SIX3 is a SIX/sine oculis family homeodomain transcription factor of the Six3/6 (Optix) subfamily, expressed in the anterior neural plate, eye field, ventral forebrain, lens placode and developing pituitary. Through its Six domain and homeodomain it binds ATTA-core cis-regulatory elements; unlike Six1/2 family members it does not partner with EYA as a coactivator but recruits Groucho/TLE corepressors (TLE1, AES/TLE5) via an eh1-like motif, and acts mainly as a transcriptional repressor. It directly represses Wnt1 and Wnt8b, protecting the anterior neuroectoderm from posteriorizing Wnt signals so that the telencephalon, rostral diencephalon and neuroretina are specified, and represses its own promoter and gamma-crystallin. In other contexts it is an activator, directly inducing Shh in the rostral diencephalon ventral midline (via the SBE2 enhancer) and Pax6/Sox2 in presumptive lens ectoderm. SIX3 also binds geminin, antagonizing it to promote progenitor proliferation. It acts with PAX6 in eye field specification and optic vesicle proximodistal patterning, and with HESX1 in pituitary development; postnatally it is needed for ependymal cell maturation. Heterozygous loss-of-function variants cause holoprosencephaly type 2 (HPE2) and have been reported in schizencephaly.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000785 chromatin | ISA GO_REF:0000113 | ACCEPT | Summary: SIX3 binds target regulatory DNA in chromatin (ChIP on Wnt1, Wnt8b, Shh SBE2, Pax6 loci). Reason: TFClass-based ISA for a homeodomain DNA-binding TF; consistent with in vivo ChIP of Six3 at Wnt1, Wnt8b and Shh enhancer chromatin. Supporting Evidence: PMID:12569128 We demonstrate that Six3 binds to the Wnt1 promoter region in vivo and represses Wnt1 expression in the most anterior neuroectoderm. PMID:18836447 SBE2 was significantly enriched in Six3 bound chromatin isolated from forebrain compared to posterior trunk regions of E8. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of RNA Pol II cis-regulatory sequence-specific DNA binding for the Six3/6 (Optix) subfamily. Reason: SIX3 homeodomain binds ATTA-core cis-regulatory elements of Wnt1, Wnt8b, Shh (SBE2), Pax6 and rhodopsin; the IBA node placement over the Six family is sound and SIX3 itself has direct experimental support. Supporting Evidence: PMID:18836447 indicating that the binding of Six3 and Six6 to SBE2 was direct PMID:12569128 These results indicated that Six3 can bind to the Wnt1 regulatory sequences at a variety of sites in vivo and in vitro, suggesting that Six3 is a direct transcriptional repressor of Wnt1 during anterior head development. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IDA PMID:18836447 Regulation of a remote Shh forebrain enhancer by the Six3 ho... | ACCEPT | Summary: EMSA/ChIP show Six3 binds the remote Shh forebrain enhancer SBE2 directly; the HPE-associated SBE2(T) variant reduces binding. Reason: Direct experimental evidence of sequence-specific binding to an RNA Pol II cis-regulatory element (Shh enhancer). Supporting Evidence: PMID:18836447 indicating that the binding of Six3 and Six6 to SBE2 was direct PMID:18836447 Taken together, these data are consistent with our hypothesis that Six3 is a direct regulator of SBE2 activity, and that the SBE2(T) variant compromises the recruitment of Six3 and subsequent activation of Shh transcription. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic transfer (ARBA/mouse ortholog) of cis-regulatory sequence-specific DNA binding. Reason: Consistent with direct experimental evidence for human/mouse SIX3 binding to Shh, Wnt1 and Pax6 regulatory elements. Supporting Evidence: PMID:18836447 indicating that the binding of Six3 and Six6 to SBE2 was direct PMID:17066077 Using ChIP, electrophoretic mobility shift assay, and luciferase reporter assays, we determined that Six3 activates Pax6 and Sox2 expression. |
| 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 transcription factor activity for the Six family. Reason: Core molecular function: SIX3 is a sequence-specific homeodomain TF that directly represses (Wnt1, Wnt8b, crystallin) and activates (Shh, Pax6, rhodopsin) Pol II target genes. Supporting Evidence: PMID:12569128 These results indicated that Six3 can bind to the Wnt1 regulatory sequences at a variety of sites in vivo and in vitro, suggesting that Six3 is a direct transcriptional repressor of Wnt1 during anterior head development. PMID:18836447 Taken together, these data are consistent with our hypothesis that Six3 is a direct regulator of SBE2 activity, and that the SBE2(T) variant compromises the recruitment of Six3 and subsequent activation of Shh transcription. PMID:18836447 Six3 functions as a context dependent activator or repressor of target gene expression in the developing eye and forebrain |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl Compara transfer of DNA-binding TF activity from mouse Six3. Reason: Mouse Six3 has direct IDA evidence for this activity (Wnt1 repression, Pax6 activation); ortholog transfer is sound. Supporting Evidence: PMID:12569128 These results indicated that Six3 can bind to the Wnt1 regulatory sequences at a variety of sites in vivo and in vitro, suggesting that Six3 is a direct transcriptional repressor of Wnt1 during anterior head development. PMID:17066077 We conclude that Six3 directly activates Pax6 and probably also Sox2 in the PLE and regulates cell autonomously the earliest stages of mammalian lens induction. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | ISA GO_REF:0000113 | ACCEPT | Summary: TFClass-based assignment of Pol II DNA-binding TF activity. Reason: SIX3 is a bona fide homeodomain sequence-specific TF. Supporting Evidence: PMID:18836447 Six3 functions as a context dependent activator or repressor of target gene expression in the developing eye and forebrain |
| GO:0001222 transcription corepressor binding | IEA GO_REF:0000107 | ACCEPT | Summary: Electronic transfer from mouse of transcription corepressor binding (mouse Six3-MTA1). Reason: SIX3 binds Groucho/TLE corepressors through its eh1-like motif and Six domain, and MTA1; this is central to its repressor activity. Supporting Evidence: PMID:12441302 Biochemical and mutational analysis shows that the Six domain of both SIX3 and SIX6 strongly interact with the QD domain of TLE1 and AES, but that SIX3 also interacts with TLE proteins via the WDR domain. PMID:17666527 MTA1 is also a Six3-interacting corepressor that contributes to a self-negative regulation of Six3 transcription by Six3. |
| GO:0001222 transcription corepressor binding | IPI PMID:12441302 Six3 and Six6 activity is modulated by members of the grouch... | ACCEPT | Summary: IPI: SIX3 binds the Groucho corepressor TLE1 (Q04724) via its Six domain and TLE1 Q and WD domains. Reason: TLE/Groucho recruitment is the mechanism of SIX3 repressor activity and is essential for human SIX3 function in HPE assays; the interaction partner is a bona fide corepressor. Supporting Evidence: PMID:12441302 Biochemical and mutational analysis shows that the Six domain of both SIX3 and SIX6 strongly interact with the QD domain of TLE1 and AES, but that SIX3 also interacts with TLE proteins via the WDR domain. PMID:12441302 consistent with the view that both Six3 and Six6 act in combination with either Tle1 and/or Aes PMID:18791198 we can also confirm that this interaction is essential for human SIX3 co-repressor activity |
| GO:0001222 transcription corepressor binding | IPI PMID:12441302 Six3 and Six6 activity is modulated by members of the grouch... | ACCEPT | Summary: IPI: SIX3 binds AES/TLE5 (Q08117), a short Groucho family member. Reason: AES/TLE5 is a Groucho-family corepressor-like cofactor; the Six domain-QD interaction is mapped. AES may act as a dominant-negative TLE, but binding to a corepressor-family protein is correctly captured. Supporting Evidence: PMID:12441302 Biochemical and mutational analysis shows that the Six domain of both SIX3 and SIX6 strongly interact with the QD domain of TLE1 and AES, but that SIX3 also interacts with TLE proteins via the WDR domain. PMID:12441302 consistent with the view that both Six3 and Six6 act in combination with either Tle1 and/or Aes |
| GO:0001222 transcription corepressor binding | IPI PMID:14973488 Direct interaction of geminin and Six3 in eye development. | KEEP AS NON CORE | Summary: IPI: Six3 binds the replication licensing inhibitor geminin (medaka Gem, Q709D5), competing with Cdt1. Reason: The Six3-geminin interaction is well established, but its main described consequence is non-transcriptional (sequestering geminin from Cdt1 to promote proliferation). Geminin is not primarily a transcriptional corepressor in this context; the corepressor-binding term is retained because the curator read the full text, but this is not the core corepressor mechanism of SIX3 (which is Groucho/TLE). Supporting Evidence: PMID:14973488 Here, we show that Six3 efficiently competes with Cdt1 directly to bind to geminin, which reveals how Six3 can promote cell proliferation without transcription. PMID:14973488 Our data indicate that the transcription factor Six3 and the replication-initiation inhibitor geminin act antagonistically to control the balance between proliferation and differentiation during early vertebrate eye development. |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IEA GO_REF:0000107 | ACCEPT | Summary: Electronic transfer of Pol II DNA-binding transcription activator activity from mouse Six3. Reason: SIX3 directly activates some targets (Shh SBE2 in the ventral forebrain, Pax6 and Sox2 in lens ectoderm, rhodopsin); this context-dependent activator activity underlies the HPE-relevant Shh induction, alongside its better-characterised Groucho-dependent repressor activity. Supporting Evidence: PMID:17066077 Using ChIP, electrophoretic mobility shift assay, and luciferase reporter assays, we determined that Six3 activates Pax6 and Sox2 expression. PMID:18836447 Taken together, these data are consistent with our hypothesis that Six3 is a direct regulator of SBE2 activity, and that the SBE2(T) variant compromises the recruitment of Six3 and subsequent activation of Shh transcription. PMID:18836447 Six3 functions as a context dependent activator or repressor of target gene expression in the developing eye and forebrain |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | ISS GO_REF:0000024 | ACCEPT | Summary: ISS from mouse Six3 of transcription activator activity. Reason: Supported by direct activation of Pax6 (lens) and rhodopsin by mouse Six3 and Shh SBE2 activation; context-dependent but a genuine activity. Supporting Evidence: PMID:17066077 We conclude that Six3 directly activates Pax6 and probably also Sox2 in the PLE and regulates cell autonomously the earliest stages of mammalian lens induction. PMID:17666527 Six3's homeodomain interacts with specific DNA elements in the rhodopsin promoter to stimulate its transcription, resulting in increased rhodopsin expression. |
