{"gene":"ZBTB33","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":1999,"finding":"Kaiso was identified as a novel BTB/POZ zinc finger transcription factor that directly interacts with p120-catenin (p120ctn). Yeast two-hybrid screening identified Kaiso as a p120ctn-binding partner; the interaction was confirmed by co-immunoprecipitation with p120ctn-specific antibodies. Mapping studies showed the interaction involves Arm repeats 1-7 of p120ctn and the C-terminal 200 amino acids of Kaiso. Kaiso homodimerizes via its POZ domain but does not heterodimerize with BCL-6. Kaiso localizes to the nucleus and nuclear dots.","method":"Yeast two-hybrid screen, co-immunoprecipitation, immunolocalization, domain mapping","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP confirmed by multiple p120-specific antibodies, domain mapping, and replicated in subsequent studies","pmids":["10207085"],"is_preprint":false},{"year":2001,"finding":"Kaiso is a methylation-dependent transcriptional repressor that requires at least two symmetrically methylated CpG dinucleotides (preferably within 5'CGCG) for DNA binding. Kaiso is a constituent of one of two methyl-CpG binding complexes originally designated as MeCP1. The zinc finger motifs are responsible for DNA binding. Kaiso behaves as a methylation-dependent transcriptional repressor in transient transfection assays.","method":"Biochemical purification, transient transfection reporter assays, complex fractionation (MeCP1)","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro binding assays, reporter assays, biochemical fractionation; foundational paper replicated across many subsequent studies","pmids":["11445535"],"is_preprint":false},{"year":2002,"finding":"Kaiso is a dual-specificity DNA-binding protein that recognizes both a sequence-specific consensus (TCCTGCNA, minimal core CTGCNA) and methylated CpG dinucleotides via its zinc fingers. Zinc fingers 2 and 3 are necessary and sufficient for sequence-specific DNA binding. p120ctn inhibits Kaiso DNA binding at both recognition sites. Kaiso has higher affinity for the TCCTGCNA consensus than for methylated CpG sites.","method":"EMSA with GST-Kaiso fusion proteins, domain deletion analysis, SELEX-type binding assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with purified fusion proteins, mutagenesis of zinc finger domains, replicated across multiple studies","pmids":["12087177"],"is_preprint":false},{"year":2003,"finding":"Kaiso is a component of the human N-CoR corepressor complex. The Kaiso/N-CoR complex binds specific CpG-rich sequences in a methylation-dependent manner in vitro. In vivo, Kaiso recruits the N-CoR complex to the MTA2 gene promoter in a methylation-dependent manner, resulting in histone hypoacetylation and H3 lysine 9 methylation at the MTA2 locus. Kaiso is required for transcriptional repression of the methylated MTA2 locus, and this repression requires a functional N-CoR deacetylase complex.","method":"Co-immunoprecipitation, in vitro binding assays, chromatin immunoprecipitation (ChIP), reporter assays, RNAi depletion","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (Co-IP, ChIP, in vitro binding, RNAi with defined phenotype), single rigorous study","pmids":["14527417"],"is_preprint":false},{"year":2004,"finding":"Kaiso is required to maintain transcriptional silencing during early Xenopus laevis development. xKaiso depletion causes premature zygotic gene expression before the mid-blastula transition (MBT), phenocopying hypomethylated embryos. Wild-type human Kaiso mRNA rescues the xKaiso depletion phenotype, establishing functional conservation. xKaiso acts as a global repressor of methylated genes.","method":"Morpholino antisense depletion in Xenopus, mRNA rescue, gene expression profiling","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with defined phenotype, rescue by human Kaiso ortholog, replicated in multiple Xenopus studies","pmids":["15548582"],"is_preprint":false},{"year":2004,"finding":"Kaiso contains a functional nuclear localization signal (NLS) that mediates interaction with importin-alpha2 for nuclear import. Mutation of a key lysine in the NLS significantly inhibits nuclear localization. Wild-type but not NLS-defective Kaiso interacts with importin-alpha2 both in vitro and in vivo. The NLS is required for Kaiso-mediated transcriptional repression.","method":"NLS identification, beta-gal/GFP fusion reporter localization, Co-IP with importin-alpha2, minimal promoter reporter assays, site-directed mutagenesis","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — multiple