GataC (SpGATAc / Sp-GataC / gatac; UniProt O77156) - curation notes

Identity of the UniProt entry

• O77156 (O77156_STRPU, unreviewed/TrEMBL, 431 aa) is the S. purpuratus "GATA
  transcription factor" cDNA AF077674 (EMBL AAC62960.1) deposited by the Davidson
  lab from a coelomocyte cDNA screen. Its single RX line is Pancer, Rast & Davidson
  1999 (PMID:10398804), which reports the gene as "a GATA-2/3 homologue (SpGATAc)"
  PMID:10398804. The NCBI Gene record linked from the
  entry (KEGG spu:373316, NCBI Gene 373316) is named GATAc / "GATA
  transcription factor".
• Class assignment: the InterPro hits are IPR016374 "TF_GATA-2/3" and the FunFams
  are GATA-2 / GATA-3, i.e. the GATA1/2/3 (class I) family, and Poustka et al.
  2007 explicitly list "SpGataE and SpGataC (orthologs of Gata4/Gata5/Gata6 and
  Gata1/Gata2/Gata3, respectively)" PMID:17506889. Solek et al. 2013 call it
  "SpGatac, an ortholog of vertebrate Gata-1/2/3" PMID:23792116. The other sea
  urchin GATA gene, gatae (Q64HK6, GATA4/5/6 class, endomesoderm GRN), is a
  separate accession reviewed in genes/STRPU/GataE/.
• Confidence that O77156 is the GRN gene gatac: HIGH. The accession is the
  originally cloned SpGATAc cDNA, the NCBI gene name is GATAc, the domain/family
  assignments are GATA1/2/3-class, and the GRN literature (Materna & Davidson
  2012; Materna et al. 2013; Solek et al. 2013) uses gataC/SpGatac for the
  GATA1/2/3 ortholog. No second GATA1/2/3-class gene is described in the genome.
• Domain architecture (UniProt FT): two GATA-type zinc fingers (221-245 and
  274-298; PROSITE PS50114 domains 215-269 and 268-321), disordered regions at
  43-84 and 199-218. Two-finger architecture typical of vertebrate GATA1/2/3.
• PANTHER PTHR10071 "TRANSCRIPTION FACTOR GATA FAMILY MEMBER", subfamily
  PTHR10071:SF281 "BOX A-BINDING FACTOR-RELATED" (labels copied from
  interpro/panther/panther.obo, not from memory; the subfamily name is
  dominated by a different member and is not a description of GataC). O77156 is
  not in interpro/panther/panther-members.tsv.

Embryonic expression: oral non-skeletogenic mesoderm (NSM)

• gataC is one of the first two transcription factor genes specific to the oral
  NSM, switched on at 17-18 hpf: PMID:23261933
  and PMID:23261933.
• Oral-mesoderm specificity was first noted in genome-wide expression surveys:
  PMID:22306924
• The oral NSM is the blastocoelar cell (larval immunocyte) lineage:
  PMID:23261933 and PMID:23261933

Inputs into gataC (upstream circuitry)

• Delta/Notch: in the regulome-wide D/N perturbation, gataC is among the NSM
  genes lost by 18 hpf: PMID:22306924; PMID:22306924. Whether the D/N input is direct
  is not known: PMID:22306924
• Aboral repression by Gcm/GataE: PMID:23261933. Solek et
  al. 2013 took this to cis-regulatory resolution: PMID:23792116 (abstract only
  cached; the reporter constructs and Gcm-site details are in the full text,
  which is not available here).

Outputs: what GataC itself does

• Pre-gastrular GRN: GataC has no measurable output on the regulatory genes of
  the pre-gastrular NSM: PMID:23261933. So in the pre-gastrular GRN gataC is a marker/output node of
  the oral NSM regulatory state rather than a driver of it.
• Blastocoelar cell (immunocyte) development: the functional paper is Solek et
  al. 2013 (abstract only cached): PMID:23792116. The abstract does
  not give the direction of the effector-gene changes or the gene identities.
• Co-expressed hematopoietic-type cofactors: PMID:23792116.
  The Davidson lab makes the same comparison: PMID:23261933.

Adult expression: coelomocytes

• PMID:10398804
• Response to bacterial challenge (down, not up): PMID:10398804 and PMID:10398804

GO curation decisions

• No direct DNA-binding assay (EMSA/ChIP) or reporter assay of a GataC-dependent
  target module is cached for this gene, so the MF is kept at the electronic
  GO:0000981 level (ACCEPT) with the literature merged into the row; no
  activator/repressor child and no cis-regulatory-region binding term proposed.
• Only one NEW BP: GO:0002520 immune system development (IMP, PMID:23792116),
  because SpGatac knockdown alters blastocoelar cell (larval immunocyte)
  migration and immune effector gene expression, and the gene is expressed in
  adult coelomocytes. Comparator check (QuickGO): human GATA3 (P23771) carries
  GO:0002520 (IBA) and GATA1 (P15976) carries hemopoiesis descendants
  (erythrocyte/megakaryocyte differentiation, IMP), so lineage-development terms
  are the convention for this class.
• Not proposed: mesodermal cell fate specification (GataC does not affect any
  regulatory gene pre-gastrulation, so it does not perform the specification
  step; the specification is done by Delta/Notch, Gcm/GataE, Nodal-downstream
  inputs), regulation of cell migration (a transcription factor is not the
  migration machinery; the migration defect is a downstream consequence),
  positive/negative regulation of transcription (sign not given in the cached
  abstract).