Transcriptional Regulation : Methods and Protocols - Vancura, Ales.; SpringerLink (Online service) (Totowa, NJ : Humana Press : Imprint: Humana, 2012)
Genome Wide In Vivo Crosslinking of Sequence Specific Transcription Factors -- Characterization of Complex Regulatory Networks and Identification of Promoter Regulatory Elements in Yeast: "In Silico" and "Wet-Lab" Approaches -- Electrophoretic Mobility Shift Assay Analysis of NFkB Transcriptional Regulation by Nuclear IkBa -- Probing Endogenous RNA Polymerase II Pre-Initiation Complexes by Electrophoretic Mobility Shift Assay -- Elucidating Protein: DNA Complex by Oligonucleotide DNA Affinity Purification -- Chromatin Immunoprecipitation (ChIP) Assay as Tool for Analyzing Transcription Factor Activity -- Two-Step Crosslinking for Analysis of Protein-Chromatin Interactions -- Chromatin Immunoprecipitation Analysis of NFkB Transcriptional Regulation by Nuclear IkBa in Human Macrophages -- In Vivo ChIP for the Analysis of Microdissected Tissue Samples -- Quantification of Protein-DNA Interactions by In Vivo Chromatin Immunoprecipitation in Yeast -- Mapping Protein-DNA Interactions Using ChIP-Sequencing -- ChIP and ReChIP Assays:  Investigating Interactions Between Regulatory Proteins, Histone Modifications, and the DNA Sequences to which They Bind -- Transcriptional Regulation of Genes Via Hypoxia-Inducible Factor -- Exchange Protein Directly Activated By Cyclic AMP 1 (Epac1)-Regulated Recruitment of CCAAT/Enhancer Binding Proteins (C/EBPs) to the Suppressor of Cytokine Signalling-3 (SOCS-3) Promoter -- Computational Analysis of Promoter Elements and Chromatin Features in Yeast -- Chromatin Affinity Purification (ChAP) -- Determination of Histone Acetylation Status by Chromatin Immunoprecipitation -- Immunostaining of Drosophila Polytene Chromosomes to Investigate Recruitment of Chromatin Binding Proteins -- Detection of Transcriptional Activators, Co-Activators, and Chromatin Remodeling by Chromatin Immunoprecipitation Coupled with Real-Time PCR -- Chromatin Endogenous Cleavage and Psoralen Crosslinking Assays to Analyze rRNA Gene Chromatin In Vivo -- UV-Induced DNA Damage and DNA Repair in Ribosomal Genes Chromatin -- Analysis of SUC2 Promoter Structure by Nucleosome Scanning -- Chromatin Immunoprecipitation of Mouse Embryos -- Chromatin Immunoprecipitation (ChIP) in Mouse Hippocampal Cells and Tissues -- Approaches for Studying Nucleosome Movement by ATP-Dependent Chromatin Remodeling Complexes -- Mapping Protein-DNA and Protein-Protein Interactions of ATP-Dependent Chromatin Remodelers -- Evaluation of Histone Modifying Enzymes in Stem Cell Populations -- Purification of Multiprotein Histone Acetyltransferase Complexes -- Reconstitution of Active and Stoichiometric Multisubunit Lysine Acetyltransferase Complexes in Insect Cells -- Affinity Purification of MLL3/MLL4 Histone H3K4 Methyltransferase Complex -- Methods for Analyzing Histone Citrullination in Chromatin Structure and Gene Regulation -- Analysis of mRNA Abundance and Stability by Ribonuclease Protection Assay -- Array-Based Nuclear Run-On (ANRO) Analysis -- In Vivo Run on Assays to Monitor Nascent Precursor RNA Transcripts -- Genome Wide Full-Length Transcript Analysis Using 5' and 3' Paired-End-Tag Next Generation Sequencing (RNA-PET) -- Analysis of Cotranscriptionnal RNA Processing by RNA-ChIP Assay -- Quantitative Analysis of Transcription Elongation by RNA Polymerase I In Vitro -- Detection and Characterization of Transcription Termination -- Promoter-Associated Noncoding RNA from the CCND1 Promoter.
Keywords: Biochemistry; Gene expression; Biochemistry, general; Gene Expression