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.
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