Affinage

SIX3

Homeobox protein SIX3 · UniProt O95343

Length
332 aa
Mass
35.5 kDa
Annotated
2026-06-10
100 papers in source corpus 44 papers cited in narrative 44 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SIX3 is a homeodomain transcription factor that sits at the top of the gene-regulatory hierarchy specifying the anterior neural plate, forebrain, and eye, with both its Six domain and homeodomain required for activity (PMID:8575305, PMID:9655819, PMID:17066077). It acts predominantly as a Groucho/TLE-dependent transcriptional repressor, binding corepressors (Grg3/Grg4/Grg5, TLE1, AES) through an eh1-like motif in its Six domain; mutation of this motif simultaneously abolishes corepressor binding and developmental activity (PMID:11401394, PMID:12050133, PMID:12441302). Through this repressive activity SIX3 directly silences Wnt pathway components—Wnt1, Wnt8b, and R-spondin 2—to restrict caudalizing Wnt/β-catenin signaling and permit rostral diencephalon, telencephalon, and neuroretina specification (PMID:12569128, PMID:18094027, PMID:20890044, PMID:29117559). In a context-dependent activating mode, SIX3 binds and activates the long-range SHH brain enhancer SBE2 in the rostral diencephalon and directly activates Pax6 and Sox2 in the presumptive lens ectoderm to drive lens and eye induction (PMID:17066077, PMID:18836447, PMID:18694563). SIX3 also drives progenitor proliferation through a non-transcriptional mechanism, competing with Cdt1 for binding to the replication inhibitor geminin in retinal and forebrain precursors (PMID:14973488, PMID:16226737). Its own expression is autoregulated via direct binding to a TAATGTC motif in its promoter and is set by upstream inputs including Sox2 and SP8/SP9 enhancer activation and MTA1/NuRD-dependent corepression (PMID:17666527, PMID:20193042, PMID:23792023, PMID:29967281). Heterozygous loss-of-function mutations in human SIX3—including homeodomain and eh1-motif point mutations that disrupt DNA binding and corepressor interaction—cause holoprosencephaly (HPE2), with dosage determining severity through differential loss of Shh versus Foxg1 expression (PMID:10369266, PMID:18694563, PMID:18791198, PMID:27770010).

Mechanistic history

Synthesis pass · year-by-year structured walk · 16 steps
  1. 1995 Medium

    Established SIX3 as an early anterior neural/eye-field homeobox factor acting upstream of and independently from Pax6, defining its position in the developmental hierarchy.

    Evidence In situ hybridization and expression analysis in Pax6 mutant mice

    PMID:8575305

    Open questions at the time
    • No direct target genes identified
    • Repressor versus activator function unresolved at this stage
  2. 1999 High

    Demonstrated SIX3 is sufficient to induce eye-field programs by triggering ectopic lens and retinal primordia and revealed an autoregulatory feedback loop.

    Evidence Ectopic mRNA injection in medaka and zebrafish with target-gene in situ readouts

    PMID:10090721 PMID:9025075 PMID:9655819

    Open questions at the time
    • Direct versus indirect target activation not distinguished
    • Domain requirements for autoregulation not yet mapped
  3. 1999 Medium

    Linked SIX3 to human disease, identifying homeodomain mutations as the cause of holoprosencephaly (HPE2).

    Evidence Mutational analysis of HPE patient families with functional prediction

    PMID:10369266

    Open questions at the time
    • Functional consequences of mutations predicted, not measured
    • Downstream pathway affected unknown
  4. 2001 High

    Defined the molecular basis of SIX3 repression by showing it recruits Groucho/Grg corepressors through an eh1-like motif required for forebrain activity and autorepression.

    Evidence Yeast two-hybrid, Co-IP, eh1 motif mutagenesis with in vivo assays in zebrafish, chick, and rat retina

    PMID:11139622 PMID:11401394 PMID:12050133 PMID:12441302

    Open questions at the time
    • Direct genomic repression targets not yet identified
    • Switch between repressor and activator modes unexplained
  5. 2002 High

    Connected SIX3 to lens induction through a mutual cross-activation loop with Pax6 driving downstream proliferative signaling.

    Evidence In vitro DNA binding and transgenic mouse rescue of Pax6 haploinsufficiency

    PMID:12072567

    Open questions at the time
    • Direct binding sites in the Pax6 locus not finely mapped here
    • Temporal order of mutual activation incompletely resolved
  6. 2003 High

    Identified Wnt1 as a direct repression target, establishing SIX3's role in restricting caudalizing Wnt signaling to pattern the anterior brain.

    Evidence Six3 knockout mice, gain-of-function in chick/zebrafish, DNA-binding assays, and headless/tcf3 rescue

    PMID:12569128

    Open questions at the time
    • Full set of Wnt-pathway targets unknown
    • Corepressor requirement at the Wnt1 locus not yet shown
  7. 2004 High

    Revealed a non-transcriptional proliferative mechanism whereby SIX3 sequesters geminin from Cdt1 to license replication in neural/retinal precursors.

    Evidence Direct protein competition binding assays plus medaka overexpression/loss-of-function genetics

    PMID:14973488 PMID:16226737

    Open questions at the time
    • Quantitative contribution of this mechanism versus transcriptional outputs unclear
    • Regulation of the SIX3-geminin interaction unknown
  8. 2006 High

    Showed SIX3 directly activates Pax6 and Sox2 in the lens ectoderm, demonstrating a bona fide context-dependent activator function distinct from its repressive role.

    Evidence Conditional knockout, ChIP, EMSA, luciferase reporters, and chick misexpression

    PMID:17066077

    Open questions at the time
    • Coactivator partners at activated loci not defined
    • Determinants of activator versus repressor outcome unresolved
  9. 2008 High

    Established SIX3 as a direct activator of SHH via the long-range SBE2 enhancer and mechanistically tied HPE mutations to failed Shh activation.

