Martik ML et al. (2016), Developmental gene regulatory networks in sea u...

ECB-ART-44556

F1000Res 2016 Feb 22;5. doi: 10.12688/f1000research.7381.1.

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Developmental gene regulatory networks in sea urchins and what we can learn from them.

Martik ML , Lyons DC , McClay DR .

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Sea urchin embryos begin zygotic transcription shortly after the egg is fertilized. Throughout the cleavage stages a series of transcription factors are activated and, along with signaling through a number of pathways, at least 15 different cell types are specified by the beginning of gastrulation. Experimentally, perturbation of contributing transcription factors, signals and receptors and their molecular consequences enabled the assembly of an extensive gene regulatory network model. That effort, pioneered and led by Eric Davidson and his laboratory, with many additional insights provided by other laboratories, provided the sea urchin community with a valuable resource. Here we describe the approaches used to enable the assembly of an advanced gene regulatory network model describing molecular diversification during early development. We then provide examples to show how a relatively advanced authenticated network can be used as a tool for discovery of how diverse developmental mechanisms are controlled and work.

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Genes referenced: LOC100887844 LOC115919910 LOC576114

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References [+] :

Adomako-Ankomah, Growth factor-mediated mesodermal cell guidance and skeletogenesis during sea urchin gastrulation. 2013, Pubmed, Echinobase

	Figure 1. . Steps in construction and validation of developmental gene regulatory networks (dGRNs).The process begins with identification of candidate molecules. Candidates for the sea urchin dGRN were defined as transcription factors or signal transduction pathway members that were expressed in spatiotemporally specific patterns in the embryo. The regulatory linkages were established by conducting perturbation analyses in which one candidate was perturbed and asking how its loss affected expression of other candidates. These established a preliminary dGRN model. That model was challenged in many ways, including testing predictions that gene A activated gene B and gene C through cis-regulatory analysis.
	Figure 2. . The patterning sequence of development results in cell diversification.Over the 24 hours from fertilization to the pluteus larval stage of Lytechinus variagatus, the number of developmental gene regulatory network (dGRN) states increases until there are more than 15 cell types in the early larva.
	Figure 3. . Process diagram of early development.Maternal inputs initiate specification. As cells divide, signaling becomes increasingly used to shape the specification sequence of each cell type. Toward the end of that process and proximal to differentiation, transcription factor sub-circuits drive expression of genes involved in differentiation and in morphogenesis.