Erg is an ETS-family transcription factor of the ERG/FLI1 subfamily, with an N-terminal PNT (pointed/SAM) domain and a C-terminal ETS winged-helix DNA-binding domain. In the sea urchin embryo it is zygotically activated in the large micromere-derived skeletogenic mesenchyme lineage (the primary mesenchyme cells), immediately downstream of the lineage-founding regulators alx1, ets1, tbr and tel, together with the homeobox genes hex and tgif. Erg and Hex drive each other's transcription in an interlocking positive feedback loop (erg-hex, hex-tgif) that dynamically locks down the skeletogenic regulatory state once the transient initiating inputs have faded, and Erg is in turn a feed-forward driver, together with Alx1, Ets1, Tbr, Tel, Hex, FoxB and Dri, of the battery of differentiation genes that build the larval calcite endoskeleton. Knockdown of erg depresses transcripts of hex and of the downstream differentiation genes. Around the time the skeletogenic cells finish ingressing, erg is additionally switched on in the oral non-skeletogenic mesoderm, where it is confined by the aboral mesoderm regulators Gcm and GataE. In Lytechinus variegatus the erg ortholog is also required for the epithelial-mesenchymal transition of the skeletogenic cells, with Snail upstream and hex downstream of it.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference for the ETS family node (PTN000218930), seeded by the human, mouse, fly and worm ETS factors. Consistent with the S. purpuratus data: Erg carries an ETS winged-helix DNA-binding domain and, in the skeletogenic micromere GRN, its knockdown severely depresses transcripts of its target regulatory gene hex and of the skeletogenic differentiation genes for which it is a feed-forward driver. The sign of the regulation is inferred from perturbation only (no cis-regulatory or direct binding assay in this species), so the sign-neutral parent term is the correct MF. Reason: Core molecular function; the phylogenetic placement is sound for an ETS-domain factor and is corroborated by perturbation evidence in the reviewed organism. Supporting Evidence: PMID:18413610 These genes are engaged in interlocking positive double feedback loops ( erg with hex ; and hex with tgif ). Interference with expression of any of these genes severely depresses transcript levels of the others ( Fig. S3 ). Thus they dynamically stabilize all aspects of the regulatory state downstream of themselves. PMID:18413610 these differentiation genes require as drivers products of all of the now familiar components of the skeletogenic regulatory state ( alx1 , ets1 , tbr , tel , erg , hex , foxb , dri ) |
| GO:0003677 DNA binding | IEA GO_REF:0000104 | MODIFY | Summary: UniRule-derived generic DNA binding from the ETS domain. True but uninformative; the ETS domain is a sequence-specific winged-helix DNA-binding domain, and the more specific term is already present from InterPro. Reason: Replace the generic term with sequence-specific DNA binding (GO:0043565), which is what the ETS domain confers; this is a family-level inference since no direct DNA-binding assay of Sp-Erg is cached. Proposed replacements: sequence-specific DNA binding |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the ETS domain (IPR000418) and ETS family (IPR046328) signatures. Correct: Erg is a transcription factor of the skeletogenic micromere GRN whose perturbation alters transcript levels of downstream regulatory and differentiation genes. Reason: Consistent with the GRN perturbation evidence; the RNA polymerase II-specific child (IBA row) is the more informative version of the same function. Supporting Evidence: PMID:18413610 three additional genes are activated: one encoding the Ets family factor Erg ( 9 ), and the other two, hex and tgif , encoding homeobox factors ( 5 ) PMID:18413610 These genes are engaged in interlocking positive double feedback loops ( erg with hex ; and hex with tgif ). Interference with expression of any of these genes severely depresses transcript levels of the others ( Fig. S3 ). Thus they dynamically stabilize all aspects of the regulatory state downstream of themselves. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of nuclear activity for the ETS family. Expected and functionally required for a sequence-specific transcription factor; no immunolocalization of Sp-Erg is cached, but the location of an ETS-domain factor that regulates transcription of GRN target genes is not in doubt. Reason: Correct location for the demonstrated transcriptional regulatory role. Supporting Evidence: PMID:18413610 These genes are engaged in interlocking positive double feedback loops ( erg with hex ; and hex with tgif ). Interference with expression of any of these genes severely depresses transcript levels of the others ( Fig. S3 ). Thus they dynamically stabilize all aspects of the regulatory state downstream of themselves. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: UniRule/UniProt subcellular-location inference (Nucleus). Same content as the IBA row; consistent with transcription factor function. Reason: Correct location for a transcription factor; redundant with the IBA row. Supporting Evidence: PMID:18413610 These genes are engaged in interlocking positive double feedback loops ( erg with hex ; and hex with tgif ). Interference with expression of any of these genes severely depresses transcript levels of the others ( Fig. S3 ). Thus they dynamically stabilize all aspects of the regulatory state downstream of themselves. |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000104 | MODIFY | Summary: UniRule maps the ETS domain to the transcription process itself. A sequence-specific transcription factor regulates transcription of its targets rather than performing DNA-templated RNA synthesis; the regulation terms (already present from IBA and InterPro) are the appropriate process annotations. Reason: Wrong level of the process hierarchy for a regulatory factor; replace with regulation of transcription by RNA polymerase II, which is supported by the GRN perturbation data. Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: PMID:18413610 These genes are engaged in interlocking positive double feedback loops ( erg with hex ; and hex with tgif ). Interference with expression of any of these genes severely depresses transcript levels of the others ( Fig. S3 ). Thus they dynamically stabilize all aspects of the regulatory state downstream of themselves. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Generic InterPro/UniRule regulation-of-transcription term. Correct by parentage of the demonstrated function but redundant with the RNA polymerase II-specific rows and with the positive-regulation term proposed as NEW. Reason: True but uninformative parent term; the informative annotations are the RNA polymerase II-specific child and the lineage-level process terms. |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference for the ETS family. Supported in the reviewed organism: erg knockdown severely depresses hex transcript levels (erg-hex positive feedback loop) and the skeletogenic differentiation genes require Erg as a feed-forward driver. Reason: Core process, corroborated by morpholino perturbation and QPCR in S. purpuratus; a positive-regulation child is proposed as NEW. Supporting Evidence: PMID:18413610 These genes are engaged in interlocking positive double feedback loops ( erg with hex ; and hex with tgif ). Interference with expression of any of these genes severely depresses transcript levels of the others ( Fig. S3 ). Thus they dynamically stabilize all aspects of the regulatory state downstream of themselves. PMID:18413610 The alx1 and erg genes play both roles, but the ets1 gene ( 9 ) is used in these gene batteries only as the A driver |
| GO:0006357 regulation of transcription by RNA polymerase II | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the ETS family signature; same content as the IBA row and equally supported by the GRN perturbation data. Reason: Correct; redundant with the IBA row. Supporting Evidence: PMID:18413610 these differentiation genes require as drivers products of all of the now familiar components of the skeletogenic regulatory state ( alx1 , ets1 , tbr , tel , erg , hex , foxb , dri ) |
| GO:0030154 cell differentiation | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT inference of a role in cell differentiation, seeded largely by vertebrate ETS factors acting in hematopoietic, endothelial and neural differentiation. Erg does act in differentiation in the sea urchin embryo (it stabilizes the skeletogenic mesenchyme regulatory state and drives the skeletogenic differentiation gene battery), so the term is not wrong, but it is too generic to be informative. Reason: Generic; the specific processes (mesodermal cell fate commitment, positive regulation of biomineral tissue development) are proposed as NEW. Supporting Evidence: PMID:18413610 these differentiation genes require as drivers products of all of the now familiar components of the skeletogenic regulatory state ( alx1 , ets1 , tbr , tel , erg , hex , foxb , dri ) |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the ETS domain (IPR000418) and pointed domain (IPR003118). The ETS domain is a sequence-specific winged-helix DNA-binding domain; no direct binding assay of Sp-Erg is cached, but sequence-specific binding is the family-defining property and is the basis of the transcription factor activity supported by perturbation data. Reason: Correct at family level and consistent with the transcriptional regulatory role; proposed as the replacement for the generic DNA binding row. Supporting Evidence: PMID:16997294 five of the nine sea urchin ets genes expressed during embryogenesis are exclusively (Sp-Ets1/2, Sp-Erg, Sp-Ese) or additionally (Sp-Tel, Sp-Pea) expressed in mesenchyme cells and/or their progenitors. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IMP PMID:18413610 Global regulatory logic for specification of an embryonic ce... | NEW | Summary: In the skeletogenic micromere GRN, erg and hex form an interlocking positive feedback loop: interference with erg expression severely depresses hex transcript levels (QPCR after morpholino perturbation, Fig. S3), and Erg is one of the transcription factors required, as both an A and a B feed-forward driver, for expression of the skeletogenic differentiation genes. Reason: Perturbation evidence (morpholino knockdown, QPCR of target transcripts) in S. purpuratus shows a positive input of Erg into hex and into the differentiation gene battery, so the positive-regulation child of the accepted GO:0006357 is warranted; IMP because no direct cis-regulatory assay of an Erg-dependent module is available. Supporting Evidence: PMID:18413610 These genes are engaged in interlocking positive double feedback loops ( erg with hex ; and hex with tgif ). Interference with expression of any of these genes severely depresses transcript levels of the others ( Fig. S3 ). Thus they dynamically stabilize all aspects of the regulatory state downstream of themselves. PMID:18413610 The alx1 and erg genes play both roles, but the ets1 gene ( 9 ) is used in these gene batteries only as the A driver PMID:18413610 these differentiation genes require as drivers products of all of the now familiar components of the skeletogenic regulatory state ( alx1 , ets1 , tbr , tel , erg , hex , foxb , dri ) |