    Evidence DNA affinity-capture, transgenic enhancer assays, ChIP, and HPE allele knockin/mutation testing

    PMID:18694563 PMID:18791198 PMID:18836447

    Open questions at the time
    • Coactivators enabling SHH activation not identified
    • How a repressor-prone factor activates SBE2 not mechanistically resolved
  10. 2010 High

    Extended the Wnt-repression program to Wnt8b in the neuroretina, establishing SIX3-mediated Wnt suppression as essential for neuroretina specification.

    Evidence Conditional knockout, ChIP, and Wnt8b transgenic epistasis

    PMID:20682799 PMID:20890044

    Open questions at the time
    • Whether one corepressor complex serves all Wnt targets unknown
    • Cell-type specificity of target choice unexplained
  11. 2010 High

    Defined SIX3 autoregulation at the DNA level by identifying a non-canonical TAATGTC recognition motif clustered in its own promoter.

    Evidence In vitro binding with single-nucleotide substitution, ChIP, and zebrafish reporter assays

    PMID:17666527 PMID:20193042

    Open questions at the time
    • Genome-wide preference for TAATGTC versus canonical sites unmeasured
    • Structural basis of motif selectivity unknown
  12. 2016 High

    Resolved how SIX3 dosage dictates HPE severity by separating Shh-dependent (semilobar) from Foxg1-dependent (alobar) phenotypes.

    Evidence Hypomorphic allele dosage series with pathway-specific in vivo Shh rescue

    PMID:20193042 PMID:27770010

    Open questions at the time
    • Whether Foxg1 is a direct SIX3 target not established
    • Threshold mechanism distinguishing the two pathways unknown
  13. 2017 High

    Mapped SIX3 function to a defined anteroventral optic vesicle progenitor population and added R-spondin 2 to its directly repressed Wnt-modulating targets.

    Evidence Lineage tracing, conditional KO, iPSC/ESC organoids, and Rspo2 transgenic epistasis

    PMID:28579317 PMID:29117559

    Open questions at the time
    • Mechanism of non-cell-autonomous repression of optic vesicle formation unclear
    • Direct binding at the Rspo2 locus not detailed
  14. 2018 High

    Defined the upstream transcriptional and epigenetic control of SIX3, identifying Sox2 and SP8/SP9 as direct enhancer/promoter activators and the LSD1/NuRD(MTA3) complex as a SIX3 partner controlling Wnt1/EMT genes.

    Evidence ChIP-seq, transgenic enhancer assays, conditional knockouts, and AP-MS complex identification

    PMID:23792023 PMID:29463994 PMID:29967281

    Open questions at the time
    • Composition of the SIX3 corepressor complex in neural contexts not fully defined
    • Whether NuRD recruitment generalizes to developmental targets unknown
  15. 2020 High

    Established post-transcriptional and epigenetic silencing of SIX3 as a tumor-relevant axis via EGFR/MAPK-ZNF263-driven promoter methylation and TRIM27-mediated protein degradation.

    Evidence Co-IP, ChIP, ubiquitination assays, and pathway epistasis in cancer cells

    PMID:28595628 PMID:32051553 PMID:33264103

    Open questions at the time
    • Physiological relevance of these regulators in normal development untested
    • Direct SIX3 binding at AURKA/AURKB versus indirect effects partly unresolved
  16. 2021 Medium

    Revealed a postnatal cell-identity maintenance role, with SIX3 sustaining adult β-cell and D2 MSN differentiation programs and suppressing alternative fates.

    Evidence shRNA knockdown in human islets with transcriptomics, and conditional KO/overexpression in mouse striatum

    PMID:33446570 PMID:34014554

    Open questions at the time
    • Direct target genes maintaining cell identity not defined
    • Whether identity maintenance uses the same corepressor machinery as development unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • The molecular determinant that switches SIX3 between Groucho-dependent repression and context-specific activation of SHH/Pax6/Sox2 remains unresolved.
  • No structural model explaining repressor/activator partner selection
  • Coactivators required for SBE2/Pax6 activation not identified
  • How upstream chromatin state biases target choice unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 6 GO:0140110 transcription regulator activity 6 GO:0098772 molecular function regulator activity 3 GO:0140313 molecular sequestering activity 2
Localization
GO:0005654 nucleoplasm 3 GO:0005634 nucleus 2
Pathway
R-HSA-1266738 Developmental Biology 5 R-HSA-162582 Signal Transduction 5 R-HSA-1643685 Disease 5 R-HSA-74160 Gene expression (Transcription) 5 R-HSA-1640170 Cell Cycle 3
Partners
AESEYA4GEMININMTA1NR4A3PAX6TLE1TRIM27
Complex memberships
SIX3-Groucho/TLE corepressor complexSIX3/LSD1/NuRD(MTA3)

