id: A0A9L0JBM7 gene_symbol: HOXA2 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9793 label: Equus asinus description: HOXA2 (homeobox protein Hox-A2) is a homeodomain transcription factor of the Antp homeobox family, proboscipedia subfamily, and the paralog group 2 member of the HOXA cluster. It binds specific DNA sequences in RNA polymerase II cis-regulatory regions through its homeodomain and, depending on the target and cofactors (PBX/MEIS), represses or activates transcription in the nucleus. In the mammalian embryo it acts in cranial neural crest-derived mesenchyme of the second pharyngeal arch as a selector gene that confers second-arch (hyoid) identity, so that loss of function transforms second-arch skeletal elements into first-arch (mandibular and middle-ear) structures; it is also expressed in hindbrain rhombomeres 2-3 and the spinal cord. Human HOXA2 variants cause microtia with hearing impairment and cleft palate. The donkey protein A0A9L0JBM7 is a full-length 373-residue product, 97.6% identical to human HOXA2 with an identical homeodomain and hexapeptide. existing_annotations: - term: id: GO:0000122 label: negative regulation of transcription by RNA polymerase II evidence_type: IEA original_reference_id: GO_REF:0000108 qualifier: involved_in supporting_entities: - GO:0001227 review: summary: Negative regulation of transcription by RNA polymerase II, inferred (GO_REF:0000108) from the repressor-activity annotation. Mouse Hoxa2 binds the Six2 promoter and downregulates Six2 in second-arch mesenchyme (PMID:15634706). action: ACCEPT reason: The process follows directly from HOXA2's own DNA-binding repressor activity; the TF itself performs the regulation. Transfer is phylogenetically grounded, as donkey A0A9L0JBM7, human O43364 and mouse P31245 are all members of PANTHER subfamily PTHR45664:SF3 (HOMEOBOX PROTEIN HOX-A2), and the donkey homeodomain is 100% identical to human. supported_by: - reference_id: PMID:15634706 supporting_text: Hoxa2 regulation of Six2 is confined to a 0.9 kb fragment of the Six2 promoter and that Hoxa2 binds to this promoter region - reference_id: PMID:15634706 supporting_text: High levels of Six2 are observed in the Hoxa2 loss-of-function mutant. - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md supporting_text: 'human region 143-202: 60 of 60 residues aligned, 60 identical' - term: id: GO:0000978 label: RNA polymerase II cis-regulatory region sequence-specific DNA binding evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables supporting_entities: - UniProtKB:P31245 - ensembl:ENSMUSP00000014848 - PANTHER:PTN000674557 review: summary: RNA polymerase II cis-regulatory region sequence-specific DNA binding (combined IEA, from the mouse ortholog and PANTHER node PTN000674557). Mouse Hoxa2 binds the Six2 promoter (PMID:15634706), and Hox/Pbx sites in the Krox20 element C enhancer mediate direct activation (PMID:18787068). action: ACCEPT reason: Most specific DNA-binding term supported for the PTHR45664:SF3 subfamily; the donkey homeodomain, which carries all DNA-contacting residues, is identical to human. supported_by: - reference_id: PMID:15634706 supporting_text: Hoxa2 binds to this promoter region - reference_id: PMID:18787068 supporting_text: element C contains multiple binding sites for Meis and Hox/Pbx factors and that these proteins synergize to activate the enhancer - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md supporting_text: 'human region 143-202: 60 of 60 residues aligned, 60 identical' - term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables supporting_entities: - InterPro:IPR017970 - PANTHER:PTN000674557 review: summary: DNA-binding transcription factor activity, RNA polymerase II-specific (combined IEA; homeobox signature and PANTHER node). HOXA2 is a homeodomain sequence-specific transcription factor that both represses (Six2) and, with Pbx/Meis, activates (Krox20) target genes. action: ACCEPT reason: Core molecular function of a HOX protein. Because HOXA2 acts as both repressor and activator depending on target and cofactor context, this general RNA Pol II TF activity term is the appropriate core term alongside the repressor child term. supported_by: - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/O43364-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Sequence-specific transcription factor which is part of a - reference_id: PMID:15634706 supporting_text: The Hoxa2 transcription factor acts during development of the second branchial arch. - reference_id: PMID:18787068 