| GO:0001654 eye development | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that Six3/6 subfamily members function in eye development. Reason: Eye development is a core role: Six3 loss abolishes eyes/forebrain in medaka and neuroretina in mouse, and Six3 cooperates with Pax6 in the eye field and lens. Supporting Evidence: PMID:12163408 Inactivation of Six3 function by morpholino knock-down results in the lack of forebrain and eyes. PMID:12163408 During both processes of vertebrate eye formation, Six3 cooperates with Pax6. PMID:20890044 In Six3 conditional-mutant mouse embryos, specification of the neuroretina was abrogated, but that of the retinal pigmented epithelium was normal. |
| GO:0001654 eye development | IDA PMID:18791198 Mutations in the human SIX3 gene in holoprosencephaly are lo... | ACCEPT | Summary: IDA (zebrafish assays of human SIX3 alleles) supporting a role in eye development. Reason: Human SIX3 activity assayed in zebrafish eye/forebrain; consistent with medaka and mouse loss-of-function data. Supporting Evidence: PMID:18791198 Here, we report the development of a set of robust and sensitive assays of human SIX3 function in zebrafish PMID:18791198 We can now confirm that 89% of these putative deleterious mutations are significant loss-of-function alleles. PMID:12163408 Inactivation of Six3 function by morpholino knock-down results in the lack of forebrain and eyes. |
| GO:0002070 epithelial cell maturation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: ISS/IEA from mouse: Six3 required for postnatal ependymal cell maturation. Reason: Mouse conditional loss of Six3 prevents ependymal cells from suppressing radial glia traits; a genuine but later, tissue-specific role. Supporting Evidence: PMID:22071110 Here, we show that Six3 is necessary for ependymal cell maturation during postnatal stages of brain development. PMID:22071110 In its absence, ependymal cells fail to suppress radial glia characteristics, resulting in a defective lateral wall, abnormal neuroblast migration and differentiation, and hydrocephaly. |
| GO:0002070 epithelial cell maturation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS/IEA from mouse: ependymal (epithelial) cell maturation. Reason: Same as above; mouse evidence (Lavado & Oliver 2011). Supporting Evidence: PMID:22071110 Here, we show that Six3 is necessary for ependymal cell maturation during postnatal stages of brain development. |
| GO:0002088 lens development in camera-type eye | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: lens development. Reason: Six3 directly activates Pax6/Sox2 in presumptive lens ectoderm and is required for lens induction (mouse conditional deletion). Part of the eye development role; retained as a specific sub-process. Supporting Evidence: PMID:17066077 We conclude that Six3 directly activates Pax6 and probably also Sox2 in the PLE and regulates cell autonomously the earliest stages of mammalian lens induction. PMID:12072567 we found that either transcription factor binds regulatory sequences from the counterpart gene and that both genes mutually activate their expression |
| GO:0002088 lens development in camera-type eye | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: lens development. Reason: Mouse lens induction requires Six3 activation of Pax6. Supporting Evidence: PMID:17066077 We conclude that Six3 directly activates Pax6 and probably also Sox2 in the PLE and regulates cell autonomously the earliest stages of mammalian lens induction. |
| GO:0003404 optic vesicle morphogenesis | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: optic vesicle morphogenesis. Reason: Ectopic Six3 induces optic vesicle-like structures in mouse; Six3 patterns the optic vesicle in medaka. Specific aspect of eye development. Supporting Evidence: PMID:11458394 ectopic Six3 expression promotes the formation of ectopic optic vesicle-like structures in the hindbrain-midbrain region of developing mouse embryos PMID:12163408 graded interference reveals an additional role of Six3 in the proximodistal patterning of the optic vesicle |
| GO:0003404 optic vesicle morphogenesis | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: optic vesicle morphogenesis. Reason: As above; mouse gain-of-function evidence. Supporting Evidence: PMID:11458394 ectopic Six3 expression promotes the formation of ectopic optic vesicle-like structures in the hindbrain-midbrain region of developing mouse embryos |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: IEA: DNA binding (InterPro homeodomain). Reason: Correct but uninformative parent of the sequence-specific cis-regulatory DNA binding terms already accepted. Supporting Evidence: PMID:18836447 indicating that the binding of Six3 and Six6 to SBE2 was direct |
| GO:0005515 protein binding | IPI PMID:12543801 The homeotic protein Six3 is a coactivator of the nuclear re... | MODIFY | Summary: IPI with NR4A3/NOR-1 (Q92570): Six3 binds the NOR-1 DNA-binding domain and modulates NOR-1 and EWS/NOR-1 transcriptional activity. Reason: Generic protein binding is uninformative. The partner NOR-1 is a sequence-specific nuclear-receptor TF whose DNA-binding domain is bound by the Six3 homeodomain; replace with RNA polymerase II-specific DNA-binding transcription factor binding. The context (extraskeletal myxoid chondrosarcoma) is not part of normal SIX3 biology, so this is non-core. Proposed replacements: RNA polymerase II-specific DNA-binding transcription factor binding Supporting Evidence: PMID:12543801 Glutathione S-transferase fusion protein assays show that Six3 binds in vitro the DNA-binding domain of NOR-1 and the EWS domain of EWS/NOR-1 and that the homeodomain of Six3 is required for these interactions. PMID:12543801 Cotransfection experiments show that Six3 stimulates the transcriptional activity of NOR-1, whereas it represses that of EWS/NOR-1. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: nucleus. Reason: Nuclear homeodomain TF; consistent with chromatin binding. Supporting Evidence: PMID:12569128 We demonstrate that Six3 binds to the Wnt1 promoter region in vivo and represses Wnt1 expression in the most anterior neuroectoderm. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: IEA: nucleus. Reason: Nuclear TF. Supporting Evidence: PMID:12569128 We demonstrate that Six3 binds to the Wnt1 promoter region in vivo and represses Wnt1 expression in the most anterior neuroectoderm. |
| GO:0005634 nucleus | ISS GO_REF:0000024 | ACCEPT | Summary: ISS from mouse: nucleus. Reason: Nuclear TF. Supporting Evidence: PMID:12569128 We demonstrate that Six3 binds to the Wnt1 promoter region in vivo and represses Wnt1 expression in the most anterior neuroectoderm. |
| GO:0005667 transcription regulator complex | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: transcription regulator complex. Reason: SIX3 acts in complexes with Groucho/TLE corepressors (and MTA1/HDAC2) on target promoters. Supporting Evidence: PMID:12441302 consistent with the view that both Six3 and Six6 act in combination with either Tle1 and/or Aes PMID:17666527 MTA1 is also a Six3-interacting corepressor that contributes to a self-negative regulation of Six3 transcription by Six3. |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: regulation of transcription by RNA polymerase II. Reason: SIX3 directly represses and activates Pol II target genes; more specific negative/positive regulation terms also apply. Supporting Evidence: PMID:12569128 These results indicated that Six3 can bind to the Wnt1 regulatory sequences at a variety of sites in vivo and in vitro, suggesting that Six3 is a direct transcriptional repressor of Wnt1 during anterior head development. PMID:18836447 Taken together, these data are consistent with our hypothesis that Six3 is a direct regulator of SBE2 activity, and that the SBE2(T) variant compromises the recruitment of Six3 and subsequent activation of Shh transcription. |
| GO:0007420 brain development | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: brain development. Reason: Six3 is required for forebrain (telencephalon, rostral diencephalon) formation; brain development is an appropriate IBA-level grouping. Supporting Evidence: PMID:12569128 In Six3(-/-) mice, the prosencephalon was severely truncated, and the expression of Wnt1 was rostrally expanded PMID:12163408 Inactivation of Six3 function by morpholino knock-down results in the lack of forebrain and eyes. PMID:10369266 We propose that SIX3 is the HPE2 gene, essential for the development of the anterior neural plate and eye in humans. |
| GO:0007420 brain development | TAS PMID:10369266 Mutations in the homeodomain of the human SIX3 gene cause ho... | MODIFY | Summary: TAS (HPE2 gene identification): brain development. Reason: Correct but the role is specifically in anterior neural plate/forebrain development (holoprosencephaly); forebrain development is more precise. Proposed replacements: forebrain development Supporting Evidence: PMID:10369266 We propose that SIX3 is the HPE2 gene, essential for the development of the anterior neural plate and eye in humans. PMID:12569128 In Six3(-/-) mice, the prosencephalon was severely truncated, and the expression of Wnt1 was rostrally expanded |
| GO:0007601 visual perception | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: IEA (ARBA): visual perception. Reason: The same term is marked as an over-annotation on the author-statement row of this review, and the claim is the same here. SIX3 patterns the eye field, lens and neuroretina during development, and visual impairment in its absence is a consequence of abnormal eye development, not participation in the sensory process. Rows that share a term are judged alike, so the machine-generated row is marked in the same way rather than removed. Supporting Evidence: PMID:12163408 Inactivation of Six3 function by morpholino knock-down results in the lack of forebrain and eyes. PMID:20890044 Six3 directly repressed Wnt8b expression in vivo |
| GO:0007601 visual perception | TAS PMID:10369266 Mutations in the homeodomain of the human SIX3 gene cause ho... | MARK AS OVER ANNOTATED | Summary: TAS: visual perception (from HPE2 gene paper). Reason: The paper describes a role in eye and anterior neural plate development, not in visual perception; eye development captures this. Supporting Evidence: PMID:10369266 We propose that SIX3 is the HPE2 gene, essential for the development of the anterior neural plate and eye in humans. |
| GO:0009946 proximal/distal axis specification | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: proximal/distal axis specification. Reason: Graded Six3 knockdown in medaka reveals a role in proximodistal patterning of the optic vesicle. Supporting Evidence: PMID:12163408 graded interference reveals an additional role of Six3 in the proximodistal patterning of the optic vesicle |
| GO:0009946 proximal/distal axis specification | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS: proximal/distal axis specification (optic vesicle). Reason: Medaka evidence (Carl et al. 2002). Supporting Evidence: PMID:12163408 graded interference reveals an additional role of Six3 in the proximodistal patterning of the optic vesicle |
| GO:0010467 gene expression | IMP PMID:28972157 Transcriptome analysis reveals determinant stages controllin... | MARK AS OVER ANNOTATED | Summary: IMP (CRISPR knockout in hESCs): SIX3 required for neural determination of hESCs; annotated to gene expression. Reason: 'Gene expression' is uninformative for a sequence-specific TF and adds nothing beyond its transcription regulation terms; the phenotype (failure of neural commitment) is better captured by forebrain/neural development terms. Supporting Evidence: PMID:28972157 intrinsic hub transcription factors, including the schizophrenia-associated SIX3 gene and septo-optic dysplasia-related HESX1 gene, are required to program hESC neural determination |
| GO:0014016 neuroblast differentiation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: neuroblast differentiation (ependymal niche study). Reason: Mouse Six3 conditional mutants show abnormal SVZ neuroblast differentiation secondary to ependymal defects; indirect, non-core. Supporting Evidence: PMID:22071110 In its absence, ependymal cells fail to suppress radial glia characteristics, resulting in a defective lateral wall, abnormal neuroblast migration and differentiation, and hydrocephaly. |
| GO:0014016 neuroblast differentiation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: neuroblast differentiation. Reason: As above. Supporting Evidence: PMID:22071110 In its absence, ependymal cells fail to suppress radial glia characteristics, resulting in a defective lateral wall, abnormal neuroblast migration and differentiation, and hydrocephaly. |
| GO:0021537 telencephalon development | ISS GO_REF:0000024 | ACCEPT | Summary: ISS from mouse: telencephalon development. Reason: Six3-null mice lack telencephalon and rostral diencephalon due to rostral expansion of Wnt1; a core developmental role. Supporting Evidence: PMID:12569128 In Six3(-/-) mice, the prosencephalon was severely truncated, and the expression of Wnt1 was rostrally expanded PMID:18694563 the anterior expansion of canonical Wnt signaling in Six3-null embryos results in the absence of the telencephalon and rostral diencephalon |
| GO:0021798 forebrain dorsal/ventral pattern formation | IDA PMID:18791198 Mutations in the human SIX3 gene in holoprosencephaly are lo... | ACCEPT | Summary: IDA (zebrafish assays of human SIX3): forebrain dorsal/ventral pattern formation. Reason: SIX3 directly activates Shh in the ventral forebrain midline; failure causes HPE (failure of ventral forebrain/hemisphere separation). Supporting Evidence: PMID:18694563 These results identify Six3 as a direct regulator of Shh expression and reveal a crossregulatory loop between Shh and Six3 in the ventral forebrain. PMID:18791198 We can now confirm that 89% of these putative deleterious mutations are significant loss-of-function alleles. |
| GO:0021846 cell proliferation in forebrain | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: cell proliferation in forebrain. Reason: Six3 promotes neural progenitor proliferation (mouse telencephalon; geminin sequestration); a downstream developmental outcome. Supporting Evidence: PMID:17576749 We find that retrovirus-mediated misexpression of Six3 causes clonal expansion of isolated cortical progenitor cells by shortening their cell cycle and by prolonging their amplification period, while maintaining them in an immature precursor state. |
| GO:0021846 cell proliferation in forebrain | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: cell proliferation in forebrain. Reason: As above. Supporting Evidence: PMID:17576749 We find that retrovirus-mediated misexpression of Six3 causes clonal expansion of isolated cortical progenitor cells by shortening their cell cycle and by prolonging their amplification period, while maintaining them in an immature precursor state. |
| GO:0021978 telencephalon regionalization | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: telencephalon regionalization. Reason: Six3 haploinsufficiency disrupts ventral forebrain patterning via Shh; acceptable non-core developmental term. Supporting Evidence: PMID:18694563 These results identify Six3 as a direct regulator of Shh expression and reveal a crossregulatory loop between Shh and Six3 in the ventral forebrain. |
| GO:0021978 telencephalon regionalization | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: telencephalon regionalization. Reason: As above. Supporting Evidence: PMID:18694563 These results identify Six3 as a direct regulator of Shh expression and reveal a crossregulatory loop between Shh and Six3 in the ventral forebrain. PMID:18694563 Haploinsufficiency of Six3 caused by deletion of one allele of Six3 or by replacement of wild-type Six3 with HPE-associated Six3 mutant alleles was sufficient to recapitulate in mouse models most of the phenotypic features of human HPE. |
