This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Smith, J. S.
Right arrow Articles by Boeke, J. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Smith, J. S.
Right arrow Articles by Boeke, J. D.

 Previous Article  |  Next Article 

Molecular and Cellular Biology, April 1999, p. 3184-3197, Vol. 19, No. 4
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

A Genetic Screen for Ribosomal DNA Silencing Defects Identifies Multiple DNA Replication and Chromatin-Modulating Factors

Jeffrey S. Smith, Emerita Caputo, and Jef D. Boeke*

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205

Received 20 October 1998/Returned for modification 3 December 1998/Accepted 21 December 1998

Transcriptional silencing in Saccharomyces cerevisiae occurs at several genetic loci, including the ribosomal DNA (rDNA). Silencing at telomeres (telomere position effect [TPE]) and the cryptic mating-type loci (HML and HMR) depends on the silent information regulator genes, SIR1, SIR2, SIR3, and SIR4. However, silencing of polymerase II-transcribed reporter genes integrated within the rDNA locus (rDNA silencing) requires only SIR2. The mechanism of rDNA silencing is therefore distinct from TPE and HM silencing. Few genes other than SIR2 have so far been linked to the rDNA silencing process. To identify additional non-Sir factors that affect rDNA silencing, we performed a genetic screen designed to isolate mutations which alter the expression of reporter genes integrated within the rDNA. We isolated two classes of mutants: those with a loss of rDNA silencing (lrs) phenotype and those with an increased rDNA silencing (irs) phenotype. Using transposon mutagenesis, lrs mutants were found in 11 different genes, and irs mutants were found in 22 different genes. Surprisingly, we did not isolate any genes involved in rRNA transcription. Instead, multiple genes associated with DNA replication and modulation of chromatin structure were isolated. We describe these two gene classes, and two previously uncharacterized genes, LRS4 and IRS4. Further characterization of the lrs and irs mutants revealed that many had alterations in rDNA chromatin structure. Several lrs mutants, including those in the cdc17 and rfc1 genes, caused lengthened telomeres, consistent with the hypothesis that telomere length modulates rDNA silencing. Mutations in the HDB (RPD3) histone deacetylase complex paradoxically increased rDNA silencing by a SIR2-dependent, SIR3-independent mechanism. Mutations in rpd3 also restored mating competence selectively to sir3Delta MATalpha strains, suggesting restoration of silencing at HMR in a sir3 mutant background.

* Corresponding author. Mailing address: Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe St., 617 Hunterian Building, Baltimore, MD 21205. Phone: (410) 955-2481. Fax: (410) 614-2987. E-mail: jboeke{at}jhmi.edu.

