HDAC3 (histone deacetylase 3)

Gene

• Entrez ID: 8841
• Gene name: Histone deacetylase 3
• Gene symbol: HDAC3
• Synonyms: HD3, KDAC3, RPD3, RPD3-2
• Chromosome: 5
• Chromosome location: 5q31.3
• Summary: Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene b

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1554216303	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs1554216308	T>C	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT732569	hsa-miR-4286	Immunofluorescence, Luciferase reporter assay, Western blotting	33973278
MIRT734466	hsa-miR-132-3p	Microarray, RNA-seq	31669733
MIRT737020	hsa-miR-193b-3p	Western blotting, qRT-PCR	32098619
MIRT1042435	hsa-miR-1261	CLIP-seq
MIRT1042436	hsa-miR-1915	CLIP-seq
MIRT1042437	hsa-miR-3124-3p	CLIP-seq
MIRT1042438	hsa-miR-324-5p	CLIP-seq
MIRT1042439	hsa-miR-3925-3p	CLIP-seq
MIRT1042440	hsa-miR-3927	CLIP-seq
MIRT1042441	hsa-miR-4257	CLIP-seq
MIRT1042442	hsa-miR-4690-3p	CLIP-seq
MIRT1042443	hsa-miR-4733-5p	CLIP-seq
MIRT1042444	hsa-miR-548ac	CLIP-seq
MIRT1042445	hsa-miR-548ae	CLIP-seq
MIRT1042446	hsa-miR-548aj	CLIP-seq
MIRT1042447	hsa-miR-548am	CLIP-seq
MIRT1042448	hsa-miR-548d-3p	CLIP-seq
MIRT1042449	hsa-miR-548x	CLIP-seq
MIRT1042450	hsa-miR-548z	CLIP-seq
MIRT1042451	hsa-miR-589	CLIP-seq
MIRT1042452	hsa-miR-765	CLIP-seq
MIRT1042453	hsa-miR-766	CLIP-seq
MIRT2008952	hsa-miR-1225-3p	CLIP-seq
MIRT2008953	hsa-miR-1258	CLIP-seq
MIRT2008954	hsa-miR-1321	CLIP-seq
MIRT2008955	hsa-miR-216a	CLIP-seq
MIRT2008956	hsa-miR-216b	CLIP-seq
MIRT2008957	hsa-miR-3127-3p	CLIP-seq
MIRT2008958	hsa-miR-3152-3p	CLIP-seq
MIRT2008959	hsa-miR-3162-5p	CLIP-seq
MIRT2008960	hsa-miR-4694-5p	CLIP-seq
MIRT2008961	hsa-miR-4739	CLIP-seq
MIRT2008962	hsa-miR-4756-5p	CLIP-seq
MIRT2008963	hsa-miR-4762-5p	CLIP-seq
MIRT2008964	hsa-miR-671-5p	CLIP-seq
MIRT1042453	hsa-miR-766	CLIP-seq
MIRT1042436	hsa-miR-1915	CLIP-seq
MIRT2241315	hsa-miR-3936	CLIP-seq
MIRT2241316	hsa-miR-4688	CLIP-seq
MIRT1042452	hsa-miR-765	CLIP-seq
MIRT2437560	hsa-miR-1236	CLIP-seq
MIRT2008956	hsa-miR-216b	CLIP-seq
MIRT2008963	hsa-miR-4762-5p	CLIP-seq
MIRT2437561	hsa-miR-670	CLIP-seq
MIRT2437560	hsa-miR-1236	CLIP-seq
MIRT2008956	hsa-miR-216b	CLIP-seq
MIRT2008963	hsa-miR-4762-5p	CLIP-seq
MIRT2437561	hsa-miR-670	CLIP-seq
MIRT2545021	hsa-miR-1231	CLIP-seq
MIRT2545022	hsa-miR-362-5p	CLIP-seq
MIRT2545023	hsa-miR-4288	CLIP-seq
MIRT2545024	hsa-miR-4742-3p	CLIP-seq
MIRT2545025	hsa-miR-500b	CLIP-seq
MIRT2545026	hsa-miR-501-5p	CLIP-seq
MIRT2545027	hsa-miR-632	CLIP-seq
MIRT2545021	hsa-miR-1231	CLIP-seq
MIRT2545022	hsa-miR-362-5p	CLIP-seq
MIRT2545023	hsa-miR-4288	CLIP-seq
MIRT2545024	hsa-miR-4742-3p	CLIP-seq
MIRT2545025	hsa-miR-500b	CLIP-seq
MIRT2545026	hsa-miR-501-5p	CLIP-seq
MIRT2545027	hsa-miR-632	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
HDAC4	Unknown	11804585
YY1	Unknown	19279113

