Affinage

SIX3

Homeobox protein SIX3 · UniProt O95343

Length
332 aa
Mass
35.5 kDa
Annotated
2026-04-28
100 papers in source corpus 44 papers cited in narrative 44 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SIX3 is a homeodomain transcription factor that orchestrates anterior neural plate patterning, eye development, and forebrain specification by functioning as both a transcriptional repressor and activator depending on cofactor context. As a repressor, SIX3 recruits Groucho/TLE corepressors via an eh1-like motif in its Six domain to directly silence Wnt1, Wnt8b, Rspo2, and Bmp4, thereby protecting anterior neuroectoderm from posteriorizing signals and enabling neuroretinal and telencephalic specification (PMID:12050133, PMID:12569128, PMID:20890044, PMID:29117559); as an activator, it directly binds and stimulates transcription of Pax6, Sox2, Shh (via the remote SBE2 enhancer), and rhodopsin, often cooperating with cofactors such as Crx, NRL, and EYA family members (PMID:17066077, PMID:18836447, PMID:17666527). SIX3 also promotes cell proliferation non-transcriptionally by competing with Cdt1 for geminin binding, thereby relieving replication licensing inhibition (PMID:14973488). Haploinsufficiency of SIX3 causes holoprosencephaly (HPE2) in humans and mice through failure to activate Shh in the rostral diencephalon ventral midline, with disease severity correlating with dosage-dependent effects on Shh and Foxg1 expression (PMID:10369266, PMID:18694563, PMID:27770010).

Mechanistic history

Synthesis pass · year-by-year structured walk · 15 steps
  1. 1995 High

    Identification of Six3 as a vertebrate homologue of Drosophila sine oculis established that a homeodomain transcription factor with anterior-restricted expression exists independently of the Pax6 pathway, opening the question of its specific function in head development.

    Evidence Gene cloning, sequence analysis, in situ hybridization in wild-type and Pax6 mutant mouse embryos

    PMID:8575305

    Open questions at the time
    • No target genes identified
    • No loss-of-function phenotype characterized
    • Relationship to other anterior transcription factors undefined
  2. 1996 High

    Demonstrating that ectopic Six3 expression induces lens formation and retinal primordia in fish established Six3 as a sufficient master regulator of eye field identity, not merely a marker.

    Evidence Ectopic RNA injection in medaka with histological and marker analysis

    PMID:10090721 PMID:9025075

    Open questions at the time
    • No loss-of-function data
    • Target gene cascades downstream of Six3 unknown
    • Mechanism of action (activator vs. repressor) unresolved
  3. 1999 High

    Discovery that homeodomain mutations in human SIX3 cause holoprosencephaly (HPE2) established that SIX3 is essential for forebrain midline development and linked its transcriptional activity to a major human congenital malformation.

    Evidence Positional cloning and mutational analysis in HPE patient families

    PMID:10369266

    Open questions at the time
    • Direct transcriptional targets in forebrain unknown
    • Mechanism by which mutations cause HPE unresolved
    • Animal model of haploinsufficiency not yet available
  4. 2001 High

    Identifying Six3 as a Groucho/TLE-dependent transcriptional repressor that uses an eh1-like motif resolved the long-standing question of whether Six3 acts as an activator or repressor, revealing that its primary developmental function in forebrain expansion requires corepressor recruitment.

    Evidence Yeast two-hybrid, Co-IP, site-directed mutagenesis of eh1 motif, zebrafish overexpression phenotyping

    PMID:11401394 PMID:12050133 PMID:12441302

    Open questions at the time
    • Direct genomic targets of repression not identified by ChIP
    • Whether Six3 also has activator functions remained unclear
    • Role of individual Groucho/TLE family members not distinguished in vivo
  5. 2003 High

    Six3-null mouse analysis revealed that Six3 directly binds and represses Wnt1 transcription in the anterior neuroectoderm, and genetic epistasis showed Six3 acts upstream of Wnt signaling, establishing the first direct target gene and the core mechanism by which Six3 protects forebrain identity.

