HDA15 histone deacetylase 15 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: HDA15
Official Full Name: histone deacetylase 15
Primary source: TAIR:AT3G18520
Locus tag: AT3G18520
See related: Araport:AT3G18520
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: ATHDA15; histone deacetylase 15
Summary: Encodes a protein with similarity to histone deacetylases. Plants expressing RNAi directed against this gene show a moderate resistance to agrobacterium-mediated root transformation.
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Genomic context

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See HDA15 in Genome Data Viewer

Location:: chromosome: 3

Exon count:: 18

Sequence:: Chromosome: 3; NC_003074.8 (6361159..6365705)

Chromosome 3 - NC_003074.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003074.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

AtHDA15 binds directly to COP1 positively regulating photomorphogenesis.
Title: AtHDA15 binds directly to COP1 positively regulating photomorphogenesis.
HY5 Interacts with the Histone Deacetylase HDA15 to Repress Hypocotyl Cell Elongation in Photomorphogenesis.
Title: HY5 Interacts with the Histone Deacetylase HDA15 to Repress Hypocotyl Cell Elongation in Photomorphogenesis.
The hda15 mutation resulted in upregulation of many warm temperature-responsive as well as metabolic genes at 20 and 27 degrees C. HDA15 is associated with thermosensory mark genes at 20 degrees C and that the association is decreased after shifting to 27 degrees C, indicating that HDA15 is a direct repressor of plant thermal-responsive genes at normal temperature.
Title: Arabidopsis histone deacetylase HDA15 directly represses plant response to elevated ambient temperature.
MYB96 interacts with the histone modifier HDA15 to suppress negative regulators of early abscisic acid signaling
Title: MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis.
Genetic evidence indicated that HDA15 acts downstream of PHYB and represses seed germination in the dark dependent on PIF1.
Title: Identification of HDA15-PIF1 as a key repression module directing the transcriptional network of seed germination in the dark.
indicate that HDA15 and PIF3 cotarget to the genes involved in chlorophyll biosynthesis and photosynthesis in the dark and repress gene expression.
Title: PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings.
HDA15 shuttles in and out of the nucleus upon light exposure.
Title: Subcellular localization of class II HDAs in Arabidopsis thaliana: nucleocytoplasmic shuttling of HDA15 is driven by light.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001338339.1

Supported by ESTs:

NM_001338340.1

Supported by ESTs:

NM_112737.3

Supported by ESTs:

NM_180278.3

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables histone deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
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 zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-mediated transformation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression, epigenetic	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within photomorphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of abscisic acid-activated signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of photomorphogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in protein homotetramerization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of photosynthesis, light reaction	IDA Inferred from Direct Assay more info	PubMed
involved_in response to heat	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 nucleolus	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 15

NP_566612.1

histone deacetylase 15 (HDA15); FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: DNA mediated transformation, histone deacetylation; LOCATED IN: intracellular; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, RanBP2-type (InterPro:IPR001876), Histone deacetylase superfamily (InterPro:IPR000286); BEST Arabidopsis thaliana protein match is: histone deacetylase 5 (TAIR:AT5G61060.1); Has 9240 Blast hits to 9035 proteins in 1456 species: Archae - 223; Bacteria - 3186; Metazoa - 1508; Fungi - 639; Plants - 555; Viruses - 0; Other Eukaryotes - 3129 (source: NCBI BLink).

NP_850609.2

histone deacetylase 15 (HDA15); FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: DNA mediated transformation, histone deacetylation; LOCATED IN: intracellular; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, RanBP2-type (InterPro:IPR001876), Histone deacetylase superfamily (InterPro:IPR000286); BEST Arabidopsis thaliana protein match is: histone deacetylase 5 (TAIR:AT5G61060.1); Has 9308 Blast hits to 9105 proteins in 1476 species: Archae - 223; Bacteria - 3234; Metazoa - 1500; Fungi - 655; Plants - 551; Viruses - 0; Other Eukaryotes - 3145 (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

NC_003074.8 Reference assembly

Range

6361159..6365705

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_112737.3 → NP_566612.1 histone deacetylase 15 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_566612.1

Status: REVIEWED

UniProtKB/Swiss-Prot

F4J8S2, Q3EB46, Q8GXJ1, Q8LD93, Q9LS38

UniProtKB/TrEMBL

A0A654F8G9

Conserved Domains (1) summary

cd09992
Location:171 → 461

HDAC_classII; Histone deacetylases and histone-like deacetylases, classII
NM_001338339.1 → NP_001326233.1 histone deacetylase 15 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1I9LNM9, A0A654F8G9
NM_001338340.1 → NP_001326232.1 histone deacetylase 15 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1I9LNM8, A0A654F8G9
NM_180278.3 → NP_850609.2 histone deacetylase 15 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_850609.2

Status: REVIEWED

UniProtKB/TrEMBL

A0A654F8G9, F4J8S1

Conserved Domains (1) summary

cd09992
Location:171 → 461

HDAC_classII; Histone deacetylases and histone-like deacetylases, classII