Biology:HDAC3

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Short description: Protein-coding gene in humans

A representation of the 3D structure of the protein myoglobin showing turquoise α-helices.
Generic protein structure example

Histone deacetylase 3 is an enzyme encoded by the HDAC3 gene in both humans and mice.[1][2][3][4]

Function

Histones are alkaline positively charged proteins that package and organize DNA into structural units known as nucleosomes, the primary protein component of chromatin.[5] Posttranslational, enzyme-mediated lysine acetylation and deacetylation of histone tails modify local chromatin structure by altering the electrostatic interaction between the negatively charged DNA backbone and the histones.[6][7] HDAC3 is a Class I member of the histone deacetylase superfamily, which is divided into four classes based on function and sequence homology.[8] HDAC3 is recruited to enhancers, where it modulates the epigenome and regulates nearby gene expression. It is found exclusively in the cell nucleus, and is the only endogenous histone deacetylase biochemically purified as part of the nuclear receptor corepressor complex containing NCOR and SMRT (NCOR2). Unlike other HDACs, HDAC3 therefore plays a distinct role in regulating the transcriptional activity of nuclear receptors.[8]

Role in intestinal homeostasis

Histone deacetylases can be regulated by endogenous factors, dietary components, synthetic inhibitors, and bacteria-derived signals. Studies in mice with a specific deletion of HDAC3 in intestinal epithelial cells (IECs) have shown deregulated gene expression in IECs. In these deletion-mutant mice, the loss of Paneth cells, impaired IEC function, and changes in the intestinal composition of commensal bacteria were observed. These adverse effects did not occur in germ-free mice, indicating that they depend on intestinal microbial colonization. However, they are not caused by the presence of an altered microbiota, since normal germ-free mice colonized with the mutant-associated microbiota did not develop the same defects.

Although the precise mechanisms and signals remain unclear, HDAC3 is known to interact with commensal bacteria–derived signals from the gut microbiota. These interactions calibrate epithelial cell responses that are essential for establishing a balanced relationship between the host and its commensal microbes and for maintaining intestinal homeostasis.[9][10][11][12]

Interactions

HDAC3 has been shown to interact with:

