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1.  NEW REGULATORY CIRCUIT CONTROLLING SPATIAL AND TEMPORAL GENE EXPRESSION IN THE SEA URCHIN EMBRYO ORAL ECTODERM GRN 
Developmental biology  2013;382(1):268-279.
The sea urchin oral ectoderm gene regulatory network (GRN) model has increased in complexity as additional genes are added to it, revealing its multiple spatial regulatory state domains. The formation of the oral ectoderm begins with an oral-aboral redox gradient, which is interpreted by the cis-regulatory system of the nodal gene to cause its expression on the oral side of the embryo. Nodal signaling drives cohorts of regulatory genes within the oral ectoderm and its derived subdomains. Activation of these genes occurs sequentially, spanning the entire blastula stage. During this process the stomodeal subdomain emerges inside of the oral ectoderm, and bilateral subdomains defining the lateral portions of the future ciliary band emerge adjacent to the central oral ectoderm. Here we examine two regulatory genes encoding repressors, sip1 and ets4, which selectively prevent transcription of oral ectoderm genes until their expression is cleared from the oral ectoderm as an indirect consequence of Nodal signaling. We show that the timing of transcriptional de-repression of sip1 and ets4 targets which occurs upon their clearance explains the dynamics of oral ectoderm gene expression. In addition two other repressors, the direct Nodal target not, and the feed forward Nodal target goosecoid, repress expression of regulatory genes in the central animal oral ectoderm thereby confining their expression to the lateral domains of the animal ectoderm. These results have permitted construction of an enhanced animal ectoderm GRN model highlighting the repressive interactions providing precise temporal and spatial control of regulatory gene expression.
doi:10.1016/j.ydbio.2013.07.027
PMCID: PMC3783610  PMID: 23933172
Sea urchin; oral ectoderm; sip1; ets4; gene regulatory network
2.  The Sea Urchin Genome as a Window on Function 
The Biological bulletin  2008;214(3):266-273.
The emphasis on the sequencing of genomes seems to make this task an end in itself. However, genome sequences and the genes that are predicted from them are really an opportunity to examine the biological function of the organism constructed by that genome. This point is illustrated here by examples in which the newly annotated gene complement reveals surprises about the way Strongylocentrotus purpuratus, the purple sea urchin, goes about its business. The three topics considered here are the nature of the innate immune system; the unexpected complexity of sensory function implied by genes encoding sensory proteins; and the remarkable intricacy of the regulatory gene complement in embryogenesis.
PMCID: PMC3981829  PMID: 18574103
3.  Diversification of Oral and Aboral Mesodermal Regulatory States in Pregastrular Sea Urchin Embryos 
Developmental biology  2012;375(1):92-104.
Summary
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.
doi:10.1016/j.ydbio.2012.11.033
PMCID: PMC3570723  PMID: 23261933
mesoderm; nodal signaling; oral/aboral axis; not; gcm; gataE; gene regulatory network
4.  Direct and indirect control of oral ectoderm regulatory gene expression by Nodal signaling in the sea urchin embryo 
Developmental biology  2012;369(2):377-385.
The Nodal signaling pathway is known from earlier work to be an essential mediator of oral ectoderm specification in the sea urchin embryo, and indirectly, of aboral ectoderm specification as well. Following expression of the Nodal ligand in the future oral ectoderm during cleavage, a sequence of regulatory gene activations occurs within this territory which depends directly or indirectly on nodal gene expression. Here we describe additional regulatory genes that contribute to the oral ectoderm regulatory state during specification in Strongylocentrotus purpuratus, and show how their spatial expression changes dynamically during development. By means of system wide perturbation analyses we have significantly improved current knowledge of the epistatic relations amongst the regulatory genes of the oral ectoderm. From these studies there emerge diverse circuitries relating downstream regulatory genes directly and indirectly to Nodal signaling. A key intermediary regulator, the role of which had not previously been discerned, is the not gene. In addition to activating several genes earlier described as targets of Nodal signaling, the not gene product acts to repress other oral ectoderm genes, contributing crucially to the bilateral spatial organization of the embryonic oral ectoderm.
doi:10.1016/j.ydbio.2012.06.022
PMCID: PMC3423475  PMID: 22771578
nodal signaling; gene regulatory network; oral ectoderm specification
5.  A comprehensive analysis of Delta signaling in pre-gastrular sea urchin embryos 
Developmental Biology  2012;364(1):77-87.
