A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos

Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Developmental Biology (Impact Factor: 3.55). 11/2009; 340(2):200-8. DOI: 10.1016/j.ydbio.2009.11.020
Source: PubMed


Comparisons of orthologous developmental gene regulatory networks (GRNs) from different organisms explain how transcriptional regulation can, or cannot, change over time to cause morphological evolution and stasis. Here, we examine a subset of the GRN connections in the central vegetal pole mesoderm of the late sea star blastula and compare them to the GRN for the same embryonic territory of sea urchins. In modern sea urchins, this territory gives rise to skeletogenic mesoderm; in sea stars, it develops into other mesodermal derivatives. Orthologs of many transcription factors that function in the sea urchin skeletogenic mesoderm are co-expressed in the sea star vegetal pole, although this territory does not form a larval skeleton. Systematic perturbation of erg, hex, tbr, and tgif gene function was used to construct a snapshot of the sea star mesoderm GRN. A comparison of this network to the sea urchin skeletogenic mesoderm GRN revealed a conserved, recursively wired subcircuit operating in both organisms. We propose that, while these territories have evolved different functions in sea urchins and sea stars, this subcircuit is part of an ancestral GRN governing echinoderm vegetal pole mesoderm development. The positive regulatory feedback between these transcription factors may explain the conservation of this subcircuit.

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    • "To this aim, we coinjected each construct with either 400 µM control morpholino antisense oligonucleotide (MASO) or PmTbr-specific translation blocking MASO. These modified oligonucleotides bind in a sequence specific manner to the translation start site of the transcript to block translation and have been used successfully in previous work from our lab (Hinman et al. 2007; McCauley et al. 2010). At this concentration, the Tbr MASO drastically reduces, but does not eliminate, Tbr protein. "
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    ABSTRACT: Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. It is well documented that GRNs can evolve extensively through mutations to cis-regulatory modules. Transcription factor proteins that bind these cis-regulatory modules may also evolve to produce novelty. Coding changes are considered to be rarer, however, because transcription factors are multifunctional and hence are more constrained to evolve in ways that will not produce widespread detrimental effects. Recent technological advances have unearthed a surprising variation in DNA binding abilities, such that individual transcription factors may recognize both a preferred primary motif and an additional secondary motif. This provides a source of modularity in function. Here, we demonstrate that orthologous transcription factors can also evolve a changed preference for a secondary binding motif, thereby offering an unexplored mechanism for GRN evolution. Using Protein Binding Microarray, Surface Plasmon Resonance, and in vivo reporter assays, we demonstrate an important difference in DNA binding preference between Tbrain protein orthologs in two species of echinoderms, the sea star, Patiria miniata, and the sea urchin, Strongylocentrotus purpuratus. While both orthologs recognize the same primary motif, only the sea star Tbr also has a secondary binding motif. Our in vivo assays demonstrate that this difference may allow for greater evolutionary change in timing of regulatory control. This uncovers a layer of transcription factor binding divergence that could exist for many pairs of orthologs. We hypothesize that this divergence provides modularity that allows orthologous transcription factors to evolve novel roles in gene regulatory networks through modification of binding to secondary sites.
    Molecular Biology and Evolution 07/2014; 31(10). DOI:10.1093/molbev/msu213 · 9.11 Impact Factor
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    • "Current phylogeny (Pisani et al., 2012) shows the eleutherozoan outgroup to the echinoids, ophiuroids and holothuroids, to be the asteroids or sea stars, the divergence dating back to the origins of the eleutherozoans, probably in the lower Ordovician if not before. Indeed sea stars have no pigment cell lineage and expression of gcm and gataE is conspicuously absent from embryonic sea star mesoderm (Hinman and Davidson, 2007; Mccauley et al., 2010). On the other hand, the sea star embryonic mesoderm generates blastocoelar cell types similar to those descendent from oral NSM of sea urchins. "
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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.
    Developmental Biology 12/2012; 375(1). DOI:10.1016/j.ydbio.2012.11.033 · 3.55 Impact Factor
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    • "In the sea urchin micromeres, hesc is itself repressed by Pmar1 in response to nuclearized β-catenin, thereby de-repressing the skeleton circuits [64]. This double-negative pmar1/hesc gate appears unique to sea urchins as the mechanism that coupled the pre-existing programs of skeletogenesis and maternal β-catenin-mediated vegetal specification to produce the novelty of the embryonic skeleton, as it is not involved in adult sea urchin skeletogenesis [19,53]. Recent evidence suggests that other, as yet unknown, mechanisms related to the unequal cleavage that produces the micromeres are also involved [65]. "
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    ABSTRACT: Background The gastrula stage represents the point in development at which the three primary germ layers diverge. At this point the gene regulatory networks that specify the germ layers are established and the genes that define the differentiated states of the tissues have begun to be activated. These networks have been well-characterized in sea urchins, but not in other echinoderms. Embryos of the brittle star Ophiocoma wendtii share a number of developmental features with sea urchin embryos, including the ingression of mesenchyme cells that give rise to an embryonic skeleton. Notable differences are that no micromeres are formed during cleavage divisions and no pigment cells are formed during development to the pluteus larval stage. More subtle changes in timing of developmental events also occur. To explore the molecular basis for the similarities and differences between these two echinoderms, we have sequenced and characterized the gastrula transcriptome of O. wendtii. Methods Development of Ophiocoma wendtii embryos was characterized and RNA was isolated from the gastrula stage. A transcriptome data base was generated from this RNA and was analyzed using a variety of methods to identify transcripts expressed and to compare those transcripts to those expressed at the gastrula stage in other organisms. Results Using existing databases, we identified brittle star transcripts that correspond to 3,385 genes, including 1,863 genes shared with the sea urchin Strongylocentrotus purpuratus gastrula transcriptome. We characterized the functional classes of genes present in the transcriptome and compared them to those found in this sea urchin. We then examined those members of the germ-layer specific gene regulatory networks (GRNs) of S. purpuratus that are expressed in the O. wendtii gastrula. Our results indicate that there is a shared ‘genetic toolkit’ central to the echinoderm gastrula, a key stage in embryonic development, though there are also differences that reflect changes in developmental processes. Conclusions The brittle star expresses genes representing all functional classes at the gastrula stage. Brittle stars and sea urchins have comparable numbers of each class of genes and share many of the genes expressed at gastrulation. Examination of the brittle star genes in which sea urchin orthologs are utilized in germ layer specification reveals a relatively higher level of conservation of key regulatory components compared to the overall transcriptome. We also identify genes that were either lost or whose temporal expression has diverged from that of sea urchins.
    EvoDevo 09/2012; 3(1):19. DOI:10.1186/2041-9139-3-19 · 3.03 Impact Factor
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