Evidence

Reading pass · 44 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1995 Six3 is a homeobox transcription factor expressed in the anterior neural plate, optic vesicles, lens, olfactory placodes, and ventral forebrain; its expression in Pax6 (Small eye) mutant mice is not affected, establishing it as acting independently of Pax6 at early stages. In situ hybridization, chromosomal mapping, expression analysis in Pax6 mutant mice Development Medium 8575305
1996 Ectopic expression of mouse Six3 in medaka fish embryos promotes ectopic lens formation in the area of the otic vesicle, demonstrating Six3 is sufficient to initiate lens formation independently of retinal tissue. Ectopic mRNA injection in medaka fish embryos, histological analysis Mechanisms of development High 9025075
1998 Overexpression of Six3 in zebrafish embryos causes rostral forebrain enlargement and enhanced pax2 expression; disruption of either the Six domain or the homeodomain abolishes these effects, establishing both domains as essential for Six3 function. mRNA injection in zebrafish embryos, domain deletion mutant analysis Development High 9655819
1999 Overexpression of Six3 RNA in medaka fish initiates ectopic Pax6 and Rx2 expression, resulting in formation of ectopic retinal primordia; injected mouse Six3 also induces ectopic expression of endogenous medaka Six3, uncovering a feedback autoregulatory loop. mRNA injection in medaka embryos, in situ hybridization Genes & development High 10090721
1999 Four different missense mutations in the homeodomain of human SIX3 are associated with holoprosencephaly and are predicted to interfere with transcriptional activation, establishing SIX3 as the HPE2 gene. Mutational analysis of HPE patients, chromosomal mapping, functional prediction Nature genetics Medium 10369266
2001 Six3 interacts with the Groucho corepressor family member Grg3 via eh1-like motifs in the Six domain; point mutations in the eh1-like motifs reduce both forebrain-enlarging activity and Grg3 interaction, demonstrating Six3 functions as a Groucho-dependent transcriptional repressor in eye and forebrain formation. Yeast two-hybrid, mRNA injection in zebrafish, dominant activator/repressor constructs, eh1 motif mutagenesis Developmental biology High 11401394
2001 Six3 acts as a transcriptional repressor at the gamma-crystallin (CRYGF) promoter, repressing it to ~10% of basal activity; functional assays define a Six3-responsive element between -101 and -123, and Six3 and Prox1 act antagonistically on CRYG promoters. Cell transfection reporter assay, randomly mutated promoter fragment analysis Nucleic acids research Medium 11139622
2001 Six3 promotes formation of ectopic optic vesicle-like structures in the hindbrain-midbrain region of developing mouse embryos upon ectopic expression; Six3 expression in the murine lens placodal ectoderm is controlled by Pax6. Ectopic Six3 expression in mouse embryos, analysis of Pax6 mutants Developmental dynamics Medium 11458394
2001 NOR-1 (NR4A3) orphan nuclear receptor interacts with Six3 in vitro and in yeast; the interaction requires the DNA binding and AF2 domains of NOR-1; Six3 negatively regulates NOR-1 transcriptional activity through the NBRE response element in a dose-dependent manner. Yeast two-hybrid, GST pulldown, cotransfection reporter assay Developmental neuroscience Medium 11173923
2002 Grg4 and Grg5, mouse Groucho homologs, physically interact with Six3 (and Six6); interaction requires the Q domain of Grg5 and a conserved phenylalanine in an eh1-like motif in the Six domain of Six3; Six3 acts as a potent transcriptional repressor via this interaction, and this interaction is required for Six3 auto-repression; disruption of the Groucho-interaction domain prevents lens placode invagination in chick and alters photoreceptor phenotype in rat retina. Co-immunoprecipitation, yeast two-hybrid, PCR DNA-binding motif identification, retroviral infection of rat retinae, chick in ovo electroporation with wild-type vs. eh1-mutant Six3 Development High 12050133
2002 Both Six3 and Six6 directly interact with TLE1 (Groucho family) and AES via the Six domain QD domain interface; Six3 additionally interacts with TLE proteins via the WDR domain; gain-of-function in medaka shows synergistic activity between SIX3/SIX6 and TLE1, while AES abrogates SIX3/6 overexpression phenotypes. Yeast two-hybrid with Six3/Six6 as baits, biochemical and mutational analysis, gain-of-function in medaka Development High 12441302
2002 Pax6 and Six3 mutually activate each other's expression in the developing mouse lens; both transcription factors bind regulatory sequences of the counterpart gene in vitro and in transgenic approaches; Six3 expression in lenses of Pax6 heterozygous mice is specifically reduced, and lens-specific Six3 expression rescues the Pax6 haploinsufficient lens phenotype by activating platelet-derived growth factor alpha-R/cyclin D1 signaling. In vitro DNA-binding assays, transgenic mouse rescue experiments, cyclin D1 pathway analysis PNAS High 12072567
2003 Six3 is a direct negative regulator of Wnt1 expression in the anterior neuroectoderm; in Six3-/- mice Wnt1 expression is rostrally expanded; ectopic Six3 expression in chick and zebrafish represses Wnt1; in vivo and in vitro DNA-binding assays confirm direct Six3 binding to Wnt1 regulatory sequences; Six3 rescues the headless/tcf3 zebrafish mutant phenotype through Wnt repression. Six3 knockout mice, ectopic Six3 expression in chick/zebrafish, in vivo and in vitro DNA-binding assays, phenotypic rescue of headless/tcf3 mutants Genes & development High 12569128
2003 Six3 acts as a cofactor for the NOR-1 (NR4A3) orphan nuclear receptor; Six3 binds the DNA-binding domain of NOR-1 and the EWS domain of EWS/NOR-1 via its homeodomain in vitro; Six3 stimulates NOR-1 transcriptional activity but represses EWS/NOR-1 activity in cotransfection assays. GST fusion protein assays, mammalian two-hybrid, cotransfection reporter assays in immortalized chondrocytes Cancer research Medium 12543801
2004 Six3 physically competes with Cdt1 to bind geminin (the DNA replication inhibitor); Six3 efficiently displaces Cdt1 from geminin, revealing a non-transcriptional mechanism by which Six3 promotes cell proliferation in retinal precursors; overexpression of geminin in medaka induces forebrain/eye defects rescued by Six3; loss of geminin potentiates Six3 gain-of-function phenotypes. Yeast two-hybrid, direct protein competition binding assays, medaka overexpression/loss-of-function genetics Nature High 14973488
2004 Three HPE-associated SIX3 homeodomain mutations have distinct functional consequences: L226V does not alter interaction with NOR-1; V250A produces a highly unstable protein; R257P abolishes in vivo interaction with NOR-1, suggesting different mutations affect different signaling pathways. GST pulldown assays, transient cotransfection in Neuro-2a cells, reporter assays Human mutation Medium 15523651