| GO:0021983 pituitary gland development | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: pituitary gland development. Reason: Six3/Hesx1 compound heterozygotes have severe pituitary defects; pituitary role is genuine but secondary to forebrain/eye functions. Supporting Evidence: PMID:18775421 Our research has revealed a role for Six3 in normal pituitary development PMID:18775421 Rathke's pouch is initially expanded in Six3+/- ;Hesx1Cre/+ compound embryos due to an increase in cell proliferation. |
| GO:0021983 pituitary gland development | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: pituitary gland development. Reason: As above. Supporting Evidence: PMID:18775421 Our research has revealed a role for Six3 in normal pituitary development |
| GO:0042127 regulation of cell population proliferation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: regulation of cell population proliferation. Reason: Six3 promotes progenitor proliferation (retina, lens, telencephalon, Rathke's pouch); general but correct. Supporting Evidence: PMID:17576749 We find that retrovirus-mediated misexpression of Six3 causes clonal expansion of isolated cortical progenitor cells by shortening their cell cycle and by prolonging their amplification period, while maintaining them in an immature precursor state. PMID:14973488 Our data indicate that the transcription factor Six3 and the replication-initiation inhibitor geminin act antagonistically to control the balance between proliferation and differentiation during early vertebrate eye development. |
| GO:0042127 regulation of cell population proliferation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: regulation of cell population proliferation. Reason: As above. Supporting Evidence: PMID:18775421 Rathke's pouch is initially expanded in Six3+/- ;Hesx1Cre/+ compound embryos due to an increase in cell proliferation. PMID:14973488 Our data indicate that the transcription factor Six3 and the replication-initiation inhibitor geminin act antagonistically to control the balance between proliferation and differentiation during early vertebrate eye development. |
| GO:0042826 histone deacetylase binding | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: histone deacetylase binding (mouse Six3-MTA1/HDAC2). Reason: Mouse Six3 associates with the MTA1/HDAC2 corepressor complex for autorepression; plausible additional corepression mechanism, not the principal one. Supporting Evidence: PMID:17666527 MTA1 is also a Six3-interacting corepressor that contributes to a self-negative regulation of Six3 transcription by Six3. |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000107 | ACCEPT | Summary: IEA from mouse: sequence-specific DNA binding. Reason: SIX3 binds ATTA-core motifs (Wnt1, SBE2, Pax6, crystallin elements). Supporting Evidence: PMID:12569128 These results indicated that Six3 can bind to the Wnt1 regulatory sequences at a variety of sites in vivo and in vitro, suggesting that Six3 is a direct transcriptional repressor of Wnt1 during anterior head development. PMID:18836447 indicating that the binding of Six3 and Six6 to SBE2 was direct |
| GO:0045665 negative regulation of neuron differentiation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: negative regulation of neuron differentiation. Reason: Six3 misexpression keeps cortical progenitors undifferentiated; a developmental outcome of its TF activity. Supporting Evidence: PMID:17576749 In vivo upregulation of Six3 expression in single progenitor cells of the embryonic telencephalon keeps them in an undifferentiated state. |
| GO:0045665 negative regulation of neuron differentiation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: negative regulation of neuron differentiation. Reason: As above. Supporting Evidence: PMID:17576749 In vivo upregulation of Six3 expression in single progenitor cells of the embryonic telencephalon keeps them in an undifferentiated state. |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:18791198 Mutations in the human SIX3 gene in holoprosencephaly are lo... | MODIFY | Summary: IDA: negative regulation of DNA-templated transcription (zebrafish assays of human SIX3; eh1/Groucho-dependent corepressor activity). Reason: SIX3 represses RNA Pol II target genes (Wnt1, Wnt8b, crystallin, own promoter) via Groucho/TLE; the Pol II-specific child term is more precise. Proposed replacements: negative regulation of transcription by RNA polymerase II Supporting Evidence: PMID:18791198 we can also confirm that this interaction is essential for human SIX3 co-repressor activity PMID:12569128 These results indicated that Six3 can bind to the Wnt1 regulatory sequences at a variety of sites in vivo and in vitro, suggesting that Six3 is a direct transcriptional repressor of Wnt1 during anterior head development. PMID:12050133 demonstrated that Six3 acts as a potent transcriptional repressor upon its interaction with Groucho-related members |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IEA GO_REF:0000108 | ACCEPT | Summary: IEA (inter-ontology inference from activator activity): positive regulation of transcription by RNA polymerase II. Reason: SIX3 directly activates Shh, Pax6 and rhodopsin; context-dependent but genuine and HPE-relevant. Supporting Evidence: PMID:18836447 Taken together, these data are consistent with our hypothesis that Six3 is a direct regulator of SBE2 activity, and that the SBE2(T) variant compromises the recruitment of Six3 and subsequent activation of Shh transcription. PMID:17066077 We conclude that Six3 directly activates Pax6 and probably also Sox2 in the PLE and regulates cell autonomously the earliest stages of mammalian lens induction. |
