SIX6 (OPTX2) is a SIX/sine oculis family homeodomain transcription factor of the Six3/6 (Optix) subfamily, closely related to SIX3 and encoded in the SIX1-SIX4-SIX6 cluster on chromosome 14q23. It is expressed in the developing and adult neural retina, optic stalk/optic nerve region, ventral hypothalamus and pituitary. Through its Six domain and homeodomain it binds cis-regulatory DNA (for example the Shh SBE2 forebrain enhancer) and acts mainly as a transcriptional repressor, recruiting Groucho/TLE (TLE1, AES/TLE5) and Dachshund corepressors via its Six domain. In mouse, Six6-Dach complexes directly repress cyclin-dependent kinase inhibitor genes such as p27Kip1, expanding early retinal and pituitary progenitor pools; Six6 loss causes retinal and pituitary hypoplasia, and with Six3 it contributes to eye-field specification. In humans, 14q22-q23 deletions encompassing SIX6 are associated with bilateral anophthalmia and pituitary anomalies, homozygous truncation causes complex microphthalmia with optic disc anomalies and retinal dystrophy, and common coding variants (e.g. Asn141His) at the SIX1/SIX6 locus are associated with optic nerve cup-to-disc ratio and primary open-angle glaucoma.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000785 chromatin | ISA GO_REF:0000113 | ACCEPT | Summary: TFClass-based ISA: chromatin. Reason: Sequence-specific homeodomain TF that occupies target promoters (e.g. p27Kip1) with Dach corepressors. Supporting Evidence: PMID:12130660 Six6, in association with Dach corepressors, regulates proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: RNA Pol II cis-regulatory region sequence-specific DNA binding (Six3/6 subfamily). Reason: SIX6 binds the Shh SBE2 enhancer directly and represses the p27Kip1 promoter; the IBA node over the SIX family is sound and SIX6 has its own experimental support. Supporting Evidence: PMID:18836447 indicating that the binding of Six3 and Six6 to SBE2 was direct PMID:12130660 Six6, in association with Dach corepressors, regulates proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. |
| 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: IDA: Six6 binds the Shh forebrain enhancer SBE2 directly in EMSA. Reason: Direct binding of Six6 to a defined Pol II cis-regulatory enhancer element. Supporting Evidence: PMID:18836447 indicating that the binding of Six3 and Six6 to SBE2 was direct PMID:18836447 Our finding that the DNA sequence containing SBE2(C) functions as a Six3/6 binding site raised the possibility that the SBE2(T) variant interferes with the recruitment of Six3 to this site. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: IEA (ARBA/mouse ortholog): cis-regulatory region sequence-specific DNA binding. Reason: Consistent with direct EMSA and promoter-repression evidence. Supporting Evidence: PMID:18836447 indicating that the binding of Six3 and Six6 to SBE2 was direct PMID:12130660 Six6, in association with Dach corepressors, regulates proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: DNA-binding transcription factor activity, RNA polymerase II-specific. Reason: Core MF: SIX6 is a sequence-specific homeodomain TF; its best-characterised activity is direct repression (p27Kip1) with Dach and Groucho/TLE corepressors. Supporting Evidence: PMID:12130660 We have genetically established that Six6 homeodomain factor, acting as a strong tissue-specific repressor, regulates early progenitor cell proliferation during mammalian retinogenesis and pituitary development. PMID:12130660 Six6, in association with Dach corepressors, regulates proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | ISA GO_REF:0000113 | ACCEPT | Summary: TFClass ISA: DNA-binding TF activity, Pol II-specific. Reason: Bona fide homeodomain TF. Supporting Evidence: PMID:12130660 We have genetically established that Six6 homeodomain factor, acting as a strong tissue-specific repressor, regulates early progenitor cell proliferation during mammalian retinogenesis and pituitary development. |
| GO:0001654 eye development | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: eye development. Reason: Core BP: Six6 is required for retinal progenitor proliferation and eye-field development; human SIX6 deletion/truncation is associated with anophthalmia/microphthalmia and optic disc anomalies. Supporting Evidence: PMID:12130660 We have genetically established that Six6 homeodomain factor, acting as a strong tissue-specific repressor, regulates early progenitor cell proliferation during mammalian retinogenesis and pituitary development. PMID:12441302 Six3 and Six6 are two genes required for the specification and proliferation of the eye field in vertebrate embryos PMID:10512683 Genomic analyses of one of these cases demonstrated SIX6 hemizygosity, strongly suggesting that SIX6 haploinsufficiency is responsible for these developmental disorders. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: IEA (InterPro homeodomain): DNA binding. Reason: Correct but uninformative parent of sequence-specific cis-regulatory DNA binding. Supporting Evidence: PMID:18836447 indicating that the binding of Six3 and Six6 to SBE2 was direct |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: nucleus. Reason: Nuclear homeodomain TF. Supporting Evidence: PMID:12130660 Six6, in association with Dach corepressors, regulates proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: IEA (UniProt subcellular location): nucleus. Reason: Nuclear TF. Supporting Evidence: PMID:12130660 Six6, in association with Dach corepressors, regulates proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. |
