Details of Epigenetic Molecule(EM)

General Information of EM (ID: EM10074)
  Official Symbol
HDAC9
  Official Full Name
histone deacetylase 9
  Synonym
HD7;HD9;HD7b;HDAC;HDRP;MITR;HDAC7;HDAC7B;HDAC9B;HDAC9FL
  Molecule Type
Protein coding
  Position On Chromosome
chr7(Start:18086949 - End:19002416)
  Strand
+
  Uniprot Entry
Q9UKV0 
  ENSG ID
ENSG00000048052 
  Dnmivd Disease
KIRC 
Metabolite(s) with this epigenetic modification
  Metabolite Name: Alpha-muricholate
     Detailed Information Meta Info click to show the detail information of this Metabolite [1], [2]
     Description
Alpha-muricholate has been shown to activate the histone deacetylases.
  Metabolite Name: Hexanoate
     Detailed Information Meta Info click to show the detail information of this Metabolite [3]
     Description
Hexanoate has been shown to inhibite histone deacetylases (HDACs)
  Metabolite Name: Benzoate
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
Benzoate has been shown to inhibite histone deacetylase activity.
  Metabolite Name: beta-muricholate
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
beta-muricholate has been shown to activate the histone deacetylases.
  Metabolite Name: Chenodeoxycholate
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
Chenodeoxycholate has been shown to activate histone deacetylases.
  Metabolite Name: Cholate
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
Cholate has been shown to activate histone deacetylases.
  Metabolite Name: Deoxycholic acid
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
Deoxycholate has been shown to activate histone deacetylases.
  Metabolite Name: Glycocholate
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
Glycocholate has been shown to activate histone deacetylases.
  Metabolite Name: Hydroxyphenylacetic acid
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
Hydroxyphenylacetic acid has been shown to inhibite histone deacetylase activity.
  Metabolite Name: Hydroxyphenylpentanoic acid
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
Hydroxyphenylpentanoic acid has been shown to inhibite histone deacetylase activity.
  Metabolite Name: Hydroxyphenylpropanoic acid
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
Hydroxyphenylpropanoic acid has been shown to inhibite histone deacetylase (HDAC7) activity.
  Metabolite Name: Hyocholate
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
Hyocholate has been shown to activate histone deacetylases.
  Metabolite Name: omega-muricholate
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
omega-muricholate has been shown to activate the histone deacetylases.
  Metabolite Name: P-cresol
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
P-cresol has been shown to inhibite histone deacetylase activity.
  Metabolite Name: Phenylbutyrate
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
PhenylButyrate has been shown to inhibit histone deacetylase.
  Metabolite Name: Taurochenoxycholate
     Detailed Information Meta Info click to show the detail information of this Metabolite [3], [4]
     Description
Taurochenoxycholate has been shown to activate histone deacetylases.
  Metabolite Name: Hydrogen sulfide (H2S)
     Detailed Information Meta Info click to show the detail information of this Metabolite [5], [6]
     Description
Hydrogen sulfide (H2S) has been shown to modulate histone deacetylase activity.
  Metabolite Name: phenylbutyl isothiocyanate
     Detailed Information Meta Info click to show the detail information of this Metabolite [7], [8]
     Description
phenylbutyl isothiocyanate has been shown to inhibite histone deacetylase activity.
  Metabolite Name: Phenylacetate
     Detailed Information Meta Info click to show the detail information of this Metabolite [9], [10]
     Description
Phenylacetate has been shown to inhibit histone deacetylase.
  Metabolite Name: 3-(4-hydroxyphenyl)propionic acid
     Detailed Information Meta Info click to show the detail information of this Metabolite [11], [12]
     Description
3-(4-hydroxyphenyl)propionic acid is the most potent HDAC inhibitors among the polyphenol metabolites.
  Metabolite Name: Valerolactone
     Detailed Information Meta Info click to show the detail information of this Metabolite [13], [14]
     Description
Valerolactone has been shown to inhibite histone deacetylase activity.
  Metabolite Name: Propionate
     Detailed Information Meta Info click to show the detail information of this Metabolite [13], [15]
     Description
Propionate has been shown to inhibit histone deacetylase.

Protein(s) with this epigenetic modification
  Protein Name: TRP32
     Detailed Information Pro Info click to show the detail information of this protein [16]
     Description
TRP32 could be bind to host-cell DNA at G-rich motifs

References
1 Dietary metabolites derived from gut microbiota: critical modulators of epigenetic changes in mammals. Nutr Rev. 2017 May 1;75(5):374-389. doi: 10.1093/nutrit/nux001.
2 Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling mSystems. 2017 Nov 14;2(6):e00046-17. doi: 10.1128/mSystems.00046-17. eCollection 2017 Nov-Dec.
3 Gut Microbiota as Important Mediator Between Diet and DNA Methylation and Histone Modifications in the Host. Nutrients. 2020 Feb 25;12(3):597. doi: 10.3390/nu12030597.
4 Arachidonic and oleic acid exert distinct effects on the DNA methylome. Epigenetics. 2016 May 3;11(5):321-34. doi: 10.1080/15592294.2016.1161873. Epub 2016 Apr 18.
5 Hydrogen sulfide attenuates cytokine production through the modulation of chromatin remodeling. Int J Mol Med. 2015 Jun;35(6):1741-6. doi: 10.3892/ijmm.2015.2176. Epub 2015 Apr 8.
6 Hydrogen Sulfide and Sulfate Prebiotic Stimulates the Secretion of GLP-1 and Improves Glycemia in Male Mice Endocrinology. 2017 Oct 1;158(10):3416-3425. doi: 10.1210/en.2017-00391.
7 Influence of bacteria on epigenetic gene control. Cell Mol Life Sci. 2014 Mar;71(6):1045-54. doi: 10.1007/s00018-013-1487-x. Epub 2013 Oct 15.
8 Broccoli ingestion increases the glucosinolate hydrolysis activity of microbiota in the mouse gut Int J Food Sci Nutr. 2019 Aug;70(5):585-594. doi: 10.1080/09637486.2018.1554624. Epub 2019 Feb 16.
9 The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992.
10 Gestational choline supply regulates methylation of histone H3, expression of histone methyltransferases G9a (Kmt1c) and Suv39h1 (Kmt1a), and DNA methylation of their genes in rat fetal liver and brain. J Biol Chem. 2009 Jan 23;284(4):1982-9. doi: 10.1074/jbc.M807651200. Epub 2008 Nov 10.
11 Inhibition of histone-deacetylase activity by short-chain fatty acids and some polyphenol metabolites formed in the colon. J Nutr Biochem. 2008 Sep;19(9):587-93. doi: 10.1016/j.jnutbio.2007.08.002. Epub 2007 Dec 3.
12 Bacterial species involved in the conversion of dietary flavonoids in the human gut. Gut Microbes. 2016 May 3;7(3):216-34. doi: 10.1080/19490976.2016.1158395. Epub 2016 Mar 10.
13 Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells. 2010 Apr;28(4):713-20. doi: 10.1002/stem.402.
14 Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria PLoS Pathog. 2018 Sep 12;14(9):e1007191. doi: 10.1371/journal.ppat.1007191. eCollection 2018 Sep.
15 Mucin Cross-Feeding of Infant Bifidobacteria and Eubacterium hallii Microb Ecol. 2018 Jan;75(1):228-238. doi: 10.1007/s00248-017-1037-4. Epub 2017 Jul 18.
16 Bacterial Factors Targeting the Nucleus: The Growing Family of Nucleomodulins Toxins (Basel). 2020 Mar 31;12(4):220. doi: 10.3390/toxins12040220.

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