supporting_text: Krox20 is under the direct transcriptional control of both Meis (presumably Meis2) and Hox/Pbx factors in r3 - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md supporting_text: 'human region 143-202: 60 of 60 residues aligned, 60 identical' - term: id: GO:0001227 label: DNA-binding transcription repressor activity, RNA polymerase II-specific evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: enables supporting_entities: - UniProtKB:P31245 - ensembl:ENSMUSP00000014848 review: summary: DNA-binding transcription repressor activity, RNA polymerase II-specific (Ensembl Compara from mouse Hoxa2, based on PMID:15634706). action: ACCEPT reason: Mouse Hoxa2 binds the Six2 promoter and its loss derepresses Six2, so it acts as a direct repressor of this RNA Pol II target. HOXA2 also activates other targets, so this is one of two valid specific activities rather than an exclusive one. Same PANTHER subfamily (PTHR45664:SF3) as the donor. supported_by: - reference_id: PMID:15634706 supporting_text: These results strongly suggest that Six2 is a direct target of Hoxa2. - reference_id: PMID:15634706 supporting_text: High levels of Six2 are observed in the Hoxa2 loss-of-function mutant. - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md supporting_text: 'human region 143-202: 60 of 60 residues aligned, 60 identical' - term: id: GO:0003677 label: DNA binding evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables supporting_entities: - InterPro:IPR001356 - InterPro:IPR001827 - InterPro:IPR020479 - UniRule:UR000401037 review: summary: DNA binding (combined IEA from homeobox signatures). True, but entailed by the accepted RNA polymerase II cis-regulatory region sequence-specific DNA binding term. action: TOO_GENERAL reason: HOXA2 binds DNA via its homeodomain; GO:0000978 (accepted in this review) is a descendant of GO:0003677, so the generic term adds nothing. supported_by: - reference_id: PMID:15634706 supporting_text: Hoxa2 binds to this promoter region - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md supporting_text: 'human region 143-202: 60 of 60 residues aligned, 60 identical' - term: id: GO:0003700 label: DNA-binding transcription factor activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR001827 review: summary: DNA-binding transcription factor activity (InterPro2GO, Antennapedia-type homeobox signature). True, but entailed by the accepted RNA polymerase II-specific child term GO:0000981. action: TOO_GENERAL reason: The more specific RNA Pol II-specific TF activity (GO:0000981) is accepted; this parent is uninformative. supported_by: - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/O43364-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Sequence-specific transcription factor which is part of a - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in supporting_entities: - UniProtKB:P31245 - ensembl:ENSMUSP00000014848 - UniProtKB-SubCell:SL-0191 - PANTHER:PTN000674557 - UniRule:UR000401037 review: summary: Nucleus (combined IEA including mouse ortholog transfer and SubCell mapping). Mouse Hoxa-2 protein is detected in nuclei by immunohistochemistry (PMID:10536059). action: ACCEPT reason: A sequence-specific transcription factor acting on chromatin; nuclear localization is shown for the mouse ortholog in the same PANTHER subfamily and is curated for human HOXA2. supported_by: - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/O43364-uniprot.txt record_section: ["CC:SUBCELLULAR LOCATION"] supporting_text: 'SUBCELLULAR LOCATION: Nucleus.' - reference_id: PMID:10536059 supporting_text: Hoxa-2 protein is predominantly detected in the nuclei of cells in the ventral mantle region of 10-day-old mouse embryos. - term: id: GO:0006355 label: regulation of DNA-templated transcription evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in supporting_entities: - InterPro:IPR001827 - InterPro:IPR017970 review: summary: Regulation of DNA-templated transcription (InterPro2GO). True but entailed by the accepted regulation of transcription by RNA polymerase II. action: TOO_GENERAL reason: GO:0006357 (accepted in this review) is the informative descendant. supported_by: - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/O43364-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Sequence-specific transcription factor which is part of a - term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: involved_in supporting_entities: - PANTHER:PTN000674557 review: summary: Regulation of transcription by RNA polymerase II, from