id: MODULE:neural_crest_gene_regulatory_network title: Neural crest gene regulatory network module description: 'The vertebrate neural crest gene regulatory network: the transcriptional program by which signals at the edge of the neural plate are converted, through a neural plate border layer and a crest specifier layer, into migratory multipotent crest cells, of which the cranial population forms skeletogenic ectomesenchyme. A parallel competence layer, shared with pluripotent blastula cells, keeps progenitors undifferentiated. Border specifiers (Gbx2, Msx1, AP-2alpha, Pax3, Zic1) are largely ancestral chordate genes already expressed at the amphioxus neural plate border; most crest specifiers were recruited at the base of vertebrates, mainly by changes in where they are expressed, and some cranial circuit components (Ets1) were added later in jawed vertebrates. Inducing signals (Wnt, BMP, FGF) are covered by the wnt_signaling, bmp_signaling and FGF modules and are treated here as upstream context.' status: DRAFT evidence: - source_id: PMID:25564621 title: 'Establishing neural crest identity: a gene regulatory recipe.' statement: Review of the layered neural crest gene regulatory network (border, specifier, effector layers). - source_id: PMID:18562679 title: Insights from the amphioxus genome on the origin of vertebrate neural crest. statement: Amphioxus has border patterning genes at the neural plate border but lacks most crest specifier expression there. supporting_text: neural plate border patterning genes, and melanocyte differentiation genes appear conserved - source_id: file:modules/neural_crest_gene_regulatory_network-deep-research-falcon.md statement: Module deep research supports treating inducing signals as upstream inputs rather than network members. supporting_text: WNT, BMP and FGF signaling are upstream inputs - source_id: PMID:31645763 title: Evolution of the new head by gradual acquisition of neural crest regulatory circuits. statement: The cranial crest circuit was assembled gradually in gnathostomes; the ancestral crest was trunk-like. notes: 'Concrete members are the gene products reviewed in projects/NEURAL_CREST_ORIGINS.md: Xenopus laevis proteins where reviewed Swiss-Prot entries exist, human proteins otherwise. Process terms follow the replacement rule of projects/NEURAL_CREST_FORMATION_OBSOLETION.md: border genes at the proposed ''neural plate border formation'' term (plus GO:0014034 where they directly induce crest fate), crest specifiers at GO:0014036, and competence factors at the proposed ''neural crest progenitor maintenance'' term. Genes with roles in more than one layer (AP-2alpha, Snai2, Twist1, Sox9) have one annoton per role, which is how roles that are non-core at gene level (e.g. Twist1 in ectomesenchyme) become explicit parts here. Sox10-driven melanocyte and glial differentiation are downstream derivative programs and are out of scope. Both proposed terms (neural plate border formation; neural crest progenitor maintenance, proposed is_a GO:0019827) have their canonical name, definition and justification in the proposed_new_terms entries of the member gene reviews and in projects/NEURAL_CREST_FORMATION_OBSOLETION.md; they are ontology gaps, not knowledge gaps, so they are not repeated here. Not yet modelled (curation plan in projects/NEURAL_CREST_ORIGINS.md): Hairy2 acting through an FGFR4-STAT3 complex, OCT4-SOX2 redeployed to TFAP2A-bound crest enhancers (chick/human; in frog any crest Oct partner is more likely SoxE, since Sox3 is absent from crest by neurula), and the Twist1 chromatin partners CHD7/CHD8/WHSC1.' module: id: neural_crest_gene_regulatory_network label: Neural crest gene regulatory network module_type: DEVELOPMENTAL_PROCESS concepts: - preferred_term: neural crest cell differentiation term: id: GO:0014033 label: neural crest cell differentiation description: 'Umbrella term: GO:0014034 fate commitment, GO:0014032 development and GO:0001755 migration all fall under it.' context: taxa: - preferred_term: Vertebrata term: id: NCBITaxon:7742 label: Vertebrata description: The neural crest is a vertebrate innovation; the border layer is shared with other chordates. cellular_components: - preferred_term: nucleus term: id: GO:0005634 label: nucleus parts: - order: 1 role: define the neural plate border competence territory node: id: neural_plate_border_specification label: Neural plate border specification module_type: DEVELOPMENTAL_PROCESS description: Wnt, intermediate BMP and FGF signals at the edge of the neural plate are read out by a set of transcription factors that define the neural plate border, a competence territory that gives rise to neural crest, preplacodal ectoderm, dorsal neural tube and epidermis. Border specifiers act upstream of, and are required for, crest specifier expression, but individually do not impose crest fate; Pax3 and Zic1 together are necessary and sufficient to do so. concepts: - preferred_term: neural plate border formation (proposed new term) description: No GO term exists. GO:0014029 neural crest formation is defined as forming this ectodermal region but is placed under epithelial to mesenchymal transition; it is proposed for obsoletion, with this new term as one replacement (projects/NEURAL_CREST_FORMATION_OBSOLETION.md). variant_sets: - id: pax37_paralogs label: Pax3/7 border specifier (paralog deployment differs by lineage) axis: Pax3/7 paralog / vertebrate lineage selection: ONE_OR_MORE notes: Frog leads with Pax3, chick with Pax7, and mouse uses both redundantly; amphioxus has a single Pax3/7 at the border. variants: - id: pax3_variant label: Pax3 (lead paralog in frog) module_type: DEVELOPMENTAL_PROCESS annotons: - id: pax3_border label: Pax3 border specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: pax3-a term: id: UniProtKB:Q645N4 label: Paired box protein Pax-3-A description: Xenopus laevis pax3-a; reviewed in genes/XENLA/pax3-a/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: neural plate border formation (proposed new term; replaces GO:0014029, proposed for obsoletion) - preferred_term: neural crest cell fate commitment term: id: GO:0014034 label: neural crest cell fate commitment locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Paired-box activator at the border; with Zic1 directly activates crest specifier genes. evidence: - source_id: PMID:24360906 title: Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers. statement: Pax3 and Zic1 