GataE (Sp-GataE / Spgatae; UniProt Q64HK6) - curation notes

Identity of the UniProt entry

• Q64HK6 (Q64HK6_STRPU, unreviewed/TrEMBL, 567 aa) is the S. purpuratus GATA
  transcription factor deposited by the Davidson lab (EMBL AAU21562.1, gene name
  gatae); its single RX line is PMID:15567710 (Lee & Davidson 2004), the
  expression paper for Spgatae. The cDNA in that paper is GenBank AY623814, which
  is also the cDNA used to define the exon structure in Lee, Nam & Davidson 2007
  PMID:17570356. So the accession is the GRN gene, not a
  paralogue; there is no identity doubt. The sea urchin has a second GATA gene,
  gatac (GATA1/2/3 class), which is a different node of the mesoderm GRN.
• Orthology: PMID:15567710; also
  PMID:17570356. PANTHER PTHR10071 (family) / PTHR10071:SF337
  (subfamily), labels looked up in interpro/panther/panther.obo, not from memory.
• Domain architecture (UniProt FT): two GATA-type zinc fingers at 256-311 and
  311-364 (PROSITE PS50114); PMID:17570356. Long disordered N- and C-terminal regions.

Expression (timing and lineage)

• PMID:15567710
• PMID:15567710 Terminal pattern: midgut plus coelomic pouches.
• Two phases, two lineages: an early non-skeletogenic mesoderm (NSM) phase
  identical to gcm, then an endoderm phase. PMID:23261933.
  PMID:19895806. GataE protein was detected with a specific antibody
  (Kiyama & Klein 2007, PMID:17710433), which also identified the Fog1 cofactor.

cis-regulation of gatae (inputs)

• Lee, Nam & Davidson 2007 (full text cached) built a gatae BAC-GFP knock-in
  that reproduces the whole pattern and mapped two intronic modules:
  PMID:17570356 BAC deletion showed
  PMID:17570356
• Delta/Notch input (NSM phase): PMID:22306924; in the
  regulome-wide D/N perturbation, PMID:22306924.
• Gcm input (feed-forward with Delta/Notch): PMID:23261933; abstract: PMID:23261933
• Otx input (endoderm phase) and the otx-gatae feedback loop: PMID:19895806; PMID:21623371; a brachyury MASO
  effect on gatae is indirect via otx PMID:19895806.

Outputs: what GataE itself does

Direct activator of endoderm regulatory genes (endoderm specification)

• PMID:17570356
• The otx node was verified at the DNA level: [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."] and PMID:15110718 The site mutations phenocopied the gatae MASO
  PMID:15110718.
• Lock-down loop: PMID:17570356. Conserved for ~500 My with starfish: PMID:14595011 and
  PMID:14595011. Note
  that the perturbation experiments in Hinman et al. 2003 are in the starfish
  Asterina miniata; the sea urchin statements rest on Davidson et al. 2002
  (PMID:12027441, PMID:11872831).
• Requirement: PMID:17570356

Aboral NSM / pigment cell specification

• GataE MASO phenotype (two MASOs, translation- and splice-blocking):
  PMID:23261933; PMID:23261933.
• Restriction of the oral NSM state: PMID:23261933; the authors note the spatial repressor is
  PMID:23261933, so direct
  repression is not established.
• Direct activation of the pigment differentiation gene pks: PMID:20122918; corroborated by
  PMID:22509525 and gataE upstream of six1
  PMID:22509525.

Repression of an ectoderm gene (spec2a)

• Kiyama et al. 2005 (abstract only): PMID:15882584 and PMID:15882584 The ectoderm-marker effect
  is hard to interpret for a gene that is never expressed in ectoderm, and the
  repressor conclusion is hedged ("suggesting"), so I do not propose a
  repressor MF term; raised as a question instead.
• Cofactor: PMID:17710433 but Fog1 MASO had
  no effect on endomesoderm specification, so the interaction is not annotated
  (and protein binding is avoided per repo policy).

Curation decisions (summary)

• Existing rows are all IEA (InterPro2GO / UniProt SubCell). GO:0003700,
  GO:0006357 and nucleus: ACCEPT (core; direct cis-regulatory evidence). GO:0006355:
  KEEP_AS_NON_CORE (redundant generic parent). GO:0008270 zinc ion binding:
  KEEP_AS_NON_CORE (structural to the class IV zinc fingers). GO:0043565: MODIFY
  to GO:0000978.
• NEW: GO:0001228 (activator MF, IDA: Gata sites in otx module; pks module),
  GO:0000978 (IDA), GO:0045944 (IDA), GO:0001714 endodermal cell fate
  specification (IMP/IDA), GO:0007501 mesodermal cell fate specification (IMP,
  aboral NSM), GO:0050942 positive regulation of pigment cell differentiation
  (IMP + direct pks input).
• Participation test: GataE is itself the transcription factor that installs
  and locks down the endoderm regulatory state (direct inputs into otx, foxA,
  brachyury) and the aboral NSM state (direct inputs into pks, and likely
  six1/2, z166), so the specification terms are participation, not mere
  necessity. Comparators: vertebrate GATA4/5/6 carry endoderm/mesoderm
  specification and cell fate terms; Otx and Blimp1 sibling reviews in this
  repository (the other members of the lock-down loop) carry endodermal cell
  fate specification.
• gocams/index.tsv has no entry for Q64HK6 / gatae.