TreeGrafter (PANTHER node PTN000674557). HOXA2 directly regulates RNA Pol II target genes, repressing some (Six2) and activating others (Krox20 element C) with Pbx/Meis cofactors. action: ACCEPT reason: Consistent with the RNA Pol II-specific TF activity. TreeGrafter places the donkey sequence in PTHR45664:SF3, the same subfamily as the experimentally characterised mouse and human HOXA2, so the PANTHER node inheritance is sound. supported_by: - reference_id: PMID:15634706 supporting_text: These results strongly suggest that Six2 is a direct target of Hoxa2. - reference_id: PMID:18787068 supporting_text: Krox20 is under the direct transcriptional control of both Meis (presumably Meis2) and Hox/Pbx factors in r3 - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md supporting_text: aligned pairs 373; identical 364; identity over aligned pairs 97.59% - term: id: GO:0043565 label: sequence-specific DNA binding evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: enables supporting_entities: - UniProtKB:P31245 - ensembl:ENSMUSP00000014848 review: summary: Sequence-specific DNA binding (Ensembl Compara from mouse Hoxa2, PMID:15634706). True, but an ancestor of the accepted GO:0000978. action: TOO_GENERAL reason: GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding (accepted here) is_a GO:0043565 (checked against OLS hierarchical ancestors), and already conveys sequence specificity. The earlier review accepted this row on the grounds that it conveyed specificity; that reasoning does not hold, so the action is changed to TOO_GENERAL. The claim itself is true. supported_by: - reference_id: PMID:15634706 supporting_text: Hoxa2 binds to this promoter region - term: id: GO:0048706 label: embryonic skeletal system development evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in supporting_entities: - UniProtKB:P31245 - ensembl:ENSMUSP00000014848 review: summary: Embryonic skeletal system development (Ensembl Compara from mouse Hoxa2, PMID:25889273). Hoxa2 specifies second-arch skeletal identity in cranial neural crest cells; loss of function transforms hyoid into mandibular/middle-ear elements, and ectopic expression transforms first-arch elements into second-arch-like structures. action: ACCEPT reason: As a selector transcription factor acting cell-autonomously in skeletogenic cranial neural crest mesenchyme (required in NCCs, and after their migration), HOXA2 directly regulates the morphogenetic programme of these skeletal elements; this is the defining developmental role of the HOXA2 subfamily in mammals, supported by independent knockout, conditional and gain-of-function studies. supported_by: - reference_id: PMID:16221728 supporting_text: Hoxa2 is selectively required in cranial neural crest cells (NCCs) - reference_id: PMID:16221728 supporting_text: resulted in homeotic transformation of hyoid into mandibular arch skeletal derivatives - reference_id: PMID:7903600 supporting_text: Skeletal elements normally derived from the second arch were absent in the mutants. - reference_id: PMID:25889273 supporting_text: Ectopic Hoxa2 expression results in the transformation of the proximal Meckel's cartilage and of the malleus, two ventral PA1 CNCCs derivatives, into a supernumerary styloid process (SP) - term: id: GO:0060037 label: pharyngeal system development evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in supporting_entities: - UniProtKB:P31245 - ensembl:ENSMUSP00000014848 review: summary: Pharyngeal system development (Ensembl Compara from mouse Hoxa2, PMID:25889273). Hoxa2 is the selector gene for second pharyngeal arch identity. action: ACCEPT reason: Core developmental role of the ortholog, executed by HOXA2 itself as a transcription factor in second-arch neural crest mesenchyme (selector gene for second-arch identity). supported_by: - reference_id: PMID:7903601 supporting_text: second arch mesenchymal NCC identity was changed to first arch identity - reference_id: PMID:7903601 supporting_text: Hoxa-2 acts as a selector gene in the second arch - reference_id: PMID:25889273 supporting_text: ectopic Hoxa2 expression is sufficient for the morphological and molecular transformation of the first PA (PA1) CNCC derivatives into the second PA (PA2)-like structures - term: id: GO:0061061 label: muscle structure development evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in supporting_entities: - UniProtKB:P31245 - ensembl:ENSMUSP00000014848 review: summary: Muscle structure development (Ensembl Compara from a mouse IDA row citing PMID:25889273, a