2005 Six3 promotes anterior neural plate expansion in Xenopus and zebrafish through transcriptional regulation of cell cycle regulators cyclinD1 and p27Xic1, as well as anti-neurogenic genes Zic2 and Xhairy2; Six3 also represses Bmp4 expression in adjacent ectoderm, and can expand the anterior neural plate even in the presence of cell cycle inhibitors, acting via BMP antagonism; Six3 cannot induce neural tissue alone but can do so in combination with Otx2. Ectopic Six3 expression in Xenopus and zebrafish, cell cycle inhibitor treatment, RT-PCR/in situ hybridization, chordino mutant rescue Development High 15843413
2005 Six3 mediates cell proliferation in the developing forebrain by sequestering Geminin from Cdt1; Lhx2 can rescue forebrain size reduction caused by six3 morpholino knockdown in zebrafish, but Six3b cannot rescue Lhx2 knockdown, placing Lhx2 downstream of Six3 in a parallel/alternative pathway for forebrain proliferation. Antisense morpholino knockdown in zebrafish, caged-mRNA photoactivation, head-specific overexpression, genetic epistasis Developmental biology Medium 16226737
2005 In developing mice, Six3 expression in the pre-placode lens ectoderm is initially Pax6-independent but subsequently becomes Pax6-dependent for both expression and nuclear localization; an in vitro protein-protein interaction is detected between Six3 and Eya1. Immunohistochemistry in Pax6 mutant mice, in vitro protein interaction assay Gene expression patterns Medium 16024294
2006 Six3 directly activates Pax6 and Sox2 expression in the presumptive lens ectoderm (PLE); conditional deletion of Six3 in the PLE disrupts lens induction and specification, downregulates Pax6, and eliminates Sox2; ChIP, EMSA, and luciferase reporter assays confirm direct Six3 binding to Pax6 and Sox2 regulatory sequences; misexpression of Six3 in chick promotes ectopic ectodermal Pax6 expression. Conditional knockout mice, ChIP, EMSA, luciferase reporter assays, misexpression in chick embryos EMBO journal High 17066077
2007 Six3 inactivation causes progressive caudalization of the diencephalon; at 15-17 somites, Wnt1 expression is anteriorly expanded in Six3-null brains; Six3;Wnt1 double-null mice reveal that Six3-mediated repression of Wnt1 is necessary for formation of the rostral diencephalon, and that Six3 activity is required for telencephalon formation. Six3 knockout, Six3;Wnt1 double knockout mice, in situ hybridization Development High 18094027
2007 MTA1 physically interacts with Six3 chromatin in a histone deacetylase (HDAC)-dependent manner, leading to transcriptional suppression of Six3; MTA1 is also a Six3-interacting corepressor contributing to self-negative regulation of Six3 transcription; loss of MTA1 in null mice leads to elevated Six3 and enhanced recruitment of Six3 to the rhodopsin promoter; Six3 homeodomain binds specific DNA elements in the rhodopsin promoter to stimulate rhodopsin transcription; Six3 cooperates with Crx or NRL to stimulate rhodopsin-luc transcription; HPE-associated Six3 deletion mutations in helix 3 of the homeodomain abolish rhodopsin promoter binding. ChIP, co-immunoprecipitation, MTA1-null mice, knockdown in rat retinal ganglion cells, luciferase reporter assays with HPE mutations PNAS High 17666527
2007 Six3 regulates diencephalic Nodal signaling activity; reduction of Six3 function causes brain-specific deregulation of Nodal pathway activity resulting in epithalamic laterality defects; misexpression and genetic epistasis in zebrafish indicate Six3 acts in the neuroectoderm to establish bilateral repression of Nodal activity, which is subsequently alleviated ipsilaterally by left-side Nodal signaling from lateral plate mesoderm. Zebrafish morpholino knockdown, Six3 misexpression, genetic epistasis experiments Neuron Medium 17678854
2008 Six3 directly binds and activates the Shh brain enhancer-2 (SBE2) located 460 kb upstream of SHH in the hypothalamus; HPE-causing Six3 alterations fail to bind and activate SBE2; DNA affinity-capture assay identified Six3 and Six6 as candidate regulators of Shh transcription; the mutant SBE2 sequence from an HPE patient shows reduced Six3 binding affinity. DNA affinity-capture assay, transgenic mouse enhancer assay, Six3 HPE mutation binding analysis Nature genetics High 18836447
2008 Haploinsufficiency of Six3 (by deletion of one allele or replacement with HPE-associated alleles) causes HPE in mice; Shh is a direct target of Six3 in the rostral diencephalon ventral midline (RDVM); reduced Six3 fails to activate Shh expression in the mutant RDVM, leading to HPE; a crossregulatory loop between Shh and Six3 exists in the ventral forebrain. Six3 heterozygous and knockin mouse models, ChIP for direct Six3-Shh target validation, zebrafish functional assays for HPE mutations Developmental cell High 18694563
2008 89% of HPE-associated SIX3 mutations function as loss-of-function alleles in zebrafish assays; disease-associated single point mutations in the Groucho-binding eh1-like motif decrease function in all assays, confirming that Groucho co-repressor interaction is essential for human SIX3 function and HPE causation; truncated SIX3 proteins missing the homeodomain retain partial function. Zebrafish functional assays for 46 distinct SIX3 mutations, eh1 motif mutational analysis Human molecular genetics High 18791198
2009 EYA4 is co-immunoprecipitated with SIX3 from cells; SIX3 recruits EYA4 (normally cytoplasmic) to the nucleus; EYA4 cooperates with SIX3 as a transcriptional coactivator in reporter gene assays, establishing a physical and functional SIX3-EYA4 interaction. Co-immunoprecipitation, confocal microscopy for nuclear recruitment, reporter gene assays Human mutation Medium 19606496
2010 Six3 directly represses Wnt8b expression in the developing neuroretina; conditional deletion of Six3 causes ectopic rostral expansion of Wnt8b and failure of neuroretina specification; ectopic Wnt8b transgenic expression is sufficient to suppress neuroretina specification; ChIP identified Six3-responsive elements in the Wnt8b locus. Conditional Six3 knockout mice, ChIP, Wnt8b transgenic overexpression Journal of clinical investigation High 20890044
2010 MTA1s and MTA1 physically interact with Six3 chromatin and inhibit Six3 transcription in an HDAC-dependent manner, relieving Six3-mediated repression of Wnt1 promoter; deletion of MTA1s/MTA1 in MEFs results in upregulation of Six3 and downregulation of Wnt signaling; in MTA1s/MTA1-null mammary glands, increased Six3 corepressor complex is recruited to the Wnt1 promoter. Co-immunoprecipitation, ChIP in null MEFs and mammary glands, gain/loss-of-function experiments Cancer research High 20682799
