GataC (SpGATAc, Sp-GataC) is the sea urchin GATA1/2/3-class zinc-finger transcription factor, with two tandem GATA-type zinc fingers flanked by disordered regions. In the embryo it is one of the first two transcription factor genes (with prox1) to be switched on specifically in the oral non-skeletogenic mesoderm at 17-18 hours post fertilization, downstream of Delta/Notch signaling and Nodal-dependent oral-aboral patterning, and it is excluded from the aboral (pigment cell) mesoderm by the Gcm/GataE regulatory state, with Gcm acting directly on the gatac gene. The oral mesoderm cells that express it become the blastocoelar cells, the migratory immunocytes of the larva; knockdown of gatac does not alter the pre-gastrular regulatory genes but perturbs blastocoelar cell migration at gastrulation and the later expression of immune effector genes. It is co-expressed with sea urchin homologs of Scl, Lmo2 and E-proteins, the partners of vertebrate GATA1/2/3 in hematopoietic complexes. In adults gatac is expressed in coelomocytes, the circulating immune cells, where its transcripts fall sharply within hours of bacterial challenge.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IEA GO_REF:0000002 | ACCEPT | Summary: GataC is a two-zinc-finger GATA1/2/3-class transcription factor (InterPro TF_GATA-2/3 family hit). In S. purpuratus it is a transcription factor gene of the oral non-skeletogenic mesoderm whose knockdown alters the later expression of immune effector genes in blastocoelar cells, consistent with sequence-specific transcription factor activity at RNA polymerase II genes. No direct DNA-binding or reporter assay of a GataC target is cached, so the electronic term is retained as the carrier of the core molecular function rather than replaced by an activator or repressor child. Reason: Core molecular function; the family assignment is confirmed by the originating coelomocyte cDNA paper (GATA-2/3 homologue) and by the loss-of-function effect on effector gene expression. The sign of regulation is not documented in the cached literature, so no activator/repressor term is proposed. Supporting Evidence: PMID:10398804 Three coelomocyte genes reported here encode transcription factors. These are an NFKB homologue (SpNFKB); a GATA-2/3 homologue (SpGATAc); and a runt domain factor (SpRunt-1). PMID:23792116 Here we characterize the oral NSM expression and downstream function of two homologs of key vertebrate hematopoietic transcription factors: SpGatac, an ortholog of vertebrate Gata-1/2/3 and SpScl, an ortholog of Scl/Tal-2/Lyl-1. PMID:23792116 Perturbation of SpGatac affects blastocoelar cell migration at gastrulation and later expression of immune effector genes, whereas interference with SpScl function disrupts segregation of pigment and blastocoelar cell precursors. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Generic parent of the RNA polymerase II-specific term above, derived from the GATA transcription factor family signature. Correct but fully redundant with GO:0000981. Reason: True but less informative than the accepted RNA polymerase II-specific child; retained as a non-core annotation. Supporting Evidence: PMID:17506889 Examples include SpGataE and SpGataC (orthologs of Gata4/Gata5/Gata6 and Gata1/Gata2/Gata3, respectively) |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Required location of a GATA-family DNA-binding transcription factor. No immunolocalization of the S. purpuratus protein is cached, but the loss-of-function effect on effector gene expression is consistent with nuclear transcription factor activity. Reason: Functionally required location for a sequence-specific transcription factor whose knockdown changes target gene transcription. Supporting Evidence: PMID:23792116 Perturbation of SpGatac affects blastocoelar cell migration at gastrulation and later expression of immune effector genes, whereas interference with SpScl function disrupts segregation of pigment and blastocoelar cell precursors. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Generic process term from the GATA zinc-finger signatures. Correct but redundant with the RNA polymerase II regulation term below. Reason: True but uninformative; the RNA polymerase II-specific child carries the same information more precisely. |
| GO:0006357 regulation of transcription by RNA polymerase II | IEA GO_REF:0000002 | ACCEPT | Summary: GataC regulates transcription of protein-coding genes in the blastocoelar cell lineage, as shown by altered immune effector gene expression after morpholino knockdown. Within the pre-gastrular network, however, GataC knockdown does not change any regulatory gene, so its transcriptional outputs are the later differentiation-stage genes, not the specification-stage regulatory genes. Reason: Core process for a transcription factor, supported by loss-of-function effects on effector gene expression in S. purpuratus; the direction of regulation is not given in the cached abstract, so the generic regulation term (not the positive or negative child) is kept. Supporting Evidence: PMID:23792116 Perturbation of SpGatac affects blastocoelar cell migration at gastrulation and later expression of immune effector genes, whereas interference with SpScl function disrupts segregation of pigment and blastocoelar cell precursors. PMID:23261933 GataC MASO treatment does not affect any regulatory genes pre-gastrulation (Supp. Fig. 4; Solek and Rast, personal communication) |