    Evidence Six3 knockout mouse, in vivo/in vitro DNA-binding assays, ectopic expression in chick/zebrafish, headless/tcf3 rescue

    PMID:12569128

    Open questions at the time
    • Whether Wnt1 is the sole critical target or one of several Wnt genes repressed was unknown
    • The Six3-Shh regulatory relationship not yet characterized
    • Mechanism of anterior-restricted Six3 expression unresolved
  6. 2004 High

    Discovery that Six3 binds geminin and competes with Cdt1 for geminin binding revealed a non-transcriptional mechanism for promoting cell proliferation, explaining how Six3 can drive progenitor expansion independently of its DNA-binding activity.

    Evidence Yeast two-hybrid, direct protein competition assay, genetic rescue in medaka

    PMID:14973488

    Open questions at the time
    • Relative contribution of transcriptional vs. geminin-mediated proliferation not quantified
    • Whether geminin interaction occurs in mammalian forebrain progenitors not confirmed in vivo
    • Structural basis of competitive binding unknown
  7. 2006 High

    Conditional deletion of Six3 in lens ectoderm combined with ChIP and EMSA demonstrated that Six3 directly activates Pax6 and Sox2, establishing that Six3 functions as a transcriptional activator for key lens-induction genes, not solely as a repressor.

    Evidence Conditional KO in mouse, ChIP, EMSA, luciferase reporter, chick misexpression

    PMID:17066077

    Open questions at the time
    • Cofactors converting Six3 from repressor to activator mode not identified
    • Whether Six3 activator function is relevant in forebrain (not just lens) undetermined
  8. 2007 High

    Identifying MTA1 as a cofactor that epigenetically silences Six3 itself via HDAC-dependent chromatin remodeling, and demonstrating that Six3 homeodomain directly activates rhodopsin transcription (with HPE mutations ablating this binding), established a regulatory feedback on Six3 levels and extended its activator role to post-mitotic photoreceptors.

    Evidence ChIP, Co-IP, MTA1-null mouse analysis, luciferase reporter with HPE mutant proteins

    PMID:17666527

    Open questions at the time
    • Whether MTA1-mediated silencing of Six3 is relevant in forebrain HPE pathogenesis unknown
    • Full repertoire of Six3 activator targets in retina not catalogued
  9. 2008 High

    Demonstrating that Six3 directly binds and activates the remote Shh brain enhancer SBE2, and that Six3 haploinsufficiency recapitulates human HPE through failure to activate Shh in the rostral diencephalon ventral midline, closed the mechanistic gap between SIX3 mutations and HPE pathogenesis via a direct Six3→Shh regulatory axis.

    Evidence DNA affinity-capture assay, transgenic enhancer assay, ChIP at Shh locus, Six3 haploinsufficient mouse models, functional analysis of 46 HPE mutations in zebrafish

    PMID:18694563 PMID:18791198 PMID:18836447

    Open questions at the time
    • How the same transcription factor switches between repression (Wnt1) and activation (Shh) mechanistically unresolved
    • Modifier genes explaining variable HPE expressivity not identified
    • Whether all HPE mutations act through SBE2 or through additional enhancers unknown
  10. 2010 High

    ChIP-validated direct repression of Wnt8b by Six3 in the neuroretina, with transgenic Wnt8b phenocopying Six3 loss, established a second Wnt target through which Six3 specifies neuroretinal fate distinct from its Wnt1-mediated forebrain function.

    Evidence Conditional Six3 KO in mouse, ChIP, transgenic Wnt8b overexpression

    PMID:20890044

    Open questions at the time
    • Whether Wnt8b repression and Wnt1 repression employ the same corepressor complexes untested
    • Genome-wide catalog of Six3-bound Wnt pathway genes absent
  11. 2011 High

    Discovery that the lncRNA Six3OS scaffolds Ezh2 and Eya to Six3 target genes revealed an epigenetic layer of Six3 regulation operating at the chromatin level, modulating target gene specificity during retinal differentiation without affecting Six3 expression itself.

    Evidence Overexpression/knockdown, direct binding assays for Six3OS-Ezh2 and Six3OS-Eya interactions, retinal specification assays

    PMID:21936910

    Open questions at the time
    • Specific genomic loci where Six3OS acts not mapped
    • Whether Six3OS is required in vivo for eye development not tested by genetic deletion
    • Stoichiometry of the Six3/Six3OS/Ezh2/Eya complex uncharacterized
  12. 2016 High

    A hypomorphic allele series showed that Six3 dosage determines HPE severity through two distinct downstream pathways—Shh for semilobar and Foxg1 for alobar HPE—explaining the clinical spectrum of SIX3-associated HPE.

    Evidence Novel hypomorphic Six3 allele mouse model, Shh pathway activation rescue, molecular phenotyping

    PMID:27770010

    Open questions at the time
    • Whether Six3 directly regulates Foxg1 or acts indirectly not resolved
    • Therapeutic implications of Shh rescue for semilobar HPE not explored
  13. 2017 High

    Identification of Rspo2 as a direct Six3 target repressed during neuroretina differentiation, with chimeric organoid experiments revealing non-cell-autonomous effects of Six3-null cells, extended the model to include Wnt-potentiating ligands and demonstrated organoid-based reconstitution of Six3 function.

    Evidence ESC/iPSC-derived eye organoids, Six3-null iPSCs, chimeric organoid assay, transgenic mice

    PMID:29117559

    Open questions at the time
    • Identity of the non-cell-autonomous signal from Six3-null cells unknown
    • Whether Rspo2 derepression alone accounts for the organoid phenotype untested
  14. 2018 Medium

    Affinity purification identified a SIX3/LSD1/NuRD(MTA3) complex and ChIP-on-chip mapped its genomic targets including WNT1, providing a biochemical framework for how Six3 recruits histone demethylase/deacetylase machinery to achieve transcriptional repression at specific loci.

    Evidence AP-MS, ChIP-on-chip, functional tumor assays in breast cancer cells

    PMID:29463994

    Open questions at the time
    • Whether the LSD1/NuRD(MTA3) complex operates in developing forebrain or only in cancer cells not established
    • Genome-wide overlap with Groucho/TLE-dependent repression untested
    • Structural basis of the SIX3-LSD1-NuRD interaction unknown
  15. 2021 High

    Demonstrating that SIX3 knockdown in human adult pancreatic islets impairs insulin secretion and derepresses fetal/non-β-cell gene programs extended Six3 function beyond development to maintenance of mature cell identity in an endocrine context.

    Evidence shRNA knockdown in human islets, RNA-seq, ATAC-seq, insulin secretion assay

    PMID:33446570

    Open questions at the time
    • Direct SIX3 target genes in β-cells not fully distinguished from indirect effects
    • Whether SIX3 loss contributes to type 2 diabetes pathogenesis in humans unknown
    • Cofactor complex used by SIX3 in β-cells not characterized

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include: (1) the structural and cofactor basis determining whether Six3 acts as a repressor or activator at specific loci; (2) a genome-wide map of direct Six3 binding sites across developmental stages; (3) the in vivo significance of the geminin interaction in mammalian forebrain progenitors; and (4) whether SIX3-based regulatory circuits are therapeutically targetable in HPE or diabetes.
  • No crystal structure of Six3 in complex with DNA or cofactors
  • Genome-wide ChIP-seq across developmental time points lacking for most tissues
  • In vivo functional significance of many reported protein interactions (NOR-1, bHLH factors) unresolved

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140110 transcription regulator activity 9 GO:0003677 DNA binding 7
Localization
GO:0005634 nucleus 4
Pathway
R-HSA-1266738 Developmental Biology 12 R-HSA-74160 Gene expression (Transcription) 7 R-HSA-162582 Signal Transduction 6 R-HSA-1643685 Disease 4
Partners
EYA1EYA4GMNNGRG5LSD1MTA1PAX6TLE1
Complex memberships
SIX3/Groucho(TLE) corepressor complexSIX3/LSD1/NuRD(MTA3) complexSIX3/geminin complex

