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A protocol for unraveling gene regulatory networks

Nature Protocols volume 3, pages 1876–1887 (2008)Cite this article

Abstract

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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Figure 1: General strategy for analysis of GRNs.
Figure 2: Perturbation experiments for network assembly.

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Acknowledgements

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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  1. Paola Oliveri

    Present address: Present address: Department of Biology, University College London, Gower Street, London, WC1W 6BT, UK.,

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  1. Division of Biology, California Institute of Technology, Pasadena, 91125, California, USA

    Stefan C Materna & Paola Oliveri

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Correspondence to Stefan C Materna or Paola Oliveri.

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Materna, S., Oliveri, P. A protocol for unraveling gene regulatory networks. Nat Protoc 3, 1876–1887 (2008). https://doi.org/10.1038/nprot.2008.187

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