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Methods for the experimental and computational analysis of gene regulatory networks in sea urchins

Peter, Isabelle S. (2018) Methods for the experimental and computational analysis of gene regulatory networks in sea urchins. In: Echinoderms, Part B. Methods in Cell Biology. No.151. Academic Press , San Diego, CA, pp. 89-113. ISBN 9780128170724.

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The discovery of gene regulatory networks (GRNs) has opened a gate to access the genomic mechanisms controlling development. GRNs are systems of transcriptional regulatory circuits that control the differential specification of cell fates during development by regulating gene expression. The experimental analysis of GRNs involves a collection of methods, each revealing aspects of the overall control process. This review provides an overview of experimental and computational methods that have been successfully applied for solving developmental GRNs in the sea urchin embryo. The key in this approach is to obtain experimental evidence for functional interactions between transcription factors and regulatory DNA. In the second part of this review, a more generally applicable strategy is discussed that shows a path from experimental evidence to annotation of regulatory linkages to the generation of GRN models.

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Peter, Isabelle S.0000-0003-3685-3147
Additional Information:© 2019 Elsevier. Available online 11 December 2018. I am very grateful to Deanna Thomas for generating the figures and to Dr. Eric Davidson for countless discussions on this subject. This work was supported by National Institutes of Health Grant HD 037105.
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Subject Keywords:Gene regulatory networks; Regulatory circuit; Transcription factor; Development; Sea urchin; Experimental analysis; Computational modeling
Series Name:Methods in Cell Biology
Issue or Number:151
Record Number:CaltechAUTHORS:20181211-101728399
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Official Citation:Isabelle S. Peter, Chapter 2 - Methods for the experimental and computational analysis of gene regulatory networks in sea urchins, Editor(s): Amro Hamdoun, Kathy R. Foltz, Methods in Cell Biology, Academic Press, Volume 151, 2019, Pages 89-113, ISSN 0091-679X, ISBN 9780128170724, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91678
Deposited By: George Porter
Deposited On:11 Dec 2018 18:31
Last Modified:16 Nov 2021 03:43

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