Gene Regulation

Gene Regulation.- Isolation of Nuclei for use in Genome-wide DNase Hypersensitivity Assays to Probe Chromatin Structure.- DNase I Digestion of Isolated Nulcei for Genome-Wide Mapping of DNase Hypersensitivity Sites in Chromatin.- Isolation and Analysis of DNA Derived from Nucleosome-Free Regions.- Acquisition of High Quality DNA for Massive Parallel Sequencing by in vivo Chromatin Immunoprecipitation.- Luciferase Assay to Study the Activity of a Cloned Promoter DNA Fragment.- Promoter Deletion Analysis using a Dual-luciferase Reporter System.- Application of mRNA Display for in vitro Selection of DNA-binding Transcription Factor Complexes.- Isolation of Intracellular Protein:DNA Complexes using HaloCHIP; An Antibody Free Alternative to Chromatin Immunoprecipitation.- A Modified Yeast One-Hybrid System for Genome Wide Identification of Transcription Factor Binding Sites.- Identifying Specific Protein--DNA Interactions using SILAC--based Quantitative Proteomics.- Electrophoretic Mobility-Shift and Super-Shift Assays for Studies and Characterization of Protein-DNA Complexes.- Combination of Native and Denaturing PAGE for the Detection of Protein Binding Regions in Long Fragments of Genomic DNA.- Quantitative NanoProteomics Approach for Protein Complex (QNanoPX) using Gold Nanoparticle-based DNA Probe.- Chromatin Assembly and In Vitro Transcription Analyses for Evaluation of Individual Protein Activities in Multicomponent Transcriptional Complexes.- Using FRET to Monitor Protein-induced DNA Bending: The TBP-TATA Complex as a Model System.- Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA Polymerase.- Fluorescence Cross-correlation Spectroscopy (FCCS) to Observe Dimerization of Transcription Factors in Living Cells.- Nuclear Recruitment Assay as a Tool to validate Transcription Factor Interactions in Mammalian Cells.- Preparation of Cell Lines for Single-Cell Analysis of TranscriptionalActivation Dynamics.- Peptide Microarrays for Profiling of Serine/threonine Kinase Activity of Recombinant Kinases and Lysates of Cells and Tissue Samples.- Immunoaffinity Purification of Protein Complexes from Mammalian Cells.- Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex Composition.- Heavy Methyl-SILAC Labeling Coupled with Liquid Chromatography and High-resolution Mass Spectrometry to Study the Dynamics of Site-specific Histone Methylation.- Analysis of p300 Occupancy at the Early Stage of Stem Cell Differentiation by Chromatin Immunoprecipitation.- Mammalian Two-Hybrid Assays for Studies of Interaction of p300 with Transcription Factors.- Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-length Steroid Receptor Coactivator-1a with Steroid Receptors.- Use of Histone Deacetylase Inhibitors to Examine the Roles of Bromodomain and Histone Acetylation in p300-dependent Gene Expression.- Histone Deacetylases Valproic Acid as a Small Molecule Inducer to Direct the Differentiation of Pluripotent Stem Cells.- Sedimentation and Immunoprecipitation Assays for Analyzing Complexes that Repress Transcription.- Methods for Studies of Protein Interactions with Different DNA Methyltransferases.