2010 The Six3 homeodomain binds to a TAATGTC motif (a newly defined recognition sequence distinct from the common TGATAC Six family motif) at multiple sites within the six3a promoter with high affinity; ChIP confirms Six3a binding to promoter fragments containing clustered TAATGTC sites in vivo; these sites mediate autoregulation in zebrafish embryos. In vitro DNA-binding affinity assays, single-nucleotide substitution analysis, ChIP, transient reporter assays in zebrafish embryos FEBS journal High 20193042
2011 Six3 is required for ependymal cell maturation during postnatal brain development; in Six3's absence, ependymal cells fail to suppress radial glia characteristics, resulting in a defective lateral wall, abnormal neuroblast migration and differentiation, and hydrocephaly. Six3 conditional knockout in ependymal cells, histological and molecular marker analysis Development Medium 22071110
2012 In zebrafish, Six3 (six3b and six7) cooperates with Hedgehog signaling to specify ventral telencephalon; Six3 promotes ventral telencephalic fates through transient regulation of foxg1a expression and repression of Wnt/β-catenin signaling; Six3 overexpression can compensate for loss of Hh signaling in isl1- but not nkx2.1b-positive cells, indicating a Hh-independent role for Six3. Zebrafish morpholino knockdown of six3b and six7, overexpression, Hh pathway inhibition/activation assays Development Medium 22736245
2013 Sox2 directly regulates a long-range forebrain enhancer to activate Six3 expression in the rostral diencephalon; biochemical and genetic evidence establish a direct regulatory link between Sox2 and Six3 during forebrain development. Genomic ChIP-seq for Sox2 binding, in vivo transgenic enhancer assay, genetic epistasis Developmental biology High 23792023
2016 Six3 dosage determines HPE severity in mice: semilobar HPE results from severe downregulation of Shh expression in the rostral diencephalon ventral midline, while alobar HPE is caused by downregulation of Foxg1 expression in the anterior neural ectoderm; in vivo Shh pathway activation rescues semilobar but not alobar HPE. Novel hypomorphic Six3 allele mice, in vivo Shh pathway activation, gene expression analysis Development High 27770010
2017 Six3 repression of R-spondin 2 (Rspo2) is required during optic vesicle morphogenesis and neuroretina differentiation; transient ectopic Rspo2 expression in the anterior neural plate of transgenic mouse embryos is sufficient to inhibit neuroretina differentiation; Six3-null cells exert a non-cell-autonomous repressive effect on optic vesicle formation. Six3-/- iPSC eye organoid, conditional null ESC organoid, in vivo transgenic Rspo2 overexpression, chimeric eye organoid assay Cell reports High 29117559
2017 SIX3 directly binds to the promoter regions of AURKA and AURKB (aurora kinases A and B) to repress their transcription in a dose-dependent manner; SIX3 increases p53 activity at the post-translational level through negative regulation of AURKA or AURKB; SIX3 overexpression does not affect AURKA-AURKB protein stabilization interactions. ChIP, luciferase reporter assay, Co-IP for AURKA-AURKB interaction, flow cytometry, colony formation/intracranial xenograft assays Journal of hematology & oncology Medium 28595628
2017 Six3 in a small population of anteroventral optic vesicle progenitors at E8.5 is required for neuroretinal specification; Six3 deletion in these progenitors causes rostral expansion of Wnt8b and drastic reduction of Fgf8/MAPK signaling, ablating neuroretinal specification without affecting RPE; Six3-Cre positive progenies are found in neuroretina and optic stalk but not RPE. Lineage tracing with Six3-Cre in wild-type and Six3-deficient mice, gene expression analysis by ISH/immunostaining Developmental biology High 28579317
2018 SIX3 forms a complex with LSD1/NuRD(MTA3) identified by affinity purification and mass spectrometry; this complex represses WNT1 and FOXC2 (involved in EMT) as identified by ChIP-on-chip genome-wide analysis; the SIX3/LSD1/NuRD(MTA3) complex inhibits carcinogenesis and metastasis in breast cancer cells. Affinity purification + mass spectrometry, ChIP-on-chip, in vitro and in vivo functional assays Theranostics High 29463994
2018 SP8 and SP9 directly activate Six3 expression in a spatially restricted LGE subventricular zone domain; ChIP-seq shows SP9 directly binds the promoter and a putative enhancer of Six3; conditional deletion of Six3 prevents formation of most D2 MSNs, phenocopying Sp8/9 double mutants. Conditional knockout mice (Sp8/Sp9 and Six3), ChIP-seq, in situ hybridization, immunostaining Development High 29967281
2018 Six3 and Six6 are jointly required for maintenance of multipotent neuroretinal progenitors; double knockout retinas show ectopic upregulation of Wnt3a, Fzd1, Otx1 and Cdon (ciliary margin markers) and loss of neuroretinal progenitor markers Sox2, Notch1, Otx2; stimulation of Wnt/β-catenin signaling promotes ciliary margin progenitors at the cost of neuroretinal identity, indicating Six3 and Six6 together directly or indirectly suppress Wnt/β-catenin signaling. Six3/Six6 double conditional knockout mice, Wnt-3a and GSK3β inhibitor treatment of eye cups, gene expression analysis Cell reports High 30485816
2020 EGFR activation induces DNA methylation silencing of SIX3 through the MAPK pathway: activated ERK binds ZNF263, abrogates its ubiquitination and stabilizes it; ZNF263 binds the core SIX3 promoter and recruits the KAP1/HATS/DNMT corepressor complex inducing H3K27me3 and DNA methylation at the SIX3 promoter. Co-immunoprecipitation, ChIP, ubiquitination assay, MAPK pathway inhibition/activation, reporter assays Oncogene High 32051553
2020 TRIM27 E3 ubiquitin ligase ubiquitinates and degrades SIX3 protein, activating Wnt/β-catenin signaling; SIX3 negatively regulates β-catenin, S100P, TGFB3, and MMP-9 expression in NSCLC cells. Ubiquitination assay, co-immunoprecipitation, loss/gain-of-function in NSCLC cells, XAV939 pathway inhibition Aging Medium 33264103
2021 SIX3 suppression in human adult pancreatic islets by shRNA impairs insulin secretion; SIX3 loss leads to inappropriate expression of genes normally expressed in fetal β cells, adult α cells, and non-β cells, indicating SIX3 maintains developmental fate and suppresses non-β-cell gene programs; SIX2 and SIX3 regulate distinct target gene sets. shRNA knockdown in human adult islets, transcriptome analysis, chromatin accessibility studies Genes & development Medium 33446570
2021 Six3 functions in D2 MSN precursor cells to drive their differentiation; conditional deletion of Six3 blocks differentiation without affecting proliferation, and conditionally overexpressed Six3 promotes LGE precursor differentiation; abnormally differentiated D2 MSNs in Six3-KO are eliminated by apoptosis postnatally. Conditional Six3 knockout and overexpression in mice, BrdU/EdU proliferation assays, TUNEL apoptosis assay, immunostaining Neuroscience bulletin Medium 34014554

