Enzymes of Epigenetics
Author(s)
Bibliographic Information
Enzymes of Epigenetics
（Methods in enzymology / editors in chief, Sidney P. Colowick, Nathan O. Kaplan, v. 573-574）
Academic Press, 2016
- pt. A
- pt. B
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Note
Includes bibliographical references and indexes
Description and Table of Contents
- Volume
-
pt. A ISBN 9780128053652
Description
Enzymes of Epigenetics, one of two new volumes in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field.
This volume covers research methods that are employed to study epigenetic regulation and includes structural, biochemical, molecular, biological, cellular, computational, and systems approaches.
Topics include chromatin structure and histones, posttranslational histone modification enzymes and complexes, histone modification binders, DNA modifications and nucleic acid regulators, epigenetic technologies and small molecule epigenetic regulators, and biological connections
Table of Contents
Chromatin Structure and Histones 1. In Vitro Chromatin Assembly - Strategies and Quality Control Uma Muthurajan, Francesca Mattiroli, Serge Bergeron, Keda Zhou, Yajie Gu, Srinivas Chakravarthy, Pamela Dyer, Thomas Irving and Karolin Luger 2. Preparation, Crystallization and Structure Determination of Chromatin Enzyme/Nucleosome Complexes Robert K. McGinty, Ravindra D. Makde and Song Tan 3. Preparation of Recombinant Centromeric Nucleosomes and Formation of Complexes with Non-Histone Centromere Proteins Nikolina Sekulic and Ben E. Black 4. Functional Characterization of Histone Chaperones using SNAP-Tag-Based Imaging to Assess De Novo Histone Deposition Camille Clement, Isabelle Vassias, Dominique Ray-Gallet and Genevieve Almouzni 5. Analysis of Nucleosome Sliding by ATP-Dependent Chromatin Remodelling Enzymes Coral Y. Zhou and Geeta J. Narlikar
Posttranslational Histone Modification Enzymes and Complexes 6. In Vitro Activity Assays for Myst Histone Acetyltransferases and Adaptation for High-Throughput Inhibitor Screening Cheryl E. McCullough and Ronen Marmorstein 7. Preparation and Biochemical Analysis of Classical Histone Deacetylases Alejandro Villagra, Eva Sahakian and Edward Seto 8. Recombinant Preparation, Biochemical Analysis, and Structure Determination of Sirtuin Family Histone/Protein Deacylases Benjamin Suenkel and Clemens Steegborn 9. Preparation, Biochemical Analysis and Structure Determination of SET Domain Histone Methyltransferases Elisa Bergamin and Jean Francois Couture 10. Expression, Purification and Biochemical Analysis of the LSD1/KDM1A Histone Demethylase Benoit Laurent and Yang Shi 11. LSD1 Histone Demethylase Assays and Inhibition Dawn Hayward and Philip A. Cole 12. Purification, Biochemical Analysis, and Structure Determination of JmjC Lysine Demethylases Swathi Krishnan and Raymond C. Trievel 13. Preparation and Analysis of Native Chromatin Modifying Complexes Yannick Doyon and Jacques Cote
Histone Modification Binders (Readers) 14. Preparation, Biochemical Analysis and Structure Determination of the Bromodomain, an Acetyl-lysine Binding Domain Chunyan Ren, Lei Zeng and Ming-Ming Zhou 15. Preparation, Biochemical Analysis and Structure Determination of Methyllysine Readers Catherine A. Musselman and Tatiana G. Kutateladze
DNA Modifications and Nucleic Acid Regulators 16. Quantification of Oxidized 5-Methylcytosine Bases and TET Enzyme Activity Monica Yun Liu, Jamie E. DeNizio and Rahul M. Kohli 17. Characterization of how DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins Anamika Patel, Hideharu Hashimoto, Xing Zhang and Xiaodong Cheng 18. Crystallographic Studies of Telomerase Hunter Hoffman and Emmanuel Skordalakes 19. Detection and Analysis of Long Non-Coding RNAs Fan Lai, Ezra Blumenthal and Ramin Shiekhattar 20. Identifying Centromeric RNAs Involved in Histone Dynamics in Vivo Delphine Quenet, David Sturgill and Yamini Dalal
- Volume
-
pt. B ISBN 9780128053812
Description
Enzymes of Epigenetics: Part B, one of two new volumes in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field.
This volume covers research methods that are employed in the study of epigenetic regulation, including structural, biochemical, molecular, biological, cellular, computational, and systems approaches.
Topics include chromatin structure and histones, posttranslational histone modification enzymes and complexes, histone modification binders, DNA modifications and nucleic acid regulators, epigenetic technologies, and small molecule epigenetic regulators and biological connections.
Table of Contents
Epigenetic Technologies 1. Identification and Quantification of Histone PTMs using High-Resolution Mass Spectrometry Kelly R. Karch, Simone Sidoli and Benjamin A. Garcia 2. Substrate Specificity Profiling of Histone-Modifying Enzymes by Peptide Microarray Evan M. Cornett, Bradley M. Dickson, Robert M. Vaughan, Swathi Krishnan, Raymond C. Trievel, Brian D. Strahl, and Scott B. Rothbart 3. ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments Bradley M. Dickson, Evan M. Cornett, Zachary Ramjan and Scott B. Rothbart 4. Chemical Biology Approaches for Characterization of Epigenetic Regulators Dalia Barsyte-Lovejoy, Magdalena M Szewczyk, Panagiotis Prinos, Evelyne Lima-Fernandes, Suzanne Ackloo and Cheryl H. Arrowsmith 5. Mapping Lysine Acetyltransferase-Ligand Interactions by Activity-Based Capture David C. Montgomery and Jordan L. Meier 6. Investigating Histone Acetylation Stoichiometry and Turnover Rate Jing Fan, Josue Baeza and John M. Denu 7. Rapid Semisynthesis of Acetylated and Sumoylated Histone Analogs Abhinav Dhall, Caroline E. Weller and Champak Chatterjee 8. An IF-FISH Approach for Co-Visualization of Gene Loci and Nuclear Architecture in Fission Yeast Kyoung-Dong Kim, Osamu Iwasaki and Ken-ichi Noma
Small Molecule Epigenetic Regulators 9. Biology, Chemistry and Pharmacology of Sirtuins Antonio Bedalov, Sarwat Chowdhury and Julian A. Simon 10. Synthesis and Assay of SIRT1 Activating Compounds Han Dai , James L. Ellis , David A. Sinclair and Basil P. Hubbard 11. Synthesis and Assays of Inhibitors of Methyltransferases Xiao-Chuan Cai, Kanishk Kapilashrami and Minkui Luo
Epigenetics and Biological Connections 12. Exploring the Dynamic Relationship between Cellular Metabolism and Chromatin Structure using SILAC-Mass Spec and ChIP-Sequencing Philipp Mews and Shelley L. Berger 13. Current Proteomic Methods to Investigate the Dynamics of Histone Turnover in the Central Nervous System Lorna A. Farrelly, Brian D. Dill, Henrik Molina, Marc R. Birtwistle and Ian Maze 14. ChIP-Sequencing to Map the Epigenome of Senescent Cells using Benzonase Endonuclease Taranjit Singh Rai and Peter D. Adams 15. Exploiting Chromatin Biology to Understand Immunology John L. Johnson and Golnaz Vahed
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