directly activate the crest specifier genes. supporting_text: We demonstrated that the neural border specifiers Pax3 and Zic1 are direct upstream regulators of neural crest specifiers Snail1/2, Foxd3, Twist1, and Tfap2b. - source_id: PMID:24360906 title: Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers. statement: Pax3 and Zic1 directly activate the crest specifier genes. supporting_text: We showed that Pax3 binds efficiently to snail2 oligonucleotide but much less to the oligonucleotide mutated in the putative binding site (Figure 4D). - id: pax7_variant label: Pax7 (lead paralog in chick) module_type: DEVELOPMENTAL_PROCESS annotons: - id: pax7_border label: Pax7 border specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PAX7 term: id: UniProtKB:P23759 label: Paired box protein Pax-7 description: Homo sapiens PAX7; reviewed in genes/human/PAX7/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: neural plate border formation (proposed new term; replaces GO:0014029, proposed for obsoletion) locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Paired-box border factor required for crest specifier expression in chick; binds the FoxD3 NC1 enhancer with Msx1 and Ets1. evidence: - source_id: PMID:16688176 title: Specification of the neural crest occurs during gastrulation and requires Pax7. statement: Pax7 is required for crest formation and binds the FoxD3 NC1 enhancer. supporting_text: In chicken embryos, Pax7 is required for neural crest formation in vivo, because blocking its translation inhibits expression of the neural crest markers Slug, Sox9, Sox10 and HNK-1. - source_id: PMID:23284303 title: Dynamic and differential regulation of stem cell factor FoxD3 in the neural crest is Encrypted in the genome. statement: Pax7 is required for crest formation and binds the FoxD3 NC1 enhancer. supporting_text: Detailed regulatory analysis shows that initial expression of FoxD3 in both cranial and trunk neural crest requires direct input from neural plate border genes, Pax7 and Msx1/2. annotons: - id: gbx2_border label: Gbx2 border specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: gbx2 term: id: UniProtKB:Q91907 label: Homeobox protein GBX-2 description: Xenopus laevis gbx2; reviewed in genes/XENLA/gbx2/. function: preferred_term: DNA-binding transcription repressor activity, RNA polymerase II-specific term: id: GO:0001227 label: DNA-binding transcription repressor activity, RNA polymerase II-specific processes: - preferred_term: neural plate border formation (proposed new term; replaces GO:0014029, proposed for obsoletion) locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Wnt-responsive repressor acting upstream of the border factors Pax3 and Msx1; required for crest and limits the preplacodal domain. evidence: - source_id: PMID:19736322 title: The posteriorizing gene Gbx2 is a direct target of Wnt signalling and the earliest factor in neural crest induction. statement: Gbx2 is required for neural crest and acts upstream of the border factors Pax3 and Msx1. supporting_text: Loss-of-function experiments using antisense morpholinos against Gbx2 inhibit NC and expand the preplacodal domain, whereas Gbx2 overexpression leads to transformation of the preplacodal domain into NC cells. - source_id: PMID:19736322 title: The posteriorizing gene Gbx2 is a direct target of Wnt signalling and the earliest factor in neural crest induction. statement: Gbx2 is required for neural crest and acts upstream of the border factors Pax3 and Msx1. supporting_text: In addition, we demonstrate that Gbx2 is upstream of the neural fold specifiers Pax3 and Msx1. - id: msx1_border label: Msx1 border specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MSX1 term: id: UniProtKB:P28360 label: Homeobox protein MSX-1 description: Homo sapiens MSX1; reviewed in genes/human/MSX1/. function: preferred_term: DNA-binding transcription factor activity, RNA polymerase II-specific term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific processes: - preferred_term: neural plate border formation (proposed new term; replaces GO:0014029, proposed for obsoletion) locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: BMP-responsive homeodomain factor at the neural fold; induces Pax3 and Zic cell-autonomously. evidence: - source_id: PMID:14627721 title: Regulation of Msx genes by a Bmp gradient is essential for neural crest specification. statement: Intermediate BMP specifies Msx expression at the border, and Msx1 induces Pax3 and Zic. supporting_text: Our results indicate that an intermediate level of Bmp activity specifies the expression of Msx genes in the neural fold region. - source_id: PMID:15691759 title: Msx1 and Pax3 cooperate to mediate FGF8 and WNT signals during Xenopus neural crest induction. statement: Intermediate BMP specifies Msx expression at the border, and Msx1 induces Pax3 and Zic. supporting_text: Msx1 induces Pax3 and ZicR1 cell autonomously, in turn, Pax3 combined with ZicR1 activates Slug in a WNT-dependent manner. - id: tfap2a_border label: AP-2alpha border initiator participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TFAP2A term: id: UniProtKB:P05549 label: Transcription factor AP-2-alpha description: Homo sapiens TFAP2A; reviewed in genes/human/TFAP2A/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: neural plate border formation (proposed new term; replaces GO:0014029, proposed for obsoletion) locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Earliest known border specifier; mediates Wnt input to initiate the border and activate pax3. evidence: - source_id: PMID:21169220 title: Reiterative AP2a activity controls sequential steps in the neural crest gene regulatory network. statement: AP-2alpha initiates neural plate border patterning and activates pax3. supporting_text: As the earliest known NB specifier, AP2a mediates Wnt signals to initiate the NB and activate pax3; as a NC specifier, AP2a regulates further NC development independent of and downstream of NB patterning. - source_id: PMID:21169220 title: Reiterative AP2a activity controls sequential steps in the neural crest gene regulatory network. statement: AP-2alpha initiates neural plate border patterning and activates pax3. supporting_text: AP2a initiates NB patterning and is sufficient to elicit a NB-like pattern in neuralized ectoderm. - id: tfap2c_border label: AP-2gamma (TFAP2A–TFAP2C) border inducer participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TFAP2C