See also

References

  1. ↑ "Characterization of a human RPD3 ortholog, HDAC3". Proceedings of the National Academy of Sciences of the United States of America 95 (6): 2795–2800. April 1998. doi:10.1073/pnas.95.6.2795. PMID 9501169. Bibcode: 1998PNAS...95.2795E. 
  2. ↑ "Differential display cloning of a novel human histone deacetylase (HDAC3) cDNA from PHA-activated immune cells". Biochemical and Biophysical Research Communications 242 (3): 648–652. March 1998. doi:10.1006/bbrc.1997.8033. PMID 9464271. Bibcode: 1998BBRC..242..648D. 
  3. ↑ "Maintenance of cardiac energy metabolism by histone deacetylase 3 in mice" (in en). The Journal of Clinical Investigation 118 (11): 3588–3597. 2008-11-03. doi:10.1172/jci35847. ISSN 0021-9738. PMID 18830415. 
  4. ↑ "Deletion of Histone Deacetylase 3 Reveals Critical Roles in S Phase Progression and DNA Damage Control". Molecular Cell 30 (1): 61–72. Apr 2008. doi:10.1016/j.molcel.2008.02.030. PMID 18406327. 
  5. ↑ "Proteins: histones and chromatin". Current Opinion in Structural Biology 21 (6): 695–7. December 2011. doi:10.1016/j.sbi.2011.10.006. PMID 22079548. 
  6. ↑ "Regulation of chromatin by histone modifications". Cell Research 21 (3): 381–95. March 2011. doi:10.1038/cr.2011.22. PMID 21321607. 
  7. ↑ "A short guide to histone deacetylases including recent progress on class II enzymes". Experimental & Molecular Medicine 52 (2): 204–212. February 2020. doi:10.1038/s12276-020-0382-4. PMID 32071378. 
  8. ↑ 8.0 8.1 "The Role of Histone Deacetylase 3 Complex in Nuclear Hormone Receptor Action". International Journal of Molecular Sciences 22 (17): 9138. August 2021. doi:10.3390/ijms22179138. PMID 34502048. 
  9. ↑ "Metaboloepigenetics: interrelationships between energy metabolism and epigenetic control of gene expression". Journal of Cellular Physiology 227 (9): 3169–3177. Sep 2012. doi:10.1002/jcp.24054. PMID 22261928. 
  10. ↑ "The many roles of histone deacetylases in development and physiology: implications for disease and therapy". Nature Reviews. Genetics 10 (1): 32–42. Jan 2009. doi:10.1038/nrg2485. PMID 19065135. 
  11. ↑ "Dietary, metabolic, and potentially environmental modulation of the lysine acetylation machinery". International Journal of Cell Biology 2010. 2010. doi:10.1155/2010/632739. PMID 20976254. 
  12. ↑ "Dietary histone deacetylase inhibitors: from cells to mice to man". Seminars in Cancer Biology 17 (5): 363–369. Oct 2007. doi:10.1016/j.semcancer.2007.04.001. PMID 17555985. 
  13. ↑ "The transcriptional corepressor MTG16a contains a novel nucleolar targeting sequence deranged in t (16; 21)-positive myeloid malignancies". Oncogene 21 (43): 6703–6712. September 2002. doi:10.1038/sj.onc.1205882. PMID 12242670. 
  14. ↑ "ETO, a target of t(8;21) in acute leukemia, makes distinct contacts with multiple histone deacetylases and binds mSin3A through its oligomerization domain". Molecular and Cellular Biology 21 (19): 6470–6483. October 2001. doi:10.1128/MCB.21.19.6470-6483.2001. PMID 11533236. 
  15. ↑ "A central domain of cyclin D1 mediates nuclear receptor corepressor activity". Oncogene 24 (3): 431–444. January 2005. doi:10.1038/sj.onc.1208200. PMID 15558026. 
  16. ↑ "Cyclin D1 Is a Ligand-independent Co-repressor for Thyroid Hormone Receptors". Journal of Biological Chemistry 277 (32): 28733–28741. August 2002. doi:10.1074/jbc.M203380200. PMID 12048199. 
  17. ↑ "Altered interaction of HDAC5 with GATA-1 during MEL cell differentiation". Oncogene 22 (57): 9176–9184. December 2003. doi:10.1038/sj.onc.1206902. PMID 14668799. 
  18. ↑ "Histone deacetylase 3 associates with and represses the transcription factor GATA-2". Blood 98 (7): 2116–2123. October 2001. doi:10.1182/blood.V98.7.2116. PMID 11567998. 
