HDAC9 (histone deacetylase 9)

Gene

• Entrez ID: 9734
• Gene name: Histone deacetylase 9
• Gene symbol: HDAC9
• Synonyms: HD7, HD7b, HD9, HDAC, HDAC7, HDAC7B, HDAC9B, HDAC9FL, HDRP, MITR
• Chromosome: 7
• Chromosome location: 7p21.1
• 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 has sequence homology to members of the histone deacetylase family. This gene is orthologous to the Xenopus and mouse MITR genes. The MITR protein lacks the histone deacetylase catalytic domain. It represses MEF2 activity through recruitment of multicomponent corepressor complexes that include CtBP and HDACs. This encoded protein may play a role in hematopoiesis. Multiple alternatively spliced transcripts have been described for this gene but the full-length nature of some of them has not been determined. [provided by RefSeq, Jul 2008]

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT610223	hsa-miR-342-3p	HITS-CLIP	23824327
MIRT610224	hsa-miR-8485	HITS-CLIP	23824327
MIRT731680	hsa-miR-29a-5p	Luciferase reporter assay, Western blot	26441331

Transcription factors

Transcription factor	Regulation	Reference
GATA4	Repression	18332107
SALL3	Repression	18332107

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000118	Component	Histone deacetylase complex	TAS	12711221
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IDA	10655483, 11535832
GO:0001818	Process	Negative regulation of cytokine production	IDA	28855441
GO:0001975	Process	Response to amphetamine	IEA
GO:0003714	Function	Transcription corepressor activity	ISS
GO:0004407	Function	Histone deacetylase activity	IDA	11535832
GO:0005080	Function	Protein kinase C binding	IPI	20188095
GO:0005515	Function	Protein binding	IPI	12590135, 16147992, 26221039
GO:0005634	Component	Nucleus	IDA	12590135, 20188095
GO:0005654	Component	Nucleoplasm	TAS
GO:0005667	Component	Transcription regulator complex	IDA	15567413, 19303849
GO:0005737	Component	Cytoplasm	IDA	12590135, 20188095
GO:0005737	Component	Cytoplasm	TAS	12711221
GO:0006954	Process	Inflammatory response	TAS	12711221
GO:0007507	Process	Heart development	ISS
GO:0008134	Function	Transcription factor binding	IDA	11535832
GO:0008134	Function	Transcription factor binding	IPI	10748098, 15567413, 19303849
GO:0016575	Process	Histone deacetylation	IDA	11535832
GO:0030182	Process	Neuron differentiation	IEA
GO:0030183	Process	B cell differentiation	TAS	12711221
GO:0032041	Function	NAD-dependent histone deacetylase activity (H3-K14 specific)	IEA
GO:0032869	Process	Cellular response to insulin stimulus	IDA	19303849
GO:0033558	Function	Protein deacetylase activity	IDA	11535832
GO:0034739	Function	Histone deacetylase activity (H4-K16 specific)	IDA	28855441
GO:0034983	Process	Peptidyl-lysine deacetylation	IDA	11535832
GO:0035097	Component	Histone methyltransferase complex	ISS
GO:0042113	Process	B cell activation	TAS	12711221
GO:0042632	Process	Cholesterol homeostasis	IDA	28855441
GO:0042826	Function	Histone deacetylase binding	IPI	12590135
GO:0045892	Process	Negative regulation of transcription, DNA-templated	IDA	11535832
GO:0046872	Function	Metal ion binding	IEA
GO:0048742	Process	Regulation of skeletal muscle fiber development	ISS
GO:0051005	Process	Negative regulation of lipoprotein lipase activity	IDA	28855441
GO:0051153	Process	Regulation of striated muscle cell differentiation	ISS
GO:0070491	Function	Repressing transcription factor binding	IDA	12590135
GO:0070491	Function	Repressing transcription factor binding	IPI	17360565
GO:0070491	Function	Repressing transcription factor binding	ISS
GO:0070932	Process	Histone H3 deacetylation	IDA	12590135
GO:0070933	Process	Histone H4 deacetylation	IDA	12590135
GO:0090050	Process	Positive regulation of cell migration involved in sprouting angiogenesis	IMP	19351956
GO:1990678	Process	Histone H4-K16 deacetylation	IDA	28855441