Evidence

Reading pass · 44 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1995 Six3 is a murine homologue of the Drosophila sine oculis gene, encoding a homeodomain-containing transcription factor expressed in the anterior neural plate and developing eye; its expression is not affected by Pax6 loss-of-function (Small eye mutants), placing it in a parallel or independent pathway. Gene cloning, sequence analysis, chromosomal mapping, in situ hybridization in wild-type and Pax6 mutant embryos Development High 8575305
1996 Ectopic expression of mouse Six3 in medaka fish embryos is sufficient to promote ectopic lens formation, demonstrating that Six3 can trigger the genetic pathway leading to lens differentiation independently of retinal tissue. Ectopic RNA injection/overexpression in medaka fish embryos with histological and molecular marker analysis Mechanisms of development High 9025075
1999 Mutations in the homeodomain of human SIX3 cause holoprosencephaly; at least four different homeodomain mutations are associated with HPE2 and are predicted to interfere with transcriptional activation, establishing SIX3 as the HPE2 gene. Positional cloning, mutational analysis in HPE patients, chromosomal mapping of translocation breakpoints Nature genetics High 10369266
1999 Six3 overexpression in medaka fish embryos causes ectopic Pax6 and Rx2 expression in midbrain and cerebellum, leading to formation of ectopic retinal primordia; injected mouse Six3 also initiates ectopic endogenous medaka Six3 expression, revealing an autoregulatory feedback loop. RNA injection/overexpression in medaka fish embryos with molecular marker analysis Genes & development High 10090721
2001 Six3 functions as a Groucho-dependent transcriptional repressor in eye and forebrain formation; it contains eh1-related motifs that mediate interaction with the Groucho corepressor Grg3; point mutations in the eh1 motifs reduce both forebrain-enlarging activities and interaction with Grg3 in zebrafish. Yeast two-hybrid, dominant activator/repressor overexpression in zebrafish, site-directed mutagenesis, in vivo phenotypic analysis Developmental biology High 11401394
2001 Six3 acts as a transcriptional repressor of the gamma-crystallin (CRYGF) promoter, reducing its activity to ~10% of basal, and acts antagonistically to Prox1 activator at the CRYGD/e/f promoters; a Six3-responsive element was mapped between -101 and -123 of the gammaF-crystallin promoter. Cell transfection reporter assays, randomly mutated promoter fragment analysis Nucleic acids research Medium 11139622
2002 Six3 interacts with Groucho-related corepressors Grg4 and Grg5 via a conserved phenylalanine in an eh1-like motif in the Six domain of Six3; this interaction was validated by co-immunoprecipitation; Six3 binds a specific DNA motif and acts as a potent transcriptional repressor through this interaction; disruption of the Groucho interaction abolishes Six3-dependent auto-repression and eye/lens developmental functions in vivo. Co-immunoprecipitation from cell lines, DNA-binding PCR assay, in vivo retroviral overexpression in rat retina, in ovo electroporation in chick, site-directed mutagenesis Development High 12050133
2002 Six3 and Pax6 mutually activate each other's expression in the developing lens; Six3 binds regulatory sequences of the Pax6 gene and Pax6 binds regulatory sequences of Six3; lens-specific expression of Six3 rescues the Pax6 haploinsufficient lens phenotype via cell proliferation and activation of the PDGF-alpha-R/cyclin D1 signaling pathway. In vitro binding assays, transgenic rescue experiments, pathway analysis PNAS High 12072567
2003 Six3 is a direct negative regulator of Wnt1 expression in the anterior neuroectoderm; in Six3-null mice, Wnt1 expression is rostrally expanded; Six3 binds the Wnt1 locus in vivo and in vitro DNA-binding assays; ectopic Six3 in chick and fish embryos represses Wnt1; phenotypic rescue of headless/tcf3 zebrafish by mouse Six3 demonstrates Six3 acts upstream of Wnt signaling to specify forebrain fate. Six3 knockout mouse analysis, in vivo and in vitro DNA-binding assays, ectopic expression in chick and zebrafish, genetic epistasis (headless/tcf3 rescue) Genes & development High 12569128
2003 The Six domain of Six3 (and Six6) strongly interacts with the QD domain of TLE1 and AES (Groucho family members); Six3 additionally interacts with TLE proteins via the WDR domain; gain-of-function in medaka shows synergistic activity between Six3/Six6 and TLE1 in expanding the eye field; AES abrogates Six3/Six6 overexpression phenotypes. Yeast two-hybrid screen, biochemical and mutational analysis, gain-of-function in medaka fish Development High 12441302
