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Gene Regulatory Networks

Methods and Protocols

  • Book
  • © 2012

Overview

Editors:
  1. Bart Deplancke

    1. Inst. Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

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  2. Nele Gheldof

    1. Faculté de Biologie det Médecine, Centre Intégratif de Génomique, Université de Lausanne, Lausanne, Switzerland

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 786)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xi
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  2. Regulatory State Components

    1. Front Matter

      Pages 1-1
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    2. How Do You Find Transcription Factors? Computational Approaches to Compile and Annotate Repertoires of Regulators for Any Genome

      • Juan M. Vaquerizas, Sarah A. Teichmann, Nicholas M. Luscombe
      Pages 3-19

    3. Expression Pattern Analysis of Regulatory Transcription Factors in Caenorhabditis elegans

      • Huiyun Feng, Hannah L. Craig, Ian A. Hope
      Pages 21-50

    4. High-Throughput SELEX Determination of DNA Sequences Bound by Transcription Factors In Vitro

      • Nobuo Ogawa, Mark D. Biggin
      Pages 51-63

    5. Convenient Determination of Protein-Binding DNA Sequences Using Quadruple 9-Mer-Based Microarray and DsRed-Monomer Fusion Protein

      • Min-Jeong Kim, Pil Joong Chung, Tae-Ho Lee, Tae-Hoon Kim, Baek Hie Nahm, Yeon-Ki Kim
      Pages 65-77

    6. Analysis of Specific Protein–DNA Interactions by Bacterial One-Hybrid Assay

      • Marcus B. Noyes
      Pages 79-95

    7. MITOMI: A Microfluidic Platform for In Vitro Characterization of Transcription Factor–DNA Interaction

      • Sylvie Rockel, Marcel Geertz, Sebastian J. Maerkl
      Pages 97-114

    8. Detecting Protein–Protein Interactions with the Split-Ubiquitin Sensor

      • Alexander Dünkler, Judith Müller, Nils Johnsson
      Pages 115-130

    9. Genome-Wide Dissection of Posttranscriptional and Posttranslational Interactions

      • Mukesh Bansal, Andrea Califano
      Pages 131-149

    10. Linking Cellular Signalling to Gene Expression Using EXT-Encoded Reporter Libraries

      • Anna Botvinik, Moritz J. Rossner
      Pages 151-166

    11. Sample Preparation for Small RNA Massive Parallel Sequencing

      • Willemijn M. Gommans, Eugene Berezikov
      Pages 167-178

  3. Genomic Components

    1. Front Matter

      Pages 179-179
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    2. CAGE (Cap Analysis of Gene Expression): A Protocol for the Detection of Promoter and Transcriptional Networks

      • Hazuki Takahashi, Sachi Kato, Mitsuyoshi Murata, Piero Carninci
      Pages 181-200

    3. Detecting DNaseI-Hypersensitivity Sites with MLPA

      • Thomas Ohnesorg, Stefanie Eggers, Stefan J. White
      Pages 201-210

    4. Detecting Long-Range Chromatin Interactions Using the Chromosome Conformation Capture Sequencing (4C-seq) Method

      • Nele Gheldof, Marion Leleu, Daan Noordermeer, Jacques Rougemont, Alexandre Reymond
      Pages 211-225

  4. Mapping Protein–DNA Interactions

    1. Front Matter

      Pages 227-227
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  5. Mapping Protein-DNA Interactions

    1. Analyzing Transcription Factor Occupancy During Embryo Development Using ChIP-seq

      • Yad Ghavi-Helm, Eileen E. M. Furlong
      Pages 229-245

    2. Genome-Wide Profiling of DNA-Binding Proteins Using Barcode-Based Multiplex Solexa Sequencing

      • Sunil Kumar Raghav, Bart Deplancke
      Pages 247-262

    3. Computational Analysis of Protein–DNA Interactions from ChIP-seq Data

      • Jacques Rougemont, Felix Naef
      Pages 263-273
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Keywords

About this book

Gene regulatory networks play a vital role in organismal development and function by controlling gene expression. With the availability of complete genome sequences, several novel experimental and computational approaches have recently been developed which promise to significantly enhance our ability to comprehensively characterize these regulatory networks by enabling the identification of respectively their genomic or regulatory state components, or the interactions between these two in unprecedented detail. Divided into five convenient sections, Gene Regulatory Networks: Methods and Protocols details how each of these approaches contributes to a more thorough understanding of the composition and function of gene regulatory networks, while providing a comprehensive protocol on how to implement them in the laboratory. Written in the highly successful Methods in Molecular Biology™ series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

 

Authoritative and accessible, Gene Regulatory Networks: Methods and Protocols aims to provide novices and experienced researchers alike with a comprehensive and timely toolkit to study gene regulatory networks from the point of data generation to processing, visualization, and modeling.

Editors and Affiliations

  • Inst. Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

    Bart Deplancke

  • Faculté de Biologie det Médecine, Centre Intégratif de Génomique, Université de Lausanne, Lausanne, Switzerland

    Nele Gheldof

Bibliographic Information

  • Book Title: Gene Regulatory Networks

  • Book Subtitle: Methods and Protocols

  • Editors: Bart Deplancke, Nele Gheldof

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-61779-292-2

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

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

  • Hardcover ISBN: 978-1-61779-291-5Published: 22 September 2011

  • Softcover ISBN: 978-1-4939-5838-2Published: 23 August 2016

  • eBook ISBN: 978-1-61779-292-2Published: 23 September 2011

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 446

  • Topics: Human Genetics, Gene Expression

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