HDA1 histone deacetylase HDA1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: HDA1
Gene description: histone deacetylase HDA1
Primary source: FungiDB:YNL021W
Locus tag: YNL021W
See related: SGD:S000004966; AllianceGenome:SGD:S000004966; VEuPathDB:YNL021W
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 chromatin binding activity. Contributes to histone deacetylase activity. Involved in gene silencing by RNA; histone deacetylation; and regulation of transcription, DNA-templated. Part of HDA1 complex. Human ortholog(s) of this gene implicated in chondrodysplasia with platyspondyly, distinctive brachydactyly, hydrocephaly, and microphthalmia. Orthologous to several human genes including HDAC6 (histone deacetylase 6). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See HDA1 in Genome Data Viewer

Location:: chromosome: XIV

Exon count:: 1

Sequence:: Chromosome: XIV; NC_001146.8 (593227..595347)

Chromosome XIV - NC_001146.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001146.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae.
Title: Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae.
Inactivating histone deacetylase HDA promotes longevity by mobilizing trehalose metabolism.
Title: Inactivating histone deacetylase HDA promotes longevity by mobilizing trehalose metabolism.
Rpd3L and Hda1 histone deacetylase complexes contribute to the repair of replication-born double strand breaks by facilitating cohesin loading.
Title: Rpd3L and Hda1 histone deacetylases facilitate repair of broken forks by promoting sister chromatid cohesion.
Hda1C specifically deacetylates histone H4, but not histone H3, at hyperactive genes to partially inhibit elongation. Hda1C may modulate elongation by specifically deacetylating histone H4 at highly transcribed regions.
Title: Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast.
These results suggested that Bdf1p likely regulated MEF1 expression negatively by regulating HDA1 positively
Title: Regulation of Saccharomyces cerevisiae MEF1 by Hda1p affects salt resistance of bdf1Δ mutant.
Mutation or inhibition of yeast Rpd3L or Hda1 suppressed up to 90% of CTG*CAG repeat expansions.
Title: Histone deacetylase complexes promote trinucleotide repeat expansions.
These structural and functional analyses of the budding yeast class II Hda1 HDAC complex provide insight into DNA recognition and deacetylation of histones in nucleosomes.
Title: Structural and functional studies of the yeast class II Hda1 histone deacetylase complex.
These findings suggest that the Hda1 deacetylase complex affects histone function at the centromere and that Hda3 has a distinctive participation in chromosome segregation.
Title: Suppressor analysis of a histone defect identifies a new function for the hda1 complex in chromosome segregation.
Hda1 partially represses roughly 30% of Tup1-repressed genes, whereas Srb10 kinase activity contributes to the repression of approximately 15% of Tup1-repressed genes.
Title: Promoter-dependent roles for the Srb10 cyclin-dependent kinase and the Hda1 deacetylase in Tup1-mediated repression in Saccharomyces cerevisiae.

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Pathways from PubChem

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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 chromatin binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to histone deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables transcription factor binding	IBA Inferred from Biological aspect of Ancestor more info
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 epigenetic regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by transcription factor localization	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of HDA1 complex	IDA Inferred from Direct Assay more info	PubMed
part_of HDA1 complex	IPI Inferred from Physical Interaction more info	PubMed
part_of histone deacetylase complex	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: histone deacetylase HDA1

NP_014377.1

EC 3.5.1.98

Catalytic subunit of class II HDA1 histone deacetylase complex; role in azole resistance via Hsp90p, and in heat shock response; Hda1p interacts with Hda2p-Hda3p subcomplex to form an active tetramer; deletion increases histone H2B, H3 and H4 acetylation; the HDA1 histone deacetylase complex regulates aging through trehalose metabolism

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_001146.8 Reference assembly

Range

593227..595347

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001182860.1 → NP_014377.1 TPA: histone deacetylase HDA1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014377.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W1F8, P53973

UniProtKB/TrEMBL

A0A6A5Q545, A6ZS47, B3LNP4, C7GWN8, C8ZFJ7, G2WM72, N1NWQ4

Conserved Domains (2) summary

cd11600
Location:81 → 403

HDAC_Clr3; Class II Histone deacetylase Clr3 and similar proteins

pfam09757
Location:457 → 698

Arb2; Arb2 domain