Histone Deacetylases, 1st ed. 2016
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1436

This volume provides different methodologies for all classes of histone deacetylases, which includes detailed procedures on Class I and II histone deacetylase inhibitors, SIRT inhibitors, and bromodomain inhibitors. Histone Deacetylases: Methods and Protocols is divided into four sections: Sections A and B describe methodologies used to detect the activity, function, or chromatin location of HDACs 1 through 11, with Section A discussing Class I and Section B discussing class II histone deacetylases; Section C focuses on the methodologies for cloning and characterizing the acetylation of SIRTs 1 through 7; and Section D describes methods related to histone deacetylase inhibitors. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls.

Thorough and cutting-edge, Histone Deacetylases: Methods and Protocols, is a valuable resource for investigators working on epigenetics, molecular biology, and genetics.

Section A: Class I, II, and IV Histone Deacetylases

1. A Sensitive and Flexible Assay for Determining Histone Deacetylase 1 (HDAC1) Activity
Mei-Yi Wu and Ray-Chang Wu

2. Detection of Sumo Modification of Endogenous Histone Deacetylase 2 (HDAC2) in Mammalian Cells
Simona Citro and Susanna Chiocca

3. Analysis of Epigenetic Regulation of Hypoxia-Induced Epithelial-Mesenchymal Transition in Cancer Cells by Quantitative Chromatin Immunoprecipitation of Histone Deacetylase 3 (HDAC3)
Jian-Qiu Wang, Min-Zu Wu, and Lou-Juey Wu

4. Molecular and Functional Characterization of Histone Deacetylase 4 (HDAC4)
Lin Li and Xiang-Jiao Yang

5. Approaches for Studying the Subcellular Localization, Interactions, and Regulation of Histone Deacetylase 5 (HDAC5)
Amanda J. Guise and Ileana M. Cristea

6. Analysis of Expression and Functions of Histone Deacetylase 6 (HDAC 6)
Miao Li, Yan Zhuang, and Bin Shan

7. Analysis of Histone Deacetylase 7 (HDAC7) Alternative Splicing and Its Role in Embryonic Stem Cell Differentiation toward Smooth Muscle Lineage
Junyao Yang, Andriana Margariti, and Lingfang Zeng

8. Large-Scale Overproduction and Purification of Recombinant Histone Deacetylase 8 (HDAC8) from the Human-Pathogenic Flatworm Schistosoma mansoni
Martin Marek, Tajith B. Shaik, Sylvie Duclaud, Raymond J. Pierce, and Christophe Romier

9. Visualization of Histone Deacetylase 9 (HDAC9) Spatiotemporal Subcellular Localization in Primary Neuron Cultures
Noriyuki Sugo and Nobuhiko Yamamoto

10. Expression and Function of Histone Deacetylase 10 (HDAC10) in B Cell Malignancies
John Powers, Maritza Lienlaf, Patricio Perez-Villarroel, Susan Deng, Tessa Knox, Alejandro Villagra, and Eva Sahakian
11. Functional Analysis of Histone Deacetylase 11 (HDAC11)
Jie Chen, Eva Sahakian, John Powers, Maritza Lienlaf, Patricio Perez-Villarroel, Tessa Knox, and Alejandro Villagra

Section B: Class III Deacetylases

12. Sirtuin1 (SIRT1) in the Acetylation of Downstream Target Proteins
Ana R. Gomes, Jay Sze Yong, Khai Cheng Kiew, Ebru Aydin, Mattaka Khongkow, Sasiwan Laohasinnarong, and Eric W.-F. Lam

13. Protocols for Cloning, Expression, and Functional Analysis of Sirtuin2 (SIRT2)
Shaoping Ji, J. Ronald Doucette, and Adil J. Nazarali

14. Cloning and Characterization of Sirtuin3 (SIRT3)
Andy WC Man, Bo Bai, and Yu Wang

15. Identification of Sirtuin4 (SIRT4) Protein Interactions: Uncovering Candidate Acyl-Modified Mitochondrial Substrates and Enzymatic Regulators
Rommel A. Mathias, Todd M. Greco, and Ileana M. Cristea

16. Generation and Purification of Catalytically Active Recombinant Sirtuin5 (SIRT5) Protein 
Surinder Kumar and David B. Lombard

17. Sirtuin6 (SIRT6) Activity Assays
Minna Rahnasto-Rilla, Maija Lahtela-Kakkonen, and Ruin Moaddel

18. Molecular, Cellular, and Physiological Characterization of Sirtuin7 (SIRT7)
Jiyung Shin and Danica Chen

Section C: Histone Deacatylase and Deacetylase Inhibitors

19. HDAC Inhibitors
Heidi Olzscha, Mina E. Bekheet, Semira Sheikh, and Nicholas B. La Thangue

20. Assessment of the Anti-Proliferative Activity of a BET Bromodomain Inhibitor as Single Agent and in Combination in Non-Hodgkin Lymphoma Cell Lines
Elena Bernasconi, Eugenio Gaudio, Ivo Kwee, and Francesco Bertoni

21. Screening the Impact of Sirtuin Inhibitors on Inflammatory and Innate Immune Responses of Macrophages and in a Mouse Model of Endotoxic Shock
Eleonora Ciarlo and Thierry Roger

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts