NKX2-5 (CSX) is an NK-2 class homeodomain transcription factor, the vertebrate ortholog of Drosophila tinman, expressed in cardiac progenitors of the first and second heart fields and in embryonic and adult myocardium, as well as in spleen mesenchyme and pharyngeal/thyroid primordia. Its homeodomain binds NKE (TNAAGTG) elements in promoters and enhancers of cardiac genes such as NPPA/ANF, GATA4, MYL2 and miR-143/145; a C-terminal autorepressive domain makes it a modest activator on its own, and it activates or represses targets in combination with partner transcription factors, notably GATA4 and TBX5 (plus SRF/myocardin and coactivators such as FBLIM1/Cal and CAMTA2). Activity is modulated by casein kinase II phosphorylation and SUMOylation. In the mouse it is required for heart looping, ventricular myocyte specialization, second heart field/outflow tract development and formation of the atrioventricular node and conduction system in a dosage-dependent manner. Heterozygous loss-of-function variants in humans cause secundum atrial septal defect with progressive atrioventricular conduction block, and also ventricular septal defect, tetralogy of Fallot and other congenital heart defects; variants are also associated with congenital asplenia and thyroid dysgenesis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000122 negative regulation of transcription by RNA polymerase II | IMP PMID:19479054 NKX2-5 regulates the expression of beta-catenin and GATA4 in... | ACCEPT | Summary: NKX2-5 directly represses the CTNNB1 (beta-catenin) promoter through NKE elements in human fetal cardiomyocytes. Reason: IMP supported by antisense knockdown and NKE-mutant reporter assays; NKX2-5 has a C-terminal autorepressive domain and acts as a context-dependent repressor as well as activator. Supporting Evidence: PMID:19479054 Down-regulation of NKX2-5 resulted in increased beta-catenin while GATA4 was decreased PMID:19479054 the identified NKX2-5 binding sites were essential for the suppression of beta-catenin, and upregulation of GATA4 by NKX2-5 PMID:10075728 Csx/Nkx-2.5 reduced the GATA-4-induced transactivation of the GATA-4-dependent promoters |
| GO:0000122 negative regulation of transcription by RNA polymerase II | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | ACCEPT | Summary: Transfer from mouse Nkx2-5 of a repressor role; consistent with human data showing NKX2-5-dependent repression of beta-catenin. Reason: Context-dependent repression is a genuine aspect of NKX2-5 TF activity (e.g. reduction of GATA4-driven promoters, repression of CTNNB1). Supporting Evidence: PMID:10075728 Csx/Nkx-2.5 reduced the GATA-4-induced transactivation of the GATA-4-dependent promoters PMID:19479054 the identified NKX2-5 binding sites were essential for the suppression of beta-catenin, and upregulation of GATA4 by NKX2-5 |
| GO:0000785 chromatin | ISA GO_REF:0000113 | ACCEPT | Summary: TFClass-based assignment of chromatin location for a sequence-specific DNA-binding TF. Reason: NKX2-5 binds promoter NKE elements in vivo; chromatin is the appropriate site of action. Supporting Evidence: PMID:19479054 this regulation was conferred by binding of NKX2-5 to specific elements (NKEs) in the promoter region of the beta-catenin and GATA4 genes Reactome:R-HSA-9735143 NKX2-5 binds sites (called NKE sites) in the promoter upstream of the first exon of GATA4 in embryonic hearts |
| GO:0000976 transcription cis-regulatory region binding | IDA PMID:19479054 NKX2-5 regulates the expression of beta-catenin and GATA4 in... | ACCEPT | Summary: NKX2-5 binds NKE elements in the GATA4 and CTNNB1 promoters. Reason: Direct evidence of cis-regulatory region binding; GO:0000978 would be the more specific equivalent but this term is correct. Supporting Evidence: PMID:19479054 this regulation was conferred by binding of NKX2-5 to specific elements (NKEs) in the promoter region of the beta-catenin and GATA4 genes |
| GO:0000976 transcription cis-regulatory region binding | IDA PMID:29899023 NEDD9 targets COL3A1 to promote endothelial fibrosis and pul... | ACCEPT | Summary: NKX2-5 binds the COL3A1 promoter in pulmonary artery endothelial cells, enhanced by NEDD9. Reason: Experimental binding to a target gene cis-regulatory region; the endothelial context is non-cardiac but the molecular function is correct. Supporting Evidence: PMID:29899023 increased NEDD9 complex formation with Nk2 homeobox 5 (NKX2-5), and increased NKX2-5 binding to COL3A1 |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred RNA Pol II cis-regulatory sequence-specific DNA binding across the NK-2 homeodomain family; core function. Reason: Consistent with direct structural and biochemical evidence for NKX2-5 binding to NKE sites in the NPPA promoter. Supporting Evidence: PMID:22849347 Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif PMID:22849347 crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IDA PMID:22849347 Crystal structure of the human NKX2.5 homeodomain in complex... | ACCEPT | Summary: Crystal structure of the NKX2-5 homeodomain bound to the NPPA/ANF -242 NKE element. Reason: Direct structural evidence of sequence-specific binding to an RNA Pol II cis-regulatory element; core function. Supporting Evidence: PMID:22849347 crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene PMID:22849347 Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IDA PMID:26926761 Intermolecular Interactions of Cardiac Transcription Factors... | ACCEPT | Summary: Ternary crystal structure of NKX2-5 and TBX5 DNA-binding domains on a 19-bp target DNA. Reason: Direct evidence of sequence-specific cis-regulatory binding together with TBX5; core function. Supporting Evidence: PMID:26926761 Here we report a crystal structure of human NKX2.5 and TBX5 DNA binding domains in a complex with a 19 bp target DNA |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl Compara transfer from mouse Nkx2-5; matches human experimental data. Reason: Core molecular function, independently supported by human structural data. Supporting Evidence: PMID:22849347 Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IMP PMID:15649947 Common arterial trunk associated with a homeodomain mutation... | ACCEPT | Summary: Homeodomain mutation (F157L) reduces NKX2-5 specific DNA binding and transactivation of ANF and Cx40 promoters. Reason: Loss-of-function mutant analysis supports sequence-specific cis-regulatory DNA binding. Supporting Evidence: PMID:15649947 Introduction of F157L into human NKX2.5 substantially reduced its transcription activating function, its synergism with partners at the atrial natriuretic factor (ANF) and connexin-40 (Cx40) promoters and its specific DNA binding |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | ACCEPT | Summary: Transfer from mouse Nkx2-5 (100% homeodomain identity). Reason: Core molecular function; supported by human experimental data. Supporting Evidence: PMID:8900537 The predicted amino acid sequence of hCsx has 87% overall homology to the murine gene with 100% identity in the homeodomain PMID:22849347 Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of RNA Pol II-specific DNA-binding TF activity for the NK-2 clade; this is the core molecular function of NKX2-5. Reason: Well supported by direct binding and transactivation of the NPPA promoter. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 PMID:22849347 Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IEA GO_REF:0000120 | ACCEPT | Summary: Automated combined annotation of RNA Pol II-specific DNA-binding TF activity. Reason: Correct core molecular function. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | ISA GO_REF:0000113 | ACCEPT | Summary: TFClass-based assignment of RNA Pol II-specific DNA-binding TF activity. Reason: Correct core molecular function. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 |
| GO:0001216 DNA-binding transcription activator activity | IDA PMID:29325903 GATA4 Loss-of-Function Mutation and the Congenitally Bicuspi... | MODIFY | Summary: NKX2-5 synergistically activates promoters together with GATA4 in reporter assays (paper focuses on a GATA4 BAV mutation). Reason: Activator activity is correct, but the evidence (Pol II promoter reporters) supports the RNA Pol II-specific child term, as already used elsewhere for NKX2-5. Proposed replacements: DNA-binding transcription activator activity, RNA polymerase II-specific Supporting Evidence: PMID:29325903 the mutation disrupted the synergistic transcriptional activation between GATA4 and NKX2.5 PMID:9312027 Co-expression of GATA-4 and Nkx2-5 resulted in synergistic activation of the ANF promoter in heterologous cells |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IDA PMID:19578358 miR-145 and miR-143 regulate smooth muscle cell fate and pla... | ACCEPT | Summary: NKX2-5 directly activates the miR-143/145 enhancer, alone and with SRF/myocardin. Reason: Direct transcriptional activator activity at an RNA Pol II enhancer. Supporting Evidence: PMID:19578358 miR-145 and miR-143 were direct transcriptional targets of serum response factor, myocardin and Nkx2-5 |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IEA GO_REF:0000107 | ACCEPT | Summary: Transfer from mouse Nkx2-5 of activator activity. Reason: Correct core function. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IMP PMID:15649947 Common arterial trunk associated with a homeodomain mutation... | ACCEPT | Summary: Homeodomain mutant analysis shows NKX2-5 activates ANF and Cx40 promoters. Reason: Supports activator activity. Supporting Evidence: PMID:15649947 Introduction of F157L into human NKX2.5 substantially reduced its transcription activating function, its synergism with partners at the atrial natriuretic factor (ANF) and connexin-40 (Cx40) promoters and its specific DNA binding |
| GO:0001570 vasculogenesis | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | MARK AS OVER ANNOTATED | Summary: ISS transfer from mouse of a vasculogenesis role. Reason: NKX2-5 is a cardiac-restricted TF; vascular (yolk sac) defects in mouse nulls are most plausibly secondary to early cardiac failure. No evidence that NKX2-5 acts directly in vasculogenesis. Supporting Evidence: PMID:7628699 The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function |
| GO:0001947 heart looping | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | ACCEPT | Summary: Heart looping fails in Nkx2-5 null mouse embryos. Reason: Looping morphogenesis is a classic, direct developmental output of NKX2-5 activity in the heart tube; core developmental role. Supporting Evidence: PMID:7628699 looping morphogenesis, a critical determinant of heart form, was not initiated at the linear heart tube stage |
| GO:0003007 heart morphogenesis | ISS GO_REF:0000024 | ACCEPT | Summary: Heart morphogenesis transferred from mouse. Reason: Well established developmental role of NKX2-5. Supporting Evidence: PMID:7628699 The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function |
| GO:0003007 heart morphogenesis | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | ACCEPT | Summary: Heart morphogenesis transferred from mouse. Reason: Well established developmental role of NKX2-5. Supporting Evidence: PMID:7628699 The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function PMID:8900537 Targeted mutation in the mouse gene, Csx/Nkx2.5, arrests cardiac development during early embryonic stages |
| GO:0003148 outflow tract septum morphogenesis | IMP PMID:20807224 New mutations in ZFPM2/FOG2 gene in tetralogy of Fallot and ... | KEEP AS NON CORE | Summary: Human NKX2-5 Arg25Cys variant found in TOF patients; outflow tract septation defects. Reason: Human association data is weak, but NKX2-5 has a genuine role in second heart field/outflow tract development in mouse; non-core relative to its TF activity. Supporting Evidence: PMID:20807224 Mutation analysis also detected one known missense change (Arg25Cys) in NKX2.5 gene in two (1.1%) sporadic patients with TOF PMID:17350578 feedback repression of Bmp2/Smad1 signaling by Nkx2-5 critically regulates SHF proliferation and outflow tract (OFT) morphology |
| GO:0003161 cardiac conduction system development | IMP PMID:15109497 Nkx2-5 pathways and congenital heart disease; loss of ventri... | ACCEPT | Summary: Ventricular-restricted Nkx2-5 knockout causes hypoplastic AV node and progressive heart block. Reason: Conduction system development is a key dosage-sensitive role of NKX2-5, recapitulating human AV block. Supporting Evidence: PMID:15109497 At birth, mutant mice display a hypoplastic atrioventricular (AV) node and then develop selective dropout of these conduction cells PMID:15085192 the number of cells in the cardiac conduction system is directly related to Nkx2-5 gene dosage |
| GO:0003161 cardiac conduction system development | IMP PMID:27207958 Variants of Transient Receptor Potential Melastatin Member 4... | ACCEPT | Summary: Screening of childhood AV block patients identified an NKX2-5 variant (A119S); the paper mainly concerns TRPM4. Reason: Evidence in this paper is limited to a variant finding, but the role of NKX2-5 in conduction system development is well established, so the annotation is accepted. Supporting Evidence: PMID:27207958 A nonsynonymous variant was identified in NKX2.5 (A119S) PMID:15085192 the number of cells in the cardiac conduction system is directly related to Nkx2-5 gene dosage PMID:9651244 These data indicate that NKX2-5 is important for regulation of septation during cardiac morphogenesis and for maturation and maintenance of atrioventricular node function throughout life |
| GO:0003162 atrioventricular node development | IEA GO_REF:0000107 | ACCEPT | Summary: AV node development transferred from mouse. Reason: Nkx2-5 nulls lack the AV node primordium; human mutations cause AV block. Supporting Evidence: PMID:15085192 Null mutant embryos appear to lack the primordium of the atrioventricular node PMID:9651244 These data indicate that NKX2-5 is important for regulation of septation during cardiac morphogenesis and for maturation and maintenance of atrioventricular node function throughout life |
| GO:0003162 atrioventricular node development | ISS GO_REF:0000024 | ACCEPT | Summary: AV node development transferred from mouse. Reason: Nkx2-5 nulls lack the AV node primordium; human mutations cause AV block. Supporting Evidence: PMID:15085192 Null mutant embryos appear to lack the primordium of the atrioventricular node PMID:15109497 At birth, mutant mice display a hypoplastic atrioventricular (AV) node and then develop selective dropout of these conduction cells |
| GO:0003166 bundle of His development | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: His bundle development transferred from mouse. Reason: Nkx2-5 haploinsufficiency halves conduction system cell number including His-Purkinje components; a specific sub-aspect of conduction system development. Supporting Evidence: PMID:15085192 In Nkx2-5 haploinsufficiency, the conduction system has half the normal number of cells |
| GO:0003180 aortic valve morphogenesis | TAS PMID:29325903 GATA4 Loss-of-Function Mutation and the Congenitally Bicuspi... | KEEP AS NON CORE | Summary: Aortic valve morphogenesis (bicuspid aortic valve) attributed to NKX2.5 by author statement. Reason: TAS statement in a GATA4 paper; valve development is a plausible but peripheral role. Supporting Evidence: PMID:29325903 the mutation disrupted the synergistic transcriptional activation between GATA4 and NKX2.5 |
| GO:0003221 right ventricular cardiac muscle tissue morphogenesis | IMP PMID:20807224 New mutations in ZFPM2/FOG2 gene in tetralogy of Fallot and ... | MARK AS OVER ANNOTATED | Summary: Right ventricular myocardium morphogenesis inferred from TOF association. Reason: Right ventricular hypertrophy in TOF is a hemodynamic consequence of outflow obstruction, and the study reports only a rare variant association; this is over-interpretation. Supporting Evidence: PMID:20807224 Mutation analysis also detected one known missense change (Arg25Cys) in NKX2.5 gene in two (1.1%) sporadic patients with TOF |
| GO:0003228 atrial cardiac muscle tissue development | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Atrial cardiac muscle tissue development transferred from mouse. Reason: Downstream developmental phenotype; non-core. Supporting Evidence: PMID:15109497 we generated mice with a ventricular-restricted knockout of Nkx2-5, which display no structural defects but have progressive complete heart block PMID:9651244 These data indicate that NKX2-5 is important for regulation of septation during cardiac morphogenesis and for maturation and maintenance of atrioventricular node function throughout life |
| GO:0003228 atrial cardiac muscle tissue development | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Atrial cardiac muscle tissue development transferred from mouse. Reason: Downstream developmental phenotype; non-core. Supporting Evidence: PMID:9651244 These data indicate that NKX2-5 is important for regulation of septation during cardiac morphogenesis and for maturation and maintenance of atrioventricular node function throughout life |
| GO:0003285 septum secundum development | IMP PMID:10587520 Mutations in the cardiac transcription factor NKX2.5 affect ... | ACCEPT | Summary: Secundum ASD is the hallmark phenotype of NKX2-5 heterozygous mutations. Reason: Human genetic evidence; atrial septation is a defining dosage-sensitive role. Supporting Evidence: PMID:10587520 Associated phenotypes included AV block, which was the primary manifestation of cardiac disease in nearly a quarter of affected individuals, as well as atrial septal defect and ventricular septal defect PMID:9651244 These data indicate that NKX2-5 is important for regulation of septation during cardiac morphogenesis and for maturation and maintenance of atrioventricular node function throughout life |
| GO:0003677 DNA binding | IDA PMID:9858576 Identification of the in vivo casein kinase II phosphorylati... | MODIFY | Summary: NKX2-5 binds NKE/A20 consensus elements; homeodomain phosphorylation increases DNA binding. Reason: DNA binding is correct but uninformative; the evidence (binding to NKE elements of Pol II promoters) supports the sequence-specific Pol II cis-regulatory term. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:9858576 three copies of A20 Csx/Nkx2.5 binding site fused to the cardiac actin minimal promoter and luciferase reporter gene PMID:9858576 the putative nuclear localization signal (NLS) of Csx/Nkx2.5 was identified by site-directed mutagenesis to the amino terminus of the homeodomain |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | MODIFY | Summary: Homeodomain-based IEA DNA binding. Reason: Correct but uninformative; NKX2-5 DNA binding is sequence-specific binding to RNA Pol II cis-regulatory NKE elements. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:22849347 Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif |
| GO:0003682 chromatin binding | IDA PMID:16678093 The transcriptional coactivator CAMTA2 stimulates cardiac gr... | ACCEPT | Summary: Chromatin binding in the CAMTA2 study (ANF promoter context). Reason: Abstract-only; NKX2-5 occupies the ANF promoter with CAMTA2; deferring to curator. Sequence-specific cis-regulatory binding is the more informative description. Supporting Evidence: PMID:16678093 activates the ANF gene, at least in part, by associating with the cardiac homeodomain protein Nkx2-5 |
| GO:0003682 chromatin binding | IEA GO_REF:0000107 | ACCEPT | Summary: Chromatin binding transferred from mouse. Reason: Consistent with promoter occupancy. Supporting Evidence: PMID:19479054 this regulation was conferred by binding of NKX2-5 to specific elements (NKEs) in the promoter region of the beta-catenin and GATA4 genes |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:10948187 Functional analyses of three Csx/Nkx-2.5 mutations that caus... | ACCEPT | Summary: Wild-type NKX2-5 activates the ANP promoter and binds NKE sites; disease mutants lose this. Reason: Core TF activity. Supporting Evidence: PMID:10948187 The atrial natriuretic peptide (ANP) promoter was activated by wild type Csx/Nkx-2.5 (WT, approximately 8-fold) PMID:10948187 Electrophoretic mobility shift assay showed that Csx/Nkx-2.5-binding sequences were bound strongly by WT and C, weakly by B, but not by A |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:11431700 Tbx5 associates with Nkx2-5 and synergistically promotes car... | ACCEPT | Summary: NKX2-5 binds the Nppa promoter in tandem with TBX5 and activates it. Reason: Core TF activity. Supporting Evidence: PMID:11431700 Tbx5 and Nkx2-5 directly bound to the promoter of the gene for cardiac-specific natriuretic peptide precursor type A (Nppa) in tandem, and both transcription factors showed synergistic activation |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:9312027 The cardiac transcription factors Nkx2-5 and GATA-4 are mutu... | ACCEPT | Summary: NKX2-5 and GATA4 act as mutual cofactors in activation of ANF. Reason: contributes_to reflects cooperative activity with GATA4; correct. Supporting Evidence: PMID:9312027 Co-expression of GATA-4 and Nkx2-5 resulted in synergistic activation of the ANF promoter in heterologous cells PMID:9312027 The synergy involves physical Nkx2-5-GATA-4 interaction, seen in vitro and in vivo |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:9858576 Identification of the in vivo casein kinase II phosphorylati... | ACCEPT | Summary: Transactivation of NKE-containing reporters by NKX2-5. Reason: Core TF activity. Supporting Evidence: PMID:9858576 three copies of A20 Csx/Nkx2.5 binding site fused to the cardiac actin minimal promoter and luciferase reporter gene |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000107 | ACCEPT | Summary: TF activity transferred from mouse. Reason: Core TF activity. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 |
| GO:0003700 DNA-binding transcription factor activity | IMP PMID:11431700 Tbx5 associates with Nkx2-5 and synergistically promotes car... | ACCEPT | Summary: Mutant analysis showing TF activity on Nppa. Reason: Core TF activity. Supporting Evidence: PMID:11431700 Tbx5 and Nkx2-5 directly bound to the promoter of the gene for cardiac-specific natriuretic peptide precursor type A (Nppa) in tandem, and both transcription factors showed synergistic activation |
| GO:0005515 protein binding | IPI PMID:10075728 Context-dependent transcriptional cooperation mediated by ca... | MODIFY | Summary: NKX2-5 physically and functionally cooperates with GATA4 on the ANP promoter. Reason: Generic protein binding is uninformative; GATA4 is an RNA Pol II DNA-binding TF, so the informative term is DNA-binding TF binding. Proposed replacements: RNA polymerase II-specific DNA-binding transcription factor binding Supporting Evidence: PMID:10075728 this synergism was dependent on binding of Csx/Nkx-2.5 to NKE2, but not on GATA-4-DNA interactions PMID:9312027 The synergy involves physical Nkx2-5-GATA-4 interaction, seen in vitro and in vivo |
| GO:0005515 protein binding | IPI PMID:11431700 Tbx5 associates with Nkx2-5 and synergistically promotes car... | MODIFY | Summary: NKX2-5 homeodomain binds the TBX5 T-box TF. Reason: Replace generic protein binding with DNA-binding TF binding (TBX5 is a T-box TF). Proposed replacements: RNA polymerase II-specific DNA-binding transcription factor binding Supporting Evidence: PMID:11431700 the N-terminal domain and N-terminal part of the T-box of Tbx5 and the homeodomain of Nkx2-5 were necessary for their interaction |
| GO:0005515 protein binding | IPI PMID:11431700 Tbx5 associates with Nkx2-5 and synergistically promotes car... | MODIFY | Summary: NKX2-5 binds TBX5 isoform 1. Reason: Replace generic protein binding with DNA-binding TF binding. Proposed replacements: RNA polymerase II-specific DNA-binding transcription factor binding Supporting Evidence: PMID:11431700 the N-terminal domain and N-terminal part of the T-box of Tbx5 and the homeodomain of Nkx2-5 were necessary for their interaction |
| GO:0005515 protein binding | IPI PMID:12499378 Functional analysis of TBX5 missense mutations associated wi... | MODIFY | Summary: NKX2-5 interacts with TBX5; Holt-Oram mutants lose the interaction and synergy. Reason: Replace generic protein binding with DNA-binding TF binding. Proposed replacements: RNA polymerase II-specific DNA-binding transcription factor binding Supporting Evidence: PMID:12499378 All seven missense mutations greatly reduced the interaction of TBX5 with NKX2.5 in vivo and in vitro |
