From the cover: Gene networks in development and evolution special feature Sackler colloquium: Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo

Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 01/2009; 105(51):20089-94. DOI: 10.1073/pnas.0806442105
Source: PubMed


We dissect the transcriptional regulatory relationships coordinating the dynamic expression patterns of two signaling genes, wnt8 and delta, which are central to specification of the sea urchin embryo endomesoderm. cis-Regulatory analysis shows that transcription of the gene encoding the Notch ligand Delta is activated by the widely expressed Runx transcription factor, but spatially restricted by HesC-mediated repression through a site in the delta 5'UTR. Spatial transcription of the hesC gene, however, is controlled by Blimp1 repression. Blimp1 thus represses the repressor of delta, thereby permitting its transcription. The blimp1 gene is itself linked into a feedback circuit that includes the wnt8 signaling ligand gene, and we showed earlier that this circuit generates an expanding torus of blimp1 and wnt8 expression. The finding that delta expression is also controlled at the cis-regulatory level by the blimp1-wnt8 torus-generating subcircuit now explains the progression of Notch signaling from the mesoderm to the endoderm of the developing embryo. Thus the specific cis-regulatory linkages of the gene regulatory network encode the coordinated spatial expression of Wnt and Notch signaling as they sweep outward across the vegetal plate of the embryo.

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    • "Sequencing showed that only 13-tag-linked region 3 showed significant contamination. BAC DNA was obtained from stab cultures of BAC 4013 F-18 mCherry (from Sp Genome Research Resource, Caltech) grown under chloramphenicol selection and purified as described [34]. 2.3. "
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    ABSTRACT: Cyclin D genes regulate the cell cycle, growth and differentiation in response to intercellular signaling. While the promoters of vertebrate cyclin D genes have been analyzed, the cis-regulatory sequences across an entire cyclin D locus have not. Doing so would increase understanding of how cyclin D genes respond to the regulatory states established by developmental gene regulatory networks, linking cell cycle and growth control to the ontogenetic program. Therefore, we conducted a cis-regulatory analysis on the cyclin D gene, SpcycD, of the sea urchin, Strongylocentrotus purpuratus, during embryogenesis, identifying upstream and intronic sequences, located within six defined regions bearing one or more cis-regulatory modules each.
    Full-text · Article · Sep 2013 · Biochemical and Biophysical Research Communications
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    • "Heterochrony in the deployment of the skeletogenic GRN is also reflected in a program of late larval skeletogenesis in euechinoids. After the larva begins to feed, several additional skeletal elements arise that are separate from the early, embryonic skeleton (Okazaki, 1975; Smith et al., 2008). These skeletal elements are secreted, at least in part, by SMCs that ingress late in gastrulation (Yajima, 2007). "
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    ABSTRACT: A central challenge of developmental and evolutionary biology is to explain how anatomy is encoded in the genome. Anatomy emerges progressively during embryonic development, as a consequence of morphogenetic processes. The specialized properties of embryonic cells and tissues that drive morphogenesis, like other specialized properties of cells, arise as a consequence of differential gene expression. Recently, gene regulatory networks (GRNs) have proven to be powerful conceptual and experimental tools for analyzing the genetic control and evolution of developmental processes. A major current goal is to link these transcriptional networks directly to morphogenetic processes. This review highlights three experimental models (sea urchin skeletogenesis, ascidian notochord morphogenesis, and the formation of somatic muscles in Drosophila) that are currently being used to analyze the genetic control of anatomy by integrating information of several important kinds: 1) morphogenetic mechanisms at the molecular, cellular and tissue levels that are responsible for shaping a specific anatomical feature, 2) the underlying GRN circuitry deployed in the relevant cells, and 3) modifications to gene regulatory circuitry that have accompanied evolutionary changes in the anatomical feature. © 2013 Wiley Periodicals, Inc.
    Preview · Article · Jun 2013 · genesis
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    • "Finally, though this refers to all the NSM, more recent results show that the control of hesC expression needs further examination. hesC clearance from the NSM is what allows delta to be expressed there after about 19 hpf (Sweet et al., 2002; Revilla-i-Domingo et al., 2007; Smith and Davidson, 2008). As we see in Figs. 1 and 5, this is the only regulatory gene within the NSM that does not respect the oral/ aboral regulatory state segregation. "
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    ABSTRACT: Specification of the non-skeletogenic mesoderm (NSM) in sea urchin embryos depends on Delta signaling. Signal reception leads to expression of regulatory genes that later contribute to the aboral NSM regulatory state. In oral NSM, this is replaced by a distinct oral regulatory state in consequence of Nodal signaling. Through regulome wide analysis we identify the homeobox gene not as an immediate Nodal target. not expression in NSM causes extinction of the aboral regulatory state in the oral NSM, and expression of a new suite of regulatory genes. All NSM specific regulatory genes are henceforth expressed exclusively, in oral or aboral domains, presaging the mesodermal cell types that will emerge. We have analyzed the regulatory linkages within the aboral NSM gene regulatory network. A linchpin of this network is gataE which as we show is a direct Gcm target and part of a feedback loop locking down the aboral regulatory state.
    Preview · Article · Dec 2012 · Developmental Biology
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