  
• Wai, H. H., Vu, L., Oakes, M., Nomura, M. (2000). Complete deletion of yeast chromosomal rDNA repeats and integration of a new rDNA repeat: use of rDNA deletion strains for functional analysis of rDNA promoter elements in vivo. Nucleic Acids Res 28: 3524-3534 [Abstract] [Full Text]  
• Gruber, M., Wellinger, R. E., Sogo, J. M. (2000). Architecture of the Replication Fork Stalled at the 3' End of Yeast Ribosomal Genes. Mol. Cell. Biol. 20: 5777-5787 [Abstract] [Full Text]  
• Ward, T. R., Hoang, M. L., Prusty, R., Lau, C. K., Keil, R. L., Fangman, W. L., Brewer, B. J. (2000). Ribosomal DNA Replication Fork Barrier and HOT1 Recombination Hot Spot: Shared Sequences but Independent Activities. Mol. Cell. Biol. 20: 4948-4957 [Abstract] [Full Text]  
• Rothstein, R., Michel, B., Gangloff, S. (2000). Replication fork pausing and recombination or "gimme a break". Genes Dev. 14: 1-10 [Full Text]  
• Vernis, L., Chasles, M., Pasero, P., Lepingle, A., Gaillardin, C., Fournier, P. (1999). Short DNA Fragments without Sequence Similarity Are Initiation Sites for Replication in the Chromosome of the Yeast Yarrowia lipolytica. Mol. Biol. Cell 10: 757-769 [Abstract] [Full Text]  
• Kobayashi, T., Heck, D. J., Nomura, M., Horiuchi, T. (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 [Abstract] [Full Text]  
• Santamaria, D., de la Cueva, G., Martinez-Robles, M. L., Krimer, D. B., Hernandez, P., Schvartzman, J. B. (1998). DnaB Helicase Is Unable to Dissociate RNA-DNA Hybrids. ITS IMPLICATION IN THE POLAR PAUSING OF REPLICATION FORKS AT ColE1 ORIGINS. J. Biol. Chem. 273: 33386-33396 [Abstract] [Full Text]  
• Viguera, E., Hernandez, P., Krimer, D. B., Boistov, A. S., Lurz, R., Alonso, J. C., Schvartzman, J. B. (1996). The ColE1 Unidirectional Origin Acts as a Polar Replication Fork Pausing Site. J. Biol. Chem. 271: 22414-22421 [Abstract] [Full Text]  
• Sahoo, T., Mohanty, B. K., Lobert, M., Manna, A. C., Bastia, D. (1995). The Contrahelicase Activities of the Replication Terminator Proteins of Escherichia coli and Bacillus subtilis Are Helicase-specific and Impede both Helicase Translocation and Authentic DNA Unwinding. J. Biol. Chem. 270: 29138-29144 [Abstract] [Full Text]  
• Hyrien, O., Maric, C., Méchali, M. (1995). Transition in Specification of Embryonic Metazoan DNA Replication Origins. Science 270: 994-997 [Abstract]  
• Liang, C, Spitzer, J D, Smith, H S, Gerbi, S A (1993). Replication initiates at a confined region during DNA amplification in Sciara DNA puff II/9A.. Genes Dev. 7: 1072-1084 [Abstract]  
• French, S (1992). Consequences of replication fork movement through transcription units in vivo. Science 258: 1362-1365 [Abstract]  
• Rivier, D., Rine, J (1992). An origin of DNA replication and a transcription silencer require a common element. Science 256: 659-663 [Abstract]  
• Marahrens, Y, Stillman, B (1992). A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255: 817-823 [Abstract]  
• Laskey, R., Fairman, M., Blow, J. (1989). S phase of the cell cycle. Science 246: 609-614 [Abstract]