  19. ↑ 19.0 19.1 19.2 19.3 "The N-CoR-HDAC3 nuclear receptor corepressor complex inhibits the JNK pathway through the integral subunit GPS2". Molecular Cell 9 (3): 611–623. March 2002. doi:10.1016/S1097-2765(02)00468-9. PMID 11931768. 
  20. ↑ "Histone deacetylase 3 binds to and regulates the multifunctional transcription factor TFII-I". Journal of Biological Chemistry 278 (3): 1841–1847. January 2003. doi:10.1074/jbc.M206528200. PMID 12393887. 
  21. ↑ "Physical and functional interactions of histone deacetylase 3 with TFII-I family proteins and PIASxbeta". Proceedings of the National Academy of Sciences of the United States of America 99 (20): 12807–12812. October 2002. doi:10.1073/pnas.192464499. PMID 12239342. Bibcode: 2002PNAS...9912807T. 
  22. ↑ 22.0 22.1 22.2 "Human HDAC7 histone deacetylase activity is associated with HDAC3 in vivo". Journal of Biological Chemistry 276 (38): 35826–35835. September 2001. doi:10.1074/jbc.M104935200. PMID 11466315. 
  23. ↑ 23.0 23.1 "Three proteins define a class of human histone deacetylases related to yeast Hda1p". Proceedings of the National Academy of Sciences of the United States of America 96 (9): 4868–4873. April 1999. doi:10.1073/pnas.96.9.4868. PMID 10220385. Bibcode: 1999PNAS...96.4868G. 
  24. ↑ 24.0 24.1 24.2 24.3 "Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N-CoR". Molecular Cell 9 (1): 45–57. January 2002. doi:10.1016/S1097-2765(01)00429-4. PMID 11804585. 
  25. ↑ 25.0 25.1 "Regulation of histone deacetylase 4 and 5 and transcriptional activity by 14-3-3-dependent cellular localization". Proceedings of the National Academy of Sciences of the United States of America 97 (14): 7835–7840. July 2000. doi:10.1073/pnas.140199597. PMID 10869435. Bibcode: 2000PNAS...97.7835G. 
  26. ↑ "The histone deacetylase 9 gene encodes multiple protein isoforms". Journal of Biological Chemistry 278 (18): 16059–16072. May 2003. doi:10.1074/jbc.M212935200. PMID 12590135. 
  27. ↑ "Identification of a transcriptional repressor related to the noncatalytic domain of histone deacetylases 4 and 5". Proceedings of the National Academy of Sciences of the United States of America 97 (3): 1056–1061. February 2000. doi:10.1073/pnas.97.3.1056. PMID 10655483. Bibcode: 2000PNAS...97.1056Z. 
  28. ↑ "Exchange of N-CoR corepressor and Tip60 coactivator complexes links gene expression by NF-kappaB and beta-amyloid precursor protein". Cell 110 (1): 55–67. July 2002. doi:10.1016/S0092-8674(02)00809-7. PMID 12150997. 
  29. ↑ "Histone deacetylase 3, a class I histone deacetylase, suppresses MAPK11-mediated activating transcription factor-2 activation and represses TNF gene expression". Journal of Immunology (Baltimore, Md.) 173 (6): 3979–3990. September 2004. doi:10.4049/jimmunol.173.6.3979. PMID 15356147. 
  30. ↑ 30.0 30.1 30.2 "N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso". Molecular Cell 12 (3): 723–734. September 2003. doi:10.1016/j.molcel.2003.08.008. PMID 14527417. 
  31. ↑ 31.0 31.1 "Purification and functional characterization of the human N-CoR complex: the roles of HDAC3, TBL1 and TBLR1". The EMBO Journal 22 (6): 1336–1346. March 2003. doi:10.1093/emboj/cdg120. PMID 12628926. 
  32. ↑ 32.0 32.1 "Both corepressor proteins SMRT and N-CoR exist in large protein complexes containing HDAC3". The EMBO Journal 19 (16): 4342–4350. August 2000. doi:10.1093/emboj/19.16.4342. PMID 10944117. 
  33. ↑ 33.0 33.1 "A novel nuclear receptor corepressor complex, N-CoR, contains components of the mammalian SWI/SNF complex and the corepressor KAP-1". Journal of Biological Chemistry 275 (51): 40463–40470. December 2000. doi:10.1074/jbc.M007864200. PMID 11013263. 
  34. ↑ 34.0 34.1 "A core SMRT corepressor complex containing HDAC3 and TBL1, a WD40-repeat protein linked to deafness". Genes & Development 14 (9): 1048–1057. May 2000. doi:10.1101/gad.14.9.1048. PMID 10809664. 
