Abstract
The human genome in order to get accommodated within the constrained nuclear space requires remarkably high level of condensation (Tseng and Yang 2013). This condensation results in the formation of chromatin, a supremely organized nucleoprotein structure (Olins and Olins 1974). Nucleosome forms the fundamental unit of this structural polymer (chromatin). Each nucleosome has a nucleosome core formed from an octameric complex made of polycationic core histones around which 145–147 bp of DNA are wrapped (Davey et al. 2002; Korolev et al. 2018; Luger et al. 1997; McGinty and Tan 2015). Adjacent nucleosome cores of two nucleosomes are connected by linker DNA which is frequently in contact with linker histone H1 (or H5 in birds) (Andreeva et al. 1978; Simpson 1978). Apart from the significant role in genomic compaction, nucleosomes serve as signalling focal points for chromatin-templated processes (McGinty and Tan 2015).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci U S A 51:786–794
Andreeva NB, Vishnevskaia T, Gazarian KG (1978) Role of serine-rich histone (H5) in bird erythrocyte genome inactivation. Mol Biol 12:123–134
Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395
Barnes CE, English DM, Cowley SM (2019) Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription. Essays Biochem 63:97–107
Bradner JE, West N, Grachan ML, Greenberg EF, Haggarty SJ, Warnow T, Mazitschek R (2010) Chemical phylogenetics of histone deacetylases. Nat Chem Biol 6:238–243
Buggy JJ, Sideris ML, Mak P, Lorimer DD, McIntosh B, Clark JM (2000) Cloning and characterization of a novel human histone deacetylase, HDAC8. Biochem J 350(Pt 1):199–205
Cai RL, Yan-Neale Y, Cueto MA, Xu H, Cohen D (2000) HDAC1, a histone deacetylase, forms a complex with Hus1 and Rad9, two G2/M checkpoint Rad proteins. J Biol Chem 275:27909–27916
Chini CC, Escande C, Nin V, Chini EN (2010) HDAC3 is negatively regulated by the nuclear protein DBC1. J Biol Chem 285:40830–40837
Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9Å resolution††we dedicate this paper to the memory of Max Perutz who was particularly inspirational and supportive to T.J.R. in the early stages of this study. J Mol Biol 319:1097–1113
David D, Cardoso J, Marques B, Marques R, Silva ED, Santos H, Boavida MG (2003) Molecular characterization of a familial translocation implicates disruption of HDAC9 and possible position effect on TGFbeta2 in the pathogenesis of Peters’ anomaly. Genomics 81:489–503
de Leval L, Waltregny D, Boniver J, Young RH, Castronovo V, Oliva E (2006) Use of histone deacetylase 8 (HDAC8), a new marker of smooth muscle differentiation, in the classification of mesenchymal tumors of the uterus. Am J Surg Pathol 30:319–327
Denu JM (2005) The Sir 2 family of protein deacetylases. Curr Opin Chem Biol 9:431–440
Ganai S (2015) In silico approaches towards safe targeting of class I histone deacetylases. https://doi.org/10.1007/978-1-4614-6436-5_459-1, pp 1–9
Ganai SA (2016) Histone deacetylase inhibitor pracinostat in doublet therapy: a unique strategy to improve therapeutic efficacy and to tackle herculean cancer chemoresistance. Pharm Biol 54:1926–1935
Ganai SA (2017) Small-molecule modulation of HDAC6 activity: the propitious therapeutic strategy to vanquish neurodegenerative disorders. Curr Med Chem 24:4104–4120
Ganai SA (2019) HDACs and their distinct classes. In: Ganai SA (ed) Histone deacetylase inhibitors — epidrugs for neurological disorders. Springer, Singapore, pp 21–25
Gao L, Cueto MA, Asselbergs F, Atadja P (2002) Cloning and functional characterization of HDAC11, a novel member of the human histone deacetylase family. J Biol Chem 277:25748–25755
