Identity of the UniProt entry
- Q2VF23 is an unreviewed TrEMBL entry (753 aa) whose single source is the mRNA DQ177152
"Blimp1/Krox1b", submitted with Livi & Davidson 2007 (RX PubMed=16798107). It therefore
represents the early, cleavage-stage 1b splice/transcription variant of the
blimp1/krox gene that is the endomesoderm-GRN node (RefSeq NP_001073021, GeneID 751833).
The PR/SET domain (aa 86-209) and four C2H2 zinc fingers (aa 458-564) match the
description of the gene product as "a zinc finger transcription factor of the SET family
of proteins" PMID:18061160.
- Naming: "The blimp1/krox gene of Strongylocentrotus purpuratus, formerly krox1, encodes zinc
finger transcription factors which play a central role in both early and late endomesoderm
specification" PMID:16581059. The original cloning paper named it SpKrox1 PMID:9025071. Peter & Davidson 2011 call the early form blimp1b PMID:21623371.
- Confidence in the accession-to-gene link: high (the accession's own literature citation is
the Blimp1/Krox isoform paper from the Davidson lab).
What the gene is
Blimp1/Krox is the sea urchin orthologue of the vertebrate PRDM1/Blimp-1 PR-domain zinc-finger
transcription factor. It is expressed zygotically from cleavage and acts both as a
transcriptional activator and as a transcriptional repressor, depending on the target
cis-regulatory module PMID:19104065.
Two alternatively transcribed/spliced forms exist: the early 1b form (this accession) and the
late gut-specific 1a form PMID:16581059. The 1a form is driven by a separate midgut/
hindgut module that carries Brn1/2/4, Otx and Blimp1 sites PMID:16798107.
Expression
- Earliest transcripts in the macromeres/vegetal plate PMID:9025071; by the Davidson-lab in situ series, cleavage-stage expression
is in "the large micromeres and veg2 descendents" PMID:16581059, then in the ring of
mesoderm cells, then the blastopore region/posterior archenteron, and finally midgut and
hindgut of the pluteus PMID:16581059.
- The pattern is a moving torus: expressed first in skeletogenic micromeres, then the
non-skeletogenic mesoderm, then veg2 endoderm, shutting off centrally each time
PMID:18061160.
Place in the GRN
- beta-catenin/Tcf (from Wnt8 signalling), Otx and Blimp1 itself (autorepression); confirmed by
site mutagenesis in a BAC-GFP knock-in PMID:18061160.
- Tcf sites act as a Groucho-mediated toggle: mutating them causes ectopic ectodermal
reporter expression PMID:18061160.
- Autorepression was first inferred from morpholino data PMID:16581059 and then reconstructed
at the cis-regulatory level PMID:17975065.
- Later (24 h) blimp1b in veg2 endoderm depends on an Eve-controlled signal (V2) from veg1
PMID:21623371. Delta/Notch is
required to clear blimp1b from mesoderm PMID:21623371.
Outputs (direct targets with mapped sites)
- wnt8 (activation). Predicted from perturbation, then shown by site mutation
PMID:16289024;
summarized as "Blimp1 is a direct input essential for wnt8 transcription" PMID:18061160.
In the micromere lineage this is Blimp1's only essential early job PMID:18413610.
Caveat: Peter & Davidson 2011 found that the Blimp1-site mutation that reduces a small
wnt8 construct "does not affect expression of a bacterial artificial chromosome expression
construct containing the whole genomic wnt8 cis-regulatory system" and exclude the model in
which loss of Blimp1 clears wnt8 from mesoderm PMID:21623371. The activator function on
the wnt8 module is therefore real at the module level but not the sole driver of wnt8 in the
endogenous locus.
- otx (beta1/2 module) (activation, AND logic with Gatae and Otx) [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"].
- hesC (repression through an intronic Blimp1 site) [PMID:19104065 "Mutation of this site
in a hesC reporter construct caused expression to remain strong in the NSM territory";
"blimp1 mRNA overexpression nearly abolished expression of the hesC BAC-GFP reporter"]. This
permits delta transcription in the NSM ("Blimp1 thus represses the repressor of delta ,
thereby permitting its transcription").
- notch (repression) PMID:19104065.
- even-skipped (activation, with Tcf) PMID:18061160.
- blimp1 itself (autorepression; see above).
- Later endoderm outputs from perturbation (no sites mapped): brn1/2/4 and tgif
PMID:21623371; the
blimp1b-otx-gatae positive feedback loop PMID:21623371.
Loss-of-function phenotype
- blimp1 MASO blocks endomesoderm specification PMID:18061160; the 1b form "is
required for the early events of endomesoderm specification" PMID:16581059. Blimp1 MASO
also leaves hesC on in the NSM and lowers delta ~3-fold PMID:19104065.
Summary of the subcircuit
PMID:19104065
Other roles
- Germline: Blimp1 isoforms regulate germline determinants (vasa, nanos) in S. purpuratus and
the sea star PMID:40024498. Abstract only; isoform not mappable to this accession with certainty, so recorded
as a question rather than an annotation.
- Starfish orthologue AmKrox has a conserved vegetal ring expression PMID:12915305.
Curation decisions (2026-09-26)
- IBA/IEA rows for DNA-binding TF activity, cis-regulatory DNA binding, nucleus, regulation/
negative regulation of Pol II transcription and repressor activity: ACCEPT (all confirmed by
the cis-regulatory work above).
- cytoplasm IBA: KEEP_AS_NON_CORE (family-level inference, no sea urchin evidence; site of
action is nuclear).
- cell fate commitment IBA and cellular developmental process IEA: MODIFY to the specific
GO:0001714 endodermal cell fate specification.
- NEW: GO:0001228 activator activity (IDA; wnt8/otx module site mutagenesis), GO:0045944
(IDA), GO:0001714 endodermal cell fate specification (IMP; blimp1 MASO). Positive regulation
of Wnt/Notch signalling deliberately NOT proposed: Blimp1 controls transcription of the
ligand/receptor genes, one step removed from the pathway, and the wnt8 BAC result makes the
necessity claim uncertain.
- No GO-CAM contains Q2VF23 (gocams/index.tsv checked).