| GO:0005515 protein binding | IPI PMID:14757752 A novel LIM protein Cal promotes cardiac differentiation by ... | MODIFY | Summary: NKX2-5 homeodomain binds the LIM protein Cal (FBLIM1), which has transcription-promoting activity and enhances NKX2-5 activation of NPPA. Reason: Cal acts as a coactivator of NKX2-5; transcription coactivator binding is more informative than protein binding. Proposed replacements: transcription coactivator binding Supporting Evidence: PMID:14757752 the LIM domains of Cal and the homeodomain of CSX/NKX2-5 were necessary for mutual binding PMID:14757752 Cal itself possessed the transcription-promoting activity, and cotransfection of Cal enhanced CSX/NKX2-5-induced activation of atrial natriuretic peptide gene promoter |
| GO:0005515 protein binding | IPI PMID:18579533 Regulation of cardiac specific nkx2.5 gene activity by small... | REMOVE | Summary: NKX2-5 is SUMOylated by PIAS1; interaction is enzyme-substrate. Reason: Generic protein binding is uninformative; the interaction reflects NKX2-5 being a substrate of the SUMO E3 ligase rather than an NKX2-5 activity. The interaction itself is not disputed. Supporting Evidence: PMID:18579533 E3 ligase PIAS proteins PIAS1, PIASx, and PIASy, but not PIAS3, enhanced SUMO-1 attachment to Nkx2.5 on the primary SUMO acceptor site |
| GO:0005515 protein binding | IPI PMID:19797053 Myocardin-dependent activation of the CArG box-rich smooth m... | REMOVE | Summary: NKX2-5 interacts with MYOCD but without functional cooperation at the ACTG2 promoter. Reason: Generic protein binding is uninformative and the paper reports no functional consequence; removal does not dispute the interaction. Supporting Evidence: PMID:19797053 no such functional relationship is evident with the related NKX2.5 transcription factor despite its interaction with MYOCD |
| GO:0005515 protein binding | IPI PMID:26926761 Intermolecular Interactions of Cardiac Transcription Factors... | MODIFY | Summary: Crystal structure shows direct NKX2-5-TBX5 contacts on DNA. Reason: Replace generic protein binding with DNA-binding TF binding. Proposed replacements: RNA polymerase II-specific DNA-binding transcription factor binding Supporting Evidence: PMID:26926761 The ternary complex structure of NKX2.5 and TBX5 with the target DNA shows physical interactions between the two proteins through Lys158 (NKX2.5) |
| GO:0005515 protein binding | IPI PMID:29899023 NEDD9 targets COL3A1 to promote endothelial fibrosis and pul... | REMOVE | Summary: NKX2-5 forms a complex with NEDD9 in pulmonary artery endothelial cells. Reason: Generic protein binding is uninformative; NEDD9 is a scaffold protein and no specific molecular function of NKX2-5 is defined by this interaction. Supporting Evidence: PMID:29899023 increased NEDD9 complex formation with Nk2 homeobox 5 (NKX2-5), and increased NKX2-5 binding to COL3A1 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: High-throughput Y2H interaction with SHOX isoform (HuRI). Reason: Generic protein binding from a binary interactome screen without functional follow-up is uninformative; removal does not mean the interaction is false. Supporting Evidence: PMID:32296183 yeast two-hybrid (Y2H) represents the only binary PPI assay that can be operated at sufficient throughput to systematically screen the human proteome for binary PPIs |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: High-throughput Y2H interaction with TRIP10 isoform (HuRI). Reason: Generic protein binding from a binary interactome screen without functional follow-up is uninformative; removal does not mean the interaction is false. Supporting Evidence: PMID:32296183 yeast two-hybrid (Y2H) represents the only binary PPI assay that can be operated at sufficient throughput to systematically screen the human proteome for binary PPIs |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: High-throughput Y2H interaction with KRTAP8-1 (HuRI). Reason: Generic protein binding from a binary interactome screen without functional follow-up is uninformative; removal does not mean the interaction is false. Supporting Evidence: PMID:32296183 yeast two-hybrid (Y2H) represents the only binary PPI assay that can be operated at sufficient throughput to systematically screen the human proteome for binary PPIs |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: High-throughput Y2H interaction with RBPMS isoform (HuRI). Reason: Generic protein binding from a binary interactome screen without functional follow-up is uninformative; removal does not mean the interaction is false. Supporting Evidence: PMID:32296183 yeast two-hybrid (Y2H) represents the only binary PPI assay that can be operated at sufficient throughput to systematically screen the human proteome for binary PPIs |
| GO:0005515 protein binding | IPI PMID:9312027 The cardiac transcription factors Nkx2-5 and GATA-4 are mutu... | MODIFY | Summary: NKX2-5 binds GATA4 (C-terminal zinc finger) via its extended homeodomain. Reason: Replace generic protein binding with DNA-binding TF binding. Proposed replacements: RNA polymerase II-specific DNA-binding transcription factor binding Supporting Evidence: PMID:9312027 a C-terminally extended homeodomain of Nkx2-5 is required for GATA-4 binding PMID:9312027 The synergy involves physical Nkx2-5-GATA-4 interaction, seen in vitro and in vivo |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear localization inferred phylogenetically. Reason: NKX2-5 is a nuclear TF. Supporting Evidence: PMID:10948187 transfected Myc-tagged WT, B, and C were localized in the nucleus of both COS-7 cells and cardiomyocytes of neonatal rats |
| GO:0005634 nucleus | IDA PMID:10948187 Functional analyses of three Csx/Nkx-2.5 mutations that caus... | ACCEPT | Summary: Wild-type NKX2-5 localizes to the nucleus of COS-7 cells and cardiomyocytes. Reason: Direct evidence. Supporting Evidence: PMID:10948187 transfected Myc-tagged WT, B, and C were localized in the nucleus of both COS-7 cells and cardiomyocytes of neonatal rats |
| GO:0005634 nucleus | IDA PMID:29899023 NEDD9 targets COL3A1 to promote endothelial fibrosis and pul... | ACCEPT | Summary: Nuclear NKX2-5 in endothelial cells. Reason: Consistent with TF function; UniProt cites this paper for nuclear location. Supporting Evidence: PMID:29899023 increased NEDD9 complex formation with Nk2 homeobox 5 (NKX2-5), and increased NKX2-5 binding to COL3A1 |
| GO:0005634 nucleus | IDA PMID:9858576 Identification of the in vivo casein kinase II phosphorylati... | ACCEPT | Summary: NLS at the homeodomain N-terminus mediates nuclear localization. Reason: Direct evidence. Supporting Evidence: PMID:9858576 the putative nuclear localization signal (NLS) of Csx/Nkx2.5 was identified by site-directed mutagenesis to the amino terminus of the homeodomain |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Nucleus (IEA). Reason: Correct. Supporting Evidence: PMID:10948187 transfected Myc-tagged WT, B, and C were localized in the nucleus of both COS-7 cells and cardiomyocytes of neonatal rats |
| GO:0005654 nucleoplasm | IDA GO_REF:0000052 | ACCEPT | Summary: HPA immunofluorescence nucleoplasm localization. Reason: Consistent with nuclear TF function. Supporting Evidence: PMID:10948187 transfected Myc-tagged WT, B, and C were localized in the nucleus of both COS-7 cells and cardiomyocytes of neonatal rats |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-9735143 | ACCEPT | Summary: Reactome: NKX2-5 binds the GATA4 gene in the nucleoplasm. Reason: Correct location of action. Supporting Evidence: Reactome:R-HSA-9735143 NKX2-5 binds sites (called NKE sites) in the promoter upstream of the first exon of GATA4 in embryonic hearts |
| GO:0005667 transcription regulator complex | IC PMID:9312027 The cardiac transcription factors Nkx2-5 and GATA-4 are mutu... | ACCEPT | Summary: NKX2-5 forms a transcription regulatory complex with GATA4. Reason: Supported by the mutual cofactor data. Supporting Evidence: PMID:9312027 The synergy involves physical Nkx2-5-GATA-4 interaction, seen in vitro and in vivo |
| GO:0005667 transcription regulator complex | IEA GO_REF:0000107 | ACCEPT | Summary: Transcription regulator complex transferred from mouse. Reason: Consistent with GATA4/TBX5 complexes. Supporting Evidence: PMID:26926761 Here we report a crystal structure of human NKX2.5 and TBX5 DNA binding domains in a complex with a 19 bp target DNA |
| GO:0005737 cytoplasm | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Cytoplasm transferred from mouse. Reason: NKX2-5 is a nuclear TF; cytoplasmic pools are observed mainly with NLS or disease mutants, not as a site of function. Supporting Evidence: PMID:9858576 When the putative NLS of Csx/Nkx2.5 was mutated a significant amount of the cytoplasmically localized Csx/Nkx2.5 was unphosphorylated PMID:10948187 transfected Myc-tagged WT, B, and C were localized in the nucleus of both COS-7 cells and cardiomyocytes of neonatal rats |
| GO:0006355 regulation of DNA-templated transcription | IDA PMID:22849347 Crystal structure of the human NKX2.5 homeodomain in complex... | ACCEPT | Summary: Regulation of transcription supported by structural/DNA-binding data. Reason: Correct, general. Supporting Evidence: PMID:22849347 crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | ACCEPT | Summary: Regulation of transcription (InterPro). Reason: Correct, general. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: Regulation of transcription by RNA Pol II (IBA). Reason: Core process at the right level. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 PMID:19479054 the identified NKX2-5 binding sites were essential for the suppression of beta-catenin, and upregulation of GATA4 by NKX2-5 |
| GO:0007512 adult heart development | IMP PMID:9651244 Congenital heart disease caused by mutations in the transcri... | KEEP AS NON CORE | Summary: Human mutations indicate a role in maintaining AV node function throughout life. Reason: Adult maintenance is a secondary aspect of NKX2-5 function. Supporting Evidence: PMID:9651244 These data indicate that NKX2-5 is important for regulation of septation during cardiac morphogenesis and for maturation and maintenance of atrioventricular node function throughout life |
| GO:0008284 positive regulation of cell population proliferation | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | MARK AS OVER ANNOTATED | Summary: Positive regulation of cell proliferation transferred from mouse. Reason: Effects of NKX2-5 on proliferation are context dependent (feedback repression of Bmp2/Smad1 in SHF; repression of p15 in spleen) and indirect. Supporting Evidence: PMID:17350578 feedback repression of Bmp2/Smad1 signaling by Nkx2-5 critically regulates SHF proliferation and outflow tract (OFT) morphology PMID:22560297 This study establishes that a Pbx/Nkx2-5/p15 regulatory module is essential for spleen development |
| GO:0010628 positive regulation of gene expression | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Positive regulation of gene expression (IEA). Reason: Very general; better captured by positive regulation of transcription by RNA Pol II. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 |
| GO:0010667 negative regulation of cardiac muscle cell apoptotic process | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Anti-apoptotic role in cardiomyocytes transferred from mouse. Reason: Supported by transgenic data; non-core. Supporting Evidence: PMID:11889119 Overexpression of the dominant negative mutant of Csx/Nkx2-5 induced apoptosis in cultured cardiomyocytes, while expression of wild type Csx/Nkx2-5 protected cardiomyocytes from doxorubicin-induced apoptotic death |
| GO:0010667 negative regulation of cardiac muscle cell apoptotic process | IMP PMID:11889119 Csx/Nkx2-5 is required for homeostasis and survival of cardi... | KEEP AS NON CORE | Summary: Dominant-negative Nkx2-5 induces cardiomyocyte apoptosis; wild-type protects. Reason: Real but indirect, non-core role. Supporting Evidence: PMID:11889119 Overexpression of the dominant negative mutant of Csx/Nkx2-5 induced apoptosis in cultured cardiomyocytes, while expression of wild type Csx/Nkx2-5 protected cardiomyocytes from doxorubicin-induced apoptotic death |
| GO:0010765 positive regulation of sodium ion transport | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Positive regulation of sodium ion transport transferred from mouse. Reason: Likely reflects indirect effects on conduction-system gene expression; NKX2-5 does not directly regulate ion transport. Supporting Evidence: PMID:15085192 the number of cells in the cardiac conduction system is directly related to Nkx2-5 gene dosage |
| GO:0010765 positive regulation of sodium ion transport | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | MARK AS OVER ANNOTATED | Summary: Positive regulation of sodium ion transport (ISS). Reason: Indirect downstream effect. Supporting Evidence: PMID:15085192 the number of cells in the cardiac conduction system is directly related to Nkx2-5 gene dosage |
| GO:0010832 negative regulation of myotube differentiation | IMP PMID:15653675 CSX/Nkx2.5 modulates differentiation of skeletal myoblasts a... | MARK AS OVER ANNOTATED | Summary: Ectopic NKX2-5 overexpression in C2C12 myoblasts inhibits myotube formation. Reason: Gain-of-function in a non-native cell type; not a physiological role of NKX2-5. Supporting Evidence: PMID:15653675 The expression of human NKX2.5 in C2C12 myoblasts inhibited myocyte differentiation and myotube formation, and up-regulated Gata4 and Tbx5 expression |
| GO:0030097 hemopoiesis | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | MARK AS OVER ANNOTATED | Summary: Hemopoiesis transferred from mouse. Reason: NKX2-5 expression is heart/spleen restricted; no direct evidence for a hematopoietic role in human. Supporting Evidence: PMID:8900537 Targeted mutation in the mouse gene, Csx/Nkx2.5, arrests cardiac development during early embryonic stages |
| GO:0030154 cell differentiation | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Cell differentiation (IBA). Reason: Revised from ACCEPT for consistency with the mouse Nkx2-5 review (ortholog audit 2026-10-12). The IBA node (PTN000678271, NK-2 class homeobox TFs) is soundly placed and the term is correct, but it is a very general parent of the specific core process already captured (cardiac muscle cell differentiation), so it is kept as non-core rather than accepted as a core annotation. Supporting Evidence: PMID:11431700 These results indicate that two different types of cardiac transcription factors synergistically induce cardiac development |
| GO:0030154 cell differentiation | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | KEEP AS NON CORE | Summary: Cell differentiation (ISS). Reason: Revised from ACCEPT for consistency with the mouse Nkx2-5 review (ortholog audit 2026-10-12); correct but very general, with the specific core process captured by cardiac muscle cell differentiation. Supporting Evidence: PMID:11431700 These results indicate that two different types of cardiac transcription factors synergistically induce cardiac development |
| GO:0030878 thyroid gland development | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Thyroid gland development transferred from mouse. Reason: Real non-cardiac role. Supporting Evidence: PMID:16418214 Our results indicate that Nkx2-5(-/-) embryos exhibit thyroid bud hypoplasia, providing evidence that NKX2-5 plays a role in thyroid organogenesis |
| GO:0030878 thyroid gland development | IMP PMID:16418214 Missense mutation in the transcription factor NKX2-5: a nove... | KEEP AS NON CORE | Summary: Nkx2-5 null embryos show thyroid bud hypoplasia; human mutations in thyroid dysgenesis. Reason: Real non-cardiac role. Supporting Evidence: PMID:16418214 Our results indicate that Nkx2-5(-/-) embryos exhibit thyroid bud hypoplasia, providing evidence that NKX2-5 plays a role in thyroid organogenesis PMID:16418214 Functional characterization of the three mutations demonstrated reduced DNA binding and/or transactivation properties |
| GO:0032991 protein-containing complex | IDA PMID:26926761 Intermolecular Interactions of Cardiac Transcription Factors... | MODIFY | Summary: NKX2-5/TBX5 complex on DNA (crystal structure). Reason: protein-containing complex is too general; the structure is a protein-DNA complex. Proposed replacements: protein-DNA complex Supporting Evidence: PMID:26926761 Here we report a crystal structure of human NKX2.5 and TBX5 DNA binding domains in a complex with a 19 bp target DNA |
| GO:0032993 protein-DNA complex | IDA PMID:22849347 Crystal structure of the human NKX2.5 homeodomain in complex... | ACCEPT | Summary: NKX2-5 homeodomain-DNA complex crystal structure. Reason: Direct structural evidence. Supporting Evidence: PMID:22849347 crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene |
| GO:0035050 embryonic heart tube development | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | ACCEPT | Summary: Embryonic heart tube development transferred from mouse. Reason: Heart tube looping/maturation requires Nkx2-5. Supporting Evidence: PMID:7628699 looping morphogenesis, a critical determinant of heart form, was not initiated at the linear heart tube stage |
| GO:0042803 protein homodimerization activity | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Protein homodimerization transferred from mouse, where Csx/Nkx2.5 was shown to homodimerize through its homeodomain in vitro and in cells (Kasahara et al. 2001). Reason: The mouse ortholog (identical homeodomain) homodimerizes experimentally, so the transfer is reasonable. It is not core - the human HD-DNA crystal structure on a tandem NKE site shows two homeodomains bound without contacting each other, so homodimerization is not required for every mode of DNA binding and its functional weight is uncertain. Supporting Evidence: PMID:11042197 Csx/Nkx2.5 physically interacts with each other in vitro as well as in cells, and the HD is critical for homodimerization PMID:22849347 NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves |
| GO:0043066 negative regulation of apoptotic process | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | KEEP AS NON CORE | Summary: Negative regulation of apoptosis (ISS). Reason: Consistent with cardiomyocyte survival role; non-core. Supporting Evidence: PMID:11889119 Overexpression of the dominant negative mutant of Csx/Nkx2-5 induced apoptosis in cultured cardiomyocytes, while expression of wild type Csx/Nkx2-5 protected cardiomyocytes from doxorubicin-induced apoptotic death |
| GO:0043565 sequence-specific DNA binding | IDA PMID:10948187 Functional analyses of three Csx/Nkx-2.5 mutations that caus... | ACCEPT | Summary: EMSA shows sequence-specific binding of NKX2-5 to NKE sites. Reason: Core. Supporting Evidence: PMID:10948187 Electrophoretic mobility shift assay showed that Csx/Nkx-2.5-binding sequences were bound strongly by WT and C, weakly by B, but not by A |
| GO:0045666 positive regulation of neuron differentiation | IMP PMID:15653675 CSX/Nkx2.5 modulates differentiation of skeletal myoblasts a... | MARK AS OVER ANNOTATED | Summary: Ectopic NKX2-5 in myoblasts induces neuron-like cells. Reason: Overexpression artefact in a non-native cell type; no physiological neuronal role. Supporting Evidence: PMID:15653675 overexpression of NKX2.5 in C2C12 cells and primary cultures of human fetal myoblasts led to differentiation of myoblasts into neuron-like cells and expression of neuronal markers |
| GO:0045823 positive regulation of heart contraction | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Positive regulation of heart contraction (IEA). Reason: Physiological downstream consequence of cardiac development, not a direct NKX2-5 activity. Supporting Evidence: PMID:7628699 The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function |
| GO:0045823 positive regulation of heart contraction | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Positive regulation of heart contraction (ISS). Reason: Indirect. Supporting Evidence: PMID:7628699 The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function |
| GO:0045892 negative regulation of DNA-templated transcription | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | ACCEPT | Summary: Negative regulation of transcription (ISS). Reason: NKX2-5 is a context-dependent repressor. Supporting Evidence: PMID:10075728 Csx/Nkx-2.5 reduced the GATA-4-induced transactivation of the GATA-4-dependent promoters |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:11431700 Tbx5 associates with Nkx2-5 and synergistically promotes car... | ACCEPT | Summary: Activation of Nppa together with TBX5. Reason: Correct. Supporting Evidence: PMID:11431700 Tbx5 and Nkx2-5 directly bound to the promoter of the gene for cardiac-specific natriuretic peptide precursor type A (Nppa) in tandem, and both transcription factors showed synergistic activation |
| GO:0045893 positive regulation of DNA-templated transcription | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | ACCEPT | Summary: Positive regulation of transcription (ISS). Reason: Correct. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IDA PMID:10948187 Functional analyses of three Csx/Nkx-2.5 mutations that caus... | ACCEPT | Summary: NKX2-5 activates RNA Pol II target genes (e.g. NPPA, GATA4, miR-143/145, MEF2C, COL3A1). Reason: Core biological process directly executed by NKX2-5 as a DNA-binding activator. Supporting Evidence: PMID:10948187 The atrial natriuretic peptide (ANP) promoter was activated by wild type Csx/Nkx-2.5 (WT, approximately 8-fold) |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IDA PMID:19578358 miR-145 and miR-143 regulate smooth muscle cell fate and pla... | ACCEPT | Summary: NKX2-5 activates RNA Pol II target genes (e.g. NPPA, GATA4, miR-143/145, MEF2C, COL3A1). Reason: Core biological process directly executed by NKX2-5 as a DNA-binding activator. Supporting Evidence: PMID:19578358 miR-145 and miR-143 were direct transcriptional targets of serum response factor, myocardin and Nkx2-5 |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IDA PMID:29325903 GATA4 Loss-of-Function Mutation and the Congenitally Bicuspi... | ACCEPT | Summary: NKX2-5 activates RNA Pol II target genes (e.g. NPPA, GATA4, miR-143/145, MEF2C, COL3A1). Reason: Core biological process directly executed by NKX2-5 as a DNA-binding activator. Supporting Evidence: PMID:29325903 the mutation disrupted the synergistic transcriptional activation between GATA4 and NKX2.5 |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IGI PMID:16678093 The transcriptional coactivator CAMTA2 stimulates cardiac gr... | ACCEPT | Summary: NKX2-5 activates RNA Pol II target genes (e.g. NPPA, GATA4, miR-143/145, MEF2C, COL3A1). Reason: Core biological process directly executed by NKX2-5 as a DNA-binding activator. Supporting Evidence: PMID:16678093 activates the ANF gene, at least in part, by associating with the cardiac homeodomain protein Nkx2-5 |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IMP PMID:11431700 Tbx5 associates with Nkx2-5 and synergistically promotes car... | ACCEPT | Summary: NKX2-5 activates RNA Pol II target genes (e.g. NPPA, GATA4, miR-143/145, MEF2C, COL3A1). Reason: Core biological process directly executed by NKX2-5 as a DNA-binding activator. Supporting Evidence: PMID:11431700 Tbx5 and Nkx2-5 directly bound to the promoter of the gene for cardiac-specific natriuretic peptide precursor type A (Nppa) in tandem, and both transcription factors showed synergistic activation |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IMP PMID:15649947 Common arterial trunk associated with a homeodomain mutation... | ACCEPT | Summary: NKX2-5 activates RNA Pol II target genes (e.g. NPPA, GATA4, miR-143/145, MEF2C, COL3A1). Reason: Core biological process directly executed by NKX2-5 as a DNA-binding activator. Supporting Evidence: PMID:15649947 Introduction of F157L into human NKX2.5 substantially reduced its transcription activating function, its synergism with partners at the atrial natriuretic factor (ANF) and connexin-40 (Cx40) promoters and its specific DNA binding |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IMP PMID:18079734 MEF2C is activated by multiple mechanisms in a subset of T-a... | ACCEPT | Summary: NKX2-5 activates RNA Pol II target genes (e.g. NPPA, GATA4, miR-143/145, MEF2C, COL3A1). Reason: Core biological process directly executed by NKX2-5 as a DNA-binding activator. Supporting Evidence: PMID:18079734 Knockdown and overexpression assays confirmed MEF2C activation by NKX2-5 at both the RNA and protein levels |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IMP PMID:19479054 NKX2-5 regulates the expression of beta-catenin and GATA4 in... | ACCEPT | Summary: NKX2-5 activates RNA Pol II target genes (e.g. NPPA, GATA4, miR-143/145, MEF2C, COL3A1). Reason: Core biological process directly executed by NKX2-5 as a DNA-binding activator. Supporting Evidence: PMID:19479054 the identified NKX2-5 binding sites were essential for the suppression of beta-catenin, and upregulation of GATA4 by NKX2-5 |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IMP PMID:29899023 NEDD9 targets COL3A1 to promote endothelial fibrosis and pul... | ACCEPT | Summary: NKX2-5 activates RNA Pol II target genes (e.g. NPPA, GATA4, miR-143/145, MEF2C, COL3A1). Reason: Core biological process directly executed by NKX2-5 as a DNA-binding activator. Supporting Evidence: PMID:29899023 increased NEDD9 complex formation with Nk2 homeobox 5 (NKX2-5), and increased NKX2-5 binding to COL3A1 |
