Pmar1 (paired-class micromere anti-repressor) is a paired-class homeodomain transcriptional repressor of the purple sea urchin, encoded by a small cluster of near-identical pmar1 genes. It is expressed transiently and exclusively in the micromeres of the cleaving embryo, switching on at the fourth cleavage in response to nuclear beta-catenin/Tcf together with Otx and disappearing by early blastula stage. In the nucleus of the micromeres Pmar1 represses transcription of hesC, a second repressor that is otherwise expressed throughout the embryo and that silences the regulatory genes alx1, ets1, tbr and tel and the Notch ligand gene delta. This double-negative gate confines the skeletogenic regulatory state to the micromere lineage. Forced expression of Pmar1 in every cell, or of an Engrailed-Pmar1 fusion, converts most of the embryo into skeletogenic mesenchyme, and Pmar1 alone rescues specification in micromeres in which beta-catenin signalling is blocked, so Pmar1 is necessary and sufficient to initiate skeletogenic micromere specification and, through the gate, the expression of the micromere-derived Delta and endomesoderm-inducing signals.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: Domain-level electronic inference from the homeobox (InterPro IPR001356, residues 19-79). Pmar1 is a paired-class homeodomain protein whose in vivo behaviour is that of a sequence-specific transcriptional repressor, so DNA binding is a correct, if general, molecular function. No Pmar1 binding site on hesC or any other target has been mapped, so a more specific cis-regulatory-region DNA-binding term is not asserted here; the informative activity is added as a NEW repressor-activity row instead. Reason: The homeobox is the only annotated domain and the perturbation literature is consistent with a DNA-binding transcriptional repressor; the term is correct but generic. Supporting Evidence: PMID:12027443 A central role is played by a newly discovered gene encoding a paired class homeodomain transcription factor which in micromeres acts as a repressor of a repressor |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic subcellular-location inference from the homeobox rule. Pmar1 acts by repressing transcription of hesC in micromere nuclei, and an Engrailed-Pmar1 fusion reproduces its effects, so nuclear localization is the only location consistent with its function. No direct immunolocalization exists, but the inference is sound and this is the core location. Reason: A transcriptional repressor that controls hesC transcription must act in the nucleus; the electronic inference matches the functional evidence. Supporting Evidence: PMID:17636127 This gene encodes a transcriptional repressor of the paired homeodomain family. |
| GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific | IMP PMID:12027443 A regulatory gene network that directs micromere specificati... | NEW | Summary: Pmar1 is a paired-class homeodomain protein that acts in vivo as a transcriptional repressor. Global expression of pmar1 mRNA and of an Engrailed-Pmar1 repressor-domain fusion give identical derepression phenotypes (ectopic delta and skeletogenic gene expression), and forced Pmar1 expression lowers hesC transcript levels, identifying hesC as the repressed target. Direct binding of Pmar1 to hesC cis-regulatory DNA has not been mapped, so the term is supported by gain-of-function equivalence and target down-regulation rather than a reporter assay. Reason: Sign of the activity is established (repressor, via En-Pmar1 equivalence and hesC down-regulation) and the target is a zygotically transcribed regulatory gene, so the RNA polymerase II-specific repressor term is the appropriate MF; it is more informative than the electronic DNA binding row. Supporting Evidence: PMID:12027443 The repressive nature of the interactions mediated by the pmar1 gene product was shown by the identical effect of introducing mRNA encoding the Pmar1 factor, and mRNA encoding an Engrailed-Pmar1 (En-Pmar1) repressor domain fusion. PMID:17636127 It follows that the pmar1 gene product naturally acts as a repressor (also indicated by its sequence) |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IMP PMID:17636127 A missing link in the sea urchin embryo gene regulatory netw... | NEW | Summary: Pmar1 represses transcription of hesC in the micromeres. In a QPCR screen of 46 regulatory genes after forced global pmar1 expression, hesC was one of five genes significantly down-regulated at both 9 and 12 h; hesC morpholino knockdown phenocopies pmar1 overexpression, and hesC is expressed everywhere except the micromeres where Pmar1 is present. This is the regulatory step Pmar1 itself performs in the double-negative gate. Reason: Pmar1 is the gene product that carries out the repression (participation test passed); hesC is the direct process target. Downstream derepression of delta, alx1, ets1 and tbr is performed by relief of HesC and is not annotated to Pmar1. Supporting Evidence: PMID:17636127 Five of the 46 regulatory genes tested were found to be significantly down-regulated at both time points in the two experiments performed. These genes were six3 , smadIP , awh , hesC , and foxJ1 PMID:18413610 HesC is expressed zygotically early in cleavage, in all cells of the embryo except the micromeres, where Pmar1 prevents its expression. |
| GO:0007501 mesodermal cell fate specification | IMP PMID:12781680 Activation of pmar1 controls specification of micromeres in ... | NEW | Summary: Pmar1 is the lineage-initiating regulator of the skeletogenic micromere (primary mesenchyme) fate. Micromeres in which beta-catenin nuclearization is blocked remain unspecified, and expression of Pmar1 in such micromeres rescues the entire micromere program in chimeras, including the PMC differentiation program; even presumptive ectoderm cells carrying pmar1 mRNA can substitute for micromeres. Global pmar1 expression converts the whole embryo into skeletogenic mesenchyme. The specification is cell-autonomous once pmar1 is on, matching the GO definition of mesodermal cell fate specification. Reason: Pmar1 itself performs the first regulatory step of the specification circuit (repression of hesC that unlocks alx1/ets1/tbr/tel), so it participates in, rather than merely being required for, specification of the mesodermal micromere lineage. Downstream Delta/Notch signalling to secondary mesoderm and endomesoderm induction of neighbouring cells are executed by other gene products and are not annotated here. Supporting Evidence: PMID:12781680 Pmar1 is an important transcription factor necessary for initiating the micromere specification program and for the expression of two inductive signals produced by micromeres. PMID:18413610 So pmar1 is necessary and sufficient; no other Ξ²-catenin/Tcf target need be involved. PMID:12027443 This results in transformation of much of the embryo into skeletogenic mesenchyme cells that express skeletogenic markers. |
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Download this section (compressed HTML)Q: Which member(s) of the pmar1 gene cluster does Q8WRE9 represent, and do the several near-identical copies differ in expression level, timing or function?
Q: Does Pmar1 bind the hesC cis-regulatory region directly, and what is its DNA-binding specificity (paired-class homeodomain P3/P2 site preference)?
Q: Which additional repressors, if any, are controlled by Pmar1 to account for the hesC-independent early activation of alx1 and delta?
Experiment: Map Pmar1 occupancy on the hesC locus by ChIP or DNA-affinity assays with a tagged Pmar1 in cleavage-stage embryos, and test candidate sites in hesC reporter constructs for loss of micromere repression.
Hypothesis: Pmar1 represses hesC directly through one or more paired-class homeodomain sites in the hesC cis-regulatory module.
Experiment: Repeat the pmar1 mRNA-overexpression QPCR screen with a hesC morpholino background to isolate hesC-independent Pmar1 targets among early regulatory genes.
Hypothesis: Pmar1 represses at least one additional early repressor that gates alx1 and delta activation.
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The cis-regulatory target site(s) through which Pmar1 represses hesC have not been identified; direct binding of Pmar1 to the hesC locus is inferred from kinetics and sequence, not demonstrated.
OPEN BIOLOGY
Provenance (the field's own admissions):
Gap: Whether Pmar1 has repressive targets in addition to hesC (as suggested by activation of alx1 and delta before hesC is downregulated) is unresolved.
OPEN BIOLOGY
Provenance (the field's own admissions):
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