Other IDs

• MIM: 606543
• HGNC: 14065
• e!Ensembl: ENSG00000048052

Protein

• UniProt ID: Q9UKV0
• Protein name: Histone deacetylase 9 (HD9) (EC 3.5.1.98) (Histone deacetylase 7B) (HD7) (HD7b) (Histone deacetylase-related protein) (MEF2-interacting transcription repressor MITR)
• Protein function: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Represses MEF2-dependent transcription.; Isoform 3 lacks active site residues and therefore is catalytically inactive. Represses MEF2-dependent transcription by recruiting HDAC1 and/or HDAC3. Seems to inhibit skeletal myogenesis and to be involved in heart development. Protects neurons from apoptosis, both by inhibiting JUN phosphorylation by MAPK10 and by repressing JUN transcription via HDAC1 recruitment to JUN promoter.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF12203	HDAC4_Gln	37 → 124	Glutamine rich N terminal domain of histone deacetylase 4	Family
  PF00850	Hist_deacetyl	654 → 972	Histone deacetylase domain	Domain

• Sequence:

  MHSMISSVDVKSEVPVGLEPISPLDLRTDLRMMMPVVDPVVREKQLQQELLLIQQQQQIQ
  KQLLIAEFQKQHENLTRQHQAQLQEHIKELLAIKQQQELLEKEQKLEQQRQEQEVERHRR
  EQQLPPLRGKDRGRERAVASTEVKQKLQEFLLSKSATKDTPTNGKNHSVSRHPKLWYTAA
  HHTSLDQSSPPLSGTSPSYKYTLPGAQDAKDDFPLRKTASEPNLKVRSRLKQKVAERRSS
  PLLRRKDGNVVTSFKKRMFEVTESSVSSSSPGSGPSSPNNGPTGSVTENETSVLPPTPHA
  EQMVSQQRILIHEDSMNLLSLYTSPSLPNITLGLPAVPSQLNASNSLKEKQKCETQTLRQ
  GVPLPGQYGGSIPASSSHPHVTLEGKPPNSSHQALLQHLLLKEQMRQQKLLVAGGVPLHP
  QSPLATKERISPGIRGTHKLPRHRPLNRTQSAPLPQSTLAQLVIQQQHQQFLEKQKQYQQ
  QIHMNKLLSKSIEQLKQPGSHLEEAEEELQGDQAMQEDRAPSSGNSTRSDSSACVDDTLG
  QVGAVKVKEEPVDSDEDAQIQEMESGEQAAFMQQPFLEPTHTRALSVRQAPLAAVGMDGL
  EKHRLVSRTHSSPAASVLPHPAMDRPLQPGSATGIAYDPLMLKHQCVCGNSTTHPEHAGR
  IQSIWSRLQETGLLNKCERIQGRKASLEEIQLVHSEHHSLLYGTNPLDGQKLDPRILLGD
  DSQKFFSSLPCGGLGVDSDTIWNELHSSGAARMAVGCVIELASKVASGELKNGFAVVRPP
  GHHAEESTAMGFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYI
  SLHRYDEGNFFPGSGAPNEVGTGLGEGYNINIAWTGGLDPPMGDVEYLEAFRTIVKPVAK
  EFDPDMVLVSAGFDALEGHTPPLGGYKVTAKCFGHLTKQLMTLADGRVVLALEGGHDLTA
  ICDASEACVNALLGNELEPLAEDILHQSPNMNAVISLQKIIEIQSMSLKFS

• Sequence length: 1011

Pathways

KEGG:

Neutrophil extracellular trap formation
Alcoholism
Viral carcinogenesis

Reactome:

Constitutive Signaling by NOTCH1 PEST Domain Mutants
Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
Notch-HLH transcription pathway