| GO:0045944 positive regulation of transcription by RNA polymerase II | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | ACCEPT | Summary: NKX2-5 activates RNA Pol II target genes (e.g. NPPA, GATA4, miR-143/145, MEF2C, COL3A1). Reason: Core biological process directly executed by NKX2-5 as a DNA-binding activator. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 |
| GO:0048536 spleen development | IMP PMID:22560297 Congenital asplenia in mice and humans with mutations in a P... | ACCEPT | Summary: Pbx/Nkx2-5/p15 module essential for spleen development; human asplenia mutation. Reason: Revised from KEEP_AS_NON_CORE for consistency with the mouse Nkx2-5 review (ortholog audit 2026-10-12). Spleen development is a second, genetically established organ program of NKX2-5 rather than a pleiotropic side effect - Nkx2-5 is a direct effector of Pbx1 in splenic mesenchyme, and a human NKX2-5 missense allele (P236H) segregates with isolated congenital asplenia - so it is accepted and captured as a core function, as in mouse. Supporting Evidence: PMID:22560297 This study establishes that a Pbx/Nkx2-5/p15 regulatory module is essential for spleen development PMID:22560297 we identify a heterozygous missense mutation (P236H) in NKX2-5 showing reduced transactivation in vitro |
| GO:0048536 spleen development | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | ACCEPT | Summary: Spleen development transferred from mouse. Reason: Revised from KEEP_AS_NON_CORE for consistency with the mouse Nkx2-5 review (ortholog audit 2026-10-12); transfer from the 1:1 mouse ortholog is supported by the human asplenia allele (PMID:22560297). Supporting Evidence: PMID:22560297 This study establishes that a Pbx/Nkx2-5/p15 regulatory module is essential for spleen development |
| GO:0051891 positive regulation of cardioblast differentiation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Positive regulation of cardioblast differentiation (IEA). Reason: NKX2-5 promotes cardiomyocyte differentiation but also limits progenitor specification via Bmp2/Smad1 feedback; non-core. Supporting Evidence: PMID:11431700 These results indicate that two different types of cardiac transcription factors synergistically induce cardiac development PMID:17350578 leading initially to progenitor overspecification, but subsequently to failed SHF proliferation and OFT truncation |
| GO:0051891 positive regulation of cardioblast differentiation | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | KEEP AS NON CORE | Summary: Positive regulation of cardioblast differentiation (ISS). Reason: As above. Supporting Evidence: PMID:11431700 These results indicate that two different types of cardiac transcription factors synergistically induce cardiac development |
| GO:0055007 cardiac muscle cell differentiation | IEA GO_REF:0000107 | ACCEPT | Summary: Cardiac muscle cell differentiation (IEA). Reason: NKX2-5 with TBX5 promotes cardiomyocyte differentiation; ventricular MLC2v requires Nkx2-5. Supporting Evidence: PMID:11431700 These results indicate that two different types of cardiac transcription factors synergistically induce cardiac development PMID:7628699 the myosin light-chain 2V gene (MLC2V) was not expressed in mutant hearts nor in mutant ES cell-derived cardiocytes |
| GO:0055008 cardiac muscle tissue morphogenesis | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Cardiac muscle tissue morphogenesis. Reason: Downstream developmental phenotype; core process is captured by heart looping/septation/differentiation terms. Supporting Evidence: PMID:7628699 The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function |
| GO:0055008 cardiac muscle tissue morphogenesis | IMP PMID:11889119 Csx/Nkx2-5 is required for homeostasis and survival of cardi... | KEEP AS NON CORE | Summary: Cardiac muscle tissue morphogenesis. Reason: Downstream developmental phenotype; core process is captured by heart looping/septation/differentiation terms. Supporting Evidence: PMID:11889119 Csx/Nkx2-5 plays a critical role in maintaining highly differentiated cardiac phenotype |
| GO:0055008 cardiac muscle tissue morphogenesis | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Cardiac muscle tissue morphogenesis. Reason: Downstream developmental phenotype; core process is captured by heart looping/septation/differentiation terms. Supporting Evidence: PMID:7628699 The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function |
| GO:0055013 cardiac muscle cell development | IEA GO_REF:0000107 | ACCEPT | Summary: Cardiac muscle cell development (IEA). Reason: Supported by loss of ventricular myogenic specialization in nulls. Supporting Evidence: PMID:7628699 the myosin light-chain 2V gene (MLC2V) was not expressed in mutant hearts nor in mutant ES cell-derived cardiocytes |
| GO:0055013 cardiac muscle cell development | ISS GO_REF:0000024 | ACCEPT | Summary: Cardiac muscle cell development (ISS). Reason: As above. Supporting Evidence: PMID:7628699 the myosin light-chain 2V gene (MLC2V) was not expressed in mutant hearts nor in mutant ES cell-derived cardiocytes |
| GO:0055014 atrial cardiac muscle cell development | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | KEEP AS NON CORE | Summary: Atrial cardiac muscle cell development (ISS). Reason: Non-core. Supporting Evidence: PMID:15109497 we generated mice with a ventricular-restricted knockout of Nkx2-5, which display no structural defects but have progressive complete heart block |
| GO:0055015 ventricular cardiac muscle cell development | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | ACCEPT | Summary: Ventricular cardiac muscle cell development (ISS). Reason: Nkx2-5 required for ventricular myocyte specialization (MLC2v, trabecular/conduction lineage). Supporting Evidence: PMID:7628699 the myosin light-chain 2V gene (MLC2V) was not expressed in mutant hearts nor in mutant ES cell-derived cardiocytes |
| GO:0055117 regulation of cardiac muscle contraction | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Regulation of cardiac muscle contraction (IEA). Reason: Indirect physiological consequence. Supporting Evidence: PMID:7628699 The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function |
| GO:0055117 regulation of cardiac muscle contraction | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | MARK AS OVER ANNOTATED | Summary: Regulation of cardiac muscle contraction (ISS). Reason: Indirect physiological consequence. Supporting Evidence: PMID:7628699 The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function |
| GO:0060037 pharyngeal system development | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | KEEP AS NON CORE | Summary: Pharyngeal system development (ISS). Reason: Related to thyroid/pharyngeal endoderm roles; non-core. Supporting Evidence: PMID:16418214 Our results indicate that Nkx2-5(-/-) embryos exhibit thyroid bud hypoplasia, providing evidence that NKX2-5 plays a role in thyroid organogenesis |
