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A protocol for unraveling gene regulatory networks

Materna, Stefan C. and Oliveri, Paola (2008) A protocol for unraveling gene regulatory networks. Nature Protocols, 3 (12). pp. 1876-1887. ISSN 1754-2189.

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Regulatory genes form large networks that are fundamental to the developmental program. The protocol presented here describes a general approach to assemble maps of gene regulatory networks (GRNs). It combines high-resolution spatio-temporal profiling of regulatory genes, strategies to perturb gene expression and quantification of perturbation effects on other genes of the network. The map of the GRN emerges by integration of these data sources and explains developmental events in terms of functional linkages between regulatory genes. This protocol has been successfully applied to regulatory processes in the sea urchin embryo, but it is generally applicable to any developmental process that relies primarily on transcriptional regulation. Unraveling the GRN for a whole tissue or organ is a challenging undertaking and, depending on the complexity, may take anywhere from months to years to complete.

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Additional Information:© 2008 Nature Publishing Group. Published online: 13 November 2008. We thank Eric Davidson in whose lab this protocol was established for many interesting and insightful discussions. Many thanks also to Jonathan Rast, Isabelle Peter, Joel Smith and Andy Cameron for their help in preparing this manuscript. We are grateful for helpful suggestions from our anonymous reviewers. This research was supported by NIH grant HD-37105.
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Subject Keywords:Cell and developmental biology, Computational and theoretical biology, Genetic analysis, Model organisms
Issue or Number:12
Record Number:CaltechAUTHORS:20090729-102400232
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14718
Deposited By: Ruth Sustaita
Deposited On:07 Aug 2009 20:57
Last Modified:03 Oct 2019 00:52

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