Histone deacetylase

Histone deacetylase superfamily

Identifiers
Symbol| Hist_deacetyl
Pfam| PF00850
InterPro| IPR000286
SCOP| 1c3s
SUPERFAMILY| 1c3s
| Available protein structures:

Pfam| structures
PDB| RCSB PDB; PDBe; PDBj
PDBsum| structure summary

Editor-In-Chief: C. Michael Gibson, M.S., M.D. [1]

## Overview

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Histone deacetylases (EC 3.5.1.98, HDAC) are a class of enzymes that remove acetyl groups (O=C-CH3) from an ε-N-acetyl lysine amino acid on a histone, allowing the histones to wrap the DNA more tightly. This is important because DNA is wrapped around histones, and DNA expression is regulated by acetylation and de-acetylation. Its action is opposite to that of histone acetyltransferase. HDAC proteins are now also called lysine deacetylases (KDAC), to describe their function rather than their target, which also includes non-histone proteins.[1]

## HDAC super family

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Together with the acetylpolyamine amidohydrolases and the acetoin utilization proteins, the histone deacetylases form an ancient protein superfamily known as the histone deacetylase superfamily.[2]

## Classes of HDACs in higher eukaryotes

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HDACs, are classified in four classes depending on sequence homology to the yeast original enzymes and domain organization:[3]

Class | Members | Catalytic sites | Subcellular localization | Tissue distribution | Substrates | Binding partners | Knockout phenotype

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I | HDAC1 | 1 | Nucleus | Ubiquitous | Androgen receptor, SHP, p53, MyoD, E2F1, STAT3 | – | embryonic lethal, increased histone acetylation, increase in p21 and p27
HDAC2 | 1 | Nucleus | Ubiquitous | Glucocorticoid receptor, YY1, BCL6, STAT3 | – | Cardiac defect
HDAC3 | 1 | Nucleus | Ubiquitous | SHP, YY1, GATA1, RELA, STAT3, MEF2D | – | –
HDAC8 | 1 | Nucleus/cytoplasm | Ubiquitous? | – | EST1B | –
IIA | HDAC4 | 1 | Nucleus / cytoplasm | heart, skeletal muscle, brain | GCMA, GATA1, HP1 | RFXANK | Defects in chondrocyte differentiation
HDAC5 | 1 | Nucleus / cytoplasm | heart, skeletal muscle, brain | GCMA, SMAD7, HP1 | REA, estrogen receptor | Cardiac defect
HDAC7 | 1 | Nucleus / cytoplasm / mitochondria | heart, skeletal muscle, pancreas, placenta | PLAG1, PLAG2 | HIF1A, BCL6, endothelin receptor, ACTN1, ACTN4, androgen receptor, Tip60 | Maintenance of vascular integrity, increase in MMP10
HDAC9 | 1 | Nucleus / cytoplasm | brain, skeletal muscle | – | FOXP3 | Cardiac defect
IIB | HDAC6 | 2 | Mostly cytoplasm | heart, liver, kidney, placenta | α-Tubulin, HSP90, SHP, SMAD7 | RUNX2 | –
HDAC10 | 1 | Mostly cytoplasm | liver, spleen, kidney | – | – | –
III | sirtuins in mammals (SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6, SIRT7) | – | – | – | – | – | –
Sir2 in the yeast S. cerevisiae | – | – | – | – | – | –
IV | HDAC11 | 2 | Nucleus / cytoplasm | brain, heart, skeletal muscle, kidney | – | – | –

HDAC (except class III) contain zinc and are known as Zn-dependent histone deacetylases.[4]

## Subtypes

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HDAC proteins occur in four groups (see above) based on function and DNA sequence similarity. The first two groups are considered "classical" HDACs whose activities are inhibited by trichostatin A (TSA), whereas the third group is a family of NAD+-dependent proteins not affected by TSA. Homologues to these three groups are found in yeast having the names: reduced potassium dependency 3 (Rpd3), which corresponds to Class I; histone deacetylase 1 (hda1), corresponding to Class II; and silent information regulator 2 (Sir2); corresponding to Class III.[5] The fourth group is considered an atypical category of its own, based solely on DNA sequence similarity to the others.

