Hdac/Hat Function Assessment and Inhibitor Development: Methods and Protocols

ISBN-13: 9781493982264 / Angielski / Miękka / 2018 / 415 str.

Oliver H. Kramer

Spis treści

Part I: Analysis of Cellular Processes that Are Regulated by HDACs

 

1. Detection of Autophagy Induction After HDAC Inhibitor Treatment in Leukemic Cells

Anja Göder, Nisintha Mahendrarajah, and Oliver H. Krämer

2. Assessment of HDACi-Induced Protein Cleavage by Caspases

Fabian Treude, Tobias Gladbach, Jacqueline Plaster, and Jörg Hartkamp

3. Assessment of HDACi-Induced Cytotoxicity

Lisa Blümel, Christian Marx, Marie Kühne, and Jürgen Sonnemann

4. Analysis of HDACi-Induced Changes in Chromosomal Passenger Complex Localization

Britta Unruhe-Knauf and Shirley K. Knauer

5. Analysis of Histone Deacetylase-Dependent Effects on Cell Migration Using the Stripe Assay

Sonja Mertsch and Solon Thanos

6. Using Histone Deacetylase Inhibitors to Analyze the Relevance of HDACs for Translation

Darren M. Hutt, Daniela Martino Roth, Christelle Marchal, and Marion Bouchecareilh

7. Effects of HDACi on Immunological Functions

René Winkler and Christian Kosan

8. DNA Fiber Spreading Assay to Test HDACi Effects on DNA and Its Replication

Teodora Nikolova, Anja Göder, Ann Parplys, and Kerstin Borgmann

9. Assessing the Effect of Class I Histone Deacetylase Activity on DNA Double-Strand Break Repair by Homologous Recombination

Andrea Krumm and Wynand P. Roos

Part II: Primary Cell Systems and In Vivo Models to Assess HDAC Functions

10. Establishment and Characterization of Long-Term Cultures Derived from Primary Acute Myeloid Leukemia Cells for HDAC Inhibitor Research

Annette Romanski and Gesine Bug

11. Assessing the Histone Deacetylase Activity of SIRT6 in Primary Murine Hepatocytes Via Proximity Ligation Assay

Katharina Wolf and Susanne Strand

12. Purification and Analysis of Male Germ Cells from Adult Mouse Testis

Thierry Buchou, Minjia Tan, Sophie Barral, Anne-Laure Vitte, Sophie Rousseaux, Juan Arechaga, and Saadi Khochbin

13. Generation of Tissue-Specific Mouse Models to Analyze HDAC Functions

Astrid Hagelkruys, Mirjam A. Moser, and Christian Seiser

14. Engineering of Conditional Class I Hdac Knockout Mice and Generation of a Time-Spatial Knockout by a Dual Recombination System

Sieglinde Bayer and Matthias Wirth

15. Xenografting of Cancer Cell Lines for In Vivo Screening of the Therapeutic Potential of HDAC Inhibitors

Daniel Nettersheim, Sina Jostes, and Hubert Schorle

16. Generation of Xenotransplants from Human Cancer Biopsies to Assess Anti-Cancer Activities of HDACi

Christina Susanne Mullins, Stephanie Bock, Mathias Krohn, and Michael Linnebacher

Part III: Assessment of HDAC-Dependent Effects on Signaling Cascades in Primary and Permanent Cells

17. Phospho-Flow Analysis of Primary Mouse Cells after HDAC Inhibitor Treatment

Dagmar Hildebrand and Katharina F. Kubatzky

18. Evaluation of Innate Immune Gene Expression Following HDAC Inhibitor Treatment by High Throughput qPCR and PhosFlow Cytometry

David Olagnier, Cindy Chiang, and John Hiscott

19. Assessing HDAC Function in the Regulation of Signal Transducer and Activator of Transcription 5 (STAT5) Activity Using Chromatin Immunoprecipitation (ChIP)

Sophia Pinz and Anne Rascle

20. Modulation of STAT1-Driven Transcriptional Activity by Histone Deacetylases

Benjamin Y. Owusu and Lidija Klampfer

21. Proximity Ligation Assay to Quantify Foxp3 Acetylation in Regulatory T Cells

Jing Jiao, Rongxiang Han, Wayne W. Hancock, and Ulf H. Beier

Part IV: PTMs Controlling Acetylation Balances and HDAC Functions

22. Testing the Effects of SIAH Ubiquitin E3 Ligases on Lysine Acetyl Transferases

Jan Hagenbucher, Hilda Stekman, Alfonso Rodriguez-Gil, Michael Kracht, and M. Lienhard Schmitz

23. Assessment of HDACi-Induced Acetylation of Non-Histone Proteins by Mass Spectrometry

Martin Wieczorek, Karl-Heinz Gührs, and Thorsten Heinzel

24. Assessing the Role of Paralog-Specific Sumoylation of HDAC1

Simona Citro and Susanna Chiocca

25. Analysis of Histone Deacetylases Sumoylation by Immunoprecipitation Techniques

Tobias Wagner, Maren Godmann, and Thorsten Heinzel

Part V: Improved, Novel, and Specific HDACi

26. How to Distinguish Between the Activity of HDAC1-3 and HDAC6 with Western Blot

Mandy Beyer, Nicole Kiweler, Siavosh Mahboobi, and Oliver H. Krämer

27. Evaluating the Effect of HDAC8 Inhibition in Malignant Peripheral Nerve Sheath Tumors

Gonzalo Lopez and Raphael E. Pollock

28. Analyzing the Impact of Pan- and Class-Specific HDACi on Differentiation-Associated Factors

Katrin Noack and Oliver H. Krämer

29. Encapsulation of the HDACi Ex527 into Liposomes and Polymer-Based Particles

Dorle Hennig and Diana Imhof

30. Preparation of Histone Deacetylase Inhibitor Vorinostat Loaded Poly d, l-lactide-co-glycolide Polymeric Nanoparticles by Nanoprecipitation Method

Vilwanathan Ravikumar and Renu Sankar

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31. Generation and Assessment of Fusions Between HDACi and TKi

Siavosh Mahboobi, Bernadette Pilsl, and Andreas Sellmer

Blurb

This detailed collection covers how the biological functions of histone deacetylases (HDACs) and histone acetyltransferases (HATs) can be detected in various experimental settings, both in vivo and in vitro. The book also covers the generation and specificity of deacetylase inhibitors and how such agents can be used to test experimental hypotheses. Written for the popular Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step by step, readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. 

Comprehensive and practical, HDAC HAT Function Assessment and Inhibitor Development: Methods and Protocols serves as an ideal guide to this vital area of study.