Snail is the sea urchin orthologue of the Snail/Slug family of C2H2 zinc-finger transcriptional repressors, a 341-residue protein with five C-terminal zinc fingers and an N-terminal basic region, encoded by a single gene in the Strongylocentrotus purpuratus genome (Sp-sna). Snail-family factors bind E-box-type cis-regulatory sequences and repress transcription, their best-known target across animals being the epithelial cadherin gene, and they are the canonical drivers of the de-adhesion step of epithelial-mesenchymal transition (EMT). In the sea urchin embryo snail is transcribed in the skeletogenic primary mesenchyme cell (PMC) lineage immediately before these cells ingress from the vegetal plate epithelium, downstream of pmar1 and alx1, and it is shut off in the PMCs shortly after ingression; later a snail homologue is expressed transiently in subsets of non-skeletogenic mesenchyme and in the ciliated band. Functional work, done in Lytechinus variegatus, shows that Snail is required in the micromere lineage for PMC ingression, that it represses cadherin transcription and is needed for cadherin endocytosis, and that together with alx1 and twist it forms the de-adhesion sub-circuit of the EMT gene regulatory network, while being dispensable for basement-membrane penetration, directed motility and apical constriction. In S. purpuratus the gene is expressed at low levels before gastrulation and its reported PMC enrichment and regulation by Alx1 differ between studies, so its exact contribution in this species is still uncertain.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Behind this IBA is a PAINT placement on the Snail/Scratch C2H2 zinc-finger node (PTN002810938), seeded by human SNAI1/SNAI2, Drosophila and mouse Snail-family members. The sea urchin protein has the five-finger Snail-type zinc-finger array, and the L. variegatus orthologue represses cadherin transcription and is required for PMC ingression, so sequence-specific binding to RNA polymerase II cis-regulatory regions is the expected molecular activity. No direct DNA-binding assay on the S. purpuratus protein is cached. Reason: Core molecular function of a Snail-family zinc-finger repressor; the phylogenetic placement is sound and is corroborated by the orthologue data in L. variegatus. Supporting Evidence: PMID:17287249 Snail represses the transcription of cadherin, a repression that appears evolutionarily conserved throughout the animal kingdom. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference for RNA polymerase II-specific DNA-binding transcription factor activity on the Snail/Scratch node (PTN002810938). Consistent with the biology; Snail is a transcription factor of the PMC gene regulatory network and the L. variegatus orthologue represses cadherin transcription. The sign (repression) is known from the orthologue and from the family, so the repressor child GO:0001227 is proposed as a NEW row; the sign-neutral parent is kept as the phylogenetically grounded assertion. Reason: Core molecular function; correct phylogenetic placement, corroborated by perturbation data on the L. variegatus orthologue. Supporting Evidence: PMID:17287249 Here we identify a sea urchin ortholog of the Snail transcription factor, and focus on its roles regulating EMT during PMC ingression. PMID:30264451 The possible role of the transcriptional repressor, snail, in the PMC GRN is currently unsettled. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of nuclear localization for the Snail/Scratch zinc-finger family. Snail is a sequence-specific transcriptional repressor and acts in the nucleus; in L. variegatus nuclear Lv-SNAIL protein was detected by immunostaining in mesenchyme cells. Reason: Correct cellular component for a DNA-binding transcriptional repressor. Supporting Evidence: PMID:16958110 Lv-snail mRNA and protein are detectable at the midgastrula stage within the archenteron. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location keyword mapping (ARBA rule, SL-0191 Nucleus) for a Snail-family zinc-finger transcription factor. Redundant with the IBA row but correct. Reason: Correct cellular component; consistent with the IBA row and with the function as a transcriptional repressor. |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of regulation of DNA-templated transcription from the Snail/Scratch node PTN001227002. Correct but sign-neutral and general; the orthologue in L. variegatus represses cadherin transcription, so the more specific negative-regulation terms apply. The general term is retained as the phylogenetically grounded assertion, with the sign captured by the proposed GO:0001227 row. Reason: Correct process for a transcription factor; the sign-specific child is proposed separately rather than rewriting the IBA. Supporting Evidence: PMID:17287249 Snail represses the transcription of cadherin, a repression that appears evolutionarily conserved throughout the animal kingdom. |
| GO:0006357 regulation of transcription by RNA polymerase II | IEA GO_REF:0000108 | ACCEPT | Summary: Logical inter-ontology inference from the GO:0000981 molecular-function annotation. Follows from the accepted MF row and is consistent with the repression of cadherin transcription by the L. variegatus orthologue. Reason: Valid logical consequence of the accepted MF annotation; correct for a Snail-family transcription factor. Supporting Evidence: PMID:17287249 Snail represses the transcription of cadherin, a repression that appears evolutionarily conserved throughout the animal kingdom. |
| GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific | ISS PMID:17287249 The Snail repressor is required for PMC ingression in the se... | NEW | Summary: Snail-family zinc-finger factors are transcriptional repressors, and in the sea urchin the Snail orthologue represses transcription of the cadherin gene; loss of Snail blocks PMC de-adhesion. The functional data are from Lytechinus variegatus (Wu and McClay 2007; Saunders and McClay 2014), not S. purpuratus, so the evidence code is ISS by orthology rather than IMP. S. purpuratus Snail is referred to as a transcriptional repressor in the GRN literature on the strength of the family and the L. variegatus data. The sign-neutral GO:0000981 IBA row remains; this row records the sign. Reason: The repressor variant of the existing GO:0000981 term; the sign is established for the sea urchin orthologue (cadherin repression) and is the family-wide activity. Human SNAI1 carries this term by IBA, so it is the convention for the family. Flagged ISS because the perturbation work is in L. variegatus. Supporting Evidence: PMID:17287249 Snail represses the transcription of cadherin, a repression that appears evolutionarily conserved throughout the animal kingdom. PMID:24598159 These data suggested that snail repression of cadherin transcription was only part of the function of snail. PMID:30264451 The possible role of the transcriptional repressor, snail, in the PMC GRN is currently unsettled. |
| GO:0001837 epithelial to mesenchymal transition | ISS PMID:17287249 The Snail repressor is required for PMC ingression in the se... | NEW | Summary: Snail is the transcription factor that executes the de-adhesion step of PMC ingression, the classic EMT of the sea urchin embryo. Morpholino knockdown and chimera experiments in L. variegatus show it is required in micromeres for PMC ingression; it represses cadherin transcription and is needed for cadherin endocytosis; snail/twist morphant PMCs make the laminin hole, move toward the blastocoel and constrict apically but fail to de-adhere and complete EMT. Participation test passed because Snail itself performs the regulatory step (silencing cadherin) rather than merely being upstream. Comparator check passed because human SNAI1 carries GO:0001837 and GO:0010718 and the Snail family is the canonical EMT driver. Caveats for S. purpuratus are that the functional data are from L. variegatus, that Sp-sna is expressed at low levels before gastrulation, and that its PMC enrichment and response to Alx1 knockdown differ between Barsi et al. 2014 and Rafiq et al. 2014; hence ISS, not IMP. Reason: Snail is the direct repressor of cadherin in the PMC de-adhesion sub-circuit and is required for ingression; this is the core process of the gene product in the sea urchin embryo. Evidence is orthology-transferred from L. variegatus. Term choice note: Snail in this directory carries the executional term GO:0001837 epithelial to mesenchymal transition because it directly silences cadherin, whereas Twist and FoxN2/3 carry the regulatory term GO:0010718 because their inputs into the de-adhesion sub-circuit are indirect. Supporting Evidence: PMID:17287249 Functional knockdown analyses of Snail in whole embryos and chimeras demonstrate that Snail is required in micromeres for PMC ingression. PMID:17287249 Furthermore, Snail expression is required for endocytosis of cadherin, a cellular activity that accompanies PMC ingression. PMID:24598159 Our analysis of both snail and twist knockdowns showed a failure of PMCs to complete EMT in spite of four other successful cell state changes PMID:24598159 In L. variegatus , alx1, twist and snail constitute a functional sub-circuit in the GRN that controls the repression and endocytosis of cadherin required for de-adhesion ( Wu and McClay, 2007 ; Wu et al., 2008 ) PMID:30264451 Wu and McClay (2007), working with Lytechinus variegatus, provided evidence that this regulatory gene acts downstream of alx1 to regulate PMC ingression. |
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Download this section (compressed HTML)Q: Is Sp-snail required for PMC ingression in S. purpuratus, as Lv-snail is in L. variegatus, or has the de-adhesion sub-circuit been rewired between the two species?
Q: Is Sp-sna activated or repressed by Alx1 in S. purpuratus (Rafiq et al. 2014 reported an increase in Alx1 morphants, opposite to L. variegatus)?
Q: Does sea urchin Snail bind the cadherin cis-regulatory region directly (E-box occupancy), and does it recruit a co-repressor through its N-terminal SNAG-like region?
Experiment: Morpholino or CRISPR knockdown of Sp-sna in S. purpuratus with live imaging of PMC ingression and assays of cadherin mRNA and protein endocytosis, to test whether the L. variegatus role transfers.
Hypothesis: Sp-Snail is required for the de-adhesion step of PMC EMT via cadherin repression.
Experiment: Stage-resolved single-cell or NanoString quantification of Sp-sna in PMCs versus other cells across hatched blastula to mesenchyme blastula, and in Alx1 morphants, to resolve the Barsi versus Rafiq discrepancy.
Hypothesis: Sp-sna is transiently enriched in pre-ingression PMCs and is positively regulated by Alx1.
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