Vancura A. (Ed.). Transcriptional Regulation: Methods and Protocols

Humana Press, 2012. - 644 p. - 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. Comprehensive and accessible, Transcriptional Regulation: Methods and Protocols equally serves senior researchers and scientists experienced in transcriptional regulation as well as graduate students and scientists who wish to study transcriptional regulation for the first time.Contents
Promoter Elements, Transcription Factors, and Pre-Initiation Complex (PIC) Assembly
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
Chromatin Structure
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
Chromatin Modifying Complexes
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
RNA Synthesis and 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