2004 Six3 directly binds to geminin (a DNA replication-inhibitor/Cdt1 sequestrator) and competes with Cdt1 for geminin binding, thereby promoting cell proliferation without transcription; overexpression of geminin in medaka phenocopies Six3 inactivation (forebrain/eye defects), and these defects are rescued by Six3; loss of geminin promotes retinal precursor proliferation, potentiating Six3 gain-of-function. Yeast two-hybrid screen, direct protein binding competition assay, overexpression and loss-of-function in medaka fish, genetic rescue experiments Nature High 14973488
2005 Six3 expands the anterior neural plate partly through transcriptional regulation of cell cycle regulators cyclinD1 and p27Xic1 and anti-neurogenic genes Zic2 and Xhairy2; it can also expand the neural plate independently of the cell cycle by repressing Bmp4 expression in adjacent ectoderm; Six3 cannot alone induce neural tissue in animal caps but can do so in combination with Otx2. Ectopic expression in Xenopus and zebrafish, cell cycle inhibitor treatment, Bmp4 expression analysis, chordino mutant rescue Development High 15843413
2005 Lhx2 mediates an alternative/parallel pathway for cellular proliferation in the developing forebrain downstream of Six3; head-specific activation of Lhx2 completely rescues the telencephalon size reduction in six3 morphant zebrafish, whereas ectopic Six3b cannot rescue lhx2 knockdown, placing Lhx2 downstream of Six3 in this pathway. Antisense morpholino knockdown, caged-mRNA photoactivation in zebrafish, genetic epistasis Developmental biology Medium 16226737
2006 Six3 directly activates Pax6 and Sox2 expression in the presumptive lens ectoderm; conditional deletion of Six3 in the lens ectoderm causes loss of Pax6 and Sox2 expression and failure of lens induction; ChIP, EMSA, and luciferase reporter assays confirm direct binding and activation; misexpression in chick promotes ectopic ectodermal Pax6 expression domain. Conditional knockout in mouse, ChIP, electrophoretic mobility shift assay (EMSA), luciferase reporter assay, chick misexpression The EMBO journal High 17066077
2007 MTA1 physically interacts with Six3 chromatin in a histone deacetylase-dependent manner, leading to transcriptional suppression of the Six3 gene; MTA1 is also a Six3-interacting corepressor contributing to self-negative regulation of Six3; Six3's homeodomain interacts with specific DNA elements in the rhodopsin promoter to stimulate rhodopsin transcription; Six3 cooperates with Crx or NRL in stimulating rhodopsin-luc transcription; HPE-associated Six3 homeodomain deletion mutations cannot bind rhodopsin DNA or stimulate its transcription. ChIP, Co-IP, gain/loss-of-function in MTA1-null mice and retinal ganglion cells, luciferase reporter assays PNAS High 17666527
2007 Six3 represses Wnt1 transcription; in Six3-null mice, Wnt1 is anteriorly expanded causing progressive caudalization of the diencephalon; analysis of Six3;Wnt1 double-null mice demonstrates 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 genetic epistasis, developmental staging analysis Development High 18094027
2007 Six3 acts in the neuroectoderm to establish a prepattern of bilateral repression of Nodal activity in the dorsal diencephalon; reduction of Six3 function causes brain-specific deregulation of Nodal pathway activity resulting in epithalamic laterality defects; epistasis experiments position Six3 upstream of Nodal signaling in establishing brain left-right asymmetry. Zebrafish loss-of-function (morpholino), misexpression, genetic epistasis experiments Neuron High 17678854
2008 Six3 directly binds and activates the Shh brain enhancer-2 (SBE2), a remote forebrain enhancer located 460 kb upstream of SHH; HPE-causing SIX3 alterations fail to bind and activate SBE2; identified via DNA affinity-capture assay screening of SBE2 sequence. DNA affinity-capture assay, transgenic mouse enhancer assay, direct DNA-binding assay with HPE mutant proteins Nature genetics High 18836447
2008 Six3 haploinsufficiency (deletion of one Six3 allele or replacement with HPE-associated mutant alleles) is sufficient to recapitulate human HPE in mice; Shh is a direct target of Six3 in the rostral diencephalon ventral midline (RDVM); reduced Six3 fails to activate Shh in the RDVM, demonstrating a direct regulatory relationship and a crossregulatory loop between Shh and Six3 in the ventral forebrain. Six3 haploinsufficiency mouse models, ChIP for Six3 binding to Shh locus, zebrafish functional assays Developmental cell High 18694563