Molecular and Cellular Biology, April 1999, p. 3184-3197, Vol. 19, No. 4
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Buonomo, S. B.C., Wu, Y., Ferguson, D., de Lange, T. (2009). Mammalian Rif1 contributes to replication stress survival and homology-directed repair. JCB 187: 385-398 [Abstract] [Full Text]  
  • Marvin, M. E., Griffin, C. D., Eyre, D. E., Barton, D. B. H., Louis, E. J. (2009). In Saccharomyces cerevisiae, yKu and Subtelomeric Core X Sequences Repress Homologous Recombination Near Telomeres as Part of the Same Pathway. Genetics 183: 441-451 [Abstract] [Full Text]  
  • Zhou, J., Zhou, B. O., Lenzmeier, B. A., Zhou, J.-Q. (2009). Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation. Nucleic Acids Res 37: 3699-3713 [Abstract] [Full Text]  
  • Hontz, R. D., Niederer, R. O., Johnson, J. M., Smith, J. S. (2009). Genetic Identification of Factors That Modulate Ribosomal DNA Transcription in Saccharomyces cerevisiae. Genetics 182: 105-119 [Abstract] [Full Text]  
  • Yin, H., Zhang, X., Liu, J., Wang, Y., He, J., Yang, T., Hong, X., Yang, Q., Gong, Z. (2009). Epigenetic Regulation, Somatic Homologous Recombination, and Abscisic Acid Signaling Are Influenced by DNA Polymerase {epsilon} Mutation in Arabidopsis. Plant Cell 21: 386-402 [Abstract] [Full Text]  
  • Viiri, K. M., Janis, J., Siggers, T., Heinonen, T. Y. K., Valjakka, J., Bulyk, M. L., Maki, M., Lohi, O. (2009). DNA-Binding and -Bending Activities of SAP30L and SAP30 Are Mediated by a Zinc-Dependent Module and Monophosphoinositides. Mol. Cell. Biol. 29: 342-356 [Abstract] [Full Text]  
  • Waples, W. G., Chahwan, C., Ciechonska, M., Lavoie, B. D. (2009). Putting the Brake on FEAR: Tof2 Promotes the Biphasic Release of Cdc14 Phosphatase during Mitotic Exit. Mol. Biol. Cell 20: 245-255 [Abstract] [Full Text]  
  • Tremblay, M., Teng, Y., Paquette, M., Waters, R., Conconi, A. (2008). Complementary Roles of Yeast Rad4p and Rad34p in Nucleotide Excision Repair of Active and Inactive rRNA Gene Chromatin. Mol. Cell. Biol. 28: 7504-7513 [Abstract] [Full Text]  
  • Hontz, R. D., French, S. L., Oakes, M. L., Tongaonkar, P., Nomura, M., Beyer, A. L., Smith, J. S. (2008). Transcription of Multiple Yeast Ribosomal DNA Genes Requires Targeting of UAF to the Promoter by Uaf30. Mol. Cell. Biol. 28: 6709-6719 [Abstract] [Full Text]  
  • McClure, J. M., Gallo, C. M., Smith, D. L. Jr., Matecic, M., Hontz, R. D., Buck, S. W., Racette, F. G., Smith, J. S. (2008). Pnc1p-Mediated Nicotinamide Clearance Modifies the Epigenetic Properties of rDNA Silencing in Saccharomyces cerevisiae. Genetics 180: 797-810 [Abstract] [Full Text]  
  • Andersen, M. P., Nelson, Z. W., Hetrick, E. D., Gottschling, D. E. (2008). A Genetic Screen for Increased Loss of Heterozygosity in Saccharomyces cerevisiae. Genetics 179: 1179-1195 [Abstract] [Full Text]  
  • van Welsem, T., Frederiks, F., Verzijlbergen, K. F., Faber, A. W., Nelson, Z. W., Egan, D. A., Gottschling, D. E., van Leeuwen, F. (2008). Synthetic Lethal Screens Identify Gene Silencing Processes in Yeast and Implicate the Acetylated Amino Terminus of Sir3 in Recognition of the Nucleosome Core. Mol. Cell. Biol. 28: 3861-3872 [Abstract] [Full Text]  
  • Exner, V., Taranto, P., Schonrock, N., Gruissem, W., Hennig, L. (2006). Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development. Development 133: 4163-4172 [Abstract] [Full Text]  
  • Grenetier, S., Bouchoux, C., Goguel, V. (2006). CTD kinase I is required for the integrity of the rDNA tandem array. Nucleic Acids Res 34: 4996-5006 [Abstract] [Full Text]  
  • Huang, J., Brito, I. L., Villen, J., Gygi, S. P., Amon, A., Moazed, D. (2006). Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer.. Genes Dev. 20: 2887-2901 [Abstract] [Full Text]  
  • Li, C., Mueller, J. E., Bryk, M. (2006). Sir2 Represses Endogenous Polymerase II Transcription Units in the Ribosomal DNA Nontranscribed Spacer. Mol. Biol. Cell 17: 3848-3859 [Abstract] [Full Text]  
  • Viiri, K. M., Korkeamaki, H., Kukkonen, M. K., Nieminen, L. K., Lindfors, K., Peterson, P., Maki, M., Kainulainen, H., Lohi, O. (2006). SAP30L interacts with members of the Sin3A corepressor complex and targets Sin3A to the nucleolus. Nucleic Acids Res 34: 3288-3298 [Abstract] [Full Text]  
  • Tamburini, B. A., Carson, J. J., Linger, J. G., Tyler, J. K. (2006). Dominant Mutants of the Saccharomyces cerevisiae ASF1 Histone Chaperone Bypass the Need for CAF-1 in Transcriptional Silencing by Altering Histone and Sir Protein Recruitment. Genetics 173: 599-610 [Abstract] [Full Text]  
  • Oakes, M. L., Siddiqi, I., French, S. L., Vu, L., Sato, M., Aris, J. P., Beyer, A. L., Nomura, M. (2006). Role of Histone Deacetylase Rpd3 in Regulating rRNA Gene Transcription and Nucleolar Structure in Yeast. Mol. Cell. Biol. 26: 3889-3901 [Abstract] [Full Text]  
  • Clarke, A. S., Samal, E., Pillus, L. (2006). Distinct Roles for the Essential MYST Family HAT Esa1p in Transcriptional Silencing. Mol. Biol. Cell 17: 1744-1757 [Abstract] [Full Text]  
  • Conconi, A., Paquette, M., Fahy, D., Bespalov, V. A., Smerdon, M. J. (2005). Repair-Independent Chromatin Assembly onto Active Ribosomal Genes in Yeast after UV Irradiation. Mol. Cell. Biol. 25: 9773-9783 [Abstract] [Full Text]  
  • Hyland, E. M., Cosgrove, M. S., Molina, H., Wang, D., Pandey, A., Cottee, R. J., Boeke, J. D. (2005). Insights into the Role of Histone H3 and Histone H4 Core Modifiable Residues in Saccharomyces cerevisiae. Mol. Cell. Biol. 25: 10060-10070 [Abstract] [Full Text]  
  • Sharp, J. A., Rizki, G., Kaufman, P. D. (2005). Regulation of Histone Deposition Proteins Asf1/Hir1 by Multiple DNA Damage Checkpoint Kinases in Saccharomyces cerevisiae. Genetics 171: 885-899 [Abstract] [Full Text]  
  • Jambunathan, N., Martinez, A. W., Robert, E. C., Agochukwu, N. B., Ibos, M. E., Dugas, S. L., Donze, D. (2005). Multiple Bromodomain Genes Are Involved in Restricting the Spread of Heterochromatic Silencing at the Saccharomyces cerevisiae HMR-tRNA Boundary. Genetics 171: 913-922 [Abstract] [Full Text]  
  • Huang, S., Zhou, H., Katzmann, D., Hochstrasser, M., Atanasova, E., Zhang, Z. (2005). Rtt106p is a histone chaperone involved in heterochromatin-mediated silencing. Proc. Natl. Acad. Sci. USA 102: 13410-13415 [Abstract] [Full Text]  
  • Lewis, L. K., Karthikeyan, G., Cassiano, J., Resnick, M. A. (2005). Reduction of nucleosome assembly during new DNA synthesis impairs both major pathways of double-strand break repair. Nucleic Acids Res 33: 4928-4939 [Abstract] [Full Text]  
  • Wang, L., Haeusler, R. A., Good, P. D., Thompson, M., Nagar, S., Engelke, D. R. (2005). Silencing Near tRNA Genes Requires Nucleolar Localization. J. Biol. Chem. 280: 8637-8639 [Abstract] [Full Text]  
  • Morales-Johansson, H., Jenoe, P., Cooke, F. T., Hall, M. N. (2004). Negative Regulation of Phosphatidylinositol 4,5-Bisphosphate Levels by the INP51-associated Proteins TAX4 and IRS4. J. Biol. Chem. 279: 39604-39610 [Abstract] [Full Text]  
  • Dror, V., Winston, F. (2004). The Swi/Snf Chromatin Remodeling Complex Is Required for Ribosomal DNA and Telomeric Silencing in Saccharomyces cerevisiae. Mol. Cell. Biol. 24: 8227-8235 [Abstract] [Full Text]  
  • Bachman, N., Eby, Y., Boeke, J. D. (2004). Local Definition of Ty1 Target Preference by Long Terminal Repeats and Clustered tRNA Genes. Genome Res 14: 1232-1247 [Abstract] [Full Text]  
  • Iida, T., Araki, H. (2004). Noncompetitive Counteractions of DNA Polymerase {varepsilon} and ISW2/yCHRAC for Epigenetic Inheritance of Telomere Position Effect in Saccharomyces cerevisiae. Mol. Cell. Biol. 24: 217-227 [Abstract] [Full Text]  
  • Polo, S., Confalonieri, S., Salcini, A. E., Di Fiore, P. P. (2003). EH and UIM: Endocytosis and More. Sci Signal 2003: re17-re17 [Abstract] [Full Text]  
  • Benguria, A., Hernandez, P., Krimer, D. B., Schvartzman, J. B. (2003). Sir2p suppresses recombination of replication forks stalled at the replication fork barrier of ribosomal DNA in Saccharomyces cerevisiae. Nucleic Acids Res 31: 893-898 [Abstract] [Full Text]  
  • Rohde, J. R., Cardenas, M. E. (2003). The Tor Pathway Regulates Gene Expression by Linking Nutrient Sensing to Histone Acetylation. Mol. Cell. Biol. 23: 629-635 [Abstract] [Full Text]  
  • Anderson, R. M., Bitterman, K. J., Wood, J. G., Medvedik, O., Cohen, H., Lin, S. S., Manchester, J. K., Gordon, J. I., Sinclair, D. A. (2002). Manipulation of a Nuclear NAD+ Salvage Pathway Delays Aging without Altering Steady-state NAD+ Levels. J. Biol. Chem. 277: 18881-18890 [Abstract] [Full Text]  
  • Huang, Y. (2002). Transcriptional silencing in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Nucleic Acids Res 30: 1465-1482 [Abstract] [Full Text]  
  • Sandmeier, J. J., Celic, I., Boeke, J. D., Smith, J. S. (2002). Telomeric and rDNA Silencing in Saccharomyces cerevisiae Are Dependent on a Nuclear NAD+ Salvage Pathway. Genetics 160: 877-889 [Abstract] [Full Text]  
  • Fuss, J., Linn, S. (2002). Human DNA Polymerase epsilon Colocalizes with Proliferating Cell Nuclear Antigen and DNA Replication Late, but Not Early, in S Phase. J. Biol. Chem. 277: 8658-8666 [Abstract] [Full Text]  
  • Krawitz, D. C., Kama, T., Kaufman, P. D. (2002). Chromatin Assembly Factor I Mutants Defective for PCNA Binding Require Asf1/Hir Proteins for Silencing. Mol. Cell. Biol. 22: 614-625 [Abstract] [Full Text]  
  • Sharp, J. A., Franco, A. A., Osley, M. A., Kaufman, P. D. (2002). Chromatin assembly factor I and Hir proteins contribute to building functional kinetochores in S. cerevisiae. Genes Dev. 16: 85-100 [Abstract] [Full Text]  
  • Briggs, S. D., Bryk, M., Strahl, B. D., Cheung, W. L., Davie, J. K., Dent, S. Y.R., Winston, F., Allis, C. D. (2001). Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev. 15: 3286-3295 [Abstract] [Full Text]  
  • Ahmed, S., Saini, S., Arora, S., Singh, J. (2001). Chromodomain Protein Swi6-mediated Role of DNA Polymerase alpha in Establishment of Silencing in Fission Yeast. J. Biol. Chem. 276: 47814-47821 [Abstract] [Full Text]  
  • Meijsing, S. H., Ehrenhofer-Murray, A. E. (2001). The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae. Genes Dev. 15: 3169-3182 [Abstract] [Full Text]  
  • Freidkin, I., Katcoff, D. J. (2001). Specific distribution of the Saccharomyces cerevisiae linker histone homolog HHO1p in the chromatin. Nucleic Acids Res 29: 4043-4051 [Abstract] [Full Text]  
  • Bryk, M., Banerjee, M., Conte, D. Jr., Curcio, M. J. (2001). The Sgs1 Helicase of Saccharomyces cerevisiae Inhibits Retrotransposition of Ty1 Multimeric Arrays. Mol. Cell. Biol. 21: 5374-5388 [Abstract] [Full Text]  
