Transcriptional Regulation, Softcover reprint of the original 1st ed. 2012
Methods and Protocols
Methods in Molecular Biology Series, Vol. 809

Through many recent remarkable developments, perhaps the most significant advancements in the study of transcriptional regulation are the development of genome-wide approaches for measuring gene expression, exemplified by gene chips (chip), and chromatin immunoprecipitation assays (ChIP) for measuring in vivo protein-DNA interactions at any genomic loci. Transcriptional Regulation: Methods and Protocols takes this progress and builds upon it with a collection of key protocols used in expert laboratories around the world.  Divided into four convenient sections, this detailed volume explores promoter elements, transcription factors, and preinitiation complex (PIC) assembly, chromatin structure, chromatin modifying complexes, and RNA synthesis and regulation. 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 vital tips on troubleshooting and avoiding known pitfalls.

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 InvestigateRecruitment 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 CCND1Promoter.