id: Q9DFH2 gene_symbol: sox9a product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:7955 label: Danio rerio description: 'Sox9a is one of two zebrafish co-orthologs of vertebrate SOX9, produced by the teleost-specific genome duplication. It is an SRY-related HMG-box (SoxE group) transcription factor: its HMG box binds the Sox consensus DNA motif and a central transactivation region activates transcription of target genes such as col2a1a and col11a2. Sox9a is expressed in cranial neural crest-derived chondrogenic mesenchyme of the neurocranium and pharyngeal arches, the pectoral girdle (scapulocoracoid), otic placode, hindbrain glial progenitors and, in adults, in many tissues including testis Sertoli cells. It is essential for chondrocyte differentiation and for the stacking and shaping of cartilage condensations: sox9a (jellyfish) mutants lack most craniofacial and pectoral girdle cartilage. It also contributes, partly redundantly with sox9b, dlx3b/dlx4b and sox10, to otic placode and inner ear development, and is required for oligodendrocyte progenitor and astroglial development in the hindbrain. The two co-orthologs share a near-identical HMG box but divide the ancestral SOX9 expression domains between them.' existing_annotations: - term: id: GO:0000122 label: negative regulation of transcription by RNA polymerase II evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - PANTHER:PTN000741645 - UniProtKB:P48436 review: summary: 'IBA: negative regulation of transcription by RNA polymerase II, propagated from PTN000741645 (human SOX9 donor).' action: KEEP_AS_NON_CORE reason: SOX9 is chiefly a transcriptional activator but represses some targets in mammals; the Sox9a HMG box is 98.6% identical to human SOX9 (file:DANRE/sox9a/sox9a-bioinformatics/RESULTS.md), so inheritance of this capacity is plausible and there is no evidence of loss in the sox9a lineage. No zebrafish experiment directly shows Sox9a-mediated repression, so it is kept as a non-core inherited property. supported_by: - &id002 reference_id: PMID:11180959 supporting_text: We tested different domains for transactivation potential and identified a potential activation domain located in the middle of both Sox9a and Sox9b. - term: id: GO:0000978 label: RNA polymerase II cis-regulatory region sequence-specific DNA binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - MGI:MGI:98358 - MGI:MGI:98370 - MGI:MGI:98371 - PANTHER:PTN002910095 - PomBase:SPBC32C12.02 - UniProtKB:P48436 review: summary: 'IBA: RNA polymerase II cis-regulatory region sequence-specific DNA binding.' action: ACCEPT reason: Sox9a binds HMG consensus sites in vitro and occupies regulatory regions of target genes in ChIP assays; the HMG box is conserved with human SOX9. supported_by: - &id001 reference_id: PMID:11180959 supporting_text: Both Sox9a and Sox9b proteins bind to the HMG consensus DNA sequences in vitro. - &id004 reference_id: PMID:25568117 supporting_text: ChIP-PCR assay verified 11 of 21 genes for Atoh1a and 11 of 18 genes for Sox9a as reproducible targets - term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - MGI:MGI:98358 - MGI:MGI:98370 - MGI:MGI:98371 - PANTHER:PTN002910095 - PomBase:SPBC32C12.02 - RGD:620474 - UniProtKB:O18896 - UniProtKB:P48436 review: summary: 'IBA: DNA-binding transcription factor activity, RNA polymerase II-specific.' action: ACCEPT reason: Core molecular function. Sox9a binds DNA and carries a transactivation domain, and loss of sox9a abolishes expression of Sox9 target genes such as col2a1 and col11a2 in cartilage. supported_by: - *id001 - *id002 - &id003 reference_id: PMID:12397114 supporting_text: Homozygous mutant embryos had greatly reduced quantities of col2a1 message, the major collagen of cartilage. - &id016 reference_id: PMID:19210963 supporting_text: In sox9a mutants, expression of col11a2 disappeared from the neurocranium and pharyngeal arches, and was reduced in the opercle - term: id: GO:0002009 label: morphogenesis of an epithelium evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:98358 - MGI:MGI:98370 - MGI:MGI:98371 - PANTHER:PTN000741645 - UniProtKB:B7ZR65 - UniProtKB:P48434 - ZFIN:ZDB-GENE-001103-1 - ZFIN:ZDB-GENE-001103-2 - ZFIN:ZDB-GENE-011207-1 review: summary: 'IBA: morphogenesis of an epithelium (PTN000741645; donors include both zebrafish sox9a and sox9b).' action: KEEP_AS_NON_CORE reason: Sox9a contributes to formation of the otic epithelium together with dlx3b/dlx4b and