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Schizophrenia	Schizophrenia	rs74315508, rs74315509, rs13447324, rs1558507406, rs387906932, rs387906933, rs-1, 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, 20471694
Epilepsy	Epilepsy	rs113994140, rs119454947, rs28937874, rs-1, rs1589762127, rs104894166, rs28939075, rs2134001459, rs104894167, rs119488099, rs119488100, rs1805032, rs387906420, rs121917752, rs121918622, rs121434579, rs1581220270, rs281865564, rs387907313, rs397514564, rs397514670, rs768241563, rs587776973, rs587776974, rs587776975, rs879255234, rs587776976, rs587776977, rs121917993, rs398123588, rs13306758, rs587777363, rs587777364, rs587777458, rs587777459, rs541024038, rs797044545, rs730882240, rs786205703, rs794726859, rs796053126, rs796053035, rs796053216, rs796052839, rs869025201, rs797044999, rs797044998, rs797045045, rs794726762, rs869312971, rs869312972, rs879255652, rs886037938, rs886037958, rs886037959, rs886037960, rs886037961, rs886037962, rs886037965, rs886037966, rs886039245, rs886039246, rs886039251, rs886039252, rs772872014, rs886039253, rs886039256, rs757511744, rs886039261, rs886039263, rs578185749, rs886039266, rs886039268, rs886039269, rs886039273, rs368820286, rs1057518801, rs1057518688, rs1057519107, rs1057519273, rs752753379, rs767795673, rs1057519424, rs755946598, rs760609867, rs1057521066, rs1057524233, rs1060501488, rs1060501487, rs755127868, rs751533302, rs771373457, rs1475605360, rs1555401942, rs1553567864, rs200661329, rs766667249, rs1556607762, rs1555882921, rs1555882867, rs1555900914, rs1553546836, rs77216276, rs755595256, rs1554169267, rs747661902, rs2105890565, rs1021001959, rs1555441032, rs1555439541, rs1556526609, rs1315483224, rs759952667, rs1555885023, rs1553456695, rs1555942720, rs1569083500, rs1559127505, rs1206309859, rs1567139896, rs1567134495, rs1431914212, rs1569166925, rs1569255443, rs1568955379, rs1567152003, rs374158137, rs1567129567, rs1569523728, rs1568991466, rs1569186093, rs1569254004, rs1372605067, rs1569067939, rs1568963062, rs1563959514, rs1569012755, rs1559118914, rs1602338615, rs1596522356, rs1364913665, rs1596522300, rs1596526976, rs1229740428, rs1596385588, rs1596500172, rs1596505517, rs1601925213, rs1601970168, rs1602010382, rs1602903591, rs1603014297, rs1603014708, rs1601875057, rs1601970824, rs1601755632, rs1587393982, rs1592977444, rs1575562076, rs1570998206, rs1588057922, rs1596528731, rs1602349641, rs1587401875, rs2065899210, rs1596526915, rs2093486364, rs2056165149, rs2056100951, rs781482552, rs1899868619, rs1900088045, rs1898675878, rs1898686157, rs1898837245, rs1898844513, rs2082841677, rs2085727988, rs2092933941, rs2091657024, rs1899864955, rs1898844907, rs2083056830, rs2084070588, rs1899713412, rs2082695884, rs1977106116, rs1977105425, rs1443687532	26220383
Rheumatoid arthritis	Rheumatoid Arthritis, Systemic Juvenile	rs3766379, rs3792876, rs2071592, rs3087456, rs587776843, rs1566328963	27927641
Coronary artery disease	Coronary Artery Disease	rs137852988, rs121918313, rs-1, rs121918529, rs121918531, rs137852340, rs405509, rs1555800701, rs1215189537	23202125
Cerebral amyloid angiopathy	Cerebral Amyloid Angiopathy	rs104894417, rs63750579, rs63750264, rs63750066, rs63750921, rs80356710, rs80356711, rs398122414, rs1555782101	29458411
Narcolepsy	Narcolepsy	rs104894574, rs387906655	19629137
Arthritis	Systemic onset juvenile chronic arthritis	rs1594890601, rs1594882933, rs184370809, rs776489319, rs1594883470	27927641

Unknown
Disease name	Disease term	dbSNP ID	References
Ischemic stroke	Ischemic stroke	rs6025, rs1799963, rs1799983, rs-1	26708676
Mental depression	Mental Depression, Depressive disorder, Unipolar Depression	rs587778876, rs587778877	19767015, 19759294
Alopecia	Alopecia		28196072
Alopecia, male pattern	Alopecia, Male Pattern		29146897, 22693459, 27182965
Androgenetic alopecia	Androgenetic Alopecia, Alopecia, Androgenetic, 3, Alopecia, Androgenetic, 2, Alopecia, Androgenetic, 1		29146897, 22693459, 27182965
Bipolar disorder	Bipolar Disorder		26806518
Osteoarthritis of hip	Osteoarthritis of hip		30374069, 29559693
Still disease	Juvenile-Onset Still Disease		27927641
Stroke	Cerebrovascular accident, Acute Cerebrovascular Accidents		26089329, 22306652
Vascular diseases	Peripheral Arterial Diseases		26488411