| GO:0061074 regulation of neural retina development | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: regulation of neural retina development. Reason: Six3 is required for neuroretina specification by directly repressing Wnt8b in mouse; arguably closer to core eye development. Supporting Evidence: PMID:20890044 Six3 directly repressed Wnt8b expression in vivo PMID:20890044 In Six3 conditional-mutant mouse embryos, specification of the neuroretina was abrogated, but that of the retinal pigmented epithelium was normal. |
| GO:0061074 regulation of neural retina development | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: regulation of neural retina development. Reason: As above. Supporting Evidence: PMID:20890044 Six3 directly repressed Wnt8b expression in vivo |
| GO:0070306 lens fiber cell differentiation | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: IEA from mouse: lens fiber cell differentiation. Reason: Source study (Goudreau et al. 2002) addresses mutual Pax6/Six3 activation and lens growth in Pax6 heterozygotes; Six3 acts early in lens induction and represses gamma-crystallin, so a positive role in fiber differentiation is weakly supported. Supporting Evidence: PMID:12072567 we found that either transcription factor binds regulatory sequences from the counterpart gene and that both genes mutually activate their expression PMID:11139622 In both cell lines Six3 repressed the CRYGF promoter to 10% of its basal activity. |
| GO:0070306 lens fiber cell differentiation | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: ISS from mouse: lens fiber cell differentiation. Reason: As above. Supporting Evidence: PMID:12072567 we found that either transcription factor binds regulatory sequences from the counterpart gene and that both genes mutually activate their expression PMID:11139622 In both cell lines Six3 repressed the CRYGF promoter to 10% of its basal activity. |
| GO:0097402 neuroblast migration | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: IEA from mouse: neuroblast migration. Reason: Abnormal SVZ neuroblast migration in Six3 conditional mutants is secondary to defective ependymal lateral wall formation; SIX3 does not execute neuroblast migration. Supporting Evidence: PMID:22071110 In its absence, ependymal cells fail to suppress radial glia characteristics, resulting in a defective lateral wall, abnormal neuroblast migration and differentiation, and hydrocephaly. |
| GO:0097402 neuroblast migration | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: ISS from mouse: neuroblast migration. Reason: As above; indirect. Supporting Evidence: PMID:22071110 In its absence, ependymal cells fail to suppress radial glia characteristics, resulting in a defective lateral wall, abnormal neuroblast migration and differentiation, and hydrocephaly. |
| GO:1901987 regulation of cell cycle phase transition | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: regulation of cell cycle phase transition. Reason: Six3 misexpression shortens progenitor cell cycle (mouse) and sequesters geminin from Cdt1; supports a role in proliferation control. Supporting Evidence: PMID:17576749 We find that retrovirus-mediated misexpression of Six3 causes clonal expansion of isolated cortical progenitor cells by shortening their cell cycle and by prolonging their amplification period, while maintaining them in an immature precursor state. PMID:14973488 Here, we show that Six3 efficiently competes with Cdt1 directly to bind to geminin, which reveals how Six3 can promote cell proliferation without transcription. |
| GO:1901987 regulation of cell cycle phase transition | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: regulation of cell cycle phase transition. Reason: As above. Supporting Evidence: PMID:17576749 We find that retrovirus-mediated misexpression of Six3 causes clonal expansion of isolated cortical progenitor cells by shortening their cell cycle and by prolonging their amplification period, while maintaining them in an immature precursor state. PMID:14973488 Here, we show that Six3 efficiently competes with Cdt1 directly to bind to geminin, which reveals how Six3 can promote cell proliferation without transcription. |
| GO:1902692 regulation of neuroblast proliferation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: regulation of neuroblast proliferation. Reason: Mouse ependymal/SVZ study; indirect developmental outcome. Supporting Evidence: PMID:22071110 In its absence, ependymal cells fail to suppress radial glia characteristics, resulting in a defective lateral wall, abnormal neuroblast migration and differentiation, and hydrocephaly. |
| GO:1902692 regulation of neuroblast proliferation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: regulation of neuroblast proliferation. Reason: As above. Supporting Evidence: PMID:22071110 In its absence, ependymal cells fail to suppress radial glia characteristics, resulting in a defective lateral wall, abnormal neuroblast migration and differentiation, and hydrocephaly. |
