SET3 histone-binding protein SET3 [Saccharomyces cerevisiae S288C] - Gene

Summary

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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, Dec 2024]
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Genomic context

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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_001143.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001143.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Structural and functional analysis of the SET3 histone deacetylase complex.
Title: Structural and functional analysis of the SET3 histone deacetylase complex.
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.
Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation.
Title: Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation.
A Prion Epigenetic Switch Establishes an Active Chromatin State.
Title: A Prion Epigenetic Switch Establishes an Active Chromatin State.
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.
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.
analysis of distinct activities of the Rpd3(L) and Set3 histone deacetylase complexes
Title: Expression noise and acetylation profiles distinguish HDAC functions.
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.
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.
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.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein methylation	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 more info	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

General protein information

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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

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_001143.9 Reference assembly

Range

497578..499833 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179819.3 → NP_012954.3 TPA: histone-binding protein SET3 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_012954.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VX94, P36124

UniProtKB/TrEMBL

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)