GataE is the sea urchin ortholog of the vertebrate GATA4/5/6 transcription factors, a 567-residue protein with two class IV (GATA-type) zinc fingers. It is zygotically expressed from the 15 h blastula, first in a ring of prospective non-skeletogenic mesoderm cells in the vegetal plate, where it is a direct target of Delta/Notch signalling (through Su(H) sites in its early intronic cis-regulatory module) and of the Gcm transcription factor; its expression then spreads to the endoderm of the veg2 lineage under Otx control, and in the gastrula and pluteus it marks the midgut, hindgut and coelomic pouches. In the endoderm GataE is a direct activator of the endodermal regulatory genes otx (beta1/2 transcript), foxA and brachyury, and it forms a positive cross-regulatory feedback loop with otx (and blimp1b) that locks down the endoderm regulatory state; the otx-gatae loop is conserved between sea urchins and starfish. In the aboral non-skeletogenic mesoderm GataE is a linchpin of the pigment cell gene regulatory network, directly activating the pigment biosynthesis gene polyketide synthase together with Gcm and Krl, and its knockdown eliminates pigment cells and allows the oral mesoderm regulatory state to expand. GataE also binds a cis-regulatory element of the aboral ectoderm gene spec2a and physically interacts with the Friend-of-GATA cofactor SpFog1.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the GATA transcription factor signature. Fully consistent with the experimental record in S. purpuratus: GataE inputs into the beta1/2-otx module and the pks cis-regulatory region have been verified by site mutagenesis, and GATA-E binding to a spec2a element has been shown directly. Reason: Core molecular function of the gene product, supported by direct cis-regulatory evidence; the RNA polymerase II-specific activator child is proposed as NEW. Supporting Evidence: PMID:15110718 For spatial expression in the endoderm, one particular pair of Gata sites is essential and these function synergistically with an adjacent Otx site. PMID:20122918 The mutagenesis of these DNA-binding sites indicated that SpGcm, SpGataE and SpKrl are direct positive regulators of SpPks. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Subcellular-location keyword mapping. Expected location for a GATA zinc-finger transcription factor whose direct binding to genomic cis-regulatory elements has been demonstrated; an anti-SpGataE antibody exists, but the cached abstract does not describe subcellular localization explicitly. Reason: Functionally required location of a sequence-specific transcription factor with demonstrated cis-regulatory binding. Supporting Evidence: PMID:15882584 The proximal element bound to SpGATA-E, an endomesoderm-specific transcription factor. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Generic InterPro2GO process term derived from the zinc-finger signatures. Correct by parentage, but redundant with the RNA polymerase II-specific term also present and with the positive-regulation term proposed as NEW. Reason: True but uninformative; the informative terms are the RNA polymerase II-specific child and the lineage specification processes. |
| GO:0006357 regulation of transcription by RNA polymerase II | IEA GO_REF:0000002 | ACCEPT | Summary: GataE directly activates the RNA polymerase II-transcribed regulatory genes otx, foxA and brachyury and the differentiation gene pks, and binds a repressive element of spec2a; the sign-neutral parent is an accurate summary. Reason: Supported by direct cis-regulatory analysis in S. purpuratus; a positive-regulation child is proposed as NEW for the well-established activating role. Supporting Evidence: PMID:17570356 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 Ξ²1/2-otx PMID:20122918 SpGataE and SpKrl are direct positive regulators of SpPks. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Derived from the GATA-type zinc finger signature. GataE has two class IV (Cys4) zinc fingers, which coordinate zinc as a structural requirement for the DNA-binding fold; zinc binding is not itself the function of the protein. Reason: Correct structural property of the GATA zinc fingers, but a means to the DNA-binding function rather than a core function in its own right. Supporting Evidence: PMID:17570356 The two class IV zinc fingers are encoded in exons 3 and 4. |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: Generic zinc-finger-derived sequence-specific DNA binding. True, but the experimentally demonstrated binding is to defined GATA sites in RNA polymerase II cis-regulatory modules (the otx beta1/2 module, the pks upstream region and the spec2a enhancer). Reason: Replace with the more specific term supported by cis-regulatory site mutagenesis and direct element binding, RNA polymerase II cis-regulatory region sequence-specific DNA binding. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:15882584 The proximal element bound to SpGATA-E, an endomesoderm-specific transcription factor. PMID:15110718 one particular pair of Gata sites is essential and these function synergistically with an adjacent Otx site. |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IDA PMID:15110718 An otx cis-regulatory module: a key node in the sea urchin e... | NEW | Summary: GataE is a direct transcriptional activator. In the beta1/2-otx cis-regulatory module a pair of Gata sites is essential for endodermal expression and mutating them reproduces the effect of gatae morpholino; in the pks cis-regulatory region mutagenesis of the GataE site shows GataE is a direct positive regulator; network-level MASO analysis identifies gatae as a direct activator of foxA and brachyury as well. Reason: The sign is shown by reporter/site-mutagenesis assays in S. purpuratus, so the activator child of the existing generic DNA-binding transcription factor term is warranted. Supporting Evidence: PMID:15110718 For spatial expression in the endoderm, one particular pair of Gata sites is essential and these function synergistically with an adjacent Otx site. PMID:20122918 The mutagenesis of these DNA-binding sites indicated that SpGcm, SpGataE and SpKrl are direct positive regulators of SpPks. PMID:17570356 gatae is a direct activator of a number of genes encoding transcription factors, including the endodermal transcription factors foxA, brachyury , and Ξ²1/2-otx |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IDA PMID:15882584 Strongylocentrotus purpuratus transcription factor GATA-E bi... | NEW | Summary: Direct binding of SpGATA-E to the proximal element of the spec2a enhancer was shown, and functional GATA sites were mapped by mutagenesis in the otx beta1/2 module and the pks cis-regulatory region. Reason: Direct element-binding and site-mutagenesis evidence for cis-regulatory sequence-specific binding (proposed as the replacement for generic sequence-specific DNA binding). Supporting Evidence: PMID:15882584 The proximal element bound to SpGATA-E, an endomesoderm-specific transcription factor. PMID:15110718 The necessary target sites were identified in the module sequence, and 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. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IDA PMID:15110718 An otx cis-regulatory module: a key node in the sea urchin e... | NEW | Summary: GataE activates transcription of the beta1/2-otx transcription unit (essential Gata sites), of the pigment differentiation gene pks (direct positive input), and of the endodermal regulators foxA and brachyury, and its knockdown depletes six1/2 and z166 transcripts in the aboral mesoderm. Reason: Process counterpart of the activator activity; supported by cis-regulatory site mutagenesis and morpholino perturbation in S. purpuratus. Supporting Evidence: PMID:15110718 It requires gatae, otx, and krox inputs, as predicted, and it operates as an "AND" logic processor in that removal of any one of these inputs essentially destroys activity. PMID:20122918 SpGataE and SpKrl are direct positive regulators of SpPks. PMID:23261933 Transcript levels of six1/2 and z166 are also greatly reduced in embryos bearing GataE MASO, about equally to embryos bearing Gcm MASO, so gataE is likely to provide direct inputs into these genes of the aboral GRN |
| GO:0001714 endodermal cell fate specification | IMP PMID:15110718 An otx cis-regulatory module: a key node in the sea urchin e... | NEW | Summary: GataE is one of the transcription factors that installs and stabilizes the endoderm regulatory state of the veg2 lineage. It directly activates the endodermal regulatory genes otx (beta1/2), foxA and brachyury, and forms a positive cross-regulatory feedback loop with otx (and blimp1b) that locks down endoderm specification; this krox-otx-gatae loop has been conserved between sea urchin and starfish for about 500 million years. gatae morpholino abolishes the Gata-dependent endodermal activity of the otx module. Reason: Participation test passed: GataE itself performs the regulatory step (direct