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Title Nucleosomes, histones and chromatin / Edited by Carl Wu, C. David Allis.
Published Amsterdam : Academic Press, 2012.
Book Cover

 Floor4  QP601 .M49  v.513 2012    IN LIBRARY
 Floor4  QP601 .M49  v.512 2012    IN LIBRARY
Description 2 v. : ill. ; 24 cm.
Series Methods in enzymology, 0076-6879 ; v. 512-513
Methods in enzymology ; v. 512-513.
Contents Section 1. Histone and DNA Modifications, Enzymes, Chromatin Effectors -- 1.Examining Histone Posttranslational Modification Patterns by High-Resolution Mass Spectrometry / Benjamin A. Garcia -- 1.Introduction -- 2.Materials -- 3.Nuclei Isolation -- 4.Acid Extraction -- 5.Offline Reverse-Phase High-Performance Liquid Chromatography for Histone Variant Purification (Optional) -- 6.Chemical Derivatization of Histones -- 7.Stage-Tip Cleanup of Peptide Samples Prior to MS Analysis -- 8.Enrichment for Phosphorylated Peptides Using Titanium Dioxide (TiO2) Beads (Optional) -- 9.Online RP-HPLC and MS -- Acknowledgments -- References -- 2.Investigating the Cell Cycle-Associated Dynamics of Histone Modifications Using Quantitative Mass Spectrometry / Bing Zhu -- 1.Introduction -- 2.Experimental Design -- 3.Cell Culture -- 4.Extraction and Separation of Histones -- 5.Preparation of Propionic Anhydride-Derivatized Tryptic Histone Peptides --
6.Mass Spectrometric Analysis and Quantification of Histone PTMs -- Acknowledgments -- References -- 3.A Method to Site-Specifically Incorporate Methyl-Lysine Analogues into Recombinant Proteins / Kevan M. Shokat -- 1.Introduction -- 2.Protocol to Install MLA into Recombinant Proteins -- References -- 4.Methods Applied to the Study of Protein Arginine Methylation / Mark T. Bedford -- 1.Introduction -- 2.In Vitro Arginine-Methylation Assays -- 3.Enzyme Sources for In Vitro Methylation Reactions -- 4.Substrate Sources for In Vitro Methylation Assays -- 5.Cell-Based Methylation Assays -- 6.Methyl-Specific Antibodies -- 7.Using Global-Methylation Inhibitors -- 8.Using Cell-Based Reporter Systems to Screen for PRMT Inhibitors -- 9.Summary -- Acknowledgments -- References -- 5.Enzymatic Analysis of Tet Proteins: Key Enzymes in the Metabolism of DNA Methylation / Yi Zhang -- 1.Introduction -- 2.Expression and Purification of Tet Proteins --
Contents note continued: 3.Tet Activity Assays -- 4.Analysis of the Cytosine Derivatives by 2D-TLC -- 5.Analysis of the Cytosine Derivatives by Mass Spectrometry -- 6.Analysis of the Endogenous Level of Cytosine Derivatives by Mass Spectrometry -- Acknowledgments -- References -- 6.Peptide Microarrays to Interrogate the "Histone Code" / Stephen M. Fuchs -- 1.Introduction -- 2.Histone Peptide Library -- 3.Microarray Printing -- 4.Analysis of Antibodies, Effector Proteins, and Enzymes -- 5.Data Analysis -- 6.Summary and Perspectives -- Acknowledgments -- References -- 7.Identifying Chromatin Readers Using a SILAC-Based Histone Peptide Pull-Down Approach / Michiel Vermeulen -- 1.Introduction -- 2.Histone Peptide Synthesis -- 3.SILAC Labeling -- 4.Incorporation Check -- 5.Preparation of Nuclear Extract -- 6.Histone Peptide Pull-Down -- 7.In-gel Digestion -- 8.Mass Spectrometry -- 9.Data Analysis -- 10.Outlook -- Acknowledgments -- References --
8.High-Throughput Strategy to Identify Inhibitors of Histone-Binding Domains / John M. Denu -- 1.Introduction -- 2.AlphaScreen Assay Principles -- 3.Materials and Instrumentation -- 4.Design and Preparation of Histone Peptides and Histidine Tag Fusion Proteins -- 5.Initial Optimization of an AlphaScreen-Based Histone-Binding Assay -- 6.Primary Screening -- 7.Hit Selection and Secondary Screening -- 8.Concentration-Dependence Validation Studies -- 9.Assay-Specific Compound Interference -- 10.Additional Assays for Validation -- 11.Summary -- Acknowledgments -- References -- 9.Validation of Histone-Binding Partners by Peptide Pull-Downs and Isothermal Titration Calorimetry / Alexander Ruthenburg -- 1.Introduction -- 2.Initial Screening: Discovering Putative Interactions Between Histone Peptides and Potential Binding Partners -- 3.Peptide Pull-downs: Establishing Candidates for Quantitative Assessment --
4.Isothermal Titration Calorimetry (ITC): Defining Histone PTM Binding Affinities -- 5.Reagent Considerations -- 6.Summary: Peptide Pull-Downs and ITC in the Chromatin Field -- Acknowledgments -- References -- Section 2 Nucleosome and Histone Dynamics -- 10.Analysis of Histone Chaperone Antisilencing Function 1 Interactions / Mair E.A. Churchill -- 1.Introduction -- 2.Preparation of Asf -- 3.Preparation of Histone Components -- 4.Fluorescence Spectroscopy Analysis of Asf1 Binding Interactions with Histones -- 5.Electrophoretic Mobility Shift Analysis of Asf1 Binding Interactions with Histones -- 6.Summary and Implications -- Acknowledgments -- References -- 11.Quantifying Chromatin-Associated Interactions: The HI-FI System / Aaron R. Hieb -- 1.Introduction to Chromatin and the HI-FI System -- 2.Fluorescent Labeling and Preparation of Nucleosome Components -- 3.Imaging Requirements and Reaction Conditions --
Contents note continued: 4.HI-FI Binding Affinity Assay Setup and Execution -- 5.HI-FI Stoichiometric Assays Setup and Execution -- 6.HI-FI Competition Assays with FRET -- 7.Summary -- Acknowledgments -- References -- 12.Biochemical Assay for Histone H2A.Z Replacement by the Yeast SWR1 Chromatin Remodeling Complex / Ed Luk -- 1.Introduction -- 2.Preparation of Reagents -- 3.In Vitro Htz1 Replacement Assay by Chromatin Remodeling Complex SWR1 -- 4.Special Notes -- 5.Concluding Remarks -- Acknowledgments -- References -- 13.Experimental Analysis of the Mechanism of Chromatin Remodeling by RNA Polymerase II / Vasily M. Studitsky -- 1.Introduction -- 2.Materials and Methods -- 3.DNase I Footprinting of ECs Formed by E. coli RNAP During Transcription Through a Nucleosome -- 4.Mapping of ECs Formed by Pol II During Transcription Through a Nucleosome Using Restriction Endonucleases -- Acknowledgments -- References.
Subject Histones.
Basic proteins.
Related Names Wu, Carl.
Allis, C. David.
ISBN 0123919401
OCLC number 812848526