sox9b; the term is broad and not the central role of the gene. supported_by: - &id011 reference_id: PMID:12668634 supporting_text: Removal of dlx3b, dlx4b and sox9a genes together also blocks ear development, although a few residual cells form an otic epithelium. - &id007 reference_id: PMID:15689370 supporting_text: Ears are somewhat reduced in each single mutant but are mostly absent in the double mutant. - term: id: GO:0002062 label: chondrocyte differentiation evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:98371 - PANTHER:PTN002910118 - UniProtKB:P48434 - UniProtKB:P48436 review: summary: 'IBA: chondrocyte differentiation.' action: ACCEPT reason: 'Central role: sox9a mutants lack overt cartilage differentiation and chondrocyte stacking, with loss of col2a1.' supported_by: - &id008 reference_id: PMID:12397114 supporting_text: These studies show that jef (sox9a) is essential for both morphogenesis of condensations and overt cartilage differentiation. - *id003 - &id014 reference_id: PMID:15689370 supporting_text: Chondrocytes failed to stack in sox9a mutants, failed to attain proper numbers in sox9b mutants and failed in both morphogenetic processes in double mutants. - term: id: GO:0003677 label: DNA binding evidence_type: IEA original_reference_id: GO_REF:0000104 qualifier: enables supporting_entities: - UniRule:UR000400811 review: summary: 'IEA (UniRule): DNA binding.' action: ACCEPT reason: Correct but general; the more informative sequence-specific cis-regulatory DNA binding term is also accepted. supported_by: - *id001 - term: id: GO:0003682 label: chromatin binding evidence_type: IDA original_reference_id: PMID:25568117 qualifier: enables review: summary: 'IDA: chromatin binding, from ChIP-seq/ChIP-PCR of Myc-tagged Sox9a in zebrafish embryos.' action: ACCEPT reason: ChIP of tagged Sox9a identified and verified occupied target loci (e.g. eya2, tlx2), which supports chromatin binding. The more specific sequence-specific cis-regulatory binding term (GO:0000978) is the core function; this annotation is consistent with it. supported_by: - *id004 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:25617839 qualifier: enables supporting_entities: - ZFIN:ZDB-GENE-030131-2317 review: summary: 'IPI: protein binding, Ewsa co-immunoprecipitated with Sox9 in zebrafish embryo lysates.' action: REMOVE reason: Generic protein binding is uninformative. The removal does not dispute the Ewsa-Sox9 interaction. Note also that the co-IP used a commercial anti-SOX9 antibody, so the cached text does not show which zebrafish copy (Sox9a or Sox9b) was precipitated; no more specific MF can be assigned from this evidence. supported_by: - reference_id: PMID:25617839 supporting_text: The co-IP experiment for zebrafish Ewsa and Sox9 was performed with 27 hpf zebrafish embryos. - reference_id: PMID:25617839 supporting_text: anti-Sox9 (1:100)(Abcam, MA) - term: id: GO:0005634 label: nucleus evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - MGI:MGI:98358 - MGI:MGI:98370 - MGI:MGI:98371 - PANTHER:PTN002910095 - PomBase:SPBC32C12.02 - RGD:3735 - UniProtKB:B7ZR65 - UniProtKB:O18896 - UniProtKB:P48434 - UniProtKB:P48436 - UniProtKB:P56693 - UniProtKB:P57073 - Xenbase:XB-GENE-1034769 review: summary: 'IBA: nucleus (is_active_in).' action: ACCEPT reason: Sox9a is a DNA-binding transcription factor with a conserved HMG box that carries the Sox nuclear localization signals; nuclear activity is expected and consistent with its target-gene occupancy in ChIP. supported_by: - *id001 - *id004 - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0191 - UniRule:UR000400811 review: summary: 'IEA: nucleus (UniProt subcellular location mapping).' action: ACCEPT reason: Consistent with the IBA and the transcription-factor function. supported_by: - *id001 - term: id: GO:0005737 label: cytoplasm evidence_type: IMP original_reference_id: PMID:12397114 qualifier: located_in supporting_entities: - ZFIN:ZDB-GENO-980202-938 review: summary: 'IMP: cytoplasm, from Yan et al. 2002 (jef mutant / splice-blocking morpholinos).' action: MARK_AS_OVER_ANNOTATED reason: 'The observation in the cited paper concerns the sox9a mRNA, not the protein: splice-blocking morpholinos caused unspliced sox9a transcript to accumulate in the nucleus, which the authors used as an assay for morpholino efficacy. That is transcript processing/export, not where the Sox9a protein acts. Independent work (Sun et al. 2013) reports a regulated cytoplasmic