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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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