orthogonal methods including mutagenesis, in vitro and in vivo importin binding, functional reporter assay in single study","pmids":["15564377"],"is_preprint":false},{"year":2004,"finding":"Nuclear localization of p120ctn is necessary to relieve Kaiso-mediated transcriptional repression. An NLS in p120ctn was identified; mutation of key lysines in the NLS inhibited p120ctn nuclear localization. Using minimal promoter assays, p120ctn's regulatory effect on Kaiso transcriptional activity requires nuclear translocation of p120ctn, not cytoplasmic sequestration of Kaiso.","method":"NLS mutagenesis, heterologous reporter (beta-gal/GFP), minimal promoter reporter assays, nuclear fractionation","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — NLS mutagenesis with functional consequence, reporter assay validation, mechanistic follow-up of p120ctn-Kaiso pathway","pmids":["15138284"],"is_preprint":false},{"year":2004,"finding":"Kaiso represses the non-canonical Wnt ligand xWnt11 in Xenopus, and xWnt11 is a direct gene target of xKaiso. p120-catenin association relieves xKaiso repression of xWnt11 in vivo. xKaiso knockdown results in increased xWnt11 expression contributing to gastrulation defects.","method":"Morpholino depletion, mRNA rescue, dominant-negative Wnt11, reporter assays in Xenopus","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis in Xenopus with rescue experiments, direct target established, replicated across Wnt/Kaiso studies","pmids":["15543138"],"is_preprint":false},{"year":2004,"finding":"Rapsyn gene is a direct sequence-specific transcriptional target of Kaiso. Kaiso associates with the rapsyn promoter in vivo (ChIP). Delta-catenin (a brain-specific p120 subfamily member) forms a complex with Kaiso. In C2C12 myocytes, Kaiso and delta-catenin activate the rapsyn promoter in a muscle-specific manner.","method":"Chromatin immunoprecipitation (ChIP), co-immunoprecipitation, minimal promoter reporter assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — ChIP and Co-IP combined with reporter assay; multiple orthogonal methods in single study","pmids":["15282317"],"is_preprint":false},{"year":2005,"finding":"Kaiso directly represses canonical Wnt gene targets (Siamois, c-Fos, Cyclin-D1, c-Myc) in Xenopus in conjunction with TCF/LEF. Kaiso and TCF coassociate. p120-catenin relieves Kaiso-mediated repression of Siamois. Kaiso suppresses beta-catenin-induced axis duplication and TCF-3 rescues Kaiso depletion phenotypes, establishing functional interdependency between Kaiso/p120ctn and beta-catenin/TCF pathways.","method":"Xenopus embryo microinjection, co-immunoprecipitation (Kaiso-TCF), beta-catenin ChIP on Siamois promoter, reporter assays, epistasis experiments","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis in Xenopus with rescue, Co-IP of Kaiso-TCF complex, ChIP, replicated by multiple labs","pmids":["15935774"],"is_preprint":false},{"year":2005,"finding":"Kaiso associates with the matrilysin promoter in vivo via the Kaiso binding site (KBS). Kaiso specifically represses transcription of the matrilysin promoter; mutation of KBS or siRNA depletion of Kaiso abrogates this repression. Kaiso blocks beta-catenin-mediated activation of matrilysin. p120ctn overexpression inhibits Kaiso-DNA binding and repression, but only when p120ctn can translocate to the nucleus (NLS-dependent).","method":"Chromatin immunoprecipitation (ChIP), minimal promoter reporter assays, KBS mutagenesis, siRNA depletion, p120ctn nuclear localization mutant","journal":"Experimental cell research","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — ChIP, reporter assay with mutagenesis, siRNA knockdown, NLS mutant rescue; multiple orthogonal methods","pmids":["15817151"],"is_preprint":false},{"year":2005,"finding":"CTCF (enhancer blocker) interacts with Kaiso as a binding partner. The interaction occurs through the C-terminal region of CTCF and the POZ domain of Kaiso. CTCF was specifically co-immunoprecipitated by Kaiso monoclonal antibodies from nuclear lysates. A Kaiso binding site near the CTCF binding site in the 5' beta-globin insulator reduces the enhancer-blocking activity of CTCF.","method":"Yeast two-hybrid, co-immunoprecipitation from nuclear lysates, insulation assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP confirmed interaction, functional insulation assay; single lab, POZ-domain interaction confirmed by two methods","pmids":["16230345"],"is_preprint":false},{"year":2006,"finding":"Kaiso-null mice are viable and fertile with no detectable developmental abnormalities, but