  35. ↑ 35.0 35.1 "Assembly of the SMRT-histone deacetylase 3 repression complex requires the TCP-1 ring complex". Genes & Development 16 (24): 3130–3135. December 2002. doi:10.1101/gad.1037502. PMID 12502735. 
  36. ↑ 36.0 36.1 36.2 "Interaction of nuclear receptor zinc finger DNA binding domains with histone deacetylase". Molecular and Cellular Endocrinology 206 (1–2): 1–12. August 2003. doi:10.1016/S0303-7207(03)00254-5. PMID 12943985. 
  37. ↑ "The peroxisome proliferator-activated receptor delta, an integrator of transcriptional repression and nuclear receptor signaling". Proceedings of the National Academy of Sciences of the United States of America 99 (5): 2613–2618. March 2002. doi:10.1073/pnas.052707099. PMID 11867749. Bibcode: 2002PNAS...99.2613S. 
  38. ↑ 38.0 38.1 "The retinoblastoma-histone deacetylase 3 complex inhibits PPARgamma and adipocyte differentiation". Developmental Cell 3 (6): 903–910. December 2002. doi:10.1016/S1534-5807(02)00360-X. PMID 12479814. 
  39. ↑ "The growth suppressor PML represses transcription by functionally and physically interacting with histone deacetylases". Molecular and Cellular Biology 21 (7): 2259–2268. April 2001. doi:10.1128/MCB.21.7.2259-2268.2001. PMID 11259576. 
  40. ↑ "The histone deacetylase HDAC3 targets RbAp48 to the retinoblastoma protein". Nucleic Acids Research 29 (15): 3131–3136. August 2001. doi:10.1093/nar/29.15.3131. PMID 11470869. 
  41. ↑ "Duration of nuclear NF-kappaB action regulated by reversible acetylation". Science (New York, N.Y.) 293 (5535): 1653–1657. August 2001. doi:10.1126/science.1062374. PMID 11533489. Bibcode: 2001Sci...293.1653C. 
  42. ↑ "RBP1 recruits both histone deacetylase-dependent and -independent repression activities to retinoblastoma family proteins". Molecular and Cellular Biology 19 (10): 6632–6641. October 1999. doi:10.1128/mcb.19.10.6632. PMID 10490602. 
  43. ↑ "Histone deacetylase 3 interacts with runx2 to repress the osteocalcin promoter and regulate osteoblast differentiation". Journal of Biological Chemistry 279 (40): 41998–42007. October 2004. doi:10.1074/jbc.M403702200. PMID 15292260. 
  44. ↑ "Functional and physical interaction between the histone methyl transferase Suv39H1 and histone deacetylases". Nucleic Acids Research 30 (2): 475–481. January 2002. doi:10.1093/nar/30.2.475. PMID 11788710. 
  45. ↑ "Identification of histone deacetylase-3 domains that interact with the orphan nuclear receptor TR2". Biochemical and Biophysical Research Communications 310 (2): 384–390. October 2003. doi:10.1016/j.bbrc.2003.08.145. PMID 14521922. Bibcode: 2003BBRC..310..384L. 
  46. ↑ "The orphan nuclear receptor TR2 interacts directly with both class I and class II histone deacetylases". Molecular Endocrinology (Baltimore, Md.) 15 (8): 1318–1328. August 2001. doi:10.1210/mend.15.8.0682. PMID 11463856. 
  47. ↑ "Proteomic analysis of ubiquitinated proteins in normal hepatocyte cell line Chang liver cells". Proteomics 8 (14): 2885–2896. July 2008. doi:10.1002/pmic.200700887. PMID 18655026. 
  48. ↑ "Isolation and characterization of cDNAs corresponding to an additional member of the human histone deacetylase gene family". Journal of Biological Chemistry 272 (44): 28001–28007. October 1997. doi:10.1074/jbc.272.44.28001. PMID 9346952. 
  49. ↑ "Regulation of transcription factor YY1 by acetylation and deacetylation". Molecular and Cellular Biology 21 (17): 5979–5991. September 2001. doi:10.1128/MCB.21.17.5979-5991.2001. PMID 11486036. 

Further reading

This article incorporates text from the United States National Library of Medicine, which is in the public domain.



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