term: id: UniProtKB:Q92754 label: Transcription factor AP-2 gamma description: Homo sapiens TFAP2C; reviewed in genes/human/TFAP2C/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: neural plate border formation (proposed new term; replaces GO:0014029, proposed for obsoletion) locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Partners TFAP2A as a heterodimer during border induction; lost from crest at specification, when TFAP2B replaces it. evidence: - source_id: PMID:31848212 title: Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification. statement: TFAP2A/C heterodimers mediate neural plate border induction. supporting_text: TFAP2C knockdown during induction resulted in a down-regulation of the neural plate border markers MSX1, PAX7, ZIC1, and GBX2 but had no significant effects on the expression of specification genes FOXD3, ETS1, SOX9, and SOX10 - source_id: PMID:31848212 title: Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification. statement: TFAP2A/C heterodimers mediate neural plate border induction. supporting_text: TFAP2A/C heterodimers mediate neural plate border induction, whereas TFAP2A/B heterodimers promote neural crest specification - id: zic1_border label: Zic1 border specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: zic1 term: id: UniProtKB:O73689 label: Zinc finger protein ZIC 1 description: Xenopus laevis zic1; reviewed in genes/XENLA/zic1/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: neural plate border formation (proposed new term; replaces GO:0014029, proposed for obsoletion) - preferred_term: neural crest cell fate commitment term: id: GO:0014034 label: neural crest cell fate commitment locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Zinc-finger activator at the border; with Pax3 commits cells to crest, alone promotes preplacodal or neural fates. evidence: - source_id: PMID:15843410 title: Neural crest determination by co-activation of Pax3 and Zic1 genes in Xenopus ectoderm. statement: Pax3 and Zic1 are early border factors, necessary and sufficient to promote crest fate. supporting_text: Pax3 and Zic1 are expressed in an overlapping manner in the presumptive neural crest area of the Xenopus gastrula, even prior to the onset of the expression of the early bona fide neural crest marker genes Foxd3 and Slug. - source_id: PMID:24360908 title: Identification of Pax3 and Zic1 targets in the developing neural crest. statement: Pax3 and Zic1 are early border factors, necessary and sufficient to promote crest fate. supporting_text: Transcription factors pax3 and zic1 are among the earliest genes activated in NC progenitors, and they are both necessary and sufficient to promote NC fate. - order: 1 role: keep border and crest progenitors undifferentiated and proliferative node: id: progenitor_competence_maintenance label: Maintenance of border/crest progenitor competence module_type: DEVELOPMENTAL_PROCESS description: Factors shared with the pluripotent blastula keep border and premigratory crest progenitors proliferative and undifferentiated, preserving the broad potential that crest cells later deploy. Loss causes progenitor arrest or death rather than a switch to another fate, so these factors support crest formation without specifying crest identity. No GO process term captures this role; a new term, neural crest progenitor maintenance, is proposed for it. concepts: - preferred_term: neural crest progenitor maintenance (proposed new term) description: Proposed as a child of GO:0019827 stem cell population maintenance, replacing GO:0014029 for competence factors (projects/NEURAL_CREST_FORMATION_OBSOLETION.md). annotons: - id: myc_competence label: c-Myc competence factor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: myc-a term: id: UniProtKB:P06171 label: Transcriptional regulator Myc-A description: Xenopus laevis myc-a; reviewed in genes/XENLA/myc-a/. function: preferred_term: DNA-binding transcription factor activity, RNA polymerase II-specific term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific processes: - preferred_term: neural crest progenitor maintenance (proposed new term; replaces GO:0014029, proposed for obsoletion) locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Blastula-inherited Myc/Max E-box factor at the border before slug; required for crest precursors. evidence: - source_id: PMID:12791268 title: The protooncogene c-myc is an essential regulator of neural crest formation in xenopus. statement: c-Myc is at the border before slug and is required for crest precursors. supporting_text: c-myc is localized at the neural plate border prior to the expression of early neural crest markers, such as slug - source_id: PMID:12791268 title: The protooncogene c-myc is an essential regulator of neural crest formation in xenopus. statement: c-Myc is at the border before slug and is required for crest precursors. supporting_text: A morpholino-mediated "knockdown" of c-Myc protein results in the absence of neural crest precursor cells and a resultant loss of neural crest derivatives - id: id3_competence label: Id3 bHLH inhibitor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: id3-a term: id: UniProtKB:Q91399 label: DNA-binding protein inhibitor ID-3-A description: Xenopus laevis id3-a; reviewed in genes/XENLA/id3-a/. function: preferred_term: transcription regulator inhibitor activity term: id: GO:0140416 label: transcription regulator inhibitor activity processes: - preferred_term: neural crest progenitor maintenance (proposed new term; replaces GO:0014029, proposed for obsoletion) - preferred_term: negative regulation of cell differentiation term: id: GO:0045596 label: negative regulation of cell differentiation locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Dominant-negative HLH protein that keeps crest progenitors cycling and undifferentiated. evidence: - source_id: PMID:15769946 title: 'To proliferate or to die: role of Id3 in cell cycle progression and survival of neural crest progenitors.' statement: Id3 maintains the cycling crest progenitor pool rather than specifying crest fate. supporting_text: This appears to be mediated by cell cycle inhibition followed by cell death of the neural crest progenitor pool, rather than a cell fate switch. - source_id: PMID:15769946 title: 'To proliferate or to die: role of Id3 in cell cycle progression and survival of neural crest progenitors.' statement: Id3 maintains the cycling crest