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Gene Review

RPD3  -  Rpd3p

Saccharomyces cerevisiae S288c

Synonyms: Histone deacetylase RPD3, MOF6, N0305, REC3, SDI2, ...
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High impact information on RPD3


Biological context of RPD3

  • GCN5-dependent histone H3 acetylation and RPD3-dependent histone H4 deacetylation have distinct, opposing effects on IME2 transcription, during meiosis and during vegetative growth, in budding yeast [4].
  • The profiles demonstrate that 40% of endogenous genes located within 20 kb of telomeres are down-regulated by RPD3 deletion [5].
  • Finally, bioinformatic analyses indicate that the yeast HDACs RPD3, SIR2, and HDA1 play distinct roles in regulating genes involved in cell cycle progression, amino acid biosynthesis, and carbohydrate transport and utilization, respectively [5].
  • Deletion of RPD3 is not lethal but confers phenotypes identical to those caused by spontaneous mutations [6].
  • Finally, we find that gcn5 and rpd3 single mutants are not defective in meiosis if acetate is absent and respiration is promoted by a metabolically unrelated carbon source [4].

Anatomical context of RPD3


Associations of RPD3 with chemical compounds


Physical interactions of RPD3

  • The Saccharomyces cerevisiae Sin3 transcriptional repressor is part of a large multiprotein complex that includes the Rpd3 histone deacetylase [15].
  • Deletion of RPD3 histone deacetylase causes earlier origin firing and concurrent binding of the replication factor Cdc45p to origins [16].
  • We demonstrate that Rpd3 interacts with both Tup1 and Ssn6 [17].
  • Hog1 interacts physically with Rpd3 in vivo and in vitro and, on stress, targets the deacetylase to specific osmostress-responsive genes [18].
  • Taken together, these data provide evidence that during anaerobiosis, the Rpd3 complex acts at the DAN1 promoter to antagonize the chromatin-mediated repression caused by Mot3 and Rox1 and that chromatin remodeling by Swi/Snf is necessary for normal expression [19].

Regulatory relationships of RPD3

  • In this paper we show that full activation of the HO promoter in vivo requires the Gcn5 protein and that defects in this protein can be suppressed by deletion of the RPD3 gene, which encodes a histone deacetylase [20].
  • Using a genetic screen, we isolated three TATA-binding protein (TBP) mutants that increase transcription from promoters that are repressed by the Cyc8-Tup1 or Sin3-Rpd3 corepressors or that lack an enhancer element, but not from an equivalently weak promoter with a mutated TATA element [21].
  • Ume1p represses meiotic gene transcription in Saccharomyces cerevisiae through interaction with the histone deacetylase Rpd3p [22].
  • Role of Histone Deacetylase Rpd3 in Regulating rRNA Gene Transcription and Nucleolar Structure in Yeast [23].

Other interactions of RPD3

  • The HDA1 protein (a subunit of the HDA activity) shares sequence similarity to RPD3, a factor required for optimal transcription of certain yeast genes [24].
  • These and other results suggest that Gcn5 and Rpd3 play distinct roles, modulating transcription initiation in opposite directions under two different cellular conditions [4].
  • We show that the extent of transcriptional regulation of many, apparently unrelated, genes in Saccharomyces cerevisiae is dependent on RPD1 (and RPD3 [M. Vidal and R. F. Gaber, Mol. Cell. Biol. 11:6317-6327, 1991]) [25].
  • Furthermore, similar levels of HDAC activity were detected in immunoprecipitates of HA-Pho23, HA-Rpd3, or HA-Sap30 [26].
  • The ability of Ume6p, Sin3p and Rpd3p to differentially regulate expression of the phospholipid biosynthetic genes affects phospholipid composition [12].

Analytical, diagnostic and therapeutic context of RPD3

  • Deletion of the RPD3 gene extended life span, and there was no additive effect of caloric restriction [27].
  • We showed that Myc-Raf60 co-fractionated with Rpd3-TAP by gel filtration chromatography, and both Myc-Rpd3 and Sin3 co-immunoprecipitated with HA-Raf60 [28].
  • To elucidate the mechanism underlying RPD3-mediated repression, we screened all promoters in yeast for occupancy by Rpd3p before and after treatment with rapamycin [29].