Gao C, Li X, Lam M, Liu Y, Chakraborty S, Kao H-Y (2006) CRM1 mediates nuclear export of HDAC7 independently of HDAC7 phosphorylation and association with 14-3-3s. FEBS Lett 580:5096–5104
Grozinger CM, Hassig CA, Schreiber SL (1999) Three proteins define a class of human histone deacetylases related to yeast Hda1p. Proc Natl Acad Sci U S A 96:4868–4873
Guardiola AR, Yao TP (2002) Molecular cloning and characterization of a novel histone deacetylase HDAC10. J Biol Chem 277:3350–3356
Hai Y, Christianson DW (2016) Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Nat Chem Biol 12:741–747
Haigis MC, Sinclair DA (2010) Mammalian sirtuins: biological insights and disease relevance. Annu Rev Pathol 5:253–295
Houtkooper RH, Pirinen E, Auwerx J (2012) Sirtuins as regulators of metabolism and healthspan. Nat Rev Mol Cell Biol 13:225–238
Hubbert C, Guardiola A, Shao R, Kawaguchi Y, Ito A, Nixon A, Yoshida M, Wang XF, Yao TP (2002) HDAC6 is a microtubule-associated deacetylase. Nature 417:455–458
Khan N, Jeffers M, Kumar S, Hackett C, Boldog F, Khramtsov N, Qian X, Mills E, Berghs SC, Carey N, Finn PW, Collins LS, Tumber A, Ritchie JW, Jensen PB, Lichenstein HS, Sehested M (2007) Determination of the class and isoform selectivity of small-molecule histone deacetylase inhibitors. Biochem J 409:581–589
Korolev N, Lyubartsev AP, Nordenskiöld L (2018) A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. Sci Rep 8:1543
Kupis W, Pałyga J, Tomal E, Niewiadomska E (2016) The role of sirtuins in cellular homeostasis. J Physiol Biochem 72:371–380
Lahm A, Paolini C, Pallaoro M, Nardi MC, Jones P, Neddermann P, Sambucini S, Bottomley MJ, Lo Surdo P, Carfí A, Koch U, De Francesco R, Steinkühler C, Gallinari P (2007) Unraveling the hidden catalytic activity of vertebrate class IIa histone deacetylases. Proc Natl Acad Sci U S A 104:17335–17340
Lawlor L, Yang XB (2019) Harnessing the HDAC–histone deacetylase enzymes, inhibitors and how these can be utilised in tissue engineering. Int J Oral Sci 11:20
Lee H, Rezai-Zadeh N, Seto E (2004) Negative regulation of histone deacetylase 8 activity by cyclic AMP-dependent protein kinase A. Mol Cell Biol 24:765–773
Li X, Song S, Liu Y, Ko SH, Kao HY (2004) Phosphorylation of the histone deacetylase 7 modulates its stability and association with 14-3-3 proteins. J Biol Chem 279:34201–34208
Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 a resolution. Nature 389:251–260
Martin D, Li Y, Yang J, Wang G, Margariti A, Jiang Z, Yu H, Zampetaki A, Hu Y, Xu Q, Zeng L (2014) Unspliced X-box-binding protein 1 (XBP1) protects endothelial cells from oxidative stress through interaction with histone deacetylase 3. J Biol Chem 289:30625–30634
McGinty RK, Tan S (2015) Nucleosome structure and function. Chem Rev 115:2255–2273
McKinsey TA, Zhang CL, Lu J, Olson EN (2000) Signal-dependent nuclear export of a histone deacetylase regulates muscle differentiation. Nature 408:106–111
Miska EA, Karlsson C, Langley E, Nielsen SJ, Pines J, Kouzarides T (1999) HDAC4 deacetylase associates with and represses the MEF2 transcription factor. EMBO J 18:5099–5107
Mottamal M, Zheng S, Huang TL, Wang G (2015) Histone deacetylase inhibitors in clinical studies as templates for new anticancer agents. Molecules (Basel, Switzerland) 20:3898–3941
Nutsford AN, Galvin HD, Ahmed F, Husain M (2019) The class IV human deacetylase, HDAC11, exhibits anti-influenza A virus properties via its involvement in host innate antiviral response. Cell Microbiol 21:e12989
