Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Expression of Spgatae, the Strongylocentrotus purpuratus ortholog of vertebrate GATA4/5/6 factors.
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Spgatae is the sea urchin ortholog of vertebrate gata4/5/6 by phylogenetic analysis.
"Spgatae is the sea urchin ortholog of the vertebrate gata4/5/6 genes, as confirmed by phylogenetic analysis."
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Zygotic expression begins in the 15 h blastula in a ring of prospective mesoderm cells, expands to the whole vegetal plate at mesenchyme blastula, and later marks midgut, hindgut, archenteron-tip mesoderm and coelomic pouches.
"Spgatae transcripts were first detected in a ring of prospective mesoderm cells in the vegetal plate. Spgatae expression then expands to include the entire vegetal plate at the mesenchyme blastula stage."
Exclusive developmental functions of gatae cis-regulatory modules in the Strongylocentrorus purpuratus embryo.
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gatae is required for normal development and, before gastrulation, is a direct activator of the endodermal regulatory genes foxA, brachyury and beta1/2-otx.
"reveal that prior to gastrulation gatae is a direct activator of a number of genes encoding transcription factors, including the endodermal transcription factors foxA, brachyury , and β1/2-otx"
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gatae and beta1/2-otx cross-regulate in a positive feedback loop that locks down endoderm specification.
"These two genes cross-regulate, generating a positive feedback loop which serves to lock down the state of endoderm specification"
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Two intronic cis-regulatory modules control gatae; module 10 is necessary and sufficient for the early endomesodermal phase and module 24 drives late gut endoderm expression.
"Module 10 produces early expression in mesoderm and endoderm cells up to the early gastrula stage, while module 24 generates late endodermal expression at gastrula and pluteus stages."
An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network.
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The beta1/2-otx cis-regulatory module requires gatae, otx and krox inputs as an AND logic processor; a pair of Gata sites is essential for endodermal expression and acts synergistically with an adjacent Otx site.
"For spatial expression in the endoderm, one particular pair of Gata sites is essential and these function synergistically with an adjacent Otx site."
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Mutation of the target sites reproduces the effect of gatae morpholino knockdown on the construct.
"mutation of these sites was demonstrated to produce the same respective effects on construct expression as does blocking its regulatory inputs by treatment with morpholino antisense oligonucleotides"
Diversification of oral and aboral mesodermal regulatory states in pregastrular sea urchin embryos.
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gataE is a direct Gcm target and a linchpin of the aboral non-skeletogenic mesoderm GRN, part of a feedback loop that locks down the aboral regulatory state.
"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."
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GataE morpholino embryos lack pigment cells and show strongly reduced six1/2 and z166 transcripts, indicating direct GataE inputs into aboral NSM genes.
"At 48 hpf GataE MASO embryos lack pigment cells altogether, as shown by the absence of pks expression"
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Blocking gcm or gataE expands the oral NSM regulatory genes ese, prox1, gataC and erg.
"If gcm or gataE expression are blocked by treatment with MASOs we see an expansion of ese, prox1, gataC, and erg expression"
Cis-regulatory analysis of the sea urchin pigment cell gene polyketide synthase.
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Mutagenesis of the SpGcm, SpGataE and SpKrl sites in the SpPks cis-regulatory region shows that SpGataE is a direct positive regulator of the pigment cell gene pks.
"The mutagenesis of these DNA-binding sites indicated that SpGcm, SpGataE and SpKrl are direct positive regulators of SpPks."
A comprehensive analysis of Delta signaling in pre-gastrular sea urchin embryos.
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gataE is a direct target of Delta/Notch signalling through functional Su(H) sites in its cis-regulatory module, with Gcm acting as an additional feed-forward activator in the NSM.
"The cis-regulatory module controlling gataE expression also contains functional Su(H) sites, thus proving that, like gcm, gataE is a direct target of D/N signaling"
The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage.
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gataE is first expressed exclusively in mesoderm precursors but becomes a component of the endoderm GRN; otx expression depends on Otx, GataE and Blimp1b.
"their data show that otx expression depends on Otx itself, GataE and Blimp1b, which are themselves encoded by Otx target genes."
A gene regulatory network controlling the embryonic specification of endoderm.
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The pre-gastrular veg2 endoderm GRN includes the positive feedback circuit between blimp1b, otx and gatae.
"The models proposed here include previously identified linkages such as the positive feedback circuit between blimp1b, otx and gatae."
Developmental gene regulatory network architecture across 500 million years of echinoderm evolution.
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The krox-otx-gatae feedback loop is conserved between sea urchin and starfish; gatae positively cross-regulates otx and is a major regulator of endodermal control genes including foxa and brachyury.
"The gatae gene is soon also engaged in this loop, requiring otx expression for function, and it, in turn, positively crossregulates otx ."
Strongylocentrotus purpuratus transcription factor GATA-E binds to and represses transcription at an Otx-Goosecoid cis-regulatory element within the aboral ectoderm-specific spec2a enhancer.
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SpGATA-E binds the proximal Otx/Gsc element of the spec2a enhancer, and GATA-E MASO increases activity from this element, suggesting a repressive role at this site.
"The proximal element bound to SpGATA-E, an endomesoderm-specific transcription factor."
SpGataE, a Strongylocentrotus purpuratus ortholog of mammalian Gata4/5/6: protein expression, interaction with putative target gene spec2a, and identification of friend of Gata factor SpFog1.
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An anti-SpGataE antibody was generated; SpGataE physically interacts with the Fog ortholog SpFog1, but Fog1 knockdown does not affect endomesoderm specification.
"we identified an S. purpuratus fog ortholog, spfog1, and showed that SpGataE and SpFog1 physically interacted."
Cis-regulatory logic driving glial cells missing: self-sustaining circuitry in later embryogenesis.
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gataE is downstream of gcm and upstream of six1 in the mesodermal GRN; six1 transcripts are specifically depleted by gataE MASO, and pks has direct GataE inputs.
"six1 is one of just two transcription factor mRNAs, the level of which is significantly depressed following knockdown of gataE transcripts"
A genomic regulatory network for development.
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The endomesoderm GRN, of which gatae is a node, was derived from large-scale perturbation analysis and cis-regulatory analysis.
"The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology."
A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.
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The provisional network was built from morpholino, dominant-repressor, ectopic-expression and pathway-blockade perturbations of the regulatory genes, including gatae.
"The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network."