Pmar1 (Q8WRE9, Strongylocentrotus purpuratus) — curation notes

Identity

UniProt Q8WRE9 (unreviewed, TrEMBL) is the original pmar1 cDNA clone
(EMBL AAL38537, "Paired class homeodomain repressor", gene name PMAR1) reported
by Oliveri, Carrick & Davidson 2002. 237 aa; homeobox at residues 19-79
(PROSITE PS50071); PANTHER PTHR45793 / SF5 (id not asserted in the review, see
CLAUDE.md rule on PANTHER labels).
pmar1 is not a single-copy gene: "there is a cluster of several very similar
pmar1 genes" PMID:18413610. The euechinoid
hbox12/pmar1/micro1 family shows extensive copy-number variation and
species-specific divergence in Paracentrotus PMID:28350855. The Hemicentrotus orthologue is
micro1 [PMID:16078091, title]. Q8WRE9 therefore stands for one member of a
near-identical cluster; the perturbation literature (mRNA injection, En-fusion,
chimera rescue) addresses the family product, not a specific copy.

Paired-class homeodomain transcriptional repressor, expressed only in
micromeres during cleavage/early blastula: "pmar1 is expressed only during
cleavage and early blastula stages, and exclusively in micromeres. It is
initially activated as soon as the micromeres are formed, in response to Otx and
beta-Catenin/Tcf inputs." PMID:12027443.
Timing: "Expression of pmar1 in the micromere lineage ( Fig. 2 B ) is specific
and transient, detectable initially right at late fourth cleavage, and gone 12–15
h later." PMID:18413610; peak transcript at 8 h post-fertilization
PMID:18413610.
Inputs: nuclear beta-catenin/Tcf plus Otx PMID:18413610.
Output: the double-negative gate. Pmar1 represses hesC, the globally
expressed second repressor; hesC in turn represses delta, alx1, ets1,
tbr, tel everywhere except the micromeres [PMID:17636127 "A gene encoding a
transcriptional repressor, pmar1 , is activated specifically in micromeres,
where it represses transcription of a second repressor that is otherwise active
globally."; PMID:18413610 "HesC is expressed zygotically early in cleavage, in
all cells of the embryo except the micromeres, where Pmar1 prevents its
expression."].

Forced global expression of Pmar1 mRNA and of an Engrailed-Pmar1 repressor
fusion have identical effects, i.e. derepression of delta and of the
skeletogenic gene battery, converting most of the embryo into skeletogenic
mesenchyme: "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. In both cases, the effects are derepression: of the delta gene; and of
skeletogenic genes" PMID:12027443. "This results in transformation of much of
the embryo into skeletogenic mesenchyme cells that express skeletogenic
markers." PMID:12027443.
Revilla-i-Domingo 2007 restates the inference: "It follows that the pmar1 gene
product naturally acts as a repressor (also indicated by its sequence)"
PMID:17636127.

Chimera/transplant rescue: beta-catenin-blocked micromeres are unspecified;
adding Pmar1 rescues all micromere functions: "When such beta-catenin-blocked
micromeres also express Pmar1, all observed micromere functions are rescued.
The rescue includes expression of the primary mesenchyme cell (PMC)
differentiation program, expression and execution of the Delta signal to induce
secondary mesoderm cell (SMC) specification in macromere progeny, and expression
of the early endomesoderm induction signal" PMID:12781680.
Conclusion: "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:12781680.
"So pmar1 is necessary and sufficient; no other β-catenin/Tcf target need be
involved." PMID:18413610. Ectopic-fated cells work too: "This transplantation
experiment can even be done successfully with cells from the part of the embryo
normally fated to become ectoderm providing they contain pmar1 mRNA."
PMID:18413610.

Screen: 46 regulatory genes assayed by QPCR after pmar1 mRNA overexpression;
hesC among the five down-regulated at 9 and 12 h: "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:17636127.
hesC MASO phenocopies pmar1 MOE: "As logically required, blockade of hesC mRNA
translation and global overexpression of pmar1 mRNA have the same effect, which
is to cause all of the cells of the embryo to express micromere-specific
genes." PMID:17636127.
Directness caveat: "Although this remains to be finally authenticated by
identification of the cis -regulatory target sites, HesC interactions with the
target genes of Fig. 1 D are likely to be direct, as is likely to be the
interaction of Pmar1 with the hesC regulatory apparatus." PMID:17636127. No
Pmar1 binding site on hesC has been mapped in any cached paper.

R11 element ~13 kb downstream of delta "responds to the pmar1 repression system
just as predicted for the delta gene in the endomesoderm GRN" PMID:15385170.
This is an indirect readout (Pmar1 -| HesC -| delta), useful for the repressor
logic but not for a direct Pmar1 target.

Sharma & Ettensohn 2010: alx1 and delta are activated before hesC is
downregulated; "We postulate the existence of additional, unidentified
repressors that are controlled by pmar1, and propose that the ability of pmar1
to derepress alx1 and delta is regulated by the unequal division of vegetal
blastomeres." PMID:20181745. So Pmar1 likely has hesC-independent repressive
targets.
Yamazaki 2020: cidaroid pmar1 and starfish phb "promote activation of
endomesoderm regulatory gene orthologs via an unknown repressor that is not
HesC" PMID:32001441 — the Pmar1-hesC link is a euechinoid innovation.

IEA DNA binding (homeobox InterPro/UniRule): ACCEPT — correct domain-level
inference for a homeodomain protein; the informative claim (repressor activity)
is added as NEW rather than by rewriting the IEA row.
IEA nucleus: ACCEPT — a transcriptional repressor acting on hesC
transcription; no direct localization data, but the inference is sound.
NEW GO:0001227 (DNA-binding transcription repressor activity, RNA polymerase
II-specific), IMP, PMID:12027443 (+17636127): sign of activity established by
En-Pmar1 equivalence and hesC down-regulation.
NEW GO:0000122 (negative regulation of transcription by RNA polymerase II),
IMP, PMID:17636127: hesC transcript falls on forced Pmar1 expression.
NEW GO:0007501 (mesodermal cell fate specification), IMP, PMID:12781680
(+18413610, 12027443): Pmar1 is the lineage-initiating regulator whose
expression is necessary and sufficient to specify skeletogenic (mesodermal)
micromere fate; passes the participation test because Pmar1 itself performs
the first regulatory step of the specification circuit.
Not proposed: Notch signalling / Delta expression, endoderm induction,
skeletogenesis — downstream consequences of the gate, performed by other gene
products (Delta, HesC targets, ES ligand).
gocams/index.tsv has no entry for Q8WRE9.