2008 HPE-associated SIX3 mutations are loss-of-function alleles (89% confirmed in zebrafish assays); disease-associated mutations in the Groucho-binding eh1-like motif decrease Six3 function in all assays, confirming that Six3-Groucho co-repressor interaction is essential for human SIX3 activity and HPE pathogenesis; truncated Six3 versions lacking the homeodomain retain partial function. Zebrafish gain-of-function and loss-of-function assays for 46 distinct SIX3 mutations, structure-function analysis Human molecular genetics High 18791198
2010 Six3 directly represses Wnt8b expression in the developing neuroretina; conditional deletion of Six3 causes ectopic Wnt8b expression which is sufficient to suppress neuroretina specification; ChIP identified Six3-responsive elements in the Wnt8b locus; transgenic ectopic Wnt8b expression phenocopies Six3 deletion in blocking neuroretina specification. Conditional Six3 knockout in mouse, ChIP, transgenic Wnt8b overexpression, comparative molecular analysis Journal of Clinical Investigation High 20890044
2010 MTA1s and MTA1 physically interact with Six3 chromatin and inhibit Six3 transcription in a histone deacetylase-dependent manner; this allows derepression of Wnt1 transcription (which Six3 normally represses); in MTA1/MTA1s null cells, Six3 is upregulated and Six3 corepressor complex recruitment to the Wnt1 promoter is increased. ChIP, gain/loss-of-function (knockdown and knockout), multiple model systems including MEFs and mammary glands Cancer research High 20682799
2011 Six3OS, a long noncoding RNA transcribed from the distal promoter region of Six3, binds directly to Ezh2 and Eya family members, acting as a molecular scaffold to recruit histone modification enzymes to Six3 target genes, thereby modulating Six3 activity during retinal cell specification without affecting Six3 expression levels. Overexpression and knockdown analysis, direct binding assays (Six3OS-Ezh2 and Six3OS-Eya interactions), retinal cell specification assays Neural development High 21936910
2011 Six3 is required for ependymal cell maturation; in its absence, ependymal cells fail to suppress radial glia characteristics, resulting in defective lateral wall, abnormal neuroblast migration and differentiation, and hydrocephaly; Six3 is expressed in ependymal cells during formation of the lateral wall of the lateral ventricles. Six3 conditional knockout in mouse, cellular marker analysis, localization studies Development High 22071110
2012 Six3 promotes ventral telencephalic fates by transiently regulating foxg1a expression and repressing the Wnt/β-catenin pathway; Six3 cooperates with Hedgehog signaling to specify ventral telencephalon, with an Hh-independent role in isl1-positive (but not nkx2.1b-positive) cells. Zebrafish six3b;six7 double morphant analysis, genetic epistasis with Hedgehog pathway, overexpression experiments Development Medium 22736245
2013 Sox2 directly regulates a long-range forebrain enhancer to activate Six3 expression in the rostral diencephalon; biochemical (ChIP) and genetic evidence indicate a direct regulatory link between Sox2 and Six3 during forebrain development. Genomic ChIP-based identification, in vivo transgenic reporter assay, biochemical and genetic validation Developmental biology Medium 23792023
2016 Six3 dosage-dependently determines HPE phenotype severity in mice: semilobar HPE results from severe downregulation of Shh expression in the rostral diencephalon ventral midline, while alobar HPE results from downregulation of Foxg1 expression in the anterior neural ectoderm; in vivo activation of Shh signaling rescues the semilobar but not alobar phenotype, establishing two distinct downstream pathways. Novel hypomorphic Six3 allele mouse model, Shh pathway activation rescue, molecular phenotyping Development High 27770010
2017 Six3 directly represses R-spondin 2 (Rspo2) expression during neuroretina differentiation; transient ectopic expression of Rspo2 in the anterior neural plate of transgenic mice is sufficient to inhibit neuroretina differentiation; Six3-null cells exert a non-cell-autonomous repressive effect on optic vesicle formation and neuroretina differentiation in chimeric eye organoids. Eye organoid system using ESC/iPSC-derived optic vesicles, Six3-/- iPSC generation, conditional null ESCs, transgenic mouse experiments, chimeric organoid assay Cell reports High 29117559