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000118	Component	Histone deacetylase complex	IBA	21873635
GO:0000118	Component	Histone deacetylase complex	IDA	18326024
GO:0000118	Component	Histone deacetylase complex	TAS	12711221
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IDA	16569215, 18417529, 18854353
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IMP	12628926
GO:0001226	Function	RNA polymerase II transcription corepressor binding	IPI	12535528
GO:0001934	Process	Positive regulation of protein phosphorylation	IDA	25190803
GO:0003682	Function	Chromatin binding	IDA	16569215, 18417529
GO:0003714	Function	Transcription corepressor activity	IDA	16569215, 18417529
GO:0003714	Function	Transcription corepressor activity	IMP	12628926
GO:0004407	Function	Histone deacetylase activity	IBA	21873635
GO:0004407	Function	Histone deacetylase activity	IMP	16924111, 18326024
GO:0004407	Function	Histone deacetylase activity	TAS	12711221
GO:0005515	Function	Protein binding	IPI	10898795, 11006275, 11013263, 11259576, 11641274, 11861901, 15016912, 15194749, 15805470, 16432238, 16461912, 16847267, 16917504, 16924111, 16980585, 17053781, 17075044, 17172643, 17895379, 17956988, 18279852, 18854353, 19409814, 20385135, 21030595, 21258344, 21624135, 21914818, 221
GO:0005634	Component	Nucleus	IDA	18326024, 18347167, 21030595
GO:0005634	Component	Nucleus	TAS	12711221
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	25190803
GO:0005737	Component	Cytoplasm	TAS	12711221
GO:0005794	Component	Golgi apparatus	IDA
GO:0005829	Component	Cytosol	IDA	21030595
GO:0005886	Component	Plasma membrane	IDA
GO:0006325	Process	Chromatin organization	TAS	12711221
GO:0006476	Process	Protein deacetylation	IDA	17172643, 21030595
GO:0007623	Process	Circadian rhythm	TAS
GO:0008134	Function	Transcription factor binding	IPI	16569215
GO:0008134	Function	Transcription factor binding	TAS	12711221
GO:0010832	Process	Negative regulation of myotube differentiation	IMP	10983972
GO:0017053	Component	Transcription repressor complex	IDA	11804585, 12628926, 16569215, 18417529
GO:0019216	Process	Regulation of lipid metabolic process	TAS
GO:0019899	Function	Enzyme binding	IPI	11641274
GO:0030332	Function	Cyclin binding	IPI	18417529
GO:0031398	Process	Positive regulation of protein ubiquitination	ISS
GO:0031647	Process	Regulation of protein stability	IDA	25190803
GO:0032008	Process	Positive regulation of TOR signaling	IMP	25190803
GO:0032041	Function	NAD-dependent histone deacetylase activity (H3-K14 specific)	IEA
GO:0032922	Process	Circadian regulation of gene expression	ISS
GO:0033558	Function	Protein deacetylase activity	IDA	17172643
GO:0042307	Process	Positive regulation of protein import into nucleus	IDA	25190803
GO:0042752	Process	Regulation of circadian rhythm	ISS
GO:0042826	Function	Histone deacetylase binding	IPI	10869435, 12590135, 23867755
GO:0043066	Process	Negative regulation of apoptotic process	TAS	10777477
GO:0045892	Process	Negative regulation of transcription, DNA-templated	IMP	16924111
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA	21873635
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	25190803
GO:0046329	Process	Negative regulation of JNK cascade	IMP	11931768
GO:0051059	Function	NF-kappaB binding	IPI	17785205
GO:0051225	Process	Spindle assembly	IMP	18326024
GO:0070932	Process	Histone H3 deacetylation	IBA	21873635
GO:0070933	Process	Histone H4 deacetylation	IBA	21873635
GO:0071498	Process	Cellular response to fluid shear stress	IDA	25190803
GO:0072686	Component	Mitotic spindle	IDA	18326024
GO:0120162	Process	Positive regulation of cold-induced thermogenesis	ISS	28614293

Other IDs

• MIM: 605166
• HGNC: 4854
• e!Ensembl: ENSG00000171720

Protein

• UniProt ID: O15379
• Protein name: Histone deacetylase 3 (HD3) (EC 3.5.1.98) (Protein deacetylase HDAC3) (EC 3.5.1.-) (Protein deacylase HDAC3) (EC 3.5.1.-) (RPD3-2) (SMAP45)
• Protein function: Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4), and some other non-histone substrates (PubMed:21030595, PubMed:21444723, PubMed:23911289, PubMed:25301942,
• PDB: 4A69
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00850	Hist_deacetyl	22 → 314	Histone deacetylase domain	Domain

• Sequence:

  MAKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCR
  FHSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNN
  KICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEA
  FYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVI
  NQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTV
  RNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQ
  TIFENLKMLNHAPSVQIHDVPADLLTYDRTDEADAEERGPEENYSRPEAPNEFYDGDHDN
  DKESDVEI

• Sequence length: 428

Pathways

KEGG:

Neutrophil extracellular trap formation
Thyroid hormone signaling pathway
Alcoholism
Viral carcinogenesis

Reactome:

PPARA activates gene expression
Transcriptional activation of mitochondrial biogenesis
Constitutive Signaling by NOTCH1 PEST Domain Mutants
Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
HDACs deacetylate histones
Notch-HLH transcription pathway
Transcriptional regulation of white adipocyte differentiation
Regulation of lipid metabolism by PPARalpha
Circadian Clock
NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux
HCMV Early Events

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Schizophrenia	Schizophrenia	rs74315508, rs74315509, rs13447324, rs1558507406, rs387906932, rs387906933, rs863223354, rs863223355, rs776061422, rs863223349, rs748809996, rs759748655, rs863223353, rs863223350, rs863223356, rs781821239, rs863223348, rs863223346, rs863223347, rs863223351, rs863223352, rs61734270, rs797045205, rs869312829, rs869312830, rs770913157, rs869312832, rs869312831, rs781720548, rs1262969313	25445625, 17961987, 25196196, 20471694

Unknown
Disease name	Disease term	dbSNP ID	References
Heart diseases	Heart Diseases		18625706
Movement disorders	Movement Disorders		19109904, 17416969, 22230954, 10491319, 10860984, 22363205, 27543892, 25209348, 10944117, 23770587, 20691407, 25425123, 11742974, 11509652, 17158926, 26795593, 25800122, 25339172, 25102098, 18830415, 15837933, 21545841, 22495309, 10748092, 15897262