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HDA9 histone deacetylase 9 [ Arabidopsis thaliana (thale cress) ]

Gene ID: 823594, updated on 18-Sep-2024

Summary

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Official Symbol
HDA9
Official Full Name
histone deacetylase 9
Primary source
TAIR:AT3G44680
Locus tag
AT3G44680
See related
Araport:AT3G44680
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Arabidopsis thaliana (ecotype: Columbia)
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as
AtHDA9; HDA09; HISTONE DEACETYLASE; histone deacetylase 9
Summary
Class I RPD3 type protein
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Genomic context

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See HDA9 in Genome Data Viewer
Location:
chromosome: 3
Exon count:
14
Sequence:
Chromosome: 3; NC_003074.8 (16226519..16230009, complement)

Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene tyrosine phosphatase Neighboring gene histone deacetylase 10 Neighboring gene Disease resistance protein (TIR-NBS-LRR class) family Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003074.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. HISTONE DEACETYLASE 9 represses seedling traits in Arabidopsis thaliana dry seeds. van Zanten M, et al. Plant J, 2014 Nov. PMID 25146719
  2. Histone deacetylase HDA9 negatively regulates salt and drought stress responsiveness in Arabidopsis. Zheng Y, et al. J Exp Bot, 2016 Mar. PMID 26733691
  3. The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation. de Rooij PGH, et al. J Exp Bot, 2020 Oct 22. PMID 32687569, Free PMC Article
  4. HISTONE DEACETYLASE 9 Functions with Polycomb Silencing to Repress FLOWERING LOCUS C Expression. Zeng X, et al. Plant Physiol, 2020 Jan. PMID 31641076, Free PMC Article
  5. HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis. Yang J, et al. J Integr Plant Biol, 2023 Jan. PMID 36165397

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The Mediator complex subunit MED25 interacts with HDA9 and PIF4 to regulate thermomorphogenesis.
    Title: The Mediator complex subunit MED25 interacts with HDA9 and PIF4 to regulate thermomorphogenesis.
  2. HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis.
    Title: HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis.
  3. The HDA9-HY5 module epigenetically regulates flowering time in Arabidopsis thaliana.
    Title: The HDA9-HY5 module epigenetically regulates flowering time in Arabidopsis thaliana.
  4. The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation.
    Title: The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation.
  5. HOS15 and HDA9 negatively regulate immunity through histone deacetylation of intracellular immune receptor NLR genes in Arabidopsis.
    Title: HOS15 and HDA9 negatively regulate immunity through histone deacetylation of intracellular immune receptor NLR genes in Arabidopsis.
  6. HISTONE DEACETYLASE 9 Functions with Polycomb Silencing to Repress FLOWERING LOCUS C Expression.
    Title: HISTONE DEACETYLASE 9 Functions with Polycomb Silencing to Repress FLOWERING LOCUS C Expression.
  7. Histone Deacetylase HDA9 and WRKY53 Transcription Factor Are Mutual Antagonists in Regulation of Plant Stress Response.
    Title: Histone Deacetylase HDA9 and WRKY53 Transcription Factor Are Mutual Antagonists in Regulation of Plant Stress Response.
  8. HY5-HDA9 Module Transcriptionally Regulates Plant Autophagy in Response to Light-to-Dark Conversion and Nitrogen Starvation.
    Title: HY5-HDA9 Module Transcriptionally Regulates Plant Autophagy in Response to Light-to-Dark Conversion and Nitrogen Starvation.
  9. HDA9 mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance.
    Title: HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion.
  10. HDA9 specifically binds to the TOC1 promoter through the interaction with ELF3. The EC-HDA9 complex promotes H3 deacetylation at the TOC1 locus, contributing to suppressing TOC1 expression during the night.
    Title: The EC-HDA9 complex rhythmically regulates histone acetylation at the TOC1 promoter in Arabidopsis.
Submit: New GeneRIF Correction See all GeneRIFs (18)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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NM_114336.4

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables histone deacetylase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone deacetylase activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within negative regulation of seed germination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of leaf senescence IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISM
Inferred from Sequence Model
more info
  

General protein information

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Preferred Names
histone deacetylase 9
NP_190054.2
  • histone deacetylase 9 (HDA9); FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: histone deacetylation; LOCATED IN: nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Histone deacetylase (InterPro:IPR003084), Histone deacetylase superfamily (InterPro:IPR000286); BEST Arabidopsis thaliana protein match is: histone deacetylase 1 (TAIR:AT4G38130.1); Has 8723 Blast hits to 8511 proteins in 1453 species: Archae - 219; Bacteria - 3191; Metazoa - 1512; Fungi - 548; Plants - 472; Viruses - 0; Other Eukaryotes - 2781 (source: NCBI BLink).

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

  1. NC_003074.8 Reference assembly

    Range
    16226519..16230009 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_114336.4 → NP_190054.2  histone deacetylase 9 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_190054.2

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q8H0W2, Q9M1N6
    UniProtKB/TrEMBL
    A0A5S9XHU0, A0A654FCX3
    Conserved Domains (2) summary
    PTZ00063
    Location:6 → 396
    PTZ00063; histone deacetylase; Provisional
    cl17011
    Location:6 → 384
    Arginase_HDAC; Arginase-like and histone-like hydrolases
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8H0W2.1

Gene LinkOut

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