Hoxa2 overexpression study in cranial neural crest). action: MARK_AS_OVER_ANNOTATED reason: The cached abstract of PMID:25889273 describes skeletal transformations of neural crest derivatives after ectopic Hoxa2 expression and says nothing about muscle; the full text is not available locally. Pharyngeal-arch muscles derive from mesoderm, not from the Hoxa2-expressing neural crest, so any effect of Hoxa2 on muscle patterning is expected to be non-cell-autonomous, via the crest-derived connective tissue. That makes muscle structure development a downstream consequence of HOXA2's activity in another cell population rather than a process HOXA2 performs. Not removed, because the mouse curator saw the full text; the earlier KEEP_AS_NON_CORE is tightened to over-annotation for the electronic transfer to donkey. supported_by: - reference_id: PMID:25889273 supporting_text: Here we show that ectopic expression of Hoxa2 in Hox-negative CNCCs results in distinct phenotypes in different CNCC subpopulations. - term: id: GO:1990837 label: sequence-specific double-stranded DNA binding evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: enables supporting_entities: - UniProtKB:O43364 - ensembl:ENSP00000222718 review: summary: Sequence-specific double-stranded DNA binding (Ensembl Compara from a human HOXA2 IDA row citing PMID:28473536, a methylation-SELEX survey of 542 human TFs). action: TOO_GENERAL reason: True for HOXA2 (homeodomain-mediated binding measured in a systematic SELEX survey; the donkey homeodomain is identical), but GO:0000978 accepted here is a descendant of GO:1990837 (checked against OLS hierarchical ancestors), so this term is entailed. supported_by: - reference_id: PMID:28473536 supporting_text: By analysis of 542 human TFs with methylation-sensitive SELEX - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md supporting_text: 'human region 143-202: 60 of 60 residues aligned, 60 identical' references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000107 title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara findings: [] - id: GO_REF:0000108 title: Automatic assignment of GO terms using logical inference, based on on inter-ontology links findings: [] - id: GO_REF:0000118 title: TreeGrafter-generated GO annotations findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:15634706 title: Hoxa2 downregulates Six2 in the neural crest-derived mesenchyme. findings: - statement: Hoxa2 binds a 0.9 kb Six2 promoter fragment and Six2 is upregulated in Hoxa2 mutants, identifying Six2 as a directly repressed target in second-arch mesenchyme. supporting_text: Hoxa2 regulation of Six2 is confined to a 0.9 kb fragment of the Six2 promoter and that Hoxa2 binds to this promoter region reference_review: relevance: HIGH correctness: VERIFIED review_notes: Mouse Hoxa2 (P31245); abstract-only in cache. Source of the mouse IDA repressor, DNA-binding and cis-regulatory binding annotations transferred to donkey. - id: PMID:18787068 title: Rostral hindbrain patterning involves the direct activation of a Krox20 transcriptional enhancer by Hox/Pbx and Meis factors. findings: - statement: Hox/Pbx and Meis binding sites in Krox20 element C mediate direct transcriptional activation in rhombomere 3. supporting_text: Krox20 is under the direct transcriptional control of both Meis (presumably Meis2) and Hox/Pbx factors in r3 reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Mouse; the abstract speaks of Hox/Pbx factors generally (and names Hoxb1); the Hoxa2-specific activation result behind the mouse IDA row is in the full text, which is not cached. - id: PMID:16221728 title: Temporal requirement of Hoxa2 in cranial neural crest skeletal morphogenesis. findings: - statement: Hoxa2 is required cell-autonomously in cranial neural crest, including after migration, for second-arch skeletal identity. supporting_text: Hoxa2 is selectively required in cranial neural crest cells (NCCs) reference_review: relevance: HIGH correctness: VERIFIED review_notes: Mouse conditional/temporal inactivation; abstract-only in cache. - id: PMID:25889273 title: Distinct effects of Hoxa2 overexpression in cranial neural crest populations reveal that the mammalian hyomandibular-ceratohyal boundary maps within the styloid process. findings: - statement: Ectopic Hoxa2 in Hox-negative cranial neural crest transforms first-arch derivatives into second-arch-like structures. supporting_text: ectopic Hoxa2 expression is sufficient for the morphological and molecular transformation of the first PA (PA1) CNCC derivatives into the second PA (PA2)-like structures reference_review: relevance: HIGH correctness: VERIFIED review_notes: Mouse gain-of-function study; source of the mouse IDA rows for skeletal, pharyngeal and muscle structure development. The abstract does not mention muscle; abstract-only in cache. - id: PMID:10536059 title: Differential expression of Hoxa-2 protein along the dorsal-ventral axis of the developing and adult mouse spinal cord. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Mouse immunohistochemistry showing nuclear Hoxa-2 protein; supports nucleus. - id: PMID:7903600 title: Hoxa-2 mutant mice exhibit homeotic transformation of skeletal elements derived from cranial neural crest. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Original mouse Hoxa2 knockout; second-arch skeletal elements absent, cleft palate. - id: PMID:7903601 title: A homeotic transformation is generated in the rostral branchial region of the head by disruption of Hoxa-2, which acts as a selector gene. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Independent mouse Hoxa2 knockout; second-arch neural crest identity changed to first-arch identity; Hoxa2 as second-arch selector gene. - id: PMID:28473536 title: Impact of cytosine methylation on DNA binding specificities of human transcription factors. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Systematic methylation-SELEX survey of 542 human TFs; HOXA2 is not named in the abstract; source of the human IDA GO:1990837 row. - id: file:EQUAS/HOXA2/HOXA2-bioinformatics/O43364-uniprot.txt title: UniProt record for human HOXA2 (O43364) findings: [] - id: file:EQUAS/HOXA2/HOXA2-bioinformatics/P31245-uniprot.txt title: UniProt record for mouse Hoxa2 (P31245) findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Retained; not currently quoted as support (its curated function text is identical to the human record). - id: file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md title: 'HOXA2: donkey-human sequence comparison' findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Local reproducible alignment; homeodomain and hexapeptide identical; donkey product is full length (373 aa vs 376 aa human, 3-residue deletion outside functional motifs). - id: file:EQUAS/HOXA2/HOXA2-bioinformatics/ortholog_experimental_goa.txt title: Experimental GO annotations of human and mouse HOXA2 orthologs (QuickGO) findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: QuickGO download of experimental annotations for O43364 and P31245. Retained as a record of which publications lie behind the Compara transfers, but no longer quoted as support, because a GOA listing states what is annotated, not why it is true; the primary papers are now cited instead. core_functions: - description: Homeodomain transcription factor that binds RNA polymerase II cis-regulatory sequences in the nucleus and represses (e.g. Six2) or, with PBX/MEIS cofactors, activates (e.g. Krox20) target genes, conferring second pharyngeal arch identity on cranial neural crest mesenchyme. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0006357 label: regulation of transcription by RNA polymerase II - id: GO:0060037 label: pharyngeal system development - id: GO:0048706 label: embryonic skeletal system development locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/O43364-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Sequence-specific transcription factor which is part of a - reference_id: PMID:15634706 supporting_text: These results strongly suggest that Six2 is a direct target of Hoxa2. - reference_id: PMID:7903601 supporting_text: Hoxa-2 acts as a selector gene in the second arch - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md supporting_text: 'human region 143-202: 60 of 60 residues aligned, 60 identical' - description: Sequence-specific binding of RNA polymerase II cis-regulatory DNA via the homeodomain. molecular_function: id: GO:0000978 label: RNA polymerase II cis-regulatory region sequence-specific DNA binding locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:15634706 supporting_text: Hoxa2 binds to this promoter region - reference_id: file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md supporting_text: 'human region 143-202: 60 of 60 residues aligned, 60 identical' suggested_questions: - question: Does HOXA2 regulate pharyngeal-arch muscle patterning cell-autonomously or only through crest-derived connective tissue, and should muscle structure development be propagated to orthologs from PMID:25889273?