E H Davidson

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..The structural organization of various kinds of GRN reflects their roles in the life process, and causally illuminates both developmental and evolutionary process...

..Comparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes...

..These are created by the logic outputs of network subcircuits, and in modern animals these outputs are impervious to continuous adaptive variation unlike genes operating more peripherally in the network...

..Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time...

..The sequence will accelerate progress toward complete understanding of the genomic regulatory system that controls developmental specification and morphogenetic function, thus illuminating basic developmental process in all animals...

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..Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages...

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..These subcircuits are dedicated to specific developmental functions, unlike simpler 'motifs', and may indicate a repertoire of specific devices of which developmental gene regulatory networks are composed...

..Gene regulatory networks make it possible to explain the process of development in causal terms and eventually will enable the redesign of developmental regulatory circuitry to achieve different outcomes...

..Conservation of phyletic body plans may have been due to the retention since pre-Cambrian time of GRN kernels, which underlie development of major body parts...

..In addition, we introduce new methodological tools for quantitative measurement of the output of expression constructs that promise to be of general value for cis-regulatory analysis in sea urchin embryos...

..purpuratus member of the myb family of transcription factors. Through interactions within the middle module, SpMyb functions to repress activation of CyIIIa in the oral ectoderm and skeletogenic mesenchyme...

..The finding of a single protein target site that recapitulates CyIIa expression in both primary and secondary mesenchyme cells suggests the existence of a pan-mesodermal gene expression program in the sea urchin embryo...

..The requirements for postembryonic adult body plan formation in the larval rudiment include engagement of a new level of genetic regulatory apparatus, exemplified by the Hox gene complex...

..These results are discussed with reference to known features of the runt domain family of transcription factors...

..Finally, Brachyury appears to be an excellent marker for the progeny of the set-aside cells of the sea urchin embryo...

..The MASO perturbation analysis also revealed blimp1/krox inputs into other genes of the endomesoderm regulatory network...

..The P3A1 and P3A2 factors could function as regulatory antagonists, having evolved similar target specificities from dissimilar DNA-binding domains...

..This terminal phase of expression has remained unchanged since the divergence of these two taxa half a billion years ago...

..SpZ12-1 probably functions at several developmental stages and is evidently of both maternal and embryonic provenance...

..The high complexity of the Endo16 gene regulatory system may be characteristic for genes that are spatially regulated in early embryonic development...

..CAT in skeletogenic mesenchyme and is likely to be the trans factor that mediates this repression...

..The spec2a enhancer thus consists of closely linked activator and repressor elements that function collectively to cause expression of the spec2a gene in the aboral ectoderm...

..The spatial expression patterns of the Hox genes illuminate the evolutionary process by which the pentameral echinoderm body plan emerged from a bilateral ancestor...

..This more general expression resolves to a dramatic pigment cell-specific pattern in prism and pluteus stages. SpHmx apparently encodes a cell-type-specific transcription factor of embryonic pigment cells...

..Each of the tests we describe supports the placement and function of Pmar1 in the endomesoderm GRN model...

..Its sequence contains binding sites for Brn1/2/4, Otx, and Blimp1/Krox itself, as predicted in a prior regulatory network analysis...

..In addition, they imply a functional cis-regulatory module exclusion, whereby only a single module can associate with the basal promoter and drive gene expression at any given time...

..Since proline-rich regions often serve as transcriptional activation domains, the five SpGCF1 proteins apparently possess different "activation potentials."..

..SpHox8 is a single-copy gene, and there is only one Hox gene cluster per genome in S. purpuratus...

..The results demonstrate that homeodomain transcription factors participate in multiple and diverse developmental functions, in that they are used at a range of time points and in every territory of the developing embryo...

..These genes may execute important regulatory functions in development. However, the functional meaning of the majority of this large gene family remains undefined...

..In the early bipinnaria larva transcripts are detected in the midgut and hindgut. Despite differences in early development of sea urchins and starfish, the expression of these Krox transcription factors is highly conserved...

..This gene was regulated coordinately with SM50 during development, and like SM50 was expressed exclusively in skeletogenic mesenchyme lineages...

..Many of the ESTs identified in this study represent the types of genes expected to be used in lower deuterostome immune functions...

..J. Exp. Zool. (Mol. Dev. Evol. ) 285:104-115, 1999...

..The sea urchin fox genes clearly execute many different regulatory functions, and almost all of them participate in the process of embryonic development...

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..In a second regulatory region, which initiates expression in micromere and macromere descendant cells early in cleavage, Tcf1 sites act to repress ectopic transcription in prospective ectoderm cells...

..The function of Otx proteins in endodermal development at least predated the evolution of the free-living echinoderms (Eleutherozoa)...

..The results suggest that S. purpuratus pks, fmo and sult could belong to a differentiation gene battery of pigment cells...

..Neither oral ectoderm regulatory functions nor ciliated band formation occur normally in the absence of hnf6 expression...

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..The outcome is a validated method for accurately counting GFP molecules in given cells in reporter gene transfer experiments, as we demonstrate by use of an expression construct expressed exclusively in skeletogenic cells...

..The observations suggest assignment of many regulatory genes to specific developmental sub-networks, including endomesodermal, oral, aboral, and apical...

..As logically required, blockade of hesC mRNA translation and global overexpression of pmar1 mRNA have the same effect, which is to cause all of the cells of the embryo to express micromere-specific genes...

..These observations show that despite differences in the early specification processes of the endomesoderm in starfish and sea urchins, gatae factors are expressed very similarly in these two taxa...

..The explanatory power of the GRN was shown in the lineage specification of sea urchin endomesoderm. Acquiring such networks is essential for a systematic and mechanistic understanding of the developmental process...