| GO:0008270 zinc ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: The two GATA-type zinc fingers (residues 221-245 and 274-298 in UniProt) coordinate zinc as a structural requirement for DNA binding. Correct structural property but not a function in its own right. Reason: Structural zinc coordination by the GATA fingers is a means to the DNA-binding transcription factor function, not a core function. |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Sequence-specific (GATA-motif) DNA binding is the expected activity of the GATA zinc fingers, but no binding assay (EMSA, ChIP, or site mutagenesis of a GataC-dependent module) is available for the sea urchin protein, so the more specific cis-regulatory region binding term cannot be supported from this species. Reason: Correct family-level inference; retained as a non-core annotation subsumed by the transcription factor activity term because no direct binding evidence exists for GataC itself. |
| GO:0002520 immune system development | IMP PMID:23792116 An ancient role for Gata-1/2/3 and Scl transcription factor ... | NEW | Summary: The oral non-skeletogenic mesoderm cells that express gatac give rise to the blastocoelar cells, the immunocytes of the larva. Morpholino knockdown of SpGatac perturbs blastocoelar cell migration at gastrulation and the later expression of immune effector genes, so GataC is a transcriptional driver of immunocyte development, paralleling the hematopoietic roles of vertebrate GATA1/2/3 with which it shares co-expressed Scl, Lmo2 and E-protein partners. The gene is also expressed in adult coelomocytes. Reason: Participation test: GataC is the transcription factor that regulates effector gene expression in the developing immunocytes, so it performs part of the developmental program rather than merely being required for it. Comparator check: human GATA3 carries GO:0002520 and GATA1 carries hemopoiesis descendant terms, so lineage-development terms are the convention for this class. Evidence is IMP from the SpGatac morpholino phenotype; the cached record is abstract-only, so the identity and direction of the effector genes affected are not recorded here. No mesoderm specification term is proposed because GataC knockdown does not affect any pre-gastrular regulatory gene. Supporting Evidence: PMID:23792116 Perturbation of SpGatac affects blastocoelar cell migration at gastrulation and later expression of immune effector genes, whereas interference with SpScl function disrupts segregation of pigment and blastocoelar cell precursors. PMID:23792116 Larval immunocytes, including pigment cells and several blastocoelar cell subtypes, emerge from a population of non-skeletal mesodermal (NSM) precursors that is specified at the blastula stage. PMID:23261933 The first transcription factor genes specific to the oral NSM, prox1 and gataC, are transcriptionally activated in this region between 17 and 18 hpf (Fig. 1B,T), which is significantly later than the onset of Nodal transcription at about 8–9 hpf (Fig. 1B). PMID:23261933 About one-third of the NSM cells, located in a V-shaped sector directly beneath the oral ectoderm, give rise upon gastrulation to a particular mesenchymal cell type known as blastocoelar cells (Ruffins and Ettensohn, 1996). PMID:10398804 All three of these coelomocyte genes respond sharply to bacterial challenge: SpNFKB and SpRunt-1 genes are rapidly up-regulated, while transcripts of SpGATAc factor disappear within hours of injection of bacteria. |
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Download this section (compressed HTML)Q: Which immune effector genes of the blastocoelar cells are direct GataC targets, and does GataC activate or repress them?
Q: Does GataC form an Scl/Lmo2/E-protein complex in sea urchin oral mesoderm cells as its orthologs do in vertebrate hematopoietic cells?
Q: Is the Delta/Notch input into gatac direct (Su(H) sites in the gatac cis-regulatory module) or relayed through other oral NSM regulators?
Q: What is the function of GataC in adult coelomocytes, given that its transcripts disappear rather than rise after bacterial challenge?
Experiment: ChIP-seq or DNA-affinity capture of tagged GataC in gastrula-stage embryos to map its genomic occupancy and identify direct targets among the blastocoelar cell effector genes.
Type: ChIP-seq
Experiment: Single-cell RNA-seq of control and gatac morphant larvae to define which blastocoelar cell subtypes and effector genes depend on GataC.
Type: single-cell RNA-seq
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