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HDA6 histone deacetylase 6 [ Arabidopsis thaliana (thale cress) ]

Gene ID: 836431, updated on 18-Sep-2024

Summary

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Official Symbol
HDA6
Official Full Name
histone deacetylase 6
Primary source
TAIR:AT5G63110
Locus tag
AT5G63110
See related
Araport:AT5G63110
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
ATHDA6; AXE1; histone deacetylase 6; HISTONE DEACETYLASE 6; MDC12.7; MDC12_7; RNA-MEDIATED TRANSCRIPTIONAL SILENCING 1; RPD3B; RTS1; SIL1
Summary
RPD3-like histone deacetylase. HDA6 mutations specifically increase the expression of auxin-responsive transgenes, suggesting a role in transgene silencing.
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Genomic context

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See HDA6 in Genome Data Viewer
Location:
chromosome: 5
Exon count:
6
Sequence:
Chromosome: 5; NC_003076.8 (25315506..25318347, complement)

Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene Plant thionin family protein Neighboring gene Lateral organ boundaries (LOB) domain family protein Neighboring gene S-adenosyl-L-methionine-dependent methyltransferases superfamily protein Neighboring gene P-loop containing nucleoside triphosphate hydrolases superfamily protein Neighboring gene Octicosapeptide/Phox/Bem1p family protein

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Arabidopsis HDA6 is required for freezing tolerance. To TK, et al. Biochem Biophys Res Commun, 2011 Mar 18. PMID 21329671
  2. HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. Wu K, et al. J Exp Bot, 2008. PMID 18212027
  3. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. Aufsatz W, et al. EMBO J, 2002 Dec 16. PMID 12486004, Free PMC Article
  4. Involvement of Arabidopsis histone deacetylase HDA6 in ABA and salt stress response. Chen LT, et al. J Exp Bot, 2010 Jul. PMID 20519338, Free PMC Article
  5. HISTONE DEACETYLASE 6 represses pathogen defence responses in Arabidopsis thaliana. Wang Y, et al. Plant Cell Environ, 2017 Dec. PMID 28770584

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ESR2-HDA6 complex negatively regulates auxin biosynthesis to delay callus initiation in Arabidopsis leaf explants during tissue culture.
    Title: ESR2-HDA6 complex negatively regulates auxin biosynthesis to delay callus initiation in Arabidopsis leaf explants during tissue culture.
  2. HDA6 modulates Arabidopsis pavement cell morphogenesis through epigenetic suppression of ROP6 GTPase expression and signaling.
    Title: HDA6 modulates Arabidopsis pavement cell morphogenesis through epigenetic suppression of ROP6 GTPase expression and signaling.
  3. Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response.
    Title: Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response.
  4. MSI1 and HDA6 function interdependently to control flowering time via chromatin modifications.
    Title: MSI1 and HDA6 function interdependently to control flowering time via chromatin modifications.
  5. HISTONE DEACETYLASE 6 suppresses salicylic acid biosynthesis to repress autoimmunity.
    Title: HISTONE DEACETYLASE 6 suppresses salicylic acid biosynthesis to repress autoimmunity.
  6. A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis.
    Title: A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis.
  7. Arabidopsis SUMO E3 Ligase SIZ1 Interacts with HDA6 and Negatively Regulates HDA6 Function during Flowering.
    Title: Arabidopsis SUMO E3 Ligase SIZ1 Interacts with HDA6 and Negatively Regulates HDA6 Function during Flowering.
  8. AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana.
    Title: AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana.
  9. HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis.
    Title: HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis.
  10. SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis.
    Title: SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis.
Submit: New GeneRIF Correction See all GeneRIFs (37)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

NM_125705.4

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables histone deacetylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 zinc ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within embryo development ending in seed dormancy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within post-transcriptional gene silencing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of timing of transition from vegetative to reproductive phase IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within response to abscisic acid IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within response to salt stress IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within seed maturation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within vegetative to reproductive phase transition of meristem IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of Sin3-type complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chloroplast envelope HDA 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 6
NP_201116.1
  • histone deacetylase 6 (HDA6); FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: response to salt stress, gene silencing, posttranscriptional gene silencing, response to abscisic acid stimulus, histone deacetylation; LOCATED IN: nucleus, chloroplast envelope; 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 8759 Blast hits to 8549 proteins in 1444 species: Archae - 221; Bacteria - 3162; Metazoa - 1525; Fungi - 546; Plants - 480; Viruses - 0; Other Eukaryotes - 2825 (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_003076.8 Reference assembly

    Range
    25315506..25318347 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_125705.4 → NP_201116.1  histone deacetylase 6 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_201116.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9FML2, Q9FVE5
    UniProtKB/TrEMBL
    A0A178URK5, A0A384KCB8, B1PXB9, B1PXC1
    Conserved Domains (1) summary
    cd09991
    Location:24 → 331
    HDAC_classI; Class I histone deacetylases
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9FML2.1

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