Olins AL, Olins DE (1974) Spheroid chromatin units (ν bodies). Science (New York, N.Y.) 183:330–332
Olzmann JA, Li L, Chudaev MV, Chen J, Perez FA, Palmiter RD, Chin LS (2007) Parkin-mediated K63-linked polyubiquitination targets misfolded DJ-1 to aggresomes via binding to HDAC6. J Cell Biol 178:1025–1038
Parihar P, Solanki I, Mansuri ML, Parihar MS (2015) Mitochondrial sirtuins: emerging roles in metabolic regulations, energy homeostasis and diseases. Exp Gerontol 61:130–141
Petrie K, Guidez F, Howell L, Healy L, Waxman S, Greaves M, Zelent A (2003) The histone deacetylase 9 gene encodes multiple protein isoforms. J Biol Chem 278:16059–16072
Radhakrishnan R, Li Y, Xiang S, Yuan F, Yuan Z, Telles E, Fang J, Coppola D, Shibata D, Lane WS, Zhang Y, Zhang X, Seto E (2015) Histone deacetylase 10 regulates DNA mismatch repair and may involve the deacetylation of MutS homolog 2. J Biol Chem 290:22795–22804
Sack MN, Finkel T (2012) Mitochondrial metabolism, sirtuins, and aging. Cold Spring Harb Perspect Biol 4
Santos L, Escande C, Denicola A (2016) Potential modulation of sirtuins by oxidative stress. Oxidative Med Cell Longev 2016:9831825
Shinsky SA, Christianson DW (2018) Polyamine deacetylase structure and catalysis: prokaryotic acetylpolyamine amidohydrolase and eukaryotic HDAC10. Biochemistry 57:3105–3114
Simpson RT (1978) Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry 17:5524–5531
Tolsma TO, Hansen JC (2019) Post-translational modifications and chromatin dynamics. Essays Biochem 63:89–96
Tseng C, Yang X (2013) Packaging DNA into chromosomes: how do the long threads of DNA fit into the small interphase nucleus? pp 111–129
Vaquero A (2009) The conserved role of sirtuins in chromatin regulation. Int J Dev Biol 53:303–322
Verdin E, Dequiedt F, Kasler HG (2003) Class II histone deacetylases: versatile regulators. Trends Genet 19:286–293
Villagra A, Cheng F, Wang H-W, Suarez I, Glozak M, Maurin M, Nguyen D, Wright KL, Atadja PW, Bhalla K, Pinilla-Ibarz J, Seto E, Sotomayor EM (2009) The histone deacetylase HDAC11 regulates the expression of interleukin 10 and immune tolerance. Nat Immunol 10:92–100
Waltregny D, Glénisson W, Tran SL, North BJ, Verdin E, Colige A, Castronovo V (2005) Histone deacetylase HDAC8 associates with smooth muscle alpha-actin and is essential for smooth muscle cell contractility. FASEB J 19:966–968
Yang X-J, Grégoire S (2005) Class II histone deacetylases: from sequence to function, regulation, and clinical implication. Mol Cell Biol 25:2873–2884
Yang XJ, Seto E (2007) HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention. Oncogene 26:5310–5318
Yang WM, Tsai SC, Wen YD, Fejer G, Seto E (2002) Functional domains of histone deacetylase-3. J Biol Chem 277:9447–9454
Zhou X, Richon VM, Rifkind RA, Marks PA (2000) Identification of a transcriptional repressor related to the noncatalytic domain of histone deacetylases 4 and 5. Proc Natl Acad Sci U S A 97:1056–1061
Zhou X, Marks PA, Rifkind RA, Richon VM (2001) Cloning and characterization of a histone deacetylase, HDAC9. Proc Natl Acad Sci U S A 98:10572–10577
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Ganai, S.A. (2020). Summa of Erasers of Histone Acetylation with Special Emphasis on Classical Histone Deacetylases (HDACs). In: Histone Deacetylase Inhibitors in Combinatorial Anticancer Therapy. Springer, Singapore. https://doi.org/10.1007/978-981-15-8179-3_3
Download citation
DOI: https://doi.org/10.1007/978-981-15-8179-3_3
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-15-8178-6
Online ISBN: 978-981-15-8179-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)