In sea urchin embryos Delta signaling specifies non-skeletogenic mesoderm (NSM). Despite the identification of some direct targets, several aspects of Delta Notch (D/N) signaling remain supported only by circumstantial evidence. To obtain a detailed and more complete image of Delta function we followed a systems biology approach and evaluated the effects of D/N perturbation on expression levels of 205 genes up to gastrulation. This gene set includes virtually all transcription factors that are expressed in a localized fashion by mid-gastrulation, and which thus provide spatial regulatory information to the embryo. Also included are signaling factors and some pigment cell differentiation genes. We show that the number of pregastrular D/N signaling targets among these regulatory genes is small and is almost exclusively restricted to non-skeletogenic mesoderm genes. However, Delta signaling also activates foxY in the small micromeres. As is the early NSM, the small micromeres are in direct contact with Delta expressing skeletogenic mesoderm. In contrast, no endoderm regulatory genes are activated by Delta signaling even during the second phase of delta expression, when this gene is transcribed in NSM cells adjacent to the endoderm. During this phase Delta provides an ongoing input which continues to activate foxY expression in small micromere progeny. Disruption of the second phase of Delta expression specifically abolishes specification of late mesodermal derivatives such as the coelomic pouches to which the small micromeres contribute.
doi:10.1016/j.ydbio.2012.01.017
PMCID: PMC3294105  PMID: 22306924
Delta; Notch; DAPT; FoxY; Mesoderm; Coelomic Pouch; Pigment; Small Micromeres; Sea Urchin
6.  High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development 
Gene expression patterns : GEP  2010;10(4-5):177-184.
Accurate measurements of transcript abundance are a prerequisite to understand gene activity in development. Using the NanoString nCounter, an RNA counting device, we measured the prevalence of 172 transcription factors and signaling molecules in early sea urchin development. These measurements show high fidelity over more than five orders of magnitude down to a few transcripts per embryo. Most of the genes included are locally restricted in their spatial expression, and contribute to the divergent regulatory states of cells in the developing embryo. In order to obtain high-resolution expression, profiles from fertilization to late gastrulation samples were collected at hourly intervals. The measured time courses agree well with, and substantially extend, prior relative abundance measurements obtained by quantitative PCR. High temporal resolution permits sequences of successively activated genes to be precisely delineated providing an ancillary tool for assembling maps of gene regulatory networks. The data are available via an interactive website for quick plotting of selected time courses.
doi:10.1016/j.gep.2010.04.002
PMCID: PMC2902461  PMID: 20398801
Transcription factor; Gene expression time course; mRNA prevalence measurement; Embryogenesis
7.  Logic of gene regulatory networks 
Current opinion in biotechnology  2007;18(4):351-354.
Regulatory networks of transcription factors and signaling molecules lie at the heart of development. Their architecture implements logic functions whose execution propels cells from one regulatory state to the next, thus driving development forward. As an example of a subcircuit that translates transcriptional input into developmental output we consider a particularly simple case, the regulatory processes underlying pigment cell formation in sea urchin embryos. The regulatory events in this process can be represented as elementary logic functions.
doi:10.1016/j.copbio.2007.07.008
PMCID: PMC2031216  PMID: 17689240
8.  High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution 
Developmental biology  2006;300(1):27-34.
A global scan of transcription factor usage in the sea urchin embryo was carried out in the context of the S.purpuratus genome sequencing project, and results from six individual studies are here considered. Transcript prevalence data were obtained for over 280 regulatory genes encoding sequence-specific transcription factors of every known family, but excluding genes encoding zinc finger proteins. This is a statistically inclusive proxy for the total “regulome” of the sea urchin genome. Close to 80% of the regulome is expressed at significant levels by the late gastrula stage. Most regulatory genes must be used repeatedly for different functions as development progresses. An evolutionary implication is that animal complexity at the stage when the regulome first evolved was far simpler than even the last common bilaterian ancestor, and is thus of deep antiquity.
doi:10.1016/j.ydbio.2006.10.016
PMCID: PMC1790870  PMID: 17101125
Regulome; Transcription factor usage; Indirect development

Results 1-8 (8)