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SET3 histone-binding protein SET3 [ Saccharomyces cerevisiae S288C ]

Gene ID: 853900, updated on 12-Aug-2025
Official Symbol
SET3
Official Full Name
histone-binding protein SET3
Primary source
SGD:S000001737
Locus tag
YKR029C
See related
AllianceGenome:SGD:S000001737; FungiDB:YKR029C; VEuPathDB:YKR029C
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Saccharomyces cerevisiae S288C (strain: S288C)
Lineage
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary
Enables methylated histone binding activity. Involved in negative regulation of meiotic nuclear division; protein methylation; and regulation of DNA-templated transcription. Acts upstream of or within transcription initiation-coupled chromatin remodeling. Part of Set3 complex. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 23. Orthologous to human SETD5 (SET domain containing 5). [provided by Alliance of Genome Resources, Apr 2025]
Orthologs
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See SET3 in Genome Data Viewer
Location:
chromosome: XI
Exon count:
1
Sequence:
Chromosome: XI; NC_001143.9 (497578..499833, complement)

Chromosome XI - NC_001143.9Genomic Context describing neighboring genes Neighboring gene Bch2p Neighboring gene Sap190p Neighboring gene Gmh1p Neighboring gene phospholipase D

Genomic Sequence:
NC_001143.9

Go to nucleotide: Graphics FASTA GenBank

Related articles in PubMed

  1. Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics. Kim T, et al. Cell, 2012 Sep 14. PMID 22959268, Free PMC Article
  2. Expression noise and acetylation profiles distinguish HDAC functions. Weinberger L, et al. Mol Cell, 2012 Jul 27. PMID 22683268, Free PMC Article
  3. Mitotically heritable, RNA polymerase II-independent H3K4 dimethylation stimulates INO1 transcriptional memory. Sump B, et al. Elife, 2022 May 17. PMID 35579426, Free PMC Article
  4. Requirement of Hos2 histone deacetylase for gene activity in yeast. Wang A, et al. Science, 2002 Nov 15. PMID 12434058
  5. Antisense transcription-dependent chromatin signature modulates sense transcript dynamics. Brown T, et al. Mol Syst Biol, 2018 Feb 12. PMID 29440389, Free PMC Article

See all (105) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Structural and functional analysis of the SET3 histone deacetylase complex.
    Title: Structural and functional analysis of the SET3 histone deacetylase complex.
  2. FACT interacts with Set3 HDAC and fine-tunes GAL1 transcription in response to environmental stimulation.
    Title: FACT interacts with Set3 HDAC and fine-tunes GAL1 transcription in response to environmental stimulation.
  3. Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation.
    Title: Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation.
  4. A Prion Epigenetic Switch Establishes an Active Chromatin State.
    Title: A Prion Epigenetic Switch Establishes an Active Chromatin State.
  5. Loss of HOS2 or components of the SET3 complex (SET3C) in which it acts specifically suppressed damage sensitivity and restored esa1 histone H4 acetylation.
    Title: The Set3 Complex Antagonizes the MYST Acetyltransferase Esa1 in the DNA Damage Response.
  6. Unlike activators or repressors that act as an on/off switch of transcription, Set3C instead plays an important role in the timing of transcription response during gene activation or repression.
    Title: Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics.
  7. analysis of distinct activities of the Rpd3(L) and Set3 histone deacetylase complexes
    Title: Expression noise and acetylation profiles distinguish HDAC functions.
  8. Set3 may participate in the dynamic deposition and remodeling of Htz1-containing nucleosomes.
    Title: Genetic analysis implicates the Set3/Hos2 histone deacetylase in the deposition and remodeling of nucleosomes containing H2A.Z.
  9. The Hos2p/Set3p complex (SET3C) is a novel component critical for cell survival in response to secretory stress.
    Title: Hos2p/Set3p deacetylase complex signals secretory stress through the Mpk1p cell integrity pathway.
  10. Hos2 and Set3 function at tRNA genes to promote Ty1 integration
    Title: Hos2 and Set3 promote integration of Ty1 retrotransposons at tRNA genes in Saccharomyces cerevisiae.
Submit: New GeneRIF Correction
Products Interactant Other Gene Complex Source Pubs Description

Homology

Gene Ontology Provided by SGD

Function Evidence Code Pubs
enables histone H3K4me3 reader activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K4me3 reader activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in cellular response to starvation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of meiotic nuclear division IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of meiotic nuclear division IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within transcription initiation-coupled chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of Rpd3L-Expanded complex HDA PubMed 
part_of Rpd3L-Expanded complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Set3 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Set3 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Set3 complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
Preferred Names
histone-binding protein SET3
NP_012954.3
  • Defining member of the SET3 histone deacetylase complex; which is a meiosis-specific repressor of sporulation genes; necessary for efficient transcription by RNAPII; one of two yeast proteins that contains both SET and PHD domains; SET3 has a paralog, SET4, that arose from the whole genome duplication

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_001143.9 Reference assembly

    Range
    497578..499833 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001179819.3 → NP_012954.3  TPA: histone-binding protein SET3

    See identical proteins and their annotated locations for NP_012954.3

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    D6VX94, P36124
    UniProtKB/TrEMBL
    A0A0L8VLQ5, B3LRB2, C8ZCJ3, N1P827
    Conserved Domains (2) summary
    COG2940
    Location:217 → 722
    SET; SET domain-containing protein (function unknown) [General function prediction only]
    cd15550
    Location:119 → 163
    PHD_MLL5; PHD finger found in mixed lineage leukemia 5 (MLL5)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P36124.1

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