Gene Regulation: Methods and Protocols (Methods in Molecular Biology, 977)

✍ Scribed by Minou Bina (editor)

• Publisher: Humana
• Year: 2013
• Tongue: English
• Leaves: 396
• Category: Library

✦ Synopsis

In this volume of Methods in Molecular Biology™, expert investigators offer comprehensive, complementary, and cutting-edge technologies for studies of gene regulation. The chapters of Gene Regulation: Methods and Protocols are organized to provide an integrated and a coherent view of control systems and their associated components. The protocols are broad in their scope. They include molecular, biochemical, spectroscopic techniques as well as high throughput strategies. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Comprehensive and broad in their scope, the protocols are useful to researchers in many disciplines including molecular biology, genomics, biochemistry, biomedicine, nutrition, and agricultural sciences.

✦ Table of Contents

Gene Regulation
Preface
Contributors
Chapter 1: Gene Regulation
Chapter 2: Isolation of Nuclei for Use in Genome-Wide DNase Hypersensitivity Assays to Probe Chromatin Structure
Chapter 3: DNase I Digestion of Isolated Nulcei for Genome-Wide Mapping of DNase Hypersensitivity Sites in Chromatin
Chapter 4: Isolation and Analysis of DNA Derived from Nucleosome-Free Regions
Chapter 5: Acquisition of High Quality DNA for Massive Parallel Sequencing by In Vivo Chromatin Immunoprecipitation
Chapter 6: Luciferase Assay to Study the Activity of a Cloned Promoter DNA Fragment
Chapter 7: Promoter Deletion Analysis Using a Dual-Luciferase Reporter System
Chapter 8: Application of mRNA Display for In Vitro Selection of DNA-Binding Transcription Factor Complexes
Chapter 9: Isolation of Intracellular Protein – DNA Complexes Using HaloCHIP, an Antibody-Free Alternative to Chromatin Imm...
Chapter 10: A Modified Yeast One-Hybrid System for Genome-Wide Identification of Transcription Factor Binding Sites
Chapter 11: Identifying Specific Protein–DNA Interactions Using SILAC-Based Quantitative Proteomics
Chapter 12: Electrophoretic Mobility-Shift and Super-Shift Assays for Studies and Characterization of Protein–DNA Complexes
Chapter 13: Combination of Native and Denaturing PAGE for the Detection of Protein Binding Regions in Long Fragments of Gen...
Chapter 14: Quantitative NanoProteomics Approach for Protein Complex (QNanoPX) Using Gold Nanoparticle-Based DNA Probe
Chapter 15: Chromatin Assembly and In Vitro Transcription Analyses for Evaluation of Individual Protein Activities in Multi...
Chapter 16: Using FRET to Monitor Protein-Induced DNA Bending: The TBP-TATA Complex as a Model System
Chapter 17: Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA Polyme...
Chapter 18: Fluorescence Cross-correlation Spectroscopy (FCCS) to Observe Dimerization of Transcription Factors in Living C...
Chapter 19: Nuclear Recruitment Assay as a Tool to Validate Transcription Factor Interactions in Mammalian Cells
Chapter 20: Preparation of Cell Lines for Single-Cell Analysis of Transcriptional Activation Dynamics
Chapter 21: Peptide Microarrays for Profiling of Serine/Threonine Kinase Activity of Recombinant Kinases and Lysates of Cel...
Chapter 22: Immunoaffinity Purification of Protein Complexes from Mammalian Cells
Chapter 23: Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex Composition
Chapter 24: Heavy Methyl-SILAC Labeling Coupled with Liquid Chromatography and High-Resolution Mass Spectrometry to Study t...
Chapter 25: Analysis of p300 Occupancy at the Early Stage of Stem Cell Differentiation by Chromatin Immunoprecipitation
Chapter 26: Mammalian Two-Hybrid Assays for Studies of Interaction of p300 with Transcription Factors
Chapter 27: Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-Length Steroid Receptor Coactiv...
Chapter 28: Use of Histone Deacetylase Inhibitors to Examine the Roles of Bromodomain and Histone Acetylation in p300-Depen...
Chapter 29: Histone Deacetylase Inhibitor Valproic Acid as a Small Molecule Inducer to Direct the Differentiation of Plurip...
Chapter 30: Sedimentation and Immunoprecipitation Assays for Analyzing Complexes that Repress Transcription
Chapter 31: Methods for Studies of Protein Interactions with Different DNA Methyltransferases
Index