| GO:0060261 positive regulation of transcription initiation by RNA polymerase II | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Positive regulation of transcription initiation by RNA Pol II (IEA). Reason: No specific evidence for an initiation step; positive regulation of transcription by RNA Pol II is the preferred term. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 |
| GO:0060261 positive regulation of transcription initiation by RNA polymerase II | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | KEEP AS NON CORE | Summary: Positive regulation of transcription initiation by RNA Pol II (ISS). Reason: As above. Supporting Evidence: PMID:10075728 Deletion and mutational analyses of the ANP promoter revealed that the Csx/Nkx-2.5-binding element (NKE2) located at -240 was required for high level transactivation by Csx/Nkx-2.5 |
| GO:0060411 cardiac septum morphogenesis | IEA GO_REF:0000107 | ACCEPT | Summary: Cardiac septum morphogenesis (IEA). Reason: Septal defects are a hallmark of NKX2-5 mutations. Supporting Evidence: PMID:9651244 These data indicate that NKX2-5 is important for regulation of septation during cardiac morphogenesis and for maturation and maintenance of atrioventricular node function throughout life |
| GO:0060412 ventricular septum morphogenesis | IMP PMID:10587520 Mutations in the cardiac transcription factor NKX2.5 affect ... | ACCEPT | Summary: VSD in NKX2-5 mutation carriers. Reason: Human genetic evidence. Supporting Evidence: PMID:10587520 Associated phenotypes included AV block, which was the primary manifestation of cardiac disease in nearly a quarter of affected individuals, as well as atrial septal defect and ventricular septal defect |
| GO:0060412 ventricular septum morphogenesis | IMP PMID:20807224 New mutations in ZFPM2/FOG2 gene in tetralogy of Fallot and ... | ACCEPT | Summary: VSD as part of TOF in an NKX2.5 variant carrier. Reason: Association evidence in this paper is weak, but ventricular septal defects are an established consequence of NKX2-5 variants (VSD3). Supporting Evidence: PMID:20807224 Mutation analysis also detected one known missense change (Arg25Cys) in NKX2.5 gene in two (1.1%) sporadic patients with TOF PMID:10587520 Ventricular septal defect was associated with tetralogy of Fallot or double-outlet right ventricle in 3 individuals |
| GO:0060413 atrial septum morphogenesis | IMP PMID:10587520 Mutations in the cardiac transcription factor NKX2.5 affect ... | ACCEPT | Summary: ASD in NKX2-5 mutation carriers. Reason: Hallmark phenotype. Supporting Evidence: PMID:10587520 Associated phenotypes included AV block, which was the primary manifestation of cardiac disease in nearly a quarter of affected individuals, as well as atrial septal defect and ventricular septal defect |
| GO:0060413 atrial septum morphogenesis | IMP PMID:9651244 Congenital heart disease caused by mutations in the transcri... | ACCEPT | Summary: NKX2-5 mutations cause ASD; regulation of septation. Reason: Hallmark phenotype. Supporting Evidence: PMID:9651244 These data indicate that NKX2-5 is important for regulation of septation during cardiac morphogenesis and for maturation and maintenance of atrioventricular node function throughout life |
| GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding | IPI PMID:11431700 Tbx5 associates with Nkx2-5 and synergistically promotes car... | ACCEPT | Summary: NKX2-5 binds the TBX5 TF. Reason: Informative MF for combinatorial TF partnership. Supporting Evidence: PMID:11431700 the N-terminal domain and N-terminal part of the T-box of Tbx5 and the homeodomain of Nkx2-5 were necessary for their interaction |
| GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding | IPI PMID:9858576 Identification of the in vivo casein kinase II phosphorylati... | ACCEPT | Summary: NKX2-5 binds GATA4. Reason: Informative MF for combinatorial TF partnership. Supporting Evidence: PMID:9858576 Mutant Csx/Nkx2.5 163S-A and wild-type Csx/Nkx2.5 associated equally with GST-GATA4 |
| GO:0090090 negative regulation of canonical Wnt signaling pathway | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Negative regulation of canonical Wnt signaling (IEA). Reason: NKX2-5 represses CTNNB1 transcription; indirect effect on Wnt pathway. Supporting Evidence: PMID:19479054 the identified NKX2-5 binding sites were essential for the suppression of beta-catenin, and upregulation of GATA4 by NKX2-5 |
| GO:0090090 negative regulation of canonical Wnt signaling pathway | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Negative regulation of canonical Wnt signaling (ISS). Reason: As above. Supporting Evidence: PMID:19479054 Down-regulation of NKX2-5 resulted in increased beta-catenin while GATA4 was decreased |
| GO:0090575 RNA polymerase II transcription regulator complex | IDA PMID:9312027 The cardiac transcription factors Nkx2-5 and GATA-4 are mutu... | ACCEPT | Summary: NKX2-5/GATA4 RNA Pol II transcription regulator complex. Reason: Correct. Supporting Evidence: PMID:9312027 The synergy involves physical Nkx2-5-GATA-4 interaction, seen in vitro and in vivo |
| GO:1903779 regulation of cardiac conduction | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Regulation of cardiac conduction (IEA). Reason: Reflects conduction system development/maintenance; non-core. Supporting Evidence: PMID:9651244 These data indicate that NKX2-5 is important for regulation of septation during cardiac morphogenesis and for maturation and maintenance of atrioventricular node function throughout life |
| GO:1903779 regulation of cardiac conduction | ISS PMID:8900537 Molecular cloning, chromosomal mapping, and characterization... | KEEP AS NON CORE | Summary: Regulation of cardiac conduction (ISS). Reason: As above. Supporting Evidence: PMID:9651244 These data indicate that NKX2-5 is important for regulation of septation during cardiac morphogenesis and for maturation and maintenance of atrioventricular node function throughout life |
| GO:1990664 Nkx-2.5 complex | IPI PMID:22849347 Crystal structure of the human NKX2.5 homeodomain in complex... | ACCEPT | Summary: Nkx-2.5 complex: NKX2-5 homeodomains bound to the ANF promoter element. Reason: Supported by crystal structure. Supporting Evidence: PMID:22849347 NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves |
| GO:1990837 sequence-specific double-stranded DNA binding | IDA PMID:28473536 Impact of cytosine methylation on DNA binding specificities ... | ACCEPT | Summary: NKX2-5 included in methyl-SELEX profiling of human TFs. Reason: Sequence-specific dsDNA binding; correct. Supporting Evidence: PMID:28473536 By analysis of 542 human TFs with methylation-sensitive SELEX |
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Download this section (compressed HTML)Q: Which NKX2-5 target genes in the atrioventricular node and conduction system mediate the dosage-sensitive recruitment/retention of conduction myocytes, and are they direct NKE-bound targets?
Q: Does human NKX2-5 form functionally relevant homodimers on DNA, given that the homeodomain-DNA crystal structure shows no direct contact between the two bound homeodomains?
Q: Is the NKX2-5 activity in non-cardiac contexts (pulmonary endothelium, T-ALL) physiological or a consequence of ectopic expression, and should such contexts be represented in GO?
Experiment: Perform CUT&RUN for NKX2-5 together with GATA4 and TBX5 in isogenic wild-type and NKX2-5 heterozygous human iPSC-derived atrial and AV-node-like cardiomyocytes, integrated with ATAC-seq and RNA-seq.
Hypothesis: NKX2-5 haploinsufficiency reduces occupancy at a subset of low-affinity NKE-containing enhancers controlling AV node and atrial septum genes.
Type: genome-wide DNA-binding and transcriptomic profiling
Experiment: Quantify DNA binding (EMSA/SELEX), partner binding (co-IP, BLI) and synergistic reporter activation for a panel of patient variants, and rescue assays in NKX2-5 null iPSC-cardiomyocytes.
Hypothesis: Disease-associated missense variants outside the homeodomain (e.g. R25C, P236H) impair cooperative activation with GATA4/TBX5 rather than DNA binding.
Type: variant functional characterization
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