## Subcellular distribution

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Within the Class I HDACs, HDAC 1, 2, and 8 are found primarily in the nucleus, whereas HDAC3 is found in both the nucleus and the cytoplasm, and is also membrane-associated. Class II HDACs (HDAC4, 5, 6, 7 9, and 10) are able to shuttle in and out of the nucleus, depending on different signals.[6][7]

HDAC6 is a cytoplasmic, microtuble-associated enzyme. HDAC6 deacetylates tubulin, Hsp90, and cortactin, and forms complexes with other partner proteins, and is, therefore, involved in a variety of biological processes.[8]

## Function

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### Histone modification

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Histone tails are normally positively charged due to amine groups present on their lysine and arginine amino acids. These positive charges help the histone tails to interact with and bind to the negatively charged phosphate groups on the DNA backbone. Acetylation, which occurs normally in a cell, neutralizes the positive charges on the histone by changing amines into amides and decreases the ability of the histones to bind to DNA. This decreased binding allows chromatin expansion, permitting genetic transcription to take place. Histone deacetylases remove those acetyl groups, increasing the positive charge of histone tails and encouraging high-affinity binding between the histones and DNA backbone. The increased DNA binding condenses DNA structure, preventing transcription.

Histone deacetylase is involved in a series of pathways within the living system. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), these are:

* Environmental information processing; signal transduction; notch signaling pathway PATH:ko04330
* Cellular processes; cell growth and death; cell cycle PATH:ko04110
* Human diseases; cancers; chronic myeloid leukemia PATH:ko05220

Histone acetylation plays an important role in the regulation of gene expression. Hyperacetylated chromatin is transcriptionally active, and hypoacetylated chromatin is silent. A study on mice found that a specific subset of mouse genes (7%) was deregulated in the absence of HDAC1.[9] Their study also found a regulatory crosstalk between HDAC1 and HDAC2 and suggest a novel function for HDAC1 as a transcriptional coactivator. HDAC1 expression was found to be increased in the prefrontal cortex of schizophrenia subjects,[10] negatively correlating with the expression of GAD67 mRNA.

### Non-histone effects

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It is a mistake to regard HDACs solely in the context of regulating gene transcription by modifying histones and chromatin structure, although that appears to be the predominant function. The function, activity, and stability of proteins can be controlled by post-translational modifications. Protein phosphorylation is perhaps the most widely studied and understood modification in which certain amino acid residues are phosphorylated by the action of protein kinases or dephosphorylated by the action of phosphatases. The acetylation of lysine residues is emerging as an analogous mechanism, in which non-histone proteins are acted on by acetylases and deacetylases.[11] It is in this context that HDACs are being found to interact with a variety of non-histone proteins—some of these are transcription factors and co-regulators, some are not. Note the following four examples:

* HDAC6 is associated with aggresomes. Misfolded protein aggregates are tagged by ubiquitination and removed from the cytoplasm by dynein motors via the microtubule network to an organelle termed the aggresome. HDAC 6 binds polyubiquitinated misfolded proteins and links to dynein motors, thereby allowing the misfolded protein cargo to be physically transported to chaperones and proteasomes for subsequent destruction.[12]
* PTEN is an important phosphatase involved in cell signaling via phosphoinositols and the AKT/PI3 kinase pathway. PTEN is subject to complex regulatory control via phosphorylation, ubiquitination, oxidation and acetylation. Acetylation of PTEN by the histone acetyltransferase p300/CBP-associated factor (PCAF) can repress its activity; on the converse, deacetylation of PTEN by SIRT1 deacetylase and, by HDAC1, can stimulate its activity.[13][14]
* APE1/Ref-1 (APEX1) is a multifunctional protein possessing both DNA repair activity (on abasic and single-strand break sites) and transcriptional regulatory activity associated with oxidative stress. APE1/Ref-1 is acetylated by PCAF; on the converse, it is stably associated with and deacetylated by Class I HDACs. The acetylation state of APE1/Ref-1 does not appear to affect its DNA repair activity, but it does regulate its transcriptional activity such as its ability to bind to the PTH promoter and initiate transcription of the parathyroid hormone gene.[15][16]
* NF-κB is a key transcription factor and effector molecule involved in responses to cell stress, consisting of a p50/p65 heterodimer. The p65 subunit is controlled by acetylation via PCAF and by deacetylation via HDAC3 and HDAC6.[17]

These are just some examples of constantly emerging non-histone, non-chromatin roles for HDACs.