2017 Six3 in a small population of anteroventral optic pit/vesicle progenitors at E8.5 is required for neuroretinal specification by repressing Wnt8b and maintaining Fgf8/MAPK signaling; lineage tracing showed Six3-Cre positive progenitors contribute to neuroretina and optic stalk but not RPE; Six3 deletion in these cells causes the progenitors to be lost and RPE to derive from Six3-Cre-negative cells. Cre-mediated lineage tracing in wild-type and Six3-deficient mice, conditional deletion, molecular signaling pathway analysis Developmental biology High 28579317
2018 SP8 and SP9 transcription factors drive expression of Six3 in a spatially restricted domain of the LGE subventricular zone; ChIP-Seq reveals SP9 directly binds the promoter and a putative enhancer of Six3; conditional deletion of Six3 prevents formation of most D2 MSNs, phenocopying Sp8/9 mutants, placing Six3 downstream of SP8/SP9 in a transcription pathway for D2 MSN production. Conditional deletion of Sp8, Sp9, and Six3 in mice, ChIP-Seq for SP9 binding to Six3 locus, neuronal subtype marker analysis Development High 29967281
2018 SIX3 forms a complex with LSD1/NuRD(MTA3); affinity purification and mass spectrometry identified this complex; ChIP-on-chip identified WNT1 and FOXC2 as genomic targets of the SIX3/LSD1/NuRD(MTA3) complex, which inhibits carcinogenesis and metastasis in breast cancer cells. Affinity purification/mass spectrometry, ChIP-on-chip, functional tumor assays Theranostics Medium 29463994
2018 Six3 and Six6 are jointly required for maintenance of multipotent neuroretinal progenitors by suppressing Wnt/β-catenin signaling and promoting retinogenic factors; the double KO (DKO) reveals a functional redundancy: neither single KO shows the DKO phenotype, including ectopic upregulation of Wnt3a, Fzd1, CM markers, and loss of Sox2, Notch1, and Otx2. Six3 and Six6 double conditional knockout in mice, Wnt signaling stimulation experiments, molecular marker analysis Cell reports High 30485816
2020 EGFR activation induces DNA methylation of the SIX3 promoter through MAPK pathway; ERK binds ZNF263, abrogating its ubiquitination and stabilizing it; ZNF263 binds the SIX3 core promoter and recruits KAP1/HATS/DNMT corepressor complex, inducing transcriptional silencing of SIX3 through H3K27me3 and DNA methylation. Signaling pathway manipulation, Co-IP, ChIP, promoter methylation analysis, epistasis experiments Oncogene Medium 32051553
2020 TRIM27 ubiquitinates and degrades SIX3 protein; TRIM27 acts as an E3 ubiquitin ligase for SIX3, leading to activation of Wnt/β-catenin signaling (which SIX3 normally represses) and promotion of NSCLC cell proliferation and metastasis. Co-IP, ubiquitination assays, knockdown/overexpression experiments in lung cancer cells and tissue analysis Aging Medium 33264103
2021 Six3 is required for the differentiation (but not proliferation) of D2-type medium spiny neuron precursor cells in the LGE; conditional overexpression of Six3 promotes LGE precursor differentiation; in the absence of Six3, abnormally differentiated D2 MSNs are eliminated by apoptosis postnatally. Conditional Six3 knockout and overexpression in mice, cell proliferation/apoptosis assays, neuronal marker analysis Neuroscience bulletin Medium 34014554
2021 SIX3 suppression in human adult pancreatic islets impairs insulin secretion; SIX3 loss leads to inappropriate expression of fetal β-cell genes, adult α-cell genes, and non-β-cell genes, indicating SIX3 maintains developmental fate of mature β cells; chromatin accessibility studies identified genes directly regulated by SIX3. shRNA-mediated knockdown in human islets, transcriptome analysis, chromatin accessibility (ATAC-seq), functional insulin secretion assay Genes & development High 33446570
2001 The orphan nuclear receptor NOR-1 interacts with Six3 in vitro and in yeast; the interaction requires the DNA binding and AF2 domains of NOR-1; Six3 has a negative effect on NOR-1 transactivation through the NBRE response element in a dose-dependent manner. Yeast two-hybrid screen, in vitro pull-down, cotransfection reporter assays Developmental neuroscience Medium 11173923
2003 Six3 acts as a coactivator of nuclear receptor NOR-1 and as a corepressor of the fusion protein EWS/NOR-1; Six3 binds the DNA-binding domain of NOR-1 and the EWS domain of EWS/NOR-1 in GST pull-down assays; Six3 homeodomain is required for these interactions; in vivo interaction confirmed by mammalian two-hybrid in immortalized chondrocytes. RT-PCR in EMC tumors, GST pull-down assay, mammalian two-hybrid, cotransfection reporter assays Cancer research Medium 12543801