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1995 Six3, a murine homologue of the sine oculis gene, demarcates the most anterior border of the developing neural plate and is expressed during eye development. Development (Cambridge, England) 590 8575305
2003 Six3 repression of Wnt signaling in the anterior neuroectoderm is essential for vertebrate forebrain development. Genes & development 393 12569128
1999 Mutations in the homeodomain of the human SIX3 gene cause holoprosencephaly. Nature genetics 294 10369266
2004 Direct interaction of geminin and Six3 in eye development. Nature 202 14973488
1999 Six3 overexpression initiates the formation of ectopic retina. Genes & development 186 10090721
2002 Six3-mediated auto repression and eye development requires its interaction with members of the Groucho-related family of co-repressors. Development (Cambridge, England) 178 12050133
1998 Overexpression of the forebrain-specific homeobox gene six3 induces rostral forebrain enlargement in zebrafish. Development (Cambridge, England) 163 9655819
1999 Six6 (Optx2) is a novel murine Six3-related homeobox gene that demarcates the presumptive pituitary/hypothalamic axis and the ventral optic stalk. Mechanisms of development 151 10473118
2001 The homeobox protein Six3 interacts with the Groucho corepressor and acts as a transcriptional repressor in eye and forebrain formation. Developmental biology 149 11401394
2008 Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein. Nature genetics 145 18836447
1996 Ectopic lens induction in fish in response to the murine homeobox gene Six3. Mechanisms of development 143 9025075
2006 Six3 activation of Pax6 expression is essential for mammalian lens induction and specification. The EMBO journal 139 17066077
2008 Haploinsufficiency of Six3 fails to activate Sonic hedgehog expression in the ventral forebrain and causes holoprosencephaly. Developmental cell 136 18694563
2011 The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Neural development 128 21936910
1998 Six3, a medaka homologue of the Drosophila homeobox gene sine oculis is expressed in the anterior embryonic shield and the developing eye. Mechanisms of development 127 9651515
1998 Expression of two zebrafish homologues of the murine Six3 gene demarcates the initial eye primordia. Mechanisms of development 126 9545529
2004 Molecular screening of SHH, ZIC2, SIX3, and TGIF genes in patients with features of holoprosencephaly spectrum: Mutation review and genotype-phenotype correlations. Human mutation 120 15221788
2010 Six3 demarcates the anterior-most developing brain region in bilaterian animals. EvoDevo 119 21190549
2013 The bilaterian head patterning gene six3/6 controls aboral domain development in a cnidarian. PLoS biology 118 23483856
2003 Six3 and Six6 activity is modulated by members of the groucho family. Development (Cambridge, England) 115 12441302
2009 The sea urchin animal pole domain is a Six3-dependent neurogenic patterning center. Development (Cambridge, England) 95 19270175
2010 Neuroretina specification in mouse embryos requires Six3-mediated suppression of Wnt8b in the anterior neural plate. The Journal of clinical investigation 91 20890044
2005 BMP inhibition-driven regulation of six-3 underlies induction of newt lens regeneration. Nature 91 16341014
2005 Lhx2 mediates the activity of Six3 in zebrafish forebrain growth. Developmental biology 88 16226737
2005 Six3 functions in anterior neural plate specification by promoting cell proliferation and inhibiting Bmp4 expression. Development (Cambridge, England) 76 15843413
2002 Mutually regulated expression of Pax6 and Six3 and its implications for the Pax6 haploinsufficient lens phenotype. Proceedings of the National Academy of Sciences of the United States of America 73 12072567
2009 Clinical spectrum of SIX3-associated mutations in holoprosencephaly: correlation between genotype, phenotype and function. Journal of medical genetics 71 19346217
2003 Regulation of proliferation, cell fate specification and differentiation by the homeodomain proteins Prox1, Six3, and Chx10 in the developing retina. Cell cycle (Georgetown, Tex.) 69 12851489
2000 Cloning and expression of xSix3, the Xenopus homologue of murine Six3. Mechanisms of development 69 10704858
2011 Candidate gene screen in the red flour beetle Tribolium reveals six3 as ancient regulator of anterior median head and central complex development. PLoS genetics 68 22216011
2007 Six3 inactivation causes progressive caudalization and aberrant patterning of the mammalian diencephalon. Development (Cambridge, England) 65 18094027
2001 Six3 promotes the formation of ectopic optic vesicle-like structures in mouse embryos. Developmental dynamics : an official publication of the American Association of Anatomists 64 11458394
2016 Development of the aboral domain in Nematostella requires β-catenin and the opposing activities of Six3/6 and Frizzled5/8. Development (Cambridge, England) 63 26989171
2007 Repression of Six3 by a corepressor regulates rhodopsin expression. Proceedings of the National Academy of Sciences of the United States of America 56 17666527