pool of Sox9a protein in juvenile gonad stromal cells alongside nuclear Sox9a, so a cytoplasmic location is not impossible, but Sox9a executes its transcription-factor function in the nucleus and the cited evidence does not support the protein-level claim. Marked as over-annotation rather than removed because of the independent gonadal data.' supported_by: - &id005 reference_id: PMID:12397114 supporting_text: Inhibiting splicing of the sox9a transcript in wild-type embryos with splice site-directed morpholino antisense oligonucleotides produced a phenotype like jef mutant larvae, and caused sox9a transcript to accumulate in the nucleus - &id006 reference_id: PMID:24263104 supporting_text: After MKI treatment, levels of sox9a and p-Erk1/2 were dramatically decreased in the cytoplasm, whereas nuclear sox9a and p-Erk1/2 showed little reduction. - term: id: GO:0005737 label: cytoplasm evidence_type: IMP original_reference_id: PMID:12397114 qualifier: located_in supporting_entities: - ZFIN:ZDB-MRPHLNO-070412-1 - ZFIN:ZDB-MRPHLNO-070412-2 review: summary: 'IMP: cytoplasm, from Yan et al. 2002 (jef mutant / splice-blocking morpholinos).' action: MARK_AS_OVER_ANNOTATED reason: 'The observation in the cited paper concerns the sox9a mRNA, not the protein: splice-blocking morpholinos caused unspliced sox9a transcript to accumulate in the nucleus, which the authors used as an assay for morpholino efficacy. That is transcript processing/export, not where the Sox9a protein acts. Independent work (Sun et al. 2013) reports a regulated cytoplasmic pool of Sox9a protein in juvenile gonad stromal cells alongside nuclear Sox9a, so a cytoplasmic location is not impossible, but Sox9a executes its transcription-factor function in the nucleus and the cited evidence does not support the protein-level claim. Marked as over-annotation rather than removed because of the independent gonadal data.' supported_by: - *id005 - *id006 - term: id: GO:0007507 label: heart development evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:98371 - PANTHER:PTN002910118 - UniProtKB:P48434 - UniProtKB:P48436 - ZFIN:ZDB-GENE-001103-2 review: summary: 'IBA: heart development (PTN002910118; zebrafish donor is sox9b, ZDB-GENE-001103-2).' action: MARK_AS_OVER_ANNOTATED reason: 'The cardiac role of the ancestral SOX9 gene went to sox9b in zebrafish: sox9b is required for proepicardium, epicardium and valve formation, whereas an effective sox9a morpholino did not cause cardiac malformations. The IBA propagates the function to both co-orthologs, which is correct for the ancestral node but not supported for sox9a, which appears to have lost this subfunction by expression partition. Morpholino negative evidence is not conclusive, so this is marked as an over-annotation rather than removed.' propagation_review: root_cause: PROPAGATION_BAD failure_modes: - FUNCTIONAL_DIVERGENCE - CONTEXT_OR_TISSUE_MISMATCH source_entities: - source_id: PANTHER:PTN002910118 source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: Ancestral SOX9 node; the cardiac role is sound for the node and for sox9b, but after the TGD the cardiac expression domain appears to have been retained only by sox9b. - source_id: ZFIN:ZDB-GENE-001103-2 source_label: sox9b source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: Paralog donor with IMP evidence for proepicardium, epicardium and valve development; the sox9a morpholino control in the same study showed no cardiac defect. supported_by: - reference_id: PMID:23775563 supporting_text: Knock down of sox9a expression did not cause cardiac malformations, or defects in epicardium development. - reference_id: PMID:23775563 supporting_text: Furthermore, sox9b is required for PE, epicardium, and valve formation. - reference_id: PMID:15689370 supporting_text: Analysis of mutant phenotypes strongly supports the interpretation that ancestral gene functions partitioned spatially and temporally between Sox9 co-orthologs. - term: id: GO:0030916 label: otic vesicle formation evidence_type: IGI original_reference_id: PMID:15689370 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-050322-1 review: summary: 'IGI: otic vesicle formation (sox9a;sox9b double mutant).' action: KEEP_AS_NON_CORE reason: Ears are reduced in each single mutant and mostly absent in double mutants, so sox9a acts partly redundantly with sox9b in otic vesicle formation. supported_by: - *id007 - term: id: GO:0032332 label: positive regulation of