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Transcriptional Regulation

Methods and Protocols

  • Book
  • © 2012

Overview

Editors:
  1. Ales Vancura

    1. , Department of Biological Sciences, St. John's University, Queens, USA

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  • Presents detailed protocols developed using mammalian, yeast, and Drosophila cells and tissues, which can easily be applied across species and cell types
  • Features reliable methods tested in laboratories around the world
  • Includes expert tips and implementation advice to ensure successful results

Part of the book series: Methods in Molecular Biology (MIMB, volume 809)

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Table of contents (39 protocols)

  1. Front Matter

    Pages i-xvi
    Download chapter PDF

  2. Promoter Elements, Transcription Factors, and Pre-initiation Complex Assembly

    1. Front Matter

      Pages 1-1
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  3. Promoter Elements, Transcription Factors, and Pre-Initiation Complex (PIC) Assembly

    1. Genome-Wide In Vivo Cross-linking of Sequence-Specific Transcription Factors

      • Xiao-Yong Li, Mark D. Biggin
      Pages 3-26

    2. Characterization of Complex Regulatory Networks and Identification of Promoter Regulatory Elements in Yeast: “In Silico” and “Wet-Lab” Approaches

      • Nuno P. Mira, Miguel C. Teixeira, Isabel Sá-Correia
      Pages 27-48

    3. Electrophoretic Mobility Shift Assay Analysis of NFκB Transcriptional Regulation by Nuclear IκBα

      • Ashish Juvekar, Sitharam Ramaswami, Subrata Manna, Tzu-Pei Chang, Adeel Zubair, Ivana Vancurova
      Pages 49-62

    4. Probing Endogenous RNA Polymerase II Pre-initiation Complexes by Electrophoretic Mobility Shift Assay

      • Emmanuelle Wilhelm, Christopher Takacs, Brendan Bell
      Pages 63-74

    5. Elucidating Protein: DNA Complex by Oligonucleotide DNA Affinity Purification

      • Teddy T. C. Yang, Chi-Wing Chow
      Pages 75-84

    6. Chromatin Immunoprecipitation Assay as a Tool for Analyzing Transcription Factor Activity

      • Padmaja Gade, Dhan V. Kalvakolanu
      Pages 85-104

    7. Two-Step Cross-linking for Analysis of Protein–Chromatin Interactions

      • Bing Tian, Jun Yang, Allan R. Brasier
      Pages 105-120

    8. Chromatin Immunoprecipitation Analysis of NFκB Transcriptional Regulation by Nuclear IκBα in Human Macrophages

      • Sitharam Ramaswami, Subrata Manna, Ashish Juvekar, Steven Kennedy, Ales Vancura, Ivana Vancurova
      Pages 121-134

    9. In Vivo ChIP for the Analysis of Microdissected Tissue Samples

      • Chris Murgatroyd, Anke Hoffmann, Dietmar Spengler
      Pages 135-148

    10. Quantification of Protein–DNA Interactions by In Vivo Chromatin Immunoprecipitation in Yeast

      • Amparo Pascual-Ahuir, Markus Proft
      Pages 149-156

    11. Mapping Protein–DNA Interactions Using ChIP-Sequencing

      • Charles E. Massie, Ian G. Mills
      Pages 157-173

    12. ChIP and Re-ChIP Assays: Investigating Interactions Between Regulatory Proteins, Histone Modifications, and the DNA Sequences to Which They Bind

      • Agnieszka D. Truax, Susanna F. Greer
      Pages 175-188

    13. Transcriptional Regulation of Genes via Hypoxia-Inducible Factor

      • Olga Roche, Michael Ohh
      Pages 189-199

    14. Exchange Protein Directly Activated by Cyclic AMP-1-Regulated Recruitment of CCAAT/Enhancer-Binding Proteins to the Suppressor of Cytokine Signaling-3 Promoter

      • William A. Sands, Hayley D. Woolson, Stephen J. Yarwood, Timothy M. Palmer
      Pages 201-214

  4. Chromatin Structure

    1. Front Matter

      Pages 215-215
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    2. Computational Analysis of Promoter Elements and Chromatin Features in Yeast

      • John J. Wyrick
      Pages 217-235

    3. Chromatin Affinity Purification

      • Ryoko Harada, Alain Nepveu
      Pages 237-253

    4. Determination of Histone Acetylation Status by Chromatin Immunoprecipitation

      • Luciano Galdieri, John Moon, Ales Vancura
      Pages 255-265
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Keywords

About this book

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.

Editors and Affiliations

  • , Department of Biological Sciences, St. John's University, Queens, USA

    Ales Vancura

Bibliographic Information

  • Book Title: Transcriptional Regulation

  • Book Subtitle: Methods and Protocols

  • Editors: Ales Vancura

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-61779-376-9

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2012

  • Hardcover ISBN: 978-1-61779-375-2Published: 24 November 2011

  • Softcover ISBN: 978-1-4939-5854-2Published: 23 August 2016

  • eBook ISBN: 978-1-61779-376-9Published: 25 November 2011

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 627

  • Number of Illustrations: 104 b/w illustrations

  • Topics: Biochemistry, general, Gene Expression

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