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Assessing regulatory information in developmental gene regulatory networks

Peter, Isabelle S. and Davidson, Eric H. (2017) Assessing regulatory information in developmental gene regulatory networks. Proceedings of the National Academy of Sciences of the United States of America, 114 (23). pp. 5862-5869. ISSN 0027-8424. PMCID PMC5468647. https://resolver.caltech.edu/CaltechAUTHORS:20170607-093633287

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Abstract

Gene regulatory networks (GRNs) provide a transformation function between the static genomic sequence and the primary spatial specification processes operating development. The regulatory information encompassed in developmental GRNs thus goes far beyond the control of individual genes. We here address regulatory information at different levels of network organization, from single node to subcircuit to large-scale GRNs and discuss how regulatory design features such as network architecture, hierarchical organization, and cis-regulatory logic contribute to the developmental function of network circuits. Using specific subcircuits from the sea urchin endomesoderm GRN, for which both circuit design and biological function have been described, we evaluate by Boolean modeling and in silico perturbations the import of given circuit features on developmental function. The examples include subcircuits encoding positive feedback, mutual repression, and coherent feedforward, as well as signaling interaction circuitry. Within the hierarchy of the endomesoderm GRN, these subcircuits are organized in an intertwined and overlapping manner. Thus, we begin to see how regulatory information encoded at individual nodes is integrated at all levels of network organization to control developmental process.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1073/pnas.1610616114DOIArticle
http://www.pnas.org/content/114/23/5862PublisherArticle
http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1610616114/-/DCSupplementalPublisherSupporting Information
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468647/PubMed CentralArticle
ORCID:
AuthorORCID
Peter, Isabelle S.0000-0003-3685-3147
Additional Information:© 2017 National Academy of Sciences. Edited by Douglas H. Erwin, Smithsonian National Museum of Natural History, Washington, DC, and accepted by Editorial Board Member Neil H. Shubin January 24, 2017 (received for review August 17, 2016). We thank Deanna Thomas for her help in the preparation of the figures. This work was supported by National Institutes of Health Grant HD 037105. Author contributions: I.S.P. and E.H.D. designed research; I.S.P. and E.H.D. performed research; and I.S.P. wrote the paper. The authors declare no conflict of interest. This paper results from the Arthur M. Sackler Colloquium of the National Academy of Sciences, “Gene Regulatory Networks and Network Models in Development and Evolution,” held April 12–14, 2016, at the Arnold and Mabel Beckman Center of the National Academies of Sciences and Engineering in Irvine, CA. The complete program and video recordings of most presentations are available on the NAS website at www.nasonline.org/Gene_Regulatory_Networks. This article is a PNAS Direct Submission. D.H.E. is a guest editor invited by the Editorial Board. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1610616114/-/DCSupplemental.
Funders:
Funding AgencyGrant Number
NIHHD037105
Subject Keywords:developmental GRN; network topology; circuit function; network hierarchy; Boolean modeling
Issue or Number:23
PubMed Central ID:PMC5468647
Record Number:CaltechAUTHORS:20170607-093633287
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170607-093633287
Official Citation:Isabelle S. Peter and Eric H. Davidson. Assessing regulatory information in developmental gene regulatory networks. PNAS 2017 114 (23) 5862-5869; published ahead of print June 6, 2017, doi:10.1073/pnas.1610616114
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:77994
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:07 Jun 2017 18:14
Last Modified:03 Oct 2019 18:04

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