  • Srikantha, T., Tsai, L., Daniels, K., Klar, A. J. S., Soll, D. R. (2001). The Histone Deacetylase Genes HDA1 and RPD3 Play Distinct Roles in Regulation of High-Frequency Phenotypic Switching in Candida albicans. J. Bacteriol. 183: 4614-4625 [Abstract] [Full Text]  
  • Kirchmaier, A. L., Rine, J. (2001). DNA Replication-Independent Silencing in S. cerevisiae. Science 291: 646-650 [Abstract] [Full Text]  
  • Park, J., Jensen, B., Kifer, C., Parsons, M (2001). A novel nucleolar G-protein conserved in eukaryotes. J. Cell Sci. 114: 173-185 [Abstract]  
  • Smith, J. S., Brachmann, C. B., Celic, I., Kenna, M. A., Muhammad, S., Starai, V. J., Avalos, J. L., Escalante-Semerena, J. C., Grubmeyer, C., Wolberger, C., Boeke, J. D. (2000). A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc. Natl. Acad. Sci. USA 97: 6658-6663 [Abstract] [Full Text]  
  • Thon, G., Verhein-Hansen, J. (2000). Four Chromo-domain Proteins of Schizosaccharomyces pombe Differentially Repress Transcription at Various Chromosomal Locations. Genetics 155: 551-568 [Abstract] [Full Text]  
  • Park, Y., Lustig, A. J. (2000). Telomere Structure Regulates the Heritability of Repressed Subtelomeric Chromatin in Saccharomyces cerevisiae. Genetics 154: 587-598 [Abstract] [Full Text]  
  • Gagny, B, Wiederkehr, A, Dumoulin, P, Winsor, B, Riezman, H, Haguenauer-Tsapis, R (2000). A novel EH domain protein of Saccharomyces cerevisiae, Ede1p, involved in endocytosis. J. Cell Sci. 113: 3309-3319 [Abstract]  
  • Tanaka, K., Nishide, J., Okazaki, K., Kato, H., Niwa, O., Nakagawa, T., Matsuda, H., Kawamukai, M., Murakami, Y. (1999). Characterization of a Fission Yeast SUMO-1 Homologue, Pmt3p, Required for Multiple Nuclear Events, Including the Control of Telomere Length and Chromosome Segregation. Mol. Cell. Biol. 19: 8660-8672 [Abstract] [Full Text]  
  • Ehrenhofer-Murray, A. E., Kamakaka, R. T., Rine, J. (1999). A Role for the Replication Proteins PCNA, RF-C, Polymerase {epsilon} and Cdc45 in Transcriptional Silencing in Saccharomyces cerevisiae. Genetics 153: 1171-1182 [Abstract] [Full Text]  
  • Kim, S., Benguria, A., Lai, C.-Y., Jazwinski, S. M. (1999). Modulation of Life-span by Histone Deacetylase Genes in Saccharomyces cerevisiae. Mol. Biol. Cell 10: 3125-3136 [Abstract] [Full Text]  
  • Sun, Z.-W., Hampsey, M. (1999). A General Requirement for the Sin3-Rpd3 Histone Deacetylase Complex in Regulating Silencing in Saccharomyces cerevisiae. Genetics 152: 921-932 [Abstract] [Full Text]  
  • Dua, R., Edwards, S., Levy, D. L., Campbell, J. L. (2000). Subunit Interactions within the Saccharomyces cerevisiae DNA Polymerase epsilon (pol epsilon ) Complex. DEMONSTRATION OF A DIMERIC pol epsilon. J. Biol. Chem. 275: 28816-28825 [Abstract] [Full Text]  
  • Loewith, R., Smith, J. S., Meijer, M., Williams, T. J., Bachman, N., Boeke, J. D., Young, D. (2001). Pho23 Is Associated with the Rpd3 Histone Deacetylase and Is Required for Its Normal Function in Regulation of Gene Expression and Silencing in Saccharomyces cerevisiae. J. Biol. Chem. 276: 24068-24074 [Abstract] [Full Text]  
  • Conconi, A., Bespalov, V. A., Smerdon, M. J. (2002). Transcription-coupled repair in RNA polymerase I-transcribed genes of yeast. Proc. Natl. Acad. Sci. USA 99: 649-654 [Abstract] [Full Text]  
  • Bernstein, B. E., Tong, J. K., Schreiber, S. L. (2000). Genomewide studies of histone deacetylase function in yeast. Proc. Natl. Acad. Sci. USA 97: 13708-13713 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»