RPD3/YNL330C Summary Help

Standard Name RPD3 1
Systematic Name YNL330C
Alias REC3 2 , SDI2 3 , SDS6 4 , 5 , MOF6 6
Feature Type ORF, Verified
Description Histone deacetylase, component of both the Rpd3S and Rpd3L complexes; regulates transcription, silencing, autophagy and other processes by influencing chromatin remodeling; forms at least two different complexes which have distinct functions and members; Rpd3(L) recruitment to the subtelomeric region is regulated by interaction with the arginine methyltransferase, Hmt1p (7, 8, 9, 10, 11, 12, 13, 14, 15, 16 and see Summary Paragraph)
Name Description Reduced Potassium Dependency 1
Chromosomal Location
ChrXIV:19302 to 18001 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -237 cM
Gene Ontology Annotations All RPD3 GO evidence and references
  View Computational GO annotations for RPD3
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Targets 307 genes
Regulators 3 genes
Classical genetics
Large-scale survey
1100 total interaction(s) for 725 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 146
  • Affinity Capture-RNA: 4
  • Affinity Capture-Western: 42
  • Biochemical Activity: 2
  • Co-localization: 4
  • Co-purification: 1
  • Reconstituted Complex: 5
  • Two-hybrid: 3

Genetic Interactions
  • Dosage Growth Defect: 4
  • Dosage Lethality: 255
  • Dosage Rescue: 2
  • Negative Genetic: 258
  • Phenotypic Enhancement: 30
  • Phenotypic Suppression: 39
  • Positive Genetic: 81
  • Synthetic Growth Defect: 102
  • Synthetic Lethality: 66
  • Synthetic Rescue: 56

Expression Summary
Length (a.a.) 433
Molecular Weight (Da) 48,904
Isoelectric Point (pI) 5.28
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrXIV:19302 to 18001 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -237 cM
Last Update Coordinates: 1996-07-31 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..1302 19302..18001 1996-07-31 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000005274

RPD3 encodes a histone deacetylase (7). Covalent modifications of histones, including acetylation and deacetylation, are implicated in transcriptional regulation in yeast and other eukaryotes (reviewed in 17 and 18). Rpd3p, Sin3p and Ume1p form the core of the Sin3 complex, a class I histone deacetylase complex (HDAC) that is conserved, in some form, from yeast to mammals (for review see 19 and 20). In fungi, two functionally distinct Sin3 complexes, Rpd3L and Rpd3S, have been characterized, both of which may contribute to transcriptional regulation (21, 8, 9, 13 and references therein).The larger, Rpd3L (1.2 MDA), is required for the heat stress response (14) and has been demonstrated to be involved in Sir2-mediated silencing (11) and replication origin firing (12). The smaller, Rpd3S (0.9 MDa), interacts with Set2p-methylated histones and may contribute to transcription elongation (21, 9). Other Rpd3p- or Sin3p-containing complexes have also been isolated (22) and it is hypothesized that some core HDAC components are shared between complexes with different functions (for review see 19 and 20). A second histone deactylase, Hda1p, shows sequence similarity to Rpd3p but is found in a complex distinct from the complexes containing Rpd3p (7); the Hda1p-containing and Rpd3p-containing complexes affect transcription of distinct, partially overlapping sets of genes (7, 18). Deletion of RPD3 increases histone acetylation in vivo, increases telomeric repression of transcription (7), and extends life span (23). In diploids, mutations in RPD3 cause defects in mitotic recombination and sporulation (2), and the recombination mutant rec3-1 (24) has been shown to be allelic to RPD3 (2). Three more histone deactylases, Hos1p, Hos2p, and Hos3p, have been identified in yeast; they share sequence similarity with Rpd3p and Hda1p but are less well characterized (7).

Last updated: 2010-07-20 Contact SGD

References cited on this page View Complete Literature Guide for RPD3
1) Vidal M, et al.  (1990) Direct selection for mutants with increased K+ transport in Saccharomyces cerevisiae. Genetics 125(2):313-20
2) Dora EG, et al.  (1999) RPD3 (REC3) mutations affect mitotic recombination in Saccharomyces cerevisiae. Curr Genet 35(2):68-76
3) Stillman DJ, et al.  (1994) Epistasis analysis of suppressor mutations that allow HO expression in the absence of the yeast SW15 transcriptional activator. Genetics 136(3):781-8
4) Sussel L, et al.  (1993) Epigenetic switching of transcriptional states: cis- and trans-acting factors affecting establishment of silencing at the HMR locus in Saccharomyces cerevisiae. Mol Cell Biol 13(7):3919-28
5) Sussel L, et al.  (1995) Suppressors of defective silencing in yeast: effects on transcriptional repression at the HMR locus, cell growth and telomere structure. Genetics 141(3):873-88
6) Meskauskas A, et al.  (2003) Delayed rRNA processing results in significant ribosome biogenesis and functional defects. Mol Cell Biol 23(5):1602-13
7) Rundlett SE, et al.  (1996) HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A 93(25):14503-8
8) Carrozza MJ, et al.  (2005) Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex. Biochim Biophys Acta 1731(2):77-87; discussion 75-6
9) Carrozza MJ, et al.  (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123(4):581-92
10) Nyswaner KM, et al.  (2008) Chromatin-associated genes protect the yeast genome from ty1 insertional mutagenesis. Genetics 178(1):197-214
11) Zhou J, et al.  (2009) Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation. Nucleic Acids Res 37(11):3699-713
12) Knott SR, et al.  (2009) Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. Genes Dev 23(9):1077-90
13) Kremer SB and Gross DS  (2009) SAGA and Rpd3 Chromatin Modification Complexes Dynamically Regulate Heat Shock Gene Structure and Expression. J Biol Chem 284(47):32914-31
14) Ruiz-Roig C, et al.  (2010) The Rpd3L HDAC complex is essential for the heat stress response in yeast. Mol Microbiol 76(4):1049-62
15) Yi C, et al.  (2012) Function and molecular mechanism of acetylation in autophagy regulation. Science 336(6080):474-7
16) Milliman EJ, et al.  (2012) Recruitment of rpd3 to the telomere depends on the protein arginine methyltransferase hmt1. PLoS One 7(8):e44656
17) Mizzen C, et al.  (1998) Signaling to chromatin through histone modifications: how clear is the signal? Cold Spring Harb Symp Quant Biol 63:469-81
18) Suka N, et al.  (1998) The regulation of gene activity by histones and the histone deacetylase RPD3. Cold Spring Harb Symp Quant Biol 63():391-9
19) Silverstein RA and Ekwall K  (2005) Sin3: a flexible regulator of global gene expression and genome stability. Curr Genet 47(1):1-17
20) Yang XJ and Seto E  (2008) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9(3):206-18
21) Keogh MC, et al.  (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123(4):593-605
22) Shevchenko A, et al.  (2008) Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol 9(11):R167
23) Kim S, et al.  (1999) Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae. Mol Biol Cell 10(10):3125-36
24) Esposito MS and Brown JT  (1990) Conditional hyporecombination mutants of three REC genes of Saccharomyces cerevisiae. Curr Genet 17(1):7-12