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..At this higher level of organization, common bilaterian strategies for specifying progenitor fields, locking down regulatory states, and driving development forward emerge...

..This approach will qualitatively alter the practice of GRN construction as well as validation, and will impact many additional areas of regulatory system biology...

..The accumulated STC data and an expanding expressed sequence tag database (at present including >12, 000 sequences) have been reported to GenBank and are accessible on public web sites...

..Here we integrate the architecture of regulatory interactions with the spatial restriction of regulatory gene expression to model the logic control of endoderm development...

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..Genomically encoded backup control circuitry thus provides the mechanism underlying a specific example of the regulative development for which the sea urchin embryo has long been famous...

..It demonstrates how the static physical genomic components define functional connections between the various regulatory genes that act together to conduct the dynamical developmental program...

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..Network structure not only specifies the linkages constituting the genomic regulatory code for development, but also indicates the various regulatory requirements of regional developmental processes...

..Model simulations display the effects of mutation of binding sites, or perturbation of upstream gene expression. The model is a generally useful tool for understanding gene regulation and the dynamics of cell fate specification...

..Their conservation is probably due to the necessity for interaction of proximally bound transcription factors, while a facilitated form of sequence conversion might be the mechanism of site position change...

..This study shed light on the mesoderm-endoderm fate decision and provides a functional explanation, in terms of the genomic regulatory code, for the spatial and temporal expression of a key developmental control gene...

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..The gene sets of the sea urchin place it firmly among the deuterostomes and indicate that various gene family-specific expansions and contractions characterize the evolution of animal genomes rather than the invention of new genes...

..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...

..The data are available via an interactive website for quick plotting of selected time courses...

..This method thus provides the opportunity to study regulatory requirements of skeletogenesis after ingression, and may be similarly useful in many other developmental contexts...

..These experiments show that the foxa gene is a component of three distinct embryonic gene regulatory networks...

..Confocal laser scanning microscopy data collection from a single sea urchin blastula required less than 2 min, thereby allowing gene expression in dozens of embryos to be monitored in parallel with high spatial and temporal resolution...

..We thus demonstrate directly the structure/function relationships of the genomic regulatory code, at this key node of the endomesoderm GRN...

..On further analysis one isolate was shown to contain a gut specific element as well as one that controls expression in the secondary mesenchyme cells...

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..The network includes almost 50 genes, and these are organized in subcircuits, each of which executes a particular regulatory function...

..Towards the end of embryogenesis, expression in the hindgut decreases. The terminal pattern of expression is in midgut plus coelomic pouches...

..As the results crystallize together, we can begin to see how far this powerful combination of methods and ideas is going to carry us...

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..The result helps to explain the patterns of evolutionary sequence divergence characteristic of cis-regulatory DNA...

..While these Su(H) target sites provide the cis-regulatory architecture with the core of an N signaling transcriptional response switch, both the on and off outputs from this module require additional inputs...

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..Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex...

..We conclude that the vertebrate immune system has evolved by inserting new genes into old gene regulatory networks dedicated to immunity...

..The results reported demonstrate that it might be possible to purify most of these regulatory proteins, or any other specific DNA-binding proteins of the sea urchin embryo, by using the simple procedures described for P3A2...

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..Evolutionary changes in the GRNs since divergence are limited sharply to certain cis-regulatory elements, whereas others have persisted unaltered...

..This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes...

..The kinetics of such developmental systems thus depend mainly on the initial output rates of genes activated in response to the advent of new transcription factors...

..This reconstruction alters expectations for Neoproterozoic fossil remains that could illustrate the pathways of bilaterian evolution...

..More generally, the regulatory network subelement emerging from this work shows how the specificity of micromere function depends on continuing global regulatory interactions, as well as on early localized inputs...

..These results and other data suggest that the brachyury gene transduces information about the state of endodermal specification to genes that modulate morphogenesis and genes that perform terminal functions in the gut...

..purpuratus genome and are likely to be the same genes that were involved with stereom formation in the earliest echinoderms some 520 million years ago...

..The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process...

..Here, we survey salient points of these networks, by using as reference those governing specification of the endomesoderm in sea urchin embryos and dorsal-ventral patterning in the Drosophila embryo...

..The genomic computer controls spatial gene expression in the development of the body plan, and its appearance in remote evolutionary time must be considered to have been a founding requirement for animal grade life...

..Finally, inter-specific gene transfer experiments confirm this scenario and demonstrate evolution occurring at the level of sequence changes to the cis-regulatory module...

..An emergent theme is that subcircuit design may be preserved even while the identity of genes performing given roles changes because of alteration in their cis-regulatory control systems...

..And we present the bioinformatics tools and databases of genomic sequence collections to the experimentalist. All of the individual goals detailed above are direct responses to this view. ..

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..Numerous letters from outside investigators attesting interest in this facility are included as an Appendix to this application. ..

..And we present the bioinformatics tools and databases of genomic sequence collections to the experimentalist. All of the individual goals detailed above are direct responses to this view. ..

..And we present the bioinformatics tools and databases of genomic sequence collections to the experimentalist. All of the individual goals detailed above are direct responses to this view. ..

..Our practice must get beyond struggling to ameliorate effects rather than altering causes. This research shows the way to discovery of structure and function in causal genomic control systems. ..

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..And we present the bioinformatics tools and databases of genomic sequence collections to the experimentalist. All of the individual goals detailed above are direct responses to this view. ..

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..The model will ultimately constitute a quantitative computational analysis of a genomic regulatory network, defined at the DNA sequence level, the function of which is to organize a complex, major process in animal development. ..

..In addition, the investigators need to carry out several unique computational analyses that reflect the particular features of the S. purpuratus genome. ..

..purpuratus is a heritable trait, and carry out other investigations on genetic aspects of sex in S. purpuratus. ..