display delayed onset of intestinal tumorigenesis when crossed with Apc(Min/+) mice. Kaiso is upregulated in murine intestinal tumors and expressed in human colon cancers, indicating a role in intestinal cancer promotion.","method":"Gene knockout mouse, Apc(Min/+) cross, tumor quantification, immunohistochemistry","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean knockout with defined tumor phenotype, genetic cross epistasis, replicated in subsequent mouse studies","pmids":["16354691"],"is_preprint":false},{"year":2006,"finding":"Frodo mediates stabilization of p120-catenin in response to Wnt signals, which in turn promotes Kaiso nuclear sequestration or removal. p120-catenin binds Frodo, and Frodo interacts with Dishevelled (Dsh). Wnt signals thus act through Dsh-Frodo-p120ctn to regulate the p120ctn/Kaiso signaling pathway.","method":"Co-immunoprecipitation, Xenopus embryo epistasis, protein stability assays","journal":"Developmental cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP of Frodo-p120ctn, Xenopus epistasis; single lab study placing Dsh upstream of p120ctn-Kaiso","pmids":["17084360"],"is_preprint":false},{"year":2008,"finding":"Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer. Kaiso binds the CDKN2A promoter in a methylation-dependent manner. Kaiso depletion induces tumor suppressor gene expression without affecting DNA methylation levels, sensitizing colon cancer cells to cell cycle arrest and cell death.","method":"ChIP, siRNA depletion, RT-PCR, cell cycle and apoptosis assays","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — ChIP demonstrating methylation-dependent promoter binding, RNAi with defined cellular phenotype, multiple orthogonal approaches","pmids":["18794111"],"is_preprint":false},{"year":2008,"finding":"H. pylori cag(+) strains induce translocation of p120-catenin to the nucleus, which relieves Kaiso-mediated transcriptional repression of mmp-7 (matrix metalloproteinase-7). This mechanism is cag- and p120-dependent and results in increased MMP-7 mRNA and protein levels.","method":"siRNA knockdown, nuclear fractionation, ex vivo gastric gland culture, RT-PCR","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — p120 knockdown, nuclear fractionation showing translocation, siRNA confirming Kaiso-dependence; single lab","pmids":["18653469"],"is_preprint":false},{"year":2009,"finding":"The non-methylated DNA-binding function of Kaiso (CTGCNA) is not evolutionarily conserved in frogs, fish, or chicken. In Xenopus, phenotypic abnormalities of xKaiso depletion are independent of the CTGCNA-dependent DNA-binding function. xKaiso does not regulate xWnt11 or Siamois; instead, the major phenotypic defects are premature transcription activation and activation of a p53-dependent cell-death pathway.","method":"Comparative species analysis of Kaiso DNA-binding, morpholino depletion, reporter assays, mutant Kaiso rescue experiments","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple independent experimental lines in Xenopus; contradicts some earlier findings about CTGCNA function of xKaiso","pmids":["19158185"],"is_preprint":false},{"year":2010,"finding":"Kaiso interacts with the POZ-ZF protein Znf131 via POZ-POZ domain interaction. GST pull-down and co-immunoprecipitation confirmed the Kaiso-Znf131 in vivo interaction. Znf131 is a transcriptional activator (activates artificial promoter containing ZBE). Kaiso overexpression significantly inhibits Znf131-mediated transcriptional activation, and co-expression of p120ctn relieves this Kaiso inhibition.","method":"Yeast two-hybrid, GST pull-down, co-immunoprecipitation, EMSA, CAST (SELEX), reporter assay","journal":"Experimental cell research","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — reconstituted interaction by GST pull-down and confirmed by Co-IP, plus EMSA for DNA binding and reporter assay for function; multiple orthogonal methods","pmids":["20303951"],"is_preprint":false},{"year":2010,"finding":"Kaiso localizes at the mitotic spindle and is a constituent of the pericentriolar material (PCM), belonging to a pericentrin molecular complex. During interphase, Kaiso is on microtubular structures and centrosomes; at metaphase, on centrosomes and spindle microtubules; during telophase, at the midbody. Two domains mediate spindle/centrosome targeting: SA1 (spindle-associated domain 1, center of protein) and SA2 (just before zinc fingers). Overexpression of full-length Kaiso causes mitotic cell arrest and cell death; Kaiso knockdown accelerates cell proliferation.","method":"GFP-tagged fragment