progenitor pool rather than specifying crest fate. supporting_text: overexpression of Id3 increases cell proliferation and results in expansion of the neural crest domain - id: pou5f3_competence label: Oct25 (Pou5f3) competence factor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: pou5f1.1 term: id: UniProtKB:Q7T103 label: POU domain, class 5, transcription factor 1.1 description: Xenopus laevis pou5f1.1; reviewed in genes/XENLA/pou5f1.1/. function: preferred_term: DNA-binding transcription factor activity, RNA polymerase II-specific term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific processes: - preferred_term: neural crest progenitor maintenance (proposed new term; replaces GO:0014029, proposed for obsoletion) locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: POU-V blastula pluripotency factor retained at the neural plate border; required (with its paralog) for snai2 and foxd3, and its gain expands border and crest markers. evidence: - source_id: PMID:39060477 title: Shared features of blastula and neural crest stem cells evolved at the base of vertebrates. statement: Pou5f3 is expressed at the border and is required for crest specifier expression. supporting_text: zygotic pou5f3.1 and pou5f3.2 expressed in the neural plate border and neural crest - source_id: PMID:39060477 title: Shared features of blastula and neural crest stem cells evolved at the base of vertebrates. statement: Pou5f3 is expressed at the border and is required for crest specifier expression. supporting_text: pou5f3 depletion resulted in a near-total loss of snai2 and foxd3 neural crest expression - id: hes4_competence label: Hairy2 border repressor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: hes4-a term: id: UniProtKB:Q90Z12 label: Transcription factor HES-4-A description: Xenopus laevis hes4-a; reviewed in genes/XENLA/hes4-a/. function: preferred_term: DNA-binding transcription repressor activity, RNA polymerase II-specific term: id: GO:0001227 label: DNA-binding transcription repressor activity, RNA polymerase II-specific processes: - preferred_term: neural crest progenitor maintenance (proposed new term; replaces GO:0014029, proposed for obsoletion) - preferred_term: negative regulation of BMP signaling pathway term: id: GO:0030514 label: negative regulation of BMP signaling pathway locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: bHLH-Orange repressor that holds border cells undifferentiated and tunes Bmp4 levels at the border. evidence: - source_id: PMID:14681193 title: Interplay between Notch signaling and the homeoprotein Xiro1 is required for neural crest induction in Xenopus embryos. statement: Hairy2 keeps border cells undifferentiated and tunes Bmp4 at the border. supporting_text: ensuring that levels of Bmp4 optimal for the specification of the neural plate border are attained in this region - source_id: PMID:18721802 title: Hairy2-Id3 interactions play an essential role in Xenopus neural crest progenitor specification. statement: Hairy2 keeps border cells undifferentiated and tunes Bmp4 at the border. supporting_text: Hairy2 acts downstream of FGF and BMP signals at the neural border to maintain cells in an undifferentiated state - order: 2 role: specify neural crest identity node: id: neural_crest_fate_specification label: Neural crest fate specification module_type: DEVELOPMENTAL_PROCESS description: Border inputs switch on a set of crest specifier transcription factors in the prospective crest. They act within the crest domain, cross-regulate one another, and are required for, and in combination sufficient for, crest identity. concepts: - preferred_term: neural crest cell fate specification term: id: GO:0014036 label: neural crest cell fate specification annotons: - id: foxd3_spec label: FoxD3 crest specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: foxd3-a term: id: UniProtKB:Q9DEN4 label: Forkhead box protein D3-A description: Xenopus laevis foxd3-a; reviewed in genes/XENLA/foxd3-a/. function: preferred_term: DNA-binding transcription repressor activity, RNA polymerase II-specific term: id: GO:0001227 label: DNA-binding transcription repressor activity, RNA polymerase II-specific processes: - preferred_term: neural crest cell fate commitment term: id: GO:0014034 label: neural crest cell fate commitment locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Forkhead repressor recruiting Groucho/TLE; induces crest markers when overexpressed. evidence: - source_id: PMID:11493569 title: Requirement of FoxD3-class signaling for neural crest determination in Xenopus. statement: FoxD3 is expressed in the presumptive crest and induces crest markers. supporting_text: Expression of FoxD3 in the presumptive neural crest region starts at the late gastrula stage in a manner similar to that of Slug, and overlaps with that of Zic-r1. - source_id: PMID:11493569 title: Requirement of FoxD3-class signaling for neural crest determination in Xenopus. statement: FoxD3 is expressed in the presumptive crest and induces crest markers. supporting_text: When overexpressed in the embryo and in ectodermal explants, FoxD3 induces expression of neural crest markers. - id: snai1_spec label: Snail1 early crest specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: snai1 term: id: UniProtKB:P19382 label: Protein snail homolog Sna description: Xenopus laevis snai1; reviewed in genes/XENLA/snai1/. function: preferred_term: DNA-binding transcription repressor activity, RNA polymerase II-specific term: id: GO:0001227 label: DNA-binding transcription repressor activity, RNA polymerase II-specific processes: - preferred_term: neural crest cell fate specification term: id: GO:0014036 label: neural crest cell fate specification locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Earliest crest specifier, activated in the first wave with sox8 and myc and directly by Zic1; acts upstream of Snai2. Also expressed in pluripotent blastula cells. evidence: - source_id: PMID:23509273 title: Pax3 and Zic1 drive induction and differentiation of multipotent, migratory, and functional neural crest in Xenopus embryos. statement: Snail1 is an early, Zic1-responsive crest specifier activated with sox8 and myc. supporting_text: Indeed, a group of early genes ( snail1 , sox8 , and myc ) was activated during early neurulation - source_id: PMID:24360906 title: Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers. statement: Snail1 is an early, Zic1-responsive crest specifier activated with sox8 and myc. supporting_text: Zic1 binds to snail1 putative oligonucleotide - id: snai2_spec label: Snai2 crest specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: snai2 term: id: UniProtKB:Q91924 label: Zinc finger protein SNAI2 description: Xenopus laevis snai2; reviewed in genes/XENLA/snai2/. function: preferred_term: DNA-binding transcription repressor activity, RNA polymerase II-specific term: id: GO:0001227 label: DNA-binding transcription repressor activity, RNA polymerase II-specific processes: - preferred_term: neural crest cell fate specification term: id: GO:0014036 label: neural crest cell fate specification locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: E-box repressor required to form crest precursors; acts downstream of the border factors. evidence: - source_id: PMID:10772801 title: Snail-related transcriptional repressors are required in Xenopus for both the induction of the neural crest and its subsequent migration. statement: Snai2 is required to form crest precursors and acts downstream of Zic1/Pax3. supporting_text: inhibition of XSlug function at early stages prevents the formation of neural crest precursors, while inhibition at later stages interferes with neural crest migration - source_id: PMID:25617436 title: Snail2/Slug cooperates with Polycomb repressive complex 2 (PRC2) to regulate neural crest development. statement: Snai2 is required to form crest precursors and acts downstream of Zic1/Pax3. supporting_text: By contrast, knockdown of Snail2 did not appreciably diminish either Zic1 or Pax3 levels - id: tfap2b_spec label: AP-2beta (TFAP2A–TFAP2B) crest specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TFAP2B term: id: UniProtKB:Q92481 label: Transcription factor AP-2-beta description: Homo sapiens TFAP2B; reviewed in genes/human/TFAP2B/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: neural crest cell fate specification term: id: GO:0014036 label: neural crest cell fate specification locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Comes on at the onset of specification, heterodimerises with TFAP2A and recruits it to specification enhancers; represses TFAP2C. evidence: - source_id: PMID:31848212 title: Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification. statement: TFAP2B is required for crest specification but not the border, and recruits TFAP2A to specification enhancers. supporting_text: TFAP2B knockdown produced no effects on the neural plate border but resulted in the disruption of the specification program - source_id: PMID:31848212 title: Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification. statement: TFAP2B is required for crest specification but not the border, and recruits TFAP2A to specification enhancers. supporting_text: Together, these data support the idea that TFAP2B is required for the recruitment of TFAP2A to specification loci. - id: tfap2a_spec label: AP-2alpha crest specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TFAP2A term: id: UniProtKB:P05549 label: Transcription factor AP-2-alpha description: Homo sapiens TFAP2A; reviewed in genes/human/TFAP2A/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: neural crest cell fate specification term: id: GO:0014036 label: neural crest cell fate specification locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Second, crest-intrinsic deployment of AP-2alpha after its border role. evidence: - source_id: PMID:21169220 title: Reiterative AP2a activity controls sequential steps in the neural crest gene regulatory network. statement: AP-2alpha acts again as a crest specifier after initiating the border. supporting_text: As the earliest known NB specifier, AP2a mediates Wnt signals to initiate the NB and activate pax3; as a NC specifier, AP2a regulates further NC development independent of and downstream of NB patterning. - id: twist1_snai2_inhibition label: Twist1 restraint of Snai2 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: twist1 term: id: UniProtKB:P13903 label: Twist-related protein description: Xenopus laevis twist1; reviewed in genes/XENLA/twist1/. function: preferred_term: transcription regulator inhibitor activity term: id: GO:0140416 label: transcription regulator inhibitor activity processes: - preferred_term: neural crest cell fate specification term: id: GO:0014036 label: neural crest cell fate specification locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Twist binds Snai2 directly and reduces its chromatin occupancy, restraining Snai2-driven crest expansion. evidence: - source_id: PMID:23443570 title: Interactions between Twist and other core epithelial-mesenchymal transition factors are controlled by GSK3-mediated phosphorylation. statement: Twist binds Snai2 directly and reduces its recruitment to chromatin. supporting_text: Importantly, the effects of Twist depletion can be rescued by a form of Twist that cannot be targeted by the MO - source_id: PMID:23443570 title: Interactions between Twist and other core epithelial-mesenchymal transition factors are controlled by GSK3-mediated phosphorylation. statement: Twist binds Snai2 directly and reduces its recruitment to chromatin. supporting_text: suggesting that the cells that did not express NC markers were stalled in a NPB state and/or adopted alternative fates, such as placodes variant_sets: - id: soxe_paralogs label: SoxE crest specifier (paralog deployment differs by lineage) axis: SoxE paralog / vertebrate lineage selection: ONE_OR_MORE notes: 'Which SoxE paralog leads crest specification varies: Sox8 in frog, Sox9 in chick and mouse, sox9a/b in zebrafish, independently duplicated SoxE1/2 in lamprey. The specifier role belongs to the SoxE group; paralog-specific crest roles should not be transferred by orthology.' variants: - id: sox8_variant label: Sox8 (first-wave SoxE in frog) module_type: DEVELOPMENTAL_PROCESS annotons: - id: sox8_spec label: Sox8 crest specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: sox8 term: id: UniProtKB:Q6VVD7 label: Transcription factor Sox-8 description: Xenopus laevis sox8; reviewed in genes/XENLA/sox8/. function: preferred_term: DNA-binding transcription factor activity, RNA polymerase II-specific term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific processes: - preferred_term: neural crest cell fate specification term: id: GO:0014036 label: neural crest cell fate specification locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Earliest SoxE at the lateral neural plate edge; knockdown delays crest induction. evidence: - source_id: PMID:16943273 title: Functional analysis of Sox8 during neural crest development in Xenopus. statement: Sox8 knockdown delays crest progenitor induction. supporting_text: Although morpholino-mediated knockdown of Sox8 protein did not prevent the formation of neural crest progenitors, the timing of their induction was severely affected - source_id: PMID:23509273 title: Pax3 and Zic1 drive induction and differentiation of multipotent, migratory, and functional neural crest in Xenopus embryos. statement: Sox8 knockdown delays crest progenitor induction. supporting_text: a group of early genes ( snail1 , sox8 , and myc ) was activated during early neurulation (between stages 12 and 15) - id: sox9_variant label: Sox9 module_type: DEVELOPMENTAL_PROCESS annotons: - id: sox9_spec label: Sox9 crest specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: sox9-a term: id: UniProtKB:B7ZR65 label: Transcription factor Sox-9-A description: Xenopus laevis sox9-a; reviewed in genes/XENLA/sox9-a/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: neural crest cell fate specification term: id: GO:0014036 label: neural crest cell fate specification locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: SoxE activator required for crest specification but not migration. evidence: - source_id: PMID:11807034 title: The transcription factor Sox9 is required for cranial neural crest development in Xenopus. statement: Sox9 is an activator required for crest specification, not migration. supporting_text: causes a dramatic loss of neural crest progenitors and an expansion of the neural plate - source_id: PMID:15464575 title: Early requirement of the transcriptional activator Sox9 for neural crest specification in Xenopus. statement: Sox9 is an activator required for crest specification, not migration. supporting_text: we show that Sox9 function is required for neural crest specification but not for its subsequent migration - id: sox10_variant label: Sox10 module_type: DEVELOPMENTAL_PROCESS annotons: - id: sox10_spec label: Sox10 crest specifier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: sox10 term: id: UniProtKB:Q8AXX8 label: Transcription factor Sox-10 description: Xenopus laevis sox10; reviewed in genes/XENLA/sox10/. function: preferred_term: DNA-binding transcription factor activity, RNA polymerase II-specific term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific processes: - preferred_term: neural crest cell fate specification term: id: GO:0014036 label: neural crest cell fate specification locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: SoxE factor acting in the earliest steps of crest specification; later drives pigment and glial lineages. evidence: - source_id: PMID:12885557 title: Sox10 is required for the early development of the prospective neural crest in Xenopus embryos. statement: Sox10 acts early in crest specification and expands the Slug domain. supporting_text: This effect of Sox10 depletion is produced during some of the earliest steps of neural crest specification - source_id: PMID:12812785 title: Sox10 regulates the development of neural crest-derived melanocytes in Xenopus. statement: Sox10 acts early in crest specification and expands the Slug domain. supporting_text: Overexpression of Sox10 causes a dramatic expansion of the Slug expression domain - order: 3 role: delaminate and migrate node: id: neural_crest_emigration label: Neural crest delamination and migration module_type: DEVELOPMENTAL_PROCESS description: Specified crest cells lose adhesion to the neural tube, delaminate and migrate along stereotyped routes. Some specifier factors are redeployed here as effectors. concepts: - preferred_term: neural crest cell delamination term: id: GO:0036032 label: neural crest cell delamination - preferred_term: neural crest cell migration term: id: GO:0001755 label: neural crest cell migration annotons: - id: ets1_emigration label: Ets1 delamination effector participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ets1-a term: id: UniProtKB:P18755 label: Protein c-ets-1-A description: Xenopus laevis ets1-a; reviewed in genes/XENLA/ets1-a/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: neural crest cell delamination term: id: GO:0036032 label: neural crest cell delamination - preferred_term: neural crest cell migration term: id: GO:0001755 label: neural crest cell migration locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Ets activator required in the crest for delamination and migration; part of the cranial crest circuit in jawed vertebrates. evidence: - source_id: PMID:25691536 title: Dual developmental role of transcriptional regulator Ets1 in Xenopus cardiac neural crest vs. heart mesoderm. statement: Ets1 knockdown in the crest disrupts delamination and migration. supporting_text: Using a translation-blocking antisense morpholino to knockdown Ets1 protein selectively in the NC, we observed defects in NC delamination from the neural tube, collective cell migration, as well as segregation of NC streams in the cranial and cardiac regions. - id: snai2_migration label: Snai2 migration effector participant: selector_type: GENE_PRODUCT gene_product: preferred_term: snai2 term: id: UniProtKB:Q91924 label: Zinc finger protein SNAI2 description: Xenopus laevis snai2; reviewed in genes/XENLA/snai2/. function: preferred_term: DNA-binding transcription repressor activity, RNA polymerase II-specific term: id: GO:0001227 label: DNA-binding transcription repressor activity, RNA polymerase II-specific processes: - preferred_term: neural crest cell migration term: id: GO:0001755 label: neural crest cell migration locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Later Snai2 activity, recruiting PRC2 to the E-cadherin promoter, is required for crest migration. evidence: - source_id: PMID:25617436 title: Snail2/Slug cooperates with Polycomb repressive complex 2 (PRC2) to regulate neural crest development. statement: Late Snai2 activity is required for crest migration. supporting_text: The data thus demonstrate that Snail2 helps to recruit PRC2 to the E-cad promoter to set up repressive histone modification marks that result in inhibition of E-cad expression during neural crest EMT. - source_id: PMID:10772801 title: Snail-related transcriptional repressors are required in Xenopus for both the induction of the neural crest and its subsequent migration. statement: Late Snai2 activity is required for crest migration. supporting_text: inhibition of XSlug function at early stages prevents the formation of neural crest precursors, while inhibition at later stages interferes with neural crest migration - order: 4 role: form cranial skeletogenic ectomesenchyme node: id: cranial_ectomesenchyme label: Cranial crest ectomesenchyme and skeletogenesis module_type: DEVELOPMENTAL_PROCESS description: Cranial crest cells adopt an ectomesenchymal, skeletogenic fate and build the cartilage and bone of the head. This is the vertebrate-specific output most associated with the 'new head'. concepts: - preferred_term: embryonic cranial skeleton morphogenesis term: id: GO:0048701 label: embryonic cranial skeleton morphogenesis annotons: - id: twist1_ectomesenchyme label: Twist1 ectomesenchyme driver participant: selector_type: GENE_PRODUCT gene_product: preferred_term: twist1 term: id: UniProtKB:P13903 label: Twist-related protein description: Xenopus laevis twist1; reviewed in genes/XENLA/twist1/. function: preferred_term: DNA-binding transcription factor activity, RNA polymerase II-specific term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific processes: - preferred_term: embryonic cranial skeleton morphogenesis term: id: GO:0048701 label: embryonic cranial skeleton morphogenesis locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: bHLH factor that steers cranial crest to cartilage-forming ectomesenchyme; without it, cells lose Sox9 and drift toward glial fates. evidence: - source_id: PMID:23443570 title: Interactions between Twist and other core epithelial-mesenchymal transition factors are controlled by GSK3-mediated phosphorylation. statement: Twist depletion loses Sox9 in the branchial arches and head cartilage. supporting_text: At stage 28, injected embryos exhibited reduced expression of Sox9 in the branchial arches, where it marks developing chondrocytes (Fig. 1f) and by stage 43 profound defects in cartilage formation and morphogenesis were observed - source_id: PMID:23443570 title: Interactions between Twist and other core epithelial-mesenchymal transition factors are controlled by GSK3-mediated phosphorylation. statement: Twist depletion loses Sox9 in the branchial arches and head cartilage. supporting_text: suggesting that in the absence of Twist, cranial NC cells that would normally give rise to cartilage might instead adopt glial fates - id: sox9_chondrogenesis label: Sox9 crest chondrogenesis participant: selector_type: GENE_PRODUCT gene_product: preferred_term: sox9-a term: id: UniProtKB:B7ZR65 label: Transcription factor Sox-9-A description: Xenopus laevis sox9-a; reviewed in genes/XENLA/sox9-a/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: chondrocyte differentiation term: id: GO:0002062 label: chondrocyte differentiation locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: SoxE activator required for crest-derived cranial cartilage. evidence: - source_id: PMID:11807034 title: The transcription factor Sox9 is required for cranial neural crest development in Xenopus. statement: Sox9 knockdown removes crest-derived skeletal elements. supporting_text: morpholino-treated embryos have a specific loss or reduction of neural crest-derived skeletal elements - id: tfap2a_craniofacial label: AP-2alpha craniofacial morphogenesis participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TFAP2A term: id: UniProtKB:P05549 label: Transcription factor AP-2-alpha description: Homo sapiens TFAP2A; reviewed in genes/human/TFAP2A/. function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: embryonic cranial skeleton morphogenesis term: id: GO:0048701 label: embryonic cranial skeleton morphogenesis locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: AP-2alpha in crest is required for face, skull and palate morphogenesis. evidence: - source_id: PMID:8622765 title: Transcription factor AP-2 essential for cranial closure and craniofacial development. statement: Tfap2a loss, including crest-specific loss, causes craniofacial and palate defects. supporting_text: AP-2(-/-) mice died perinatally with cranio-abdominoschisis and severe dismorphogenesis of the face, skull, sensory organs and cranial ganglia. - source_id: PMID:14975722 title: Wnt1-Cre-mediated deletion of AP-2alpha causes multiple neural crest-related defects. statement: Tfap2a loss, including crest-specific loss, causes craniofacial and palate defects. supporting_text: Neural crest-specific disruption of tcfap2a results in frequent perinatal lethality associated with neural tube closure defects and cleft secondary palate. connections: - source: neural_plate_border_specification target: neural_crest_fate_specification connection_type: PRECEDES description: Border specifiers are expressed first and are required for crest specifier expression. - source: progenitor_competence_maintenance target: neural_crest_fate_specification connection_type: PROVIDES_INPUT_FOR description: Competence factors keep border progenitors undifferentiated so that specifier inputs can act. - source: neural_crest_fate_specification target: neural_crest_emigration connection_type: PRECEDES description: Specified crest cells delaminate and migrate. - source: neural_crest_emigration target: cranial_ectomesenchyme connection_type: PRECEDES description: Migrating cranial crest populates the pharyngeal arches and forms skeletogenic ectomesenchyme. - source: gbx2_border target: pax3_border connection_type: POSITIVELY_REGULATES description: Gbx2 acts upstream of Pax3, placed by epistasis; direct binding to the pax3 locus is not demonstrated. evidence: - source_id: file:modules/neural_crest_gene_regulatory_network-deep-research-falcon.md statement: Module deep research (falcon) assessment of this edge. supporting_text: Gbx2 is positioned upstream of *msx1* and *pax3* by epistasis - source: gbx2_border target: msx1_border connection_type: POSITIVELY_REGULATES description: Gbx2 acts upstream of Msx1, placed by epistasis; direct binding to the msx1 locus is not demonstrated. evidence: - source_id: file:modules/neural_crest_gene_regulatory_network-deep-research-falcon.md statement: Module deep research (falcon) assessment of this edge. supporting_text: Gbx2 is positioned upstream of *msx1* and *pax3* by epistasis - source: tfap2a_border target: pax3_border connection_type: POSITIVELY_REGULATES description: 'AP-2alpha