Histone Deacetylases: Methods and Protocols

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