localization, immunofluorescence throughout cell cycle, domain deletion analysis, Kaiso knockdown/overexpression with proliferation readout","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — direct localization experiments with GFP constructs and domain mapping, knockdown/overexpression phenotypes; single lab","pmids":["20169156"],"is_preprint":false},{"year":2011,"finding":"Wnt3a-induced phosphorylation of p120-catenin at Ser268 and Ser269 (by CK1ε) enhances its binding to Kaiso, preventing Kaiso-mediated inhibition of the β-catenin-Tcf-4 complex. Kaiso associates with both Tcf-4 and β-catenin. p120-catenin disrupts Tcf-4-Kaiso and β-catenin-Kaiso interactions, freeing Tcf-4 and β-catenin to form their complex and enabling Kaiso to bind methylated CpG islands (e.g., CDKN2A promoter).","method":"Co-immunoprecipitation, phospho-site mutagenesis, reporter assays, ChIP, siRNA knockdown","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP showing Kaiso-Tcf4 and Kaiso-β-catenin interaction, phospho-mutants tested, ChIP; single lab","pmids":["21670201"],"is_preprint":false},{"year":2012,"finding":"Crystal structures of the Kaiso zinc finger DNA-binding domain in complex with its nonmethylated KBS DNA and with symmetrically methylated E-cadherin promoter-derived DNA were solved. Recognition of specific bases in the major groove of KBS and mCpG sites is mediated by residues in zinc fingers 1 and 2 through classical and methyl CH···O hydrogen-bonding interactions. The C-terminal extension following zinc finger 3 binds in the opposing minor groove and is required for high-affinity binding; this region is disordered in free protein and folds upon DNA binding.","method":"X-ray crystallography, structural analysis of protein-DNA complexes","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures of two distinct DNA-bound complexes, structural mechanism defined at atomic level","pmids":["22949637"],"is_preprint":false},{"year":2012,"finding":"Kaiso requires all three zinc fingers plus adjacent protein regions (N-terminal extension for stability and extended C-terminal region for augmented binding) for high-affinity DNA recognition of both methylated and sequence-specific sites. Contrary to prior findings, zinc fingers 2 and 3 alone are not sufficient for high-affinity binding.","method":"Systematic domain deletion/mutagenesis, in vitro binding assays (EMSA, ITC)","journal":"FEBS letters","confidence":"High","confidence_rationale":"Tier 1 / Moderate — systematic biochemical analysis with purified proteins and multiple binding assays; single lab study","pmids":["22300642"],"is_preprint":false},{"year":2012,"finding":"Kaiso associates with and represses the cyclin D1 promoter via both the KBS consensus site and methylated CpG dinucleotides. The methyl-CpG sites are critical for Kaiso binding to the cyclin D1 promoter, while the KBS stabilizes binding. Kaiso repressed the minimal cyclin D1 promoter-reporter in a dose-dependent, KBS-specific, and methyl-CpG-dependent manner.","method":"EMSA, ChIP, minimal promoter reporter assay, KBS mutagenesis","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — EMSA in vitro, ChIP in vivo, reporter with KBS mutagenesis; multiple orthogonal methods, single lab","pmids":["23226276"],"is_preprint":false},{"year":2012,"finding":"Kaiso interacts with the transcriptional corepressor MTG16. This interaction is mediated by Kaiso's zinc finger domains. MTG16 family members are required for efficient repression of a reporter construct containing Kaiso binding sites and the known Kaiso target MMP-7/matrilysin. ChIP places MTG16 in a complex occupying the Kaiso binding site on the MMP-7 promoter. MTG16's contribution to repression requires Kaiso binding to its DNA binding site.","method":"Yeast two-hybrid, co-immunoprecipitation, reporter assay, chromatin immunoprecipitation","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Moderate — Co-IP, ChIP, reporter assay with multiple KBS constructs; domain interaction mapped; single lab with multiple methods","pmids":["23251453"],"is_preprint":false},{"year":2012,"finding":"In vivo, ZBTB33/Kaiso binds to unmethylated regions of the genome associated with actively expressed genes and highly acetylated histones, rather than methylated DNA as predicted. DNA methylation and nucleosome occupancy restrict Kaiso access to potential binding sites.","method":"ChIP-seq for Kaiso, genome-wide DNA methylation analysis, bioinformatic integration","journal":"Epigenetics & chromatin","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP-seq with bioinformatic