activation of the endodermal regulatory genes and the lock-down feedback loop), it is not merely required upstream. Vertebrate GATA4/5/6 orthologs and the sea urchin Otx and Blimp1 nodes of the same loop carry this term. Evidence is morpholino perturbation validated at the DNA level by site mutagenesis. Supporting Evidence: PMID:17570356 These two genes cross-regulate, generating a positive feedback loop which serves to lock down the state of endoderm specification PMID:15110718 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 PMID:14595011 The gatae gene is a major regulator of many other endodermal control genes ( 4 , 5 ), among which are foxa and brachyury ( bra ) PMID:21623371 The models proposed here include previously identified linkages such as the positive feedback circuit between blimp1b, otx and gatae. |
| GO:0007501 mesodermal cell fate specification | IMP PMID:23261933 Diversification of oral and aboral mesodermal regulatory sta... | NEW | Summary: In its early phase GataE is a linchpin of the aboral non-skeletogenic mesoderm (pigment cell precursor) GRN: it is a direct Delta/Notch and Gcm target, it provides inputs into the aboral regulatory genes six1/2 and z166, and two independent GataE morpholinos abolish pigment cells and let the oral mesoderm regulatory genes (ese, prox1, gataC, erg) expand across the whole non-skeletogenic mesoderm. Reason: GataE is a transcription factor that installs the aboral mesoderm regulatory state and excludes the alternative oral state, so it participates in the specification step itself. GO:0007501 is used because the aboral NSM is mesoderm of the sea urchin embryo; no echinoderm-specific non-skeletogenic mesoderm term exists. Supporting Evidence: PMID:23261933 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. PMID:23261933 If gcm or gataE expression are blocked by treatment with MASOs we see an expansion of ese, prox1, gataC, and erg expression PMID:22306924 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 |
| GO:0050942 positive regulation of pigment cell differentiation | IMP PMID:23261933 Diversification of oral and aboral mesodermal regulatory sta... | NEW | Summary: GataE morphants lack pigment cells altogether at 48 h (no pks expression), and GataE is a direct positive regulator of polyketide synthase, the enzyme of larval echinochrome pigment biosynthesis, acting through a defined GataE site in the pks cis-regulatory region together with Gcm and Krl. Reason: Regulatory (not executional) role in pigment cell differentiation, hence the positive-regulation term. Supported by morpholino phenotype and by direct cis-regulatory input into the pigment differentiation gene. Supporting Evidence: PMID:23261933 At 48 hpf GataE MASO embryos lack pigment cells altogether, as shown by the absence of pks expression PMID:20122918 The mutagenesis of these DNA-binding sites indicated that SpGcm, SpGataE and SpKrl are direct positive regulators of SpPks. PMID:22509525 the essential pigment cell differentiation gene, pks, has direct GataE inputs (Calestani and Rogers, 2010) |
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Download this section (compressed HTML)Q: Is GataE a direct transcriptional repressor (of spec2a in the endomesoderm, and of the oral NSM genes in the aboral NSM), which would justify GO:0001227 / GO:0000122 annotations, or is the exclusion of these states mediated indirectly through GataE-activated genes such as six1/2?
Q: Which cis-regulatory module drives the late gatae expression in the coelomic pouches, which neither module 10 nor module 24 accounts for, and what role does GataE play in coelomic pouch (adult rudiment) mesoderm?
Q: Does the SpGataE-SpFog1 interaction modulate GataE activity in a context (for example spec2a repression or later gut regionalization) not tested by the Fog1 morpholino experiments?
Experiment: Site-directed mutagenesis of the GATA sites in the spec2a proximal element and in the cis-regulatory modules of ese, prox1 and gataC, combined with GataE ChIP-qPCR, to test direct repression by GataE.
Experiment: Genome-wide ChIP-seq of SpGataE (the anti-SpGataE antibody exists) at 18 h, 24 h and 48 h to distinguish direct mesodermal, endodermal and gut-regionalization targets and to map GATA sites in the foxA and brachyury modules.
Experiment: BAC-reporter scanning of the region upstream of conserved patch 1 of the gatae locus to identify the missing coelomic pouch module and its inputs.
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