chondrocyte differentiation evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:98371 - PANTHER:PTN002910118 - UniProtKB:P48436 review: summary: 'IBA: positive regulation of chondrocyte differentiation.' action: ACCEPT reason: Sox9a promotes chondrocyte differentiation by activating cartilage matrix genes; the IBA is well supported by the zebrafish mutant data. supported_by: - *id008 - *id003 - term: id: GO:0033339 label: pectoral fin development evidence_type: IMP original_reference_id: PMID:9007245 qualifier: acts_upstream_of_or_within review: summary: 'IMP: pectoral fin development, from the Tuebingen fin mutant screen (van Eeden et al. 1996).' action: KEEP_AS_NON_CORE reason: Only the abstract is cached and it does not name jellyfish; the curator presumably used the full text. The annotation is consistent with the loss of pectoral girdle cartilage in sox9a (jef) mutants reported independently, so it is kept, as a non-core developmental role that follows from its chondrogenic function. supported_by: - &id009 reference_id: PMID:12397114 supporting_text: lack cartilage elements of the neurocranium, pharyngeal arches, and pectoral girdle similar to humans with campomelic dysplasia - reference_id: PMID:19210963 supporting_text: In the wild-type pectoral apparatus, sox9a is expressed strongly in the scapulocoracoid of the pectoral girldle but was weaker in the blade of the fin bud and did not appear in the cleithrum of the pectoral girdle. - term: id: GO:0035118 label: embryonic pectoral fin morphogenesis evidence_type: IMP original_reference_id: PMID:12397114 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-980202-938 review: summary: 'IMP: embryonic pectoral fin morphogenesis.' action: KEEP_AS_NON_CORE reason: sox9a mutants and morphants lack pectoral girdle cartilage, and each co-ortholog is required for a distinct subset of the pectoral appendage. Kept as a non-core organ-level consequence of its chondrogenic function. supported_by: - *id009 - &id010 reference_id: PMID:15689370 supporting_text: Distinct subsets of the craniofacial skeleton, otic placode and pectoral appendage express each gene, and are defective in each single mutant. - term: id: GO:0035118 label: embryonic pectoral fin morphogenesis evidence_type: IMP original_reference_id: PMID:12397114 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-070412-1 - ZFIN:ZDB-MRPHLNO-070412-2 review: summary: 'IMP: embryonic pectoral fin morphogenesis.' action: KEEP_AS_NON_CORE reason: sox9a mutants and morphants lack pectoral girdle cartilage, and each co-ortholog is required for a distinct subset of the pectoral appendage. Kept as a non-core organ-level consequence of its chondrogenic function. supported_by: - *id009 - *id010 - term: id: GO:0035118 label: embryonic pectoral fin morphogenesis evidence_type: IMP original_reference_id: PMID:15689370 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-030219-2 review: summary: 'IMP: embryonic pectoral fin morphogenesis.' action: KEEP_AS_NON_CORE reason: sox9a mutants and morphants lack pectoral girdle cartilage, and each co-ortholog is required for a distinct subset of the pectoral appendage. Kept as a non-core organ-level consequence of its chondrogenic function. supported_by: - *id009 - *id010 - term: id: GO:0043049 label: otic placode formation evidence_type: IGI original_reference_id: PMID:12668634 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENE-980526-280 - ZFIN:ZDB-GENE-990415-50 review: summary: 'IGI: otic placode formation (Df(b380) deletion removing dlx3b, dlx4b and sox9a, with Fgf pathway genes).' action: KEEP_AS_NON_CORE reason: The genetic evidence is from combined loss of several genes, so sox9a is one of several partly redundant contributors; supported but not core. supported_by: - *id011 - reference_id: PMID:12668634 supporting_text: These cells fail to form if sox9b function is also blocked. - reference_id: PMID:12668634 supporting_text: Expression of sox9a but not dlx3b, dlx4b or sox9b requires Fgf3 and Fgf8. - term: id: GO:0048708 label: astrocyte differentiation evidence_type: IMP original_reference_id: PMID:20023158 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-980202-938 review: summary: 'IMP: astrocyte differentiation (sox9a tw37 mutant; loss of GS-positive astroglia in hindbrain).' action: KEEP_AS_NON_CORE reason: Full text shows sox9a is required for GS-positive astroglia in the hindbrain, a conserved SoxE gliogenic role. Non-core relative to chondrogenesis. supported_by: - &id012 reference_id: PMID:20023158 supporting_text: We have shown that in the zebrafish hindbrain, sox9a is necessary for the generation of both OLPs and GS-positive astroglia, supporting a phylogenetically conserved role. - term: id: GO:0048709 label: oligodendrocyte differentiation evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:98371 - PANTHER:PTN002910118 - ZFIN:ZDB-GENE-001103-1 review: summary: 'IBA: oligodendrocyte differentiation (donor includes zebrafish sox9a itself).' action: KEEP_AS_NON_CORE reason: Sox9a being among the donors reflects its own experimental support (Esain et al. 2010), which is appropriate for an IBA. Kept as non-core. supported_by: - *id012 - term: id: GO:0048709 label: oligodendrocyte differentiation evidence_type: IMP original_reference_id: PMID:20023158 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-980202-938 review: summary: 'IMP: oligodendrocyte differentiation (sox9a mutant; reduced OLP markers).' action: KEEP_AS_NON_CORE reason: Sox9a is needed for oligodendrocyte progenitor generation in the hindbrain; residual marker expression is attributed to sox9b. supported_by: - *id012 - reference_id: PMID:20023158 supporting_text: residual expression of glial markers in these mutants is probably due to the sox9b co-orthologue, which has an overlapping expression profile. - term: id: GO:0048839 label: inner ear development evidence_type: IGI original_reference_id: PMID:19132125 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-980202-1565 - ZFIN:ZDB-MRPHLNO-090422-7 - ZFIN:ZDB-MRPHLNO-090422-8 review: summary: 'IGI: inner ear development (with sox10 mutant and sox9 morpholinos).' action: KEEP_AS_NON_CORE reason: SoxE genes sox9a, sox9b and sox10 act redundantly to maintain sox10 and restrict fgf8 expression in the otic vesicle. supported_by: - &id013 reference_id: PMID:19132125 supporting_text: they act redundantly to maintain sox10 expression throughout otic tissue and to restrict fgf8 expression to anterior macula regions - term: id: GO:0048839 label: inner ear development evidence_type: IMP original_reference_id: PMID:19132125 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-090422-7 - ZFIN:ZDB-MRPHLNO-090422-8 review: summary: 'IMP: inner ear development (morpholinos).' action: KEEP_AS_NON_CORE reason: As above; the full text is not cached, but the abstract supports a redundant requirement for group E sox genes in otic patterning. supported_by: - *id013 - term: id: GO:0048839 label: inner ear development evidence_type: IMP original_reference_id: PMID:25568117 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-041110-2 review: summary: 'IMP: inner ear development (sox9a morpholino reduces statoacoustic ganglion).' action: KEEP_AS_NON_CORE reason: Sox9a knockdown reduces neurod expression and statoacoustic ganglion size; Sox9a acts downstream of Fgf signalling in otic neurogenesis. supported_by: - reference_id: PMID:25568117 supporting_text: When Sox9a function was knocked down by MO, neurod expression and SAG area were reduced - reference_id: PMID:25568117 supporting_text: Sox9a and Atoh1a act downstream of Fgfr-Akt signaling to specify and/or maintain the otic neuron fate during the early segmentation stage. - term: id: GO:0051216 label: cartilage development evidence_type: IMP original_reference_id: PMID:12397114 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-980202-938 review: summary: 'IMP: cartilage development.' action: ACCEPT reason: 'Core role: loss of sox9a (mutant or morpholino) eliminates most craniofacial and pectoral girdle cartilage.' supported_by: - *id008 - *id009 - reference_id: file:DANRE/sox9a/sox9a-deep-research-falcon.md supporting_text: Alcian-blue staining showed loss of all neurocranial cartilage and most pharyngeal-arch cartilage. - term: id: GO:0051216 label: cartilage development evidence_type: IMP original_reference_id: PMID:12397114 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-070412-1 - ZFIN:ZDB-MRPHLNO-070412-2 review: summary: 'IMP: cartilage development.' action: ACCEPT reason: 'Core role: loss of sox9a (mutant or morpholino) eliminates most craniofacial and pectoral girdle cartilage.' supported_by: - *id008 - term: id: GO:0051216 label: cartilage development evidence_type: IMP original_reference_id: PMID:15689370 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-030219-2 review: summary: 'IMP: cartilage development.' action: ACCEPT reason: 'Core role: loss of sox9a (mutant or morpholino) eliminates most craniofacial and pectoral girdle cartilage.' supported_by: - *id014 - *id010 - term: id: GO:0051216 label: cartilage development evidence_type: IMP original_reference_id: PMID:18950725 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-070412-1 review: summary: 'IMP: cartilage development.' action: ACCEPT reason: 'Core role: loss of sox9a (mutant or morpholino) eliminates most craniofacial and pectoral girdle cartilage.' supported_by: - &id015 reference_id: PMID:18950725 supporting_text: blocking translation of either sox9a or ff1a also blocked cartilage formation. - term: id: GO:0051216 label: cartilage development evidence_type: IMP original_reference_id: PMID:18950725 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-070412-2 review: summary: 'IMP: cartilage development.' action: ACCEPT reason: 'Core role: loss of sox9a (mutant or morpholino) eliminates most craniofacial and pectoral girdle cartilage.' supported_by: - *id015 - term: id: GO:0060536 label: cartilage morphogenesis evidence_type: IMP original_reference_id: PMID:9007254 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-980202-938 review: summary: 'IMP: cartilage morphogenesis (jellyfish mutant, Piotrowski et al. 1996).' action: ACCEPT reason: The jellyfish mutant, later shown to be sox9a, lacks almost all cartilage; Yan et al. 2002 showed Sox9a is needed for morphogenetic behaviours of condensations (stacking, individuation, shaping). supported_by: - reference_id: PMID:9007254 supporting_text: jellyfish mutant larvae are characterized by a severe reduction of all cartilaginous elements, leaving only two pieces in the position of the ceratohyal cartilages. - reference_id: PMID:12397114 supporting_text: We show that two alleles of jef contain mutations in sox9a, one of two zebrafish orthologs of the human transcription factor SOX9. - *id008 - term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific evidence_type: IDA original_reference_id: PMID:11180959 review: summary: 'Proposed: Sox9a is a sequence-specific transcriptional activator.' action: NEW reason: Chiang et al. 2001 showed that both zebrafish Sox9 proteins bind HMG consensus DNA and mapped a transactivation domain in the middle of each protein; the title describes them as similar transcription activators. Sox9a is required for expression of the SOX9 target genes col2a1 and col11a2. This refines the accepted GO:0000981 IBA. Proposed identically for sox9b, since the evidence covers both proteins. supported_by: - *id001 - *id002 - reference_id: PMID:19210963 supporting_text: After the sox9 gene duplication event, regulatory elements controlling the expression of sox9 co-orthologs apparently partitioned in a tissue-specific fashion, but the Sox9 proteins encoded by sox9a and sox9b retained the ability to regulate col11a2, presumably by binding to regulatory sites for the col11a2 gene. references: - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000104 title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:12397114 title: A zebrafish sox9 gene required for cartilage morphogenesis. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Abstract only; identifies jellyfish as sox9a. - id: PMID:12668634 title: Fgf3 and Fgf8 dependent and independent transcription factors are required for otic placode specification. findings: [] - id: PMID:15689370 title: 'A pair of Sox: distinct and overlapping functions of zebrafish sox9 co-orthologs in craniofacial and pectoral fin development.' findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Abstract only; key pair paper (single and double mutants). - id: PMID:18950725 title: Sox9a regulation of ff1a in zebrafish (Danio rerio) suggests an involvement of ff1a in cartilage development. findings: [] - id: PMID:19132125 title: A zebrafish model for Waardenburg syndrome type IV reveals diverse roles for Sox10 in the otic vesicle. findings: [] - id: PMID:20023158 title: FGF-receptor signalling controls neural cell diversity in the zebrafish hindbrain by regulating olig2 and sox9. findings: [] - id: PMID:25568117 title: Fgf-signaling-dependent Sox9a and Atoh1a regulate otic neural development in zebrafish. findings: [] - id: PMID:25617839 title: Ewing sarcoma ewsa protein regulates chondrogenesis of Meckel's cartilage through modulation of Sox9 in zebrafish. findings: [] - id: PMID:9007245 title: Genetic analysis of fin formation in the zebrafish, Danio rerio. findings: [] - id: PMID:9007254 title: 'Jaw and branchial arch mutants in zebrafish II: anterior arches and cartilage differentiation.' findings: [] - id: PMID:11180959 title: 'Two sox9 genes on duplicated zebrafish chromosomes: expression of similar transcription activators in distinct sites.' reference_review: relevance: HIGH correctness: VERIFIED review_notes: Abstract only; establishes duplicated-chromosome origin, DNA binding and transactivation of both copies, and distinct expression. - id: PMID:14579386 title: 'Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish.' reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; expression partition between co-orthologs across two teleost lineages. - id: PMID:15818483 title: Divergent expression patterns of Sox9 duplicates in teleosts indicate a lineage specific subfunctionalization. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; medaka Sox9a/Sox9b expression compared with zebrafish. - id: PMID:15939378 title: Characterization and expression pattern of zebrafish Anti-Müllerian hormone (Amh) relative to sox9a, sox9b, and cyp19a1a, during gonad development. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; sox9a in testis Sertoli cells, sox9b in oocytes. - id: PMID:19210963 title: Expression profiling of zebrafish sox9 mutants reveals that Sox9 is required for retinal differentiation. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text; compares sox9a, sox9b and double mutants for col11a2 and retinal genes. - id: PMID:23775563 title: Sox9b is required for epicardium formation and plays a role in TCDD-induced heart malformation in zebrafish. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text; includes sox9a morpholino control showing no cardiac defect. - id: PMID:23209659 title: RUNX3, EGR1 and SOX9B form a regulatory cascade required to modulate BMP-signaling during cranial cartilage development in zebrafish. reference_review: relevance: LOW correctness: VERIFIED review_notes: Full text; background statements on sox9a in chondrocyte stacking and col2a1. - id: file:DANRE/sox9a/sox9a-bioinformatics/RESULTS.md title: Region-wise identity of zebrafish Sox9a, Sox9b and human SOX9 reference_review: relevance: HIGH correctness: VERIFIED review_notes: Manual audit verified the sidecar supports conservation of the SOX9 HMG DNA-binding box in both zebrafish copies while noting that region identity alone does not compare transactivation strength. findings: - statement: HMG box 98.6% identical between Sox9a, Sox9b and human SOX9; divergence is concentrated C-terminal of the HMG box. - id: file:DANRE/sox9a/sox9a-deep-research-falcon.md title: Deep research report on sox9a (Falcon) - id: PMID:24263104 title: Sox9-related signaling controls zebrafish juvenile ovary-testis transformation. reference_review: relevance: LOW correctness: VERIFIED review_notes: Full text; reports nuclear and cytoplasmic Sox9a immunostaining in juvenile gonad. core_functions: - description: Sequence-specific DNA-binding transcriptional activator acting through the conserved SOX HMG box on RNA polymerase II target genes such as col2a1a and col11a2 in chondrocytes. molecular_function: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific directly_involved_in: - id: GO:0002062 label: chondrocyte differentiation - id: GO:0051216 label: cartilage development locations: - id: GO:0005634 label: nucleus supported_by: - *id001 - *id002 - *id008 - *id016 suggested_questions: - question: Do Sox9a and Sox9b differ in transactivation strength or partner choice (e.g. with Sox5/Sox6 or other cofactors), given that divergence between the copies is concentrated outside the HMG box? - question: Is the absence of a cardiac role for sox9a an expression-level loss (no cardiac cis-regulatory elements) or would Sox9a protein substitute for Sox9b if expressed in the heart? - question: Which Sox9 copy did the Ewsa co-immunoprecipitation (PMID:25617839) detect, given a commercial anti-SOX9 antibody was used? suggested_experiments: - description: 'Cross-rescue: express sox9a coding sequence from sox9b regulatory elements (knock-in or BAC) in sox9b fh313 mutants and test rescue of ductal, cardiac and cartilage phenotypes, to separate expression partition from protein divergence.' - description: Compare genome-wide occupancy (ChIP-seq/CUT&RUN) of tagged Sox9a and Sox9b in the same cell type (e.g. pharyngeal chondrocytes) to test whether target specificity differs.