integration; single lab; contradicts in vitro methylation-dependent binding model, creating uncertainty","pmids":["23693142"],"is_preprint":false},{"year":2012,"finding":"SMRT corepressor is tethered to promoter-proximal regions in preadipocytes primarily via KAISO through the conserved TCTCGCGAGA motif. KAISO, similar to SMRT, functions as an adipogenic repressor that modulates the mitotic clonal expansion phase of adipogenesis; KAISO knockdown increases fat accumulation and accelerates cell cycle.","method":"Genome-wide ChIP-seq for SMRT and KAISO, ChIP-seq motif analysis, siRNA knockdown with adipogenesis assay","journal":"Molecular cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide ChIP-seq plus functional knockdown; single lab, multiple methods","pmids":["22521691"],"is_preprint":false},{"year":2012,"finding":"Dyrk1A kinase is a component of the p120-catenin-Kaiso trajectory of the Wnt pathway. Dyrk1A positively modulates p120-catenin protein levels, impacting p120-catenin and Kaiso gene targets (siamois, wnt11). A consensus Dyrk phosphorylation site in p120-catenin was identified; a phosphomimetic mutant of p120-catenin shows enhanced capacity to promote Wnt-11 and Siamois expression.","method":"Xenopus epistasis/rescue, mammalian cell experiments, phosphomimetic mutagenesis, Dyrk1A Co-IP/overexpression","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phosphomimetic mutagenesis plus Xenopus epistasis and rescue; single lab","pmids":["22389395"],"is_preprint":false},{"year":2014,"finding":"KAISO is induced by DNA damage in p53-expressing cells and interacts with the p53-p300 complex. KAISO increases acetylation of p53 at K320 and K382 residues while decreasing K381 acetylation. This specific p53 acetylation pattern increases p53 DNA binding and potently induces CDKN1A and apoptotic gene transcription. In Kaiso-KO mouse embryonic fibroblasts, p53-promoter binding and upregulation of p21 and apoptosis genes are significantly compromised.","method":"Co-immunoprecipitation (KAISO-p53-p300), p53 acetylation assays, ChIP, KO mouse fibroblasts, reporter assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Moderate — Co-IP of KAISO-p53-p300 complex, p53 acetylation mapping, ChIP, KO cell phenotype; multiple orthogonal methods, single lab","pmids":["25288747"],"is_preprint":false},{"year":2015,"finding":"Nuclear p120-catenin relieves Kaiso-mediated transcriptional repression of Wnt11 in anchorage-independent ILC cells. Wnt11 upregulation in anchorage-independent conditions is controlled by nuclear p120 through inhibition of Kaiso repression. Wnt11 promotes RhoA activation causing ILC anoikis resistance.","method":"mRNA profiling, nuclear p120 fractionation, siRNA knockdown of Kaiso/Wnt11, RhoA activity assay, anoikis assay","journal":"Disease models & mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — nuclear fractionation, siRNA with defined phenotype, RhoA activity assay; single lab","pmids":["25713299"],"is_preprint":false},{"year":2016,"finding":"ZBTB33/Kaiso mediates cell-specific cell cycle regulation through direct occupancy of cyclin D1 and cyclin E1 promoters. In HeLa cells, ZBTB33 occupies and activates cyclin D1 and E1 promoters, promoting RB phosphorylation and E2F transcriptional activity to accelerate G1-to-S transition. In HEK293 cells, ZBTB33 indirectly reduces cyclin E abundance, decreasing RB phosphorylation and decelerating G1 transition.","method":"ZBTB33 depletion/overexpression, ChIP, cell cycle analysis (flow cytometry), RB phosphorylation assays, E2F reporter assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP plus knockdown/overexpression with cell cycle readout; cell-type specific effects; single lab","pmids":["27694442"],"is_preprint":false},{"year":2018,"finding":"Glutamate 535 (E535) in Kaiso zinc finger 1 is critical for preferential recognition of methylated CpG (mCpG) over unmethylated CpG, with a ~100-fold difference in affinity. E535 forms multiple direct contacts with mCpG including CH···O hydrogen bonds. NMR and X-ray crystallography with E535 mutants provided first direct experimental evidence for CH···O hydrogen bond formation between Kaiso and 5-methylcytosine.","method":"X-ray crystallography, NMR spectroscopy, in vitro protein-DNA binding assays, site-directed mutagenesis of E535","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — X-ray crystallography plus NMR plus binding assays with mutagenesis; mechanistic detail at atomic level validated by multiple structural methods","pmids":["29546986"],"is_preprint":false},{"year":2018,"finding":"Kaiso is SUMOylated at lysine 42 (K42) as a monoSUMOylation under normal physiological conditions in kidney-origin cell lines. SUMOylated Kaiso activates transcription from exogenous methylated promoters, while deSUMOylated Kaiso retains transcriptional repressor activity. Hyperosmotic stress rapidly and reversibly triggers deSUMOylation of Kaiso. Genomic K42R editing (deSUMOylated Kaiso) led to misregulation of ion transport and immune response genes; TRIM25 is a direct transcriptional target of Kaiso.","method":"SUMO site mutagenesis (K42R), CRISPR/Cas9 genome editing, reporter assays with methylated promoters, hyperosmotic stress treatment, KO mouse model (salt diet)","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — site-directed SUMO mutagenesis with functional consequence, CRISPR genome editing, in vivo mouse model; multiple orthogonal approaches, single lab","pmids":["29472715"],"is_preprint":false},{"year":2018,"finding":"Kaiso binds to methylated regions of the miR-200c promoter in a methylation-dependent manner (confirmed by ChIP), repressing miR-200c expression. EGFR signaling regulates Kaiso-mediated silencing of miR-200c. miR-200c and Kaiso regulate each other in a feedback loop, with miR-200c overexpression decreasing Kaiso, ZEB1, and EGFR.","method":"ChIP assay for Kaiso-miR-200c promoter binding, 5-aza treatment, siRNA knockdown, miR-200c overexpression","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — ChIP confirms direct methylation-dependent binding, siRNA and overexpression functional studies; single lab","pmids":["29751044"],"is_preprint":false},{"year":2020,"finding":"A conformational switch in Kaiso's E535 residue enables differential readout of methylated (mCpG) and sequence-specific (KBS) DNA. With methylated DNA, multiple direct contacts between E535 and the 5' mCpG site dominate binding, tolerating different flanking sequences. With KBS, E535 acts as an indirect screen for 5' flanking sequence, with tyrosine-DNA interactions stabilizing optimal DNA conformation. Intrinsic variations in DNA flexibility contribute to differential specificity.","method":"X-ray crystallography, targeted mutagenesis, in vitro DNA binding assays, nucleotide substitutions","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structures of mutant complexes with mutagenesis and binding assays; atomic-level mechanism; single lab follow-up to prior structural work","pmids":["32352758"],"is_preprint":false},{"year":2021,"finding":"Kaiso deficiency in human renal cancer cells leads to whole-genome hypermethylation at genic regions, enhancers, and regions with low histone modifications, while protecting these regions from demethylation. Kaiso immunoprecipitates with de novo DNA methyltransferases DNMT3a/3b but not with maintenance methyltransferase DNMT1, suggesting Kaiso modulates genome methylation by attracting de novo methyltransferases.","method":"CRISPR/Cas9-generated Kaiso-knockout cells, whole-genome methylation analysis, co-immunoprecipitation of Kaiso with DNMT3a/3b","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR KO with genome-wide methylation analysis, Co-IP with DNMTs; single lab, multiple methods","pmids":["34299205"],"is_preprint":false},{"year":2021,"finding":"ZBTB33 mutations in clonal hematopoiesis and MDS confer a competitive advantage to hematopoietic stem cells in vivo. Zbtb33-edited mouse HSPCs show increased genome-wide intron retention, suggesting ZBTB33 mutations potentially link DNA methylation reading and RNA splicing.","method":"CRISPR editing of Zbtb33 in mouse HSPCs, competitive transplantation assay, RNA-seq for intron retention","journal":"Blood cancer discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo competitive HSPC transplantation, RNA-seq; single study, novel finding linking ZBTB33 to splicing","pmids":["34568833"],"is_preprint":false},{"year":2022,"finding":"TRIM28 enhances SUMOylation of Kaiso, leading to decreased methyl-dependent transcriptional repression. The RBCC domain of TRIM28 interacts with the BTB/POZ domain and zinc fingers of Kaiso; the PHD-bromodomain of TRIM28 is sufficient for interaction with Kaiso zinc fingers. Kaiso also enhances SUMOylation of TRIM28, suggesting mutual self-enhancement of SUMOylation.","method":"Co-immunoprecipitation, domain deletion mapping, SUMOylation assays, reporter assays","journal":"Biochimie","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP with domain mapping, SUMOylation assay, functional reporter; single lab","pmids":["36252888"],"is_preprint":false},{"year":2022,"finding":"Conserