Gene Regulatory Networks: Methods and Protocols(786 Methods in Molecular Biology)

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.

Table of Contents:
How Do You Find Transcription Factors? Computational Approaches to Compile and Annotate Repertoires of Regulators for Any Genome.- Expression Pattern Analysis of Regulatory Transcription Factors in Caenorhabditis elegans.- High-throughput SELEX Determination of DNA Sequences Bound by Transcription Factors In vitro.- Convenient Determination of Protein-Binding DNA Sequences using Quadruple 9-Mer-Based Microarray and DsRed-Monomer Fusion Protein.- Analysis of Specific Protein-DNA Interactions by Bacterial One-Hybrid Assay.- MITOMI- A Microdluidic Platform for In vitro Characterization of Transcription Factor – DNA Interaction.- Detecting Protein-protein Interactions with the Split-Ubiquitin Sensor.- Genome-wide Dissection of Post-transcriptional and Post-translational Interactions.- Linking Cellular Signalling to Gene Expression using EXT Encoded Reporter Libraries.- Sample Preparation for Small RNA Massive Parallel Sequencing.- CAGE-Cap Analysis Gene Expression: A Protocol for the Detection of Promoter and Transcriptional Networks.- Detecting DNasel-hypersensitivity Sites with MLPA.- Detecting Long-range Chromatin Interactions using the Chromosome Conformation Capture Sequencing (3C-seq) Method.- Analyzing Transcription FactorOccupancy during Embryo Development using ChIP-seq.- Genome-wide Profiling of DNA Binding Proteins using Barcode-based Multiplex Solexa Sequencing.- Computational Analysis of Protein-DNA Interactions from ChIP-seq Data.- Using a Yeast Inverse One-hybrid System to Identify Functional Binding Sites of Transcription Factors.- Using cisTargetX to Predict Transcriptional Targets and Networks in Drosophila.- Proteomic Methodologies to Study Transcription Factor Function.- A High-throughput Gateway-compatible Yeast One-hybrid Screen to Detect Protein-DNA Interactions.- BioTapestry: A Tool to Visualize the Dynamic Properties of Gene Regulatory Networks.- Implicit Methods for Qualitative Modeling of Gene Regulatory Networks.