2018 SP8 and SP9 coordinately promote D2-type medium spiny neuron production by activating Six3 expression. Development (Cambridge, England) 55 29967281
2000 A new mutation in the six-domain of SIX3 gene causes holoprosencephaly. European journal of human genetics : EJHG 54 11039582
2018 Six3 and Six6 Are Jointly Required for the Maintenance of Multipotent Retinal Progenitors through Both Positive and Negative Regulation. Cell reports 51 30485816
2008 Genetic interaction between the homeobox transcription factors HESX1 and SIX3 is required for normal pituitary development. Developmental biology 51 18775421
2005 Pax6-dependence of Six3, Eya1 and Dach1 expression during lens and nasal placode induction. Gene expression patterns : GEP 51 16024294
2007 Six3 represses nodal activity to establish early brain asymmetry in zebrafish. Neuron 50 17678854
1996 Molecular characterization of breakpoints in patients with holoprosencephaly and definition of the HPE2 critical region 2p21. Human molecular genetics 49 8824878
2012 Utilizing prospective sequence analysis of SHH, ZIC2, SIX3 and TGIF in holoprosencephaly probands to describe the parameters limiting the observed frequency of mutant gene×gene interactions. Molecular genetics and metabolism 47 22310223
2008 Mutations in the human SIX3 gene in holoprosencephaly are loss of function. Human molecular genetics 45 18791198
2001 Antagonistic action of Six3 and Prox1 at the gamma-crystallin promoter. Nucleic acids research 44 11139622
2011 Six3 is required for ependymal cell maturation. Development (Cambridge, England) 39 22071110
2007 Six3 controls the neural progenitor status in the murine CNS. Cerebral cortex (New York, N.Y. : 1991) 38 17576749
2021 SIX2 and SIX3 coordinately regulate functional maturity and fate of human pancreatic β cells. Genes & development 37 33446570
2015 Expression of Hox, Cdx, and Six3/6 genes in the hoplonemertean Pantinonemertes californiensis offers insight into the evolution of maximally indirect development in the phylum Nemertea. EvoDevo 36 26244086
2013 The expression pattern of the genes engrailed, pax6, otd and six3 with special respect to head and eye development in Euperipatoides kanangrensis Reid 1996 (Onychophora: Peripatopsidae). Development genes and evolution 36 23625086
2010 Heterozygous mutations in SIX3 and SHH are associated with schizencephaly and further expand the clinical spectrum of holoprosencephaly. Human genetics 36 20157829
2010 Metastasis-associated protein 1 and its short form variant stimulates Wnt1 transcription through promoting its derepression from Six3 corepressor. Cancer research 36 20682799
2009 A novel SIX3 mutation segregates with holoprosencephaly in a large family. American journal of medical genetics. Part A 36 19353631
2020 The EGFR-ZNF263 signaling axis silences SIX3 in glioblastoma epigenetically. Oncogene 35 32051553
2003 The homeotic protein Six3 is a coactivator of the nuclear receptor NOR-1 and a corepressor of the fusion protein EWS/NOR-1 in human extraskeletal myxoid chondrosarcomas. Cancer research 35 12543801
2018 The Homeotic Protein SIX3 Suppresses Carcinogenesis and Metastasis through Recruiting the LSD1/NuRD(MTA3) Complex. Theranostics 34 29463994
2017 SIX3, a tumor suppressor, inhibits astrocytoma tumorigenesis by transcriptional repression of AURKA/B. Journal of hematology & oncology 34 28595628
2015 Homeodomain Proteins SIX3 and SIX6 Regulate Gonadotrope-specific Genes During Pituitary Development. Molecular endocrinology (Baltimore, Md.) 34 25915183
2012 Six3 cooperates with Hedgehog signaling to specify ventral telencephalon by promoting early expression of Foxg1a and repressing Wnt signaling. Development (Cambridge, England) 34 22736245
1998 Transient expression of a novel Six3-related zebrafish gene during gastrulation and eye formation. Gene 34 9714724
2002 A screen for co-factors of Six3. Mechanisms of development 33 12204251
2013 Down-regulation of SIX3 is associated with clinical outcome in lung adenocarcinoma. PloS one 32 23977152
2010 The unfolding clinical spectrum of holoprosencephaly due to mutations in SHH, ZIC2, SIX3 and TGIF genes. European journal of human genetics : EJHG 32 20531442
1999 Genomic cloning, structure, expression pattern, and chromosomal location of the human SIX3 gene. Genomics 32 9889003
2020 TRIM27 acts as an oncogene and regulates cell proliferation and metastasis in non-small cell lung cancer through SIX3-β-catenin signaling. Aging 31 33264103
2017 Genome-wide meta-analysis in Japanese populations identifies novel variants at the TMC6-TMC8 and SIX3-SIX2 loci associated with HbA1c. Scientific reports 28 29170429
2006 SIX3 mutations with holoprosencephaly. American journal of medical genetics. Part A 28 17001667
2017 An Eye Organoid Approach Identifies Six3 Suppression of R-spondin 2 as a Critical Step in Mouse Neuroretina Differentiation. Cell reports 25 29117559
2016 Six3 dosage mediates the pathogenesis of holoprosencephaly. Development (Cambridge, England) 25 27770010