2002 Six3 bHLH co-factor screen identified ATH5, ATH3, NEUROD, and ASH1 as proteins that interact specifically with XSix3; the bHLH domain of NEUROD interacts with the SIX domain of XSix3, defining a new interaction interface. Yeast two-hybrid screen, biochemical domain-mapping analysis Mechanisms of development Low 12204251
2005 An in vitro protein-protein interaction is detected between Six3 and Eya1; Six3 expression in the pre-placode lens ectoderm is initially Pax6-independent but subsequently both its expression and nuclear localization become Pax6-dependent. In vitro protein-protein interaction assay, immunohistochemistry in Pax6 mutant mice, nuclear localization analysis Gene expression patterns Low 16024294
2009 EYA4 is co-immunoprecipitated with SIX3; EYA4 protein is recruited to the nucleus by SIX3; EYA4 cooperates with SIX3 in reporter gene assays as a transcriptional coactivator, demonstrating physical and functional association between EYA4 and SIX3. Co-immunoprecipitation, confocal microscopy for subcellular localization, reporter gene assays Human mutation Medium 19606496
2010 Six3 defines a novel DNA recognition sequence (TAATGTC) for its homeodomain; this is distinct from the common Six family recognition sequence (TGATAC); in vitro binding to TAATGTC and TGATAC sites shows similar affinities suggesting two distinct DNA-binding modes; ChIP in zebrafish embryos confirmed Six3a binding to promoter fragments containing the TAATGTC motif, which is involved in autoregulation. In vitro binding affinity analysis with single-nucleotide substitutions, transient reporter assays in zebrafish embryos, ChIP in zebrafish The FEBS journal Medium 20193042
2015 SIX3 represses transcription of GnRH receptor (GnRHR) and the common α-subunit (Cga) genes in immature gonadotrope cell lines; SIX3 and SIX6 can functionally compensate for each other in gonadotrope gene regulation; SIX6 repression requires interaction with TLE corepressor proteins and competition for DNA-binding sites with Pitx1. siRNA knockdown in gonadotrope cell lines, Six6 knockout mouse analysis, reporter and binding assays Molecular endocrinology Medium 25915183
2017 SIX3 directly represses transcription of aurora kinase A (AURKA) and aurora kinase B (AURKB) in astrocytoma cells in a dose-dependent manner; ChIP confirmed SIX3 binding to AURKA and AURKB promoter regions; SIX3 increases p53 activity at the post-translational level through negative regulation of AURKA/AURKB; AURKA and AURKB interact to stabilize each other, an interaction not affected by SIX3 overexpression. ChIP, luciferase reporter assay, Co-IP for AURKA-AURKB interaction, flow cytometry, intracranial xenograft Journal of hematology & oncology Medium 28595628

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) 589 8575305
2003 Six3 repression of Wnt signaling in the anterior neuroectoderm is essential for vertebrate forebrain development. Genes & development 390 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 200 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) 177 12050133
1998 Overexpression of the forebrain-specific homeobox gene six3 induces rostral forebrain enlargement in zebrafish. Development (Cambridge, England) 163 9655819
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1998 Expression of two zebrafish homologues of the murine Six3 gene demarcates the initial eye primordia. Mechanisms of development 126 9545529
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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 66 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) 59 26989171
2018 SP8 and SP9 coordinately promote D2-type medium spiny neuron production by activating Six3 expression. Development (Cambridge, England) 55 29967281
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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
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2017 SIX3, a tumor suppressor, inhibits astrocytoma tumorigenesis by transcriptional repression of AURKA/B. Journal of hematology & oncology 33 28595628
2012 Six3 cooperates with Hedgehog signaling to specify ventral telencephalon by promoting early expression of Foxg1a and repressing Wnt signaling. Development (Cambridge, England) 33 22736245
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2005 Agonistic and antagonistic action of AP2, Msx2, Pax6, Prox1 AND Six3 in the regulation of Sox2 expression. Ophthalmic research 24 16118513
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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
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