CELL BIOLOGY: PROTEIN TRANSLATION
1 Gene Regulation 1 2 Isolation of Nuclei for Use in Genome-Wide DNase Hypersensitivity Assays to Probe Chromatin Structure 13 3 DNase I Digestion of Isolated Nulcei for Genome-Wide Mapping of DNase Hypersensitivity Sites in Chromatin 21 4 Isolation and Analysis of DNA Derived from Nucleosome-Free Regions 35 5 Acquisition of High Quality DNA for Massive Parallel Sequencing by In Vivo Chromatin Immunoprecipitation 53 6 Luciferase Assay to Study the Activity of a Cloned Promoter DNA Fragment 65 Nina Solberg and Stefan Krauss 7 Promoter Deletion Analysis Using a Dual-Luciferase Reporter System 79 8 Application of mRNA Display for In Vitro Selection of DNA-Binding Transcription Factor Complexes 95 9 Isolation of Intracellular Protein – DNA Complexes Using HaloCHIP, an Antibody-Free Alternative to Chromatin Immunoprecipitation 111 10 A Modified Yeast One-Hybrid System for Genome-Wide Identification of Transcription Factor Binding Sites 125 11 Identifying Specific Protein–DNA Interactions Using SILAC-Based Quantitative Proteomics 137 12 Electrophoretic Mobility-Shift and Super-Shift Assays for Studies and Characterization of Protein–DNA Complexes 159 13 Combination of Native and Denaturing PAGE for the Detection of Protein Binding Regions in Long Fragments of Genomic DNA 169 14 Quantitative NanoProteomics Approach for Protein Complex (QNanoPX) Using Gold Nanoparticle-Based DNA Probe 183 15 Chromatin Assembly and In Vitro Transcription Analyses for Evaluation of Individual Protein Activities in Multicomponent Transcriptional Complexes 193 16 Using FRET to Monitor Protein-Induced DNA Bending: The TBP-TATA Complex as a Model System 203 17 Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA Polymerase 217 18 Fluorescence Cross-correlation Spectroscopy (FCCS) to Observe Dimerization of Transcription Factors in Living Cells 229 19 Nuclear Recruitment Assay as a Tool to Validate Transcription Factor Interactions in Mammalian Cells 243 20 Preparation of Cell Lines for Single-Cell Analysis of Transcriptional Activation Dynamics 249 21 Peptide Microarrays for Profiling of Serine/Threonine Kinase Activity of Recombinant Kinases and Lysates of Cells and Tissue Samples 259 22 Immunoaffinity Purification of Protein Complexes from Mammalian Cells 273 23 Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex Composition 289 24 Heavy Methyl-SILAC Labeling Coupled with Liquid Chromatography and High-Resolution Mass Spectrometry to Study the Dynamics of Site-Specific Histone Methylation 299 25 Analysis of p300 Occupancy at the Early Stage of Stem Cell Differentiation by Chromatin Immunoprecipitation 315 26 Mammalian Two-Hybrid Assays for Studies of Interaction of p300 with Transcription Factors 323 27 Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-Length Steroid Receptor Coactivator-1a with Steroid Receptors 339 28 Use of Histone Deacetylase Inhibitors to Examine the Roles of Bromodomain and Histone Acetylation in p300-Dependent Gene Expression 353 29 Histone Deacetylase Inhibitor Valproic Acid as a Small Molecule Inducer to Direct the Differentiation of Pluripotent Stem Cells 359 30 Sedimentation and Immunoprecipitation Assays for Analyzing Complexes that Repress Transcription 365 31 Methods for Studies of Protein Interactions with Different DNA Methyltransferases 385