| GO:1902742 apoptotic process involved in development | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: IEA from mouse: apoptotic process involved in development. Reason: Derived from Six3 haploinsufficiency mouse study focused on Shh activation in the ventral forebrain; any apoptosis is a downstream consequence, not a SIX3-executed process. Supporting Evidence: PMID:18694563 These results identify Six3 as a direct regulator of Shh expression and reveal a crossregulatory loop between Shh and Six3 in the ventral forebrain. |
| GO:1902742 apoptotic process involved in development | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: ISS from mouse: apoptotic process involved in development. Reason: As above. Supporting Evidence: PMID:18694563 These results identify Six3 as a direct regulator of Shh expression and reveal a crossregulatory loop between Shh and Six3 in the ventral forebrain. |
| GO:1990086 lens fiber cell apoptotic process | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: IEA from mouse: lens fiber cell apoptotic process. Reason: Source study reports Six3-mediated lens growth/proliferation in Pax6 heterozygotes; a role in lens fiber apoptosis is indirect at best. Supporting Evidence: PMID:12072567 This phenotypic rescue was accompanied by cell proliferation and activation of the platelet-derived growth factor alpha-R/cyclin D1 signaling pathway. |
| GO:1990086 lens fiber cell apoptotic process | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: ISS from mouse: lens fiber cell apoptotic process. Reason: As above. Supporting Evidence: PMID:12072567 This phenotypic rescue was accompanied by cell proliferation and activation of the platelet-derived growth factor alpha-R/cyclin D1 signaling pathway. |
| GO:1990837 sequence-specific double-stranded DNA binding | IDA PMID:28473536 Impact of cytosine methylation on DNA binding specificities ... | ACCEPT | Summary: IDA (HT-SELEX / methyl-SELEX of human TFs): sequence-specific double-stranded DNA binding. Reason: SIX3 was among the human TFs profiled by HT-SELEX, giving its in vitro sequence specificity; consistent with its homeodomain TF function. Supporting Evidence: PMID:28473536 In total, HT-SELEX models now exist for 632 of the ~1400 (23) human TFs. |
| GO:2000177 regulation of neural precursor cell proliferation | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA from mouse: regulation of neural precursor cell proliferation. Reason: Six3 misexpression expands cortical progenitors; developmental outcome. Supporting Evidence: PMID:17576749 We find that retrovirus-mediated misexpression of Six3 causes clonal expansion of isolated cortical progenitor cells by shortening their cell cycle and by prolonging their amplification period, while maintaining them in an immature precursor state. |
| GO:2000177 regulation of neural precursor cell proliferation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS from mouse: regulation of neural precursor cell proliferation. Reason: As above. Supporting Evidence: PMID:17576749 We find that retrovirus-mediated misexpression of Six3 causes clonal expansion of isolated cortical progenitor cells by shortening their cell cycle and by prolonging their amplification period, while maintaining them in an immature precursor state. |
| GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific | IDA PMID:18791198 Mutations in the human SIX3 gene in holoprosencephaly are lo... | NEW | Summary: SIX3 binds Wnt1 and Wnt8b regulatory sequences and directly represses them in the anterior neuroectoderm; Groucho/TLE recruitment via its eh1-like motif confers potent repression, and HPE mutations in this motif abolish human SIX3 corepressor activity. Reason: The repressor activity is the best-characterized molecular activity of SIX3 and is not captured by any existing MF annotation (only the generic GO:0000981 and the activator term GO:0001228 are present). Evidence is from mouse (direct ChIP + repression), Groucho-dependent repression assays, and human HPE allele assays. Supporting Evidence: PMID:12569128 These results indicated that Six3 can bind to the Wnt1 regulatory sequences at a variety of sites in vivo and in vitro, suggesting that Six3 is a direct transcriptional repressor of Wnt1 during anterior head development. PMID:20890044 Six3 directly repressed Wnt8b expression in vivo PMID:12050133 demonstrated that Six3 acts as a potent transcriptional repressor upon its interaction with Groucho-related members PMID:18791198 we can also confirm that this interaction is essential for human SIX3 co-repressor activity |
Loading supporting content…
Download this section (compressed HTML)Q: Which SIX3 target genes are directly activated versus repressed in human forebrain progenitors, and what (partner, motif, or EYA/TLE availability) determines the switch?
Q: Is the SIX3-geminin interaction conserved and functionally important in mammalian (human) retinal progenitors, independent of SIX3 transcriptional activity?
Q: Should a NOT or caution be considered for GO:0001222 annotations based on geminin, given geminin's primary role as a replication-licensing inhibitor?
Experiment: CUT&RUN/ChIP-seq for SIX3 and TLE1 in human forebrain organoids, combined with SIX3 eh1-motif (HPE) mutant knock-in, to define Groucho-dependent repressed targets genome-wide.
Hypothesis: SIX3 represses a defined set of posteriorizing (Wnt pathway) genes in human anterior neural progenitors through Groucho/TLE recruitment, and HPE eh1-motif variants derepress them.
Type: ChIP-seq
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)