| GO:0005667 transcription regulator complex | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: transcription regulator complex. Reason: SIX6 functions in repressor complexes with Dach and Groucho/TLE corepressors. Supporting Evidence: PMID:12130660 Six6, in association with Dach corepressors, regulates proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. PMID:12441302 consistent with the view that both Six3 and Six6 act in combination with either Tle1 and/or Aes |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: IBA: regulation of transcription by RNA polymerase II. Reason: SIX6 directly regulates (represses) Pol II target genes such as p27Kip1. Supporting Evidence: PMID:12130660 Six6, in association with Dach corepressors, regulates proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. |
| 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. SIX6 acts in retinal, optic and pituitary progenitors 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:12130660 We have genetically established that Six6 homeodomain factor, acting as a strong tissue-specific repressor, regulates early progenitor cell proliferation during mammalian retinogenesis and pituitary development. |
| GO:0007601 visual perception | TAS PMID:10512683 Genomic cloning and characterization of the human homeobox g... | MARK AS OVER ANNOTATED | Summary: TAS (cloning paper): visual perception. Reason: The cloning paper reports retinal expression and association of SIX6 hemizygosity with anophthalmia; this supports eye development rather than visual perception. Supporting Evidence: PMID:10512683 SIX6 is closely related to SIX3 and is expressed in the developing and adult human retina. PMID:10512683 Genomic analyses of one of these cases demonstrated SIX6 hemizygosity, strongly suggesting that SIX6 haploinsufficiency is responsible for these developmental disorders. |
| GO:0009887 animal organ morphogenesis | TAS PMID:10512683 Genomic cloning and characterization of the human homeobox g... | MODIFY | Summary: TAS (cloning paper): animal organ morphogenesis. Reason: Too general. SIX6 controls retinal progenitor expansion (and pituitary development); retina development in camera-type eye is the specific organ-level process. Proposed replacements: retina development in camera-type eye Supporting Evidence: PMID:12130660 We have genetically established that Six6 homeodomain factor, acting as a strong tissue-specific repressor, regulates early progenitor cell proliferation during mammalian retinogenesis and pituitary development. PMID:10512683 Genomic analyses of one of these cases demonstrated SIX6 hemizygosity, strongly suggesting that SIX6 haploinsufficiency is responsible for these developmental disorders. |
| GO:1990837 sequence-specific double-stranded DNA binding | IDA PMID:28473536 Impact of cytosine methylation on DNA binding specificities ... | ACCEPT | Summary: IDA (HT-SELEX): sequence-specific double-stranded DNA binding. Reason: Accepted by deferring to the curator's IDA. The paper reports HT-SELEX binding specificities for hundreds of human TFs; SIX6 is not named in the cached main text, so the SIX6-specific motif lives in the paper's supplementary data. The quote shows only the scope of the screen. Sequence-specific DNA binding is in any case expected for this SIX homeodomain protein. Supporting Evidence: PMID:28473536 In total, HT-SELEX models now exist for 632 of the ~1400 (23) human TFs. |
| GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific | ISS PMID:12130660 Tissue-specific regulation of retinal and pituitary precurso... | NEW | Summary: Mouse Six6 acts as a strong tissue-specific repressor that, with Dach corepressors, directly represses CDK inhibitor genes including the p27Kip1 promoter in retinal and pituitary progenitors. Reason: Repressor activity is the best-characterised molecular activity of the Six3/6 subfamily and is not captured by existing annotations; human SIX6 also binds TLE1/AES corepressors directly. Supporting Evidence: PMID:12130660 We have genetically established that Six6 homeodomain factor, acting as a strong tissue-specific repressor, regulates early progenitor cell proliferation during mammalian retinogenesis and pituitary development. PMID:12130660 Six6, in association with Dach corepressors, regulates proliferation by directly repressing cyclin-dependent kinase inhibitors, including the p27Kip1 promoter. 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 |
| GO:0001222 transcription corepressor binding | IPI PMID:12441302 Six3 and Six6 activity is modulated by members of the grouch... | NEW | Summary: SIX6 (bait in the yeast two-hybrid screen) binds the Groucho family corepressor TLE1 and AES via its Six domain. Reason: The interaction was identified with SIX6 as bait and mapped biochemically; SIX6 and TLE1 act synergistically in medaka eye-field expansion. Mouse Six6 also binds Grg/Groucho proteins and Dach corepressors. 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 PMID:12441302 consistent with the view that both Six3 and Six6 act in combination with either Tle1 and/or Aes PMID:12050133 interact with mouse Six3 and its closely related member Six6, which may also be involved in vertebrate eye development |
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Download this section (compressed HTML)Q: What is the human SIX6 direct target repertoire in retinal progenitors and optic nerve head cells, and does the glaucoma-associated Asn141His variant alter DNA binding or corepressor recruitment?
Q: Does SIX6 ever act as an activator (e.g. at the Shh SBE2 enhancer) in vivo, or is it exclusively a repressor?
Experiment: Compare wild-type and Asn141His SIX6 in human iPSC-derived retinal organoids by CUT&RUN and RNA-seq, with p27Kip1 reporter assays and TLE1/DACH1 co-immunoprecipitation.
Hypothesis: The SIX6 Asn141His glaucoma risk variant reduces repression of p27Kip1/CDKN1B and other targets in retinal progenitors.
Type: genome-wide DNA-binding and transcriptomic profiling
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