activates pax3 directly: translation-independent induction, promoter-reporter, site mutation and EMSA/supershift (frog).' evidence: - source_id: file:modules/neural_crest_gene_regulatory_network-deep-research-falcon.md statement: Module deep research (falcon) assessment of this edge. supporting_text: A stronger direct edge is AP-2α → *pax3* - source: msx1_border target: pax3_border connection_type: POSITIVELY_REGULATES description: Msx1 induces Pax3 cell-autonomously. - source: msx1_border target: zic1_border connection_type: POSITIVELY_REGULATES description: Msx1 induces ZicR1/Zic cell-autonomously. - source: pax3_border target: snai2_spec connection_type: POSITIVELY_REGULATES description: Pax3 binds and activates snail2 directly. - source: pax3_border target: foxd3_spec connection_type: POSITIVELY_REGULATES description: Pax3/Zic1 activate foxd3 without new protein synthesis (immediate-response target); enhancer occupancy in frog not shown. - source: zic1_border target: foxd3_spec connection_type: POSITIVELY_REGULATES description: Pax3/Zic1 activate foxd3 without new protein synthesis (immediate-response target); enhancer occupancy in frog not shown. - source: zic1_border target: snai1_spec connection_type: POSITIVELY_REGULATES description: Zic1 binds a snail1 element (EMSA) and activates snail1 without new protein synthesis. - source: snai1_spec target: snai2_spec connection_type: POSITIVELY_REGULATES description: Snail1 acts upstream of Slug/Snai2 in crest specification. - source: tfap2c_border target: tfap2b_spec connection_type: POSITIVELY_REGULATES description: TFAP2A/C occupies the TFAP2B locus and is required for its activation at the onset of specification (chick). - source: tfap2b_spec target: tfap2c_border connection_type: NEGATIVELY_REGULATES description: TFAP2B represses TFAP2C cell-autonomously, stabilising the switch from the A/C to the A/B heterodimer (chick). - source: pax3_border target: tfap2b_spec connection_type: POSITIVELY_REGULATES description: Pax3/Zic1 activate tfap2b without new protein synthesis (frog immediate-response target). - source: zic1_border target: tfap2b_spec connection_type: POSITIVELY_REGULATES description: Pax3/Zic1 activate tfap2b without new protein synthesis (frog immediate-response target). - source: pax7_border target: foxd3_spec connection_type: POSITIVELY_REGULATES description: Pax7 binds the FoxD3 NC1 enhancer in vivo (ChIP) with Msx1 and Ets1; its knockdown abolishes NC1/NC2 activity (chick). - source: pou5f3_competence target: pax3_border connection_type: POSITIVELY_REGULATES description: Pou5f3 gain of function expands pax3 (and zic1, snai2) expression. - source: pax3_border target: sox8_spec connection_type: POSITIVELY_REGULATES description: Pax3/Zic1 activate sox8 with snail1 and myc. - source: pax3_border target: twist1_ectomesenchyme connection_type: POSITIVELY_REGULATES description: Pax3 activates twist1 directly. - source: twist1_snai2_inhibition target: snai2_spec connection_type: NEGATIVELY_REGULATES description: 'Twist binds Snai2 and reduces its chromatin occupancy. Stage-specific: Twist later promotes mesenchymal outputs, so this is not a permanent inhibitory edge.' evidence: - source_id: file:modules/neural_crest_gene_regulatory_network-deep-research-falcon.md statement: Module deep research (falcon) assessment of this edge. supporting_text: a permanently activating or permanently inhibiting “TWIST → SNAI2” arrow misstates the mechanism - source: hes4_competence target: id3_competence connection_type: PROVIDES_INPUT_FOR description: Hairy2 and Id3 act together (with Stat3) to keep progenitors undifferentiated. knowledge_gaps: - gap_statement: 'Parts of the network are lineage-specific: the cranial circuit (including Ets1) is absent from lamprey crest, Twist1''s early specifier role is reported only in anamniotes, and the leading SoxE paralog differs by lineage.' boundary: Affects the neural_crest_fate_specification and neural_crest_emigration parts; the module is drawn from frog and human members. gap_kind: - BIOLOGY status: OPEN significance: A pan-vertebrate module would overstate the conservation of these components; taxon-specific variants may be needed. resolution: Model taxon variants (cyclostome vs gnathostome; anamniote vs amniote) once lamprey and amniote members are reviewed. provenance: - reference_id: PMID:31645763 supporting_text: lamprey lacks most components of a transcriptional circuit that is specific to - reference_id: file:modules/neural_crest_gene_regulatory_network-deep-research-falcon.md supporting_text: ETS1 is a strong cranial regulator in chick but is not a universal vertebrate delamination factor - gap_statement: 'The hand-off from SoxB1 (Sox2/Sox3) to SoxE is a required step in moving from pluripotent blastula cells to crest, but SoxB1 factors are not members: they must be switched off for crest to form and do none of its work.' boundary: SoxB1 is treated as an upstream blastula/neural-plate state, outside the module; the hand-off sits between the competence and specification parts. gap_kind: - ONTOLOGY - BIOLOGY status: OPEN significance: The module cannot express a required repression of an upstream state; GO has no term for this kind of state transition, and adding a negative-regulation crest term to SoxB1 would fail the participation test. resolution: Model the hand-off explicitly (e.g. a NEGATIVELY_REGULATES edge from a crest specifier to an upstream SoxB1 node) once a repressor of SoxB1 in the crest is established; record SoxB1 in the reviews as non-participants. provenance: - reference_id: PMID:30144418 supporting_text: A transition from SoxB1 to SoxE transcription factors is essential for - reference_id: PMID:39060477 supporting_text: soxB1a, soxB1b, brd4 were all expressed in lamprey animal pole cells, analogous to Xenopus - gap_statement: Lin28 is a candidate competence factor, but its crest requirement is shown only in chick; the frog lin28a review found no frog crest evidence. boundary: Affects the progenitor_competence_maintenance part; Lin28 is not included as an annoton. gap_kind: - BIOLOGY - CURATION status: OPEN significance: Lin28/let-7 would link developmental timing and Myc to crest competence, but frog and chick may differ. resolution: Review chick LIN28A (Q45KJ5) and test lin28a/lin28b at the frog neural plate border. provenance: - reference_id: PMID:30520734 supporting_text: Changes in Lin28a levels impact neural crest development in vivo