2005 Agonistic and antagonistic action of AP2, Msx2, Pax6, Prox1 AND Six3 in the regulation of Sox2 expression. Ophthalmic research 24 16118513
2016 Six3 regulates optic nerve development via multiple mechanisms. Scientific reports 23 26822689
2002 The homeobox gene Six3 is a potential regulator of anterior segment formation in the chick eye. Developmental biology 22 12167403
2021 Homeobox Gene Six3 is Required for the Differentiation of D2-Type Medium Spiny Neurons. Neuroscience bulletin 21 34014554
2009 EYA4, deleted in a case with middle interhemispheric variant of holoprosencephaly, interacts with SIX3 both physically and functionally. Human mutation 21 19606496
2013 Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus. Scientific reports 20 23478590
2005 Expression analysis of SIX3 and SIX6 in human tissues reveals differences in expression and a novel correlation between the expression of SIX3 and the genes encoding isocitrate dehyhrogenase and cadherin 18. Genomics 20 15953543
2021 Long noncoding RNA DLGAP1-AS2 facilitates Wnt1 transcription through physically interacting with Six3 and drives the malignancy of gastric cancer. Cell death discovery 19 34545072
2020 six3 acts upstream of foxQ2 in labrum and neural development in the spider Parasteatoda tepidariorum. Development genes and evolution 19 32040712
2004 Coexpression of NOR1 and SIX3 proteins in extraskeletal myxoid chondrosarcomas without detectable NR4A3 fusion genes. Cancer genetics and cytogenetics 19 15262426
2017 Six3 in a small population of progenitors at E8.5 is required for neuroretinal specification via regulating cell signaling and survival in mice. Developmental biology 18 28579317
2014 Pax6- and Six3-mediated induction of lens cell fate in mouse and human ES cells. PloS one 18 25517354
2021 The transcription factors SIX3 and VAX1 are required for suprachiasmatic nucleus circadian output and fertility in female mice. Journal of neuroscience research 17 34212416
2018 Haploinsufficiency of Homeodomain Proteins Six3, Vax1, and Otx2 Causes Subfertility in Mice via Distinct Mechanisms. Neuroendocrinology 17 30261489
2017 Epigenetically controlled Six3 expression regulates glioblastoma cell proliferation and invasion alongside modulating the activation levels of WNT pathway members. Journal of neuro-oncology 17 28643150
2003 Retinal expression of zebrafish six3.1 and its regulation by Pax6. Biochemical and biophysical research communications 17 12951074
2021 miR-4306 Suppresses Proliferation of Esophageal Squamous Cell Carcinoma Cell by Targeting SIX3. Cell biochemistry and biophysics 16 34021861
2018 Haploinsufficiency of SIX3 Abolishes Male Reproductive Behavior Through Disrupted Olfactory Development, and Impairs Female Fertility Through Disrupted GnRH Neuron Migration. Molecular neurobiology 16 29589282
2013 Genomic code for Sox2 binding uncovers its regulatory role in Six3 activation in the forebrain. Developmental biology 16 23792023
1999 Sequence and location of SIX3, a homeobox gene expressed in the human eye. Ophthalmic genetics 16 10415461
2006 Expression of Six3 Opposite Strand (Six3OS) during mouse embryonic development. Gene expression patterns : GEP 15 17084678
2001 The orphan nuclear receptor NOR-1 interacts with the homeobox containing protein Six3. Developmental neuroscience 15 11173923
2001 Regulation of the human SIX3 gene promoter. Biochemical and biophysical research communications 15 11554737
2015 Anteroposterior patterning of Drosophila ocelli requires an anti-repressor mechanism within the hh pathway mediated by the Six3 gene Optix. Development (Cambridge, England) 13 26160900
2018 A novel long noncoding RNA lncWDR26 suppresses the growth and metastasis of hepatocellular carcinoma cells through interaction with SIX3. American journal of cancer research 12 29736313
2017 SIX3 deletions and incomplete penetrance in families affected by holoprosencephaly. Congenital anomalies 12 28670735
2016 Transcriptional Reactivation of OTX2, RX1 and SIX3 during Reprogramming Contributes to the Generation of RPE Cells from Human iPSCs. International journal of biological sciences 12 27019633
2004 Functional characterization of SIX3 homeodomain mutations in holoprosencephaly: interaction with the nuclear receptor NR4A3/NOR1. Human mutation 12 15523651
2010 Autoregulatory binding sites in the zebrafish six3a promoter region define a new recognition sequence for Six3 proteins. The FEBS journal 11 20193042
2004 [Analysis of the expression pattern of regulatory genes Pax6, Prox1, and Six3 during regeneration of eye structures in the newt]. Izvestiia Akademii nauk. Seriia biologicheskaia 11 15559128
2021 Deletion of Six3 in post-proliferative neurons produces weakened SCN circadian output, improved metabolic function, and dwarfism in male mice. Molecular metabolism 10 34974160
2008 [Expression of regulatory genes Pax6, Otx2, Six3, and FGF2 during newt retina regeneration]. Izvestiia Akademii nauk. Seriia biologicheskaia 10 18771023

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