  1. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Keogh, M.C., Kurdistani, S.K., Morris, S.A., Ahn, S.H., Podolny, V., Collins, S.R., Schuldiner, M., Chin, K., Punna, T., Thompson, N.J., Boone, C., Emili, A., Weissman, J.S., Hughes, T.R., Strahl, B.D., Grunstein, M., Greenblatt, J.F., Buratowski, S., Krogan, N.J. Cell (2005) [Pubmed]
  2. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Robyr, D., Suka, Y., Xenarios, I., Kurdistani, S.K., Wang, A., Suka, N., Grunstein, M. Cell (2002) [Pubmed]
  3. Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Kurdistani, S.K., Robyr, D., Tavazoie, S., Grunstein, M. Nat. Genet. (2002) [Pubmed]
  4. GCN5-dependent histone H3 acetylation and RPD3-dependent histone H4 deacetylation have distinct, opposing effects on IME2 transcription, during meiosis and during vegetative growth, in budding yeast. Burgess, S.M., Ajimura, M., Kleckner, N. Proc. Natl. Acad. Sci. U.S.A. (1999) [Pubmed]
  5. Genomewide studies of histone deacetylase function in yeast. Bernstein, B.E., Tong, J.K., Schreiber, S.L. Proc. Natl. Acad. Sci. U.S.A. (2000) [Pubmed]
  6. RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae. Vidal, M., Gaber, R.F. Mol. Cell. Biol. (1991) [Pubmed]
  7. A role for Sds3p, a component of the Rpd3p/Sin3p deacetylase complex, in maintaining cellular integrity in Saccharomyces cerevisiae. Vannier, D., Damay, P., Shore, D. Mol. Genet. Genomics (2001) [Pubmed]
  8. Functional analysis of the SIN3-histone deacetylase RPD3-RbAp48-histone H4 connection in the Xenopus oocyte. Vermaak, D., Wade, P.A., Jones, P.L., Shi, Y.B., Wolffe, A.P. Mol. Cell. Biol. (1999) [Pubmed]
  9. The multi-KH domain protein of Saccharomyces cerevisiae Scp160p contributes to the regulation of telomeric silencing. Marsellach, F.X., Huertas, D., Azorín, F. J. Biol. Chem. (2006) [Pubmed]
  10. An 8.2 kb DNA segment from chromosome XIV carries the RPD3 and PAS8 genes as well as the Saccharomyces cerevisiae homologue of the thiamine-repressed nmt1 gene and a chromosome III-duplicated gene for a putative aryl-alcohol dehydrogenase. Van Dyck, L., Pascual-Ahuir, A., Purnelle, B., Goffeau, A. Yeast (1995) [Pubmed]
  11. Developmentally regulated rpd3p homolog specific to the transcriptionally active macronucleus of vegetative Tetrahymena thermophila. Wiley, E.A., Ohba, R., Yao, M.C., Allis, C.D. Mol. Cell. Biol. (2000) [Pubmed]
  12. Combinatorial regulation of phospholipid biosynthetic gene expression by the UME6, SIN3 and RPD3 genes. Elkhaimi, M., Kaadige, M.R., Kamath, D., Jackson, J.C., Biliran, H., Lopes, J.M. Nucleic Acids Res. (2000) [Pubmed]
  13. Regulation of gene expression by glucose in Saccharomyces cerevisiae: a role for ADA2 and ADA3/NGG1. Wu, M., Newcomb, L., Heideman, W. J. Bacteriol. (1999) [Pubmed]
  14. An inhibitor-resistant histone deacetylase in the plant pathogenic fungus Cochliobolus carbonum. Brosch, G., Dangl, M., Graessle, S., Loidl, A., Trojer, P., Brandtner, E.M., Mair, K., Walton, J.D., Baidyaroy, D., Loidl, P. Biochemistry (2001) [Pubmed]
  15. Roles for the Saccharomyces cerevisiae SDS3, CBK1 and HYM1 genes in transcriptional repression by SIN3. Dorland, S., Deegenaars, M.L., Stillman, D.J. Genetics (2000) [Pubmed]
  16. Histone acetylation regulates the time of replication origin firing. Vogelauer, M., Rubbi, L., Lucas, I., Brewer, B.J., Grunstein, M. Mol. Cell (2002) [Pubmed]
  17. Tup1-Ssn6 interacts with multiple class I histone deacetylases in vivo. Davie, J.K., Edmondson, D.G., Coco, C.B., Dent, S.Y. J. Biol. Chem. (2003) [Pubmed]
  18. The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. De Nadal, E., Zapater, M., Alepuz, P.M., Sumoy, L., Mas, G., Posas, F. Nature (2004) [Pubmed]
  19. Direct role for the Rpd3 complex in transcriptional induction of the anaerobic DAN/TIR genes in yeast. Sertil, O., Vemula, A., Salmon, S.L., Morse, R.H., Lowry, C.V. Mol. Cell. Biol. (2007) [Pubmed]
  20. Mutations in chromatin components suppress a defect of Gcn5 protein in Saccharomyces cerevisiae. Pérez-Martín, J., Johnson, A.D. Mol. Cell. Biol. (1998) [Pubmed]
  21. TATA-binding protein mutants that increase transcription from enhancerless and repressed promoters in vivo. Geisberg, J.V., Struhl, K. Mol. Cell. Biol. (2000) [Pubmed]
  22. Ume1p represses meiotic gene transcription in Saccharomyces cerevisiae through interaction with the histone deacetylase Rpd3p. Mallory, M.J., Strich, R. J. Biol. Chem. (2003) [Pubmed]
  23. Role of Histone Deacetylase Rpd3 in Regulating rRNA Gene Transcription and Nucleolar Structure in Yeast. Oakes, M.L., Siddiqi, I., French, S.L., Vu, L., Sato, M., Aris, J.P., Beyer, A.L., Nomura, M. Mol. Cell. Biol. (2006) [Pubmed]
  24. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Rundlett, S.E., Carmen, A.A., Kobayashi, R., Bavykin, S., Turner, B.M., Grunstein, M. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  25. RPD1 (SIN3/UME4) is required for maximal activation and repression of diverse yeast genes. Vidal, M., Strich, R., Esposito, R.E., Gaber, R.F. Mol. Cell. Biol. (1991) [Pubmed]
  26. 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. Loewith, R., Smith, J.S., Meijer, M., Williams, T.J., Bachman, N., Boeke, J.D., Young, D. J. Biol. Chem. (2001) [Pubmed]
  27. Distinct roles of processes modulated by histone deacetylases Rpd3p, Hda1p, and Sir2p in life extension by caloric restriction in yeast. Jiang, J.C., Wawryn, J., Shantha Kumara, H.M., Jazwinski, S.M. Exp. Gerontol. (2002) [Pubmed]
  28. Raf60, a novel component of the Rpd3 histone deacetylase complex required for Rpd3 activity in Saccharomyces cerevisiae. Colina, A.R., Young, D. J. Biol. Chem. (2005) [Pubmed]
  29. Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Humphrey, E.L., Shamji, A.F., Bernstein, B.E., Schreiber, S.L. Chem. Biol. (2004) [Pubmed]
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