## HDAC inhibitors

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Main article: Histone deacetylase inhibitor

Histone deacetylase inhibitors (HDIs) have a long history of use in psychiatry and neurology as mood stabilizers and anti-epileptics, for example, valproic acid. In more recent times, HDIs are being studied as a mitigator or treatment for neurodegenerative diseases.[18][19] Also in recent years, there has been an effort to develop HDIs for cancer therapy.[20][21] Vorinostat (SAHA) was approved in 2006 for the treatment of cutaneous manifestations in patients with cutaneous T cell lymphoma (CTCL) that have failed previous treatments. A second HDI, Istodax (romidepsin), was approved in 2009 for patients with CTCL. The exact mechanisms by which the compounds may work are unclear, but epigenetic pathways are proposed.[22] In addition, a clinical trial is studying valproic acid effects on the latent pools of HIV in infected persons.[23] HDIs are currently being investigated as chemosensitizers for cytotoxic chemotherapy or radiation therapy, or in association with DNA methylation inhibitors based on in vitro synergy.[24] Recent research has focused on developing isoform selective HDIs which can aid in elucidating role of individual HDAC isoforms and device strategy for effective treatment of diseases related to relevant HDAC isoform.[25][26][27]

HDAC inhibitors have effects on non-histone proteins that are related to acetylation. HDIs can alter the degree of acetylation of these molecules and, therefore, increase or repress their activity. For the four examples given above (see Function) on HDACs acting on non-histone proteins, in each of those instances the HDAC inhibitor Trichostatin A (TSA) blocks the effect. HDIs have been shown to alter the activity of many transcription factors, including ACTR, cMyb, E2F1, EKLF, FEN 1, GATA, HNF-4, HSP90, Ku70, NFκB, PCNA, p53, RB, Runx, SF1 Sp3, STAT, TFIIE, TCF, YY1.[28][29]

Research has shown that histone deacetylase inhibitors may modulate the latency of some viruses, resulting in reactivation.[30] This has been shown to occur, for instance, with a latent human herpesvirus-6 infection.

## See also

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* Histone acetyltransferase (HAT)
* Histone deacetylase inhibitor
* Histone methyltransferase (HMT)
* Histone-modifying enzymes
* RNA polymerase control by chromatin structure

## References

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1. ↑ Choudhary C; et al. (August 2009). "Lysine acetylation targets protein complexes and co-regulates major cellular functions". Science. 325 (5942): 834–40. doi:10.1126/science.1175371. ISSN 1095-9203. PMID 19608861. Unknown parameter `|author-separator=` ignored (help)
2. ↑ Leipe DD, Landsman D (1997). "Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are members of an ancient protein superfamily". Nucleic Acids Res. 25 (18): 3693–7. doi:10.1093/nar/25.18.3693. PMC 146955. PMID 9278492.
3. ↑ Dokmanovic M, Clarke C, Marks PA (2007). "Histone deacetylase inhibitors: overview and perspectives". Mol. Cancer Res. 5 (10): 981–9. doi:10.1158/1541-7786.MCR-07-0324. PMID 17951399.CS1 maint: Multiple names: authors list (link)
4. ↑ Marks PA, Xu WS (July 2009). "Histone Deacetylase Inhibitors: Potential in Cancer Therapy". J. Cell. Biochem. 107 (4): 600–8. doi:10.1002/jcb.22185. PMC 2766855. PMID 19459166.
5. ↑ Sengupta N, Seto E (September 2004). "Regulation of histone deacetylase activities". J. Cell. Biochem. 93 (1): 57–67. doi:10.1002/jcb.20179. PMID 15352162.
6. ↑ de Ruijter AJ, van Gennip AH, Caron HN, Kemp S, van Kuilenburg AB (March 2003). "Histone deacetylases (HDACs): characterization of the classical HDAC family". Biochem. J. 370 (Pt 3): 737–49. doi:10.1042/BJ20021321. PMC 1223209. PMID 12429021.CS1 maint: Multiple names: authors list (link)
7. ↑ Longworth MS, Laimins LA (July 2006). "Histone deacetylase 3 localizes to the plasma membrane and is a substrate of Src". Oncogene. 25 (32): 4495–500. doi:10.1038/sj.onc.1209473. PMID 16532030.
8. ↑ Valenzuela-Fernández A, Cabrero JR, Serrador JM, Sánchez-Madrid F (June 2008). "HDAC6: a key regulator of cytoskeleton, cell migration and cell-cell interactions error". Trends Cell Biol. 18 (6): 291–7. doi:10.1016/j.tcb.2008.04.003. PMID 18472263.CS1 maint: Multiple names: authors list (link)
9. ↑ Zupkovitz G; Tischler J; Posch M; et al. (2006). "Negative and Positive Regulation of Gene Expression by Mouse Histone Deacetylase 1". Mol. Cell. Biol. 26 (21): 7913–28. doi:10.1128/MCB.01220-06. PMC 1636735. PMID 16940178. Unknown parameter `|author-separator=` ignored (help)
10. ↑ Sharma RP, Grayson DR, Gavin DP (2007). "Histone Deactylase 1 expression is increased in the prefrontal cortex of Schizophrenia subjects; analysis of the National Brain Databank microarray collection". Schizophrenia Research. 98 (1–3): 111–7. doi:10.1016/j.schres.2007.09.020. PMC 2254186. PMID 17961987.CS1 maint: Multiple names: authors list (link)
11. ↑ Glozak MA, Sengupta N, Zhang X, Seto E (2005). "Acetylation and deacetylation of non-histone proteins". Gene. 363: 15–23. doi:10.1016/j.gene.2005.09.010. PMID 16289629.CS1 maint: Multiple names: authors list (link)
12. ↑ Rodriguez-Gonzalez A, Lin T, Ikeda AK, Simms-Waldrip T, Fu C, Sakamoto KM (2008). "Role of the aggresome pathway in cancer: targeting histone deacetylase 6-dependent protein degradation". Cancer Res. 68 (8): 2557–60. doi:10.1158/0008-5472.CAN-07-5989. PMID 18413721.CS1 maint: Multiple names: authors list (link)
13. ↑ Ikenoue T, Inoki K, Zhao B, Guan KL (2008). "PTEN acetylation modulates its interaction with PDZ domain". Cancer Res. 68 (17): 6908–12. doi:10.1158/0008-5472.CAN-08-1107. PMID 18757404.CS1 maint: Multiple names: authors list (link)
14. ↑ Yao XH, Nyomba BL (2008). "Hepatic insulin resistance induced by prenatal alcohol exposure is associated with reduced PTEN and TRB3 acetylation in adult rat offspring". Am J Physiol Regul Integr Comp Physiol. 294 (6): R1797–806. doi:10.1152/ajpregu.00804.2007. PMID 18385463.
15. ↑ Bhakat KK, Izumi T, Yang SH, Hazra TK, Mitra S (2003). "Role of acetylated human AP-endonuclease (APE1/Ref-1) in regulation of the parathyroid hormone gene". EMBO J. 22 (23): 6299–309. doi:10.1093/emboj/cdg595. PMC 291836. PMID 14633989.CS1 maint: Multiple names: authors list (link)
16. ↑ Fantini D, Vascotto C, Deganuto M, Bivi N, Gustincich S, Marcon G, Quadrifoglio F, Damante G, Bhakat KK, Mitra S, Tell G (2008). "APE1/Ref-1 regulates PTEN expression mediated by Egr-1". Free Radic Res. 42 (1): 20–9. doi:10.1080/10715760701765616. PMC 2677450. PMID 18324520.CS1 maint: Multiple names: authors list (link)
17. ↑ Hasselgren PO (2007). "Ubiquitination, phosphorylation, and acetylation--triple threat in muscle wasting". J Cell Physiol. 213 (3): 679–89. doi:10.1002/jcp.21190. PMID 17657723.
18. ↑ Hahnen E, Hauke J, Tränkle C, Eyüpoglu IY, Wirth B, Blümcke I (February 2008). "Histone deacetylase inhibitors: possible implications for neurodegenerative disorders". Expert Opin Investig Drugs. 17 (2): 169–84. doi:10.1517/13543784.17.2.169. PMID 18230051.CS1 maint: Multiple names: authors list (link)
19. ↑ "Scientists 'reverse' memory loss". BBC News. 2007-04-29. Retrieved 2007-07-08.
20. ↑ Mwakwari S. C., Patil V., Guerrant W., Oyelere A. K. “Macrocyclic histonedeacetylase inhibitors” Curr. Top. Med. Chem. (2010), 10, 1423-1440.
21. ↑ Miller, T. A.; Witter, D. J.; Belvedere, S. J. Med. Chem.2003, 46, 5097–5116.
22. ↑ Monneret C (2007). "Histone deacetylase inhibitors for epigenetic therapy of cancer". Anticancer Drugs. 18 (4): 363–70. doi:10.1097/CAD.0b013e328012a5db. PMID 17351388.
23. ↑ Depletion of Latent HIV in CD4 Cells - Full Text View - ClinicalTrials.gov
24. ↑ Batty N; Malouf, GG; Issa, JP (August 2009). "Histone deacetylase inhibitors as anti-neoplastic agents". Cancer Letters. 280 (2): 190–200. doi:10.1016/j.canlet.2009.03.013. PMID 19345475. Unknown parameter `|unused_data=` ignored (help)
25. ↑ Patil V., Sodji Q., Kornacki J., MrksichM., Oyelere A. K. “3-Hydroxypyridin-2-thiones as a novel zinc binding group for selective HDAC inhibition” J. Med. Chem. 2013, 56, 3492-3506.
26. ↑ Mwakwari S. C., Guerrant W., Patil V., Khan S., Tekwani B., Gurard-Levin Z., Mrksich M.; Oyelere A. K. “Non-peptide macrocyclic histone deacetylase inhibitorsderived from tricyclic ketolide skeleton” J.Med Chem. 2010, 53, 6100-6111
27. ↑ Kyle V. Butler, Jay Kalin, Camille Brochier, Guilio Vistoli, Brett Langley, and Alan P. Kozikowski "Rational Design and Simple Chemistry Yield a Superior,Neuroprotective HDAC6 Inhibitor, Tubastatin A" J. Am. Chem. Soc. 2010, 132(31), 10842.
28. ↑ Drummond DC, Noble CO, Kirpotin DB, Guo Z, Scott GK, Benz CC (2005). "Clinical development of histone deacetylase inhibitors as anticancer agents". Annu Rev Pharmacol Toxicol. 45: 495–528. doi:10.1146/annurev.pharmtox.45.120403.095825. PMID 15822187.CS1 maint: Multiple names: authors list (link)
29. ↑ Yang XJ, Seto E (2007). "HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention". Oncogene. 26 (37): 5310–5318. doi:10.1038/sj.onc.1210599. PMID 17694074.
30. ↑ Arbuckle, Jesse. "The molecular biology of human herpesvirus-6 latency and telomere integration". Microbes and infection. 13 (8–9). doi:10.1016/j.micinf.2011.03.006. PMC 3130849. PMID 21458587.

