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Transcriptional regulation : methods and protocols / edited by Ales Vancura. — New York : Humana Press, c2012. – (58.17/M592/v.809) |
Contents
Contents
Preface
Contributors
PART I PROMOTER ELEMENTS， TRANSCRIPTION FACTORS， AND PRE-INITIATION COMPLEX ASSEMBLY
1 Genome-Wide In Vivo Cross-linking of Sequence-Specific Transcription Factors
2 Characterization of Complex Regulatory Networks and Identification of Promoter Regulatory Elements in Yeast: "In Silico" and "Wet-Lab" Approaches
3 Electrophoretic Mobility Shift Assay Analysis of NFK:B Transcriptional Regulation by Nuclear IκBα
4 Probing Endogenous RNA Polymerase II Pre-initiation Complexes by Electrophoretic Mobility Shift Assay
5 Elucidating Protein: DNA Complex by Oligonucleotide DNA Affinity Purification
6 Chromatin Immunoprecipitation Assay as a Tool for Analyzing Transcription Factor Activity
7 Two-Step Cross-linking for Analysis of Protein-Chromatin Interactions 105
8 Chromatin Immunoprecipitation Analysis of NFκB Transcriptional Regulation by Nuclear IκBα in Human Macrophages 121
9 In Vivo ChIP for the Analysis of Microdissected Tissue Samples
10 Quantification of Protein-DNA Interactions by In Vivo Chromatin Immunoprecipitation in Yeast
11 Mapping Protein-DNA Interactions Using ChiP-Sequencing 157
12 ChIP and Re-ChIP Assays: Investigating Interactions Between Regulatory Proteins， Histone Modifications， and the DNA Sequences to Which They Bind 17
13 Transcriptional Regulation of Genes via Hypoxia-Inducible Factor 18
14 Exchange Protein Directly Activated by Cyclic AMP-1-Regulated Recruitment of CCAAT/Enhancer-Binding Proteins to the Suppressor of Cytokine Signaling- 3 Promoter
PART II CHROMATIN STRUCTURE
15 Computational Analysis of Promoter Elements and Chromatin Features in Yeast
16 Chromatin Affinity Purification
17 Determination of Histone Acetylation Status by Chromatin Immunoprecipitation
18 Immunostaining of Drosophila Polytene Chromosomes to Investigate Recruitment of Chromatin-Binding Proteins
19 Detection of Transcriptional Activators， Co-activators， and Chromatin Remodeling by Chromatin Immunoprecipitation Coupled with Real-Time PCR 27
20 Chromatin Endogenous Cleavage and Psoralen Crosslinking Assays to Analyze rRNA Gene Chromatin In Vivo 29
21 UV-Induced DNA Damage and DNA Repair in Ribosomal Genes Chromatin 30
22 Analysis of SUC2 Promoter Structure by Nucleosome Scanning 32
23 Chromatin Immunoprecipitation of Mouse Embryos 33
24 Chromatin Immunoprecipitation in Mouse Hippocampal Cells and Tissues
PART III CHROMATIN MODIFYING COMPLEXES
25 Approaches for Studying Nucleosome Movement by ATP-Dependent Chromatin Remodeling Complexes 367
26 Mapping Protein-DNA and Protein-Protein Interactions of ATP-Dependent Chromatin Remodelers 381
27 Evaluation of Histone-Modifying Enzymes in Stem Cell Populations
28 Purification of Multiprotein Histone Acetyltransferase Complexes 427
29 Reconstitution of Active and Stoichiometric Multisubunit Lysine Acetyltransferase Complexes in Insect Cells 445
30 Affinity Purification of MLL3/MLL4 Histone H3K4 Methyltransferase Complex
31 Methods for Analyzing Histone Citrullination in Chromatin Structure and Gene Regulation
PART IV RNA SYNTHESIS AND REGULATION
32 Analysis of mRNA Abundance and Stability by Ribonuclease Protection Assay
33 Array-Based Nuclear Run-On Analysis
34 In Vivo Run-On Assays to Monitor Nascent Precursor RNA Transcripts 519
35 Genome Wide Full-Length Transcript Analysis Using 5' and 3' Paired-End-Tag Next Generation Sequencing (RNA-PET) 535
36 Analysis of Co-transcriptional RNA Processing by RNA-ChIP Assay 563
37 Quantitative Analysis of Transcription Elongation by RNA Polymerase I In Vitro
38 Detection and Characterization of Transcription Termination
39 Promoter-Associated Noncoding RNA from the CCND1 Promoter 609
Index
