Gene Regulatory Networks: Methods and Protocols

ISBN-13: 9781617792915 / Angielski / Twarda / 2011 / 446 str.

Bart Deplancke; Nele Gheldof

Opis

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.

Spis treści

Part I. Regulatory State Components

 

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

                Juan M. Vaquerizas, Sarah A. Teichmann, and Nicholas M. Luscombe

               

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

                Huiyun Feng, Hannah L. Craig, and Ian A. Hope

 

 3. High-throughput SELEX Determination of DNA Sequences Bound by Transcription Factors In vitro

                Nobuo Ogawa and Mark D. Biggin

 

 4. 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, and Yeon-Ki Kim

 

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

                Marcus B. Noyes                             

 

 6. MITOMI- A Microdluidic Platform for In vitro Characterization of Transcription Factor – DNA Interaction

                Sylvie Rockel, Marcel Geertz, and Sebastian J. Maerkl

 

 7. Detecting Protein-protein Interactions with the Split-Ubiquitin Sensor

                Alexander Dünkler, Judith Müller, and Nils Johnsson

 

 8. Genome-wide Dissection of Post-transcriptional and Post-translational Interactions

                Mukesh Bansal and Andrea Califano

 

 9. Linking Cellular Signalling to Gene Expression using EXT Encoded Reporter Libraries

                Anna Botvinik and Moritz J. Rossner

 

 10. Sample Preparation for Small RNA Massive Parallel Sequencing

                Willemijn M. Gommans and Eugene Berezikov

 

 

Part II. Genomic Components

 

 11. CAGE-Cap Analysis Gene Expression: A Protocol for the Detection of Promoter and Transcriptional Networks

                Hazuki Takahashi, Sachiko Kato, Mitsuyoshi Murata, and Piero Carninci

 

 12. Detecting DNasel-hypersensitivity Sites with MLPA

                Thomas Ohnesorg, Stefanie Eggers, and Stefan J. White

 

 13. Detecting Long-range Chromatin Interactions using the Chromosome Conformation Capture Sequencing (3C-seq) Method

                Nele Gheldof, Marion Leleu, Daan Noordermeer, Jacques Rougemont, and Alexandre Reymond

 

 

Part III. Mapping Protein-DNA Interactions

 

 14. Analyzing Transcription Factor Occupancy during Embryo Development using ChIP-seq

                Yad Ghavi-Helm and Eileen E.M. Furlong

 

 15. Genome-wide Profiling of DNA Binding Proteins using Barcode-based Multiplex Solexa Sequencing

                Bart Deplancke

 

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

                Jacques Rougemont  and Felix Naef

 

 17. Using a Yeast Inverse One-hybrid System to Identify Functional Binding Sites of Transcription Factors

                Jizhou Yan and Shawn M. Burgess

 

 18. Using cisTargetX to Predict Transcriptional Targets and Networks in Drosophila

                Delphine Potier, Zeynep Kalender Atak, Marina Naval Sanchez, Carl Herrmann, and Stein Aerts

 

 19. Proteomic Methodologies to Study Transcription Factor Function

                Harry W. Jarrett

 

 20. A High-throughput Gateway-compatible Yeast One-hybrid Screen to Detect Protein-DNA Interactions

                Korneel Hens, Jean-Daniel Feuz, and Bart Deplancke

 

 

Part IV. Visualitzation of GRNs

 

21. BioTapestry: A Tool to Visualize the Dynamic Properties of Gene Regulatory Networks

                William J. R. Longabaugh

 

 

Part V. Modeling of GRNs

 

 22. Implicit Methods for Qualitative Modeling of Gene Regulatory Networks

                Abhishek Garg, Kartik Mohanram, Giovanni De Micheli, and Ioannis Xenarios