## External links

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* Histone+deacetylase at the US National Library of Medicine Medical Subject Headings (MeSH)
* Animation at Merck

* v
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Hydrolases: carbon-nitrogen non-peptide (EC 3.5)

3.5.1: Linear amides /
Amidohydrolases|

* Asparaginase
* Glutaminase
* Urease
* Biotinidase
* Aspartoacylase
* Ceramidase
* Aspartylglucosaminidase
* Fatty acid amide hydrolase
* Histone deacetylase
* Sirtuin

3.5.2: Cyclic amides/
Amidohydrolases|

* Barbiturase
* Beta-lactamase

3.5.3: Linear amidines/
Ureohydrolases|

* Arginase
* Agmatinase
* Protein-arginine deiminase

3.5.4: Cyclic amidines/
Aminohydrolases|

* Guanine deaminase
* Adenosine deaminase
* AMP deaminase
* Inosine monophosphate synthase
* DCMP deaminase
* GTP cyclohydrolase I
* Cytidine deaminase
* AICDA
* Activation-induced cytidine deaminase

3.5.5: Nitriles/
Aminohydrolases|

* Nitrilase

3.5.99: Other|

* Riboflavinase
* Thiaminase II

* v
* t
* e

Transcription (Bacterial, Eukaryotic)

Transcriptional regulation|

| prokaryotic|

* Operon
* lac operon
* trp operon
* gab operon
* ara operon
* gal operon
* Repressor
* lac repressor
* trp repressor

|

eukaryotic|

| Histone-modifying enzymes
(histone/nucleosome):|

* Histone methylation/Histone methyltransferase
* EZH2
* Histone demethylase
* Histone acetylation and deacetylation
* Histone deacetylase HDAC1
* Histone acetyltransferase

|

DNA methylation:|

*     * DNA methyltransferase

Chromatin remodeling:|

* CHD7

both|

* Transcription coregulator
* Coactivator
* Corepressor
* Inducer

Promotion|

* Promoter
* Pribnow box
* TATA box
* BRE
* CAAT box
* Response element
* Enhancer
* E-box
* Response element
* Insulator
* Silencer
* Internal control region

Initiation|

* Bacterial
* Eukaryotic
* Archaeal transcription factor B

Elongation|

* bacterial RNA polymerase: rpoB
* eukaryotic RNA polymerase: RNA polymerase II

Termination
(bacterial,
eukaryotic)|

* Terminator
* Intrinsic termination
* Rho factor

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