| GO:0001710 mesodermal cell fate commitment | IMP PMID:18413610 Global regulatory logic for specification of an embryonic ce... | NEW | Summary: Erg is a component of the dynamic state-stabilization subcircuit (erg-hex and hex-tgif positive feedback loops) that locks down the skeletogenic mesenchyme (primary mesenchyme cell) regulatory state after the transient initiating inputs from the double-negative gate have faded. Its outputs drive hex, feed multiple other nodes of the GRN and the differentiation genes, so Erg performs the regulatory step that commits the lineage rather than merely being required for it. It is expressed exclusively in mesenchyme cells and their progenitors during the relevant period. Reason: Participation test passed: Erg is a transcription factor whose activity maintains the lineage regulatory state; the commitment term (parent of specification and determination) is chosen because Erg acts after the specification genes alx1/ets1/tbr/tel and its documented role is stabilization/lockdown of the already-specified mesodermal fate. IMP from the morpholino/QPCR perturbation data. Supporting Evidence: PMID:18413610 These genes are engaged in interlocking positive double feedback loops ( erg with hex ; and hex with tgif ). Interference with expression of any of these genes severely depresses transcript levels of the others ( Fig. S3 ). Thus they dynamically stabilize all aspects of the regulatory state downstream of themselves. PMID:18413610 The tgif-hex and erg-hex loops in the skeletogenic micromere GRN are canonical examples. Outputs of these genes not only serve as drivers for one another but also feed multiple other nodes of the GRN, so that their activity ensures the persistence of surrounding activities. PMID:16997294 five of the nine sea urchin ets genes expressed during embryogenesis are exclusively (Sp-Ets1/2, Sp-Erg, Sp-Ese) or additionally (Sp-Tel, Sp-Pea) expressed in mesenchyme cells and/or their progenitors. |
| GO:0070169 positive regulation of biomineral tissue development | IMP PMID:18413610 Global regulatory logic for specification of an embryonic ce... | NEW | Summary: The skeletogenic differentiation genes that constitute the larval calcite biomineral require Erg among their transcriptional drivers; in the feed-forward architecture of the differentiation gene batteries erg serves both as an upstream (A) and an intermediate (B) driver. Erg regulates the transcription of the biomineralization genes rather than executing mineral deposition, hence the regulation term. Reason: Perturbation-based (QPCR of differentiation gene transcripts after erg knockdown, Table S1/Fig. S3 of Oliveri 2008) positive input of Erg into the biomineralization gene battery in S. purpuratus. A morphological skeleton-minus phenotype for erg knockdown is not documented in the cached text, so the evidence is at the level of target-gene transcription; recorded as IMP. Supporting Evidence: PMID:18413610 these differentiation genes require as drivers products of all of the now familiar components of the skeletogenic regulatory state ( alx1 , ets1 , tbr , tel , erg , hex , foxb , dri ) PMID:18413610 The alx1 and erg genes play both roles, but the ets1 gene ( 9 ) is used in these gene batteries only as the A driver |
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Download this section (compressed HTML)Q: Is Erg a direct activator of hex and of the skeletogenic differentiation genes (which would justify GO:0001228 / GO:0000978 with IDA), or does it act through intermediates? A cis-regulatory dissection of the hex or an Erg-dependent differentiation-gene module has not been reported for S. purpuratus.
Q: Does erg knockdown in S. purpuratus produce the ingression (EMT) defect reported for L. variegatus erg morphants, and what is the skeletal phenotype? This would determine whether a positive regulation of epithelial to mesenchymal transition annotation is warranted for the S. purpuratus gene product.
Q: What is the function of the later oral non-skeletogenic mesoderm expression of erg (with hex and ets1/2), and does the same erg-hex loop operate there?
Experiment: ChIP-qPCR/ChIP-seq of tagged Sp-Erg in primary mesenchyme cells, combined with GFP reporter analysis of the hex cis-regulatory region with mutated ETS (GGAA/T) sites, to test direct Erg input into hex and the differentiation genes.
Experiment: Time-lapse imaging of ingression and skeletal spicule formation after erg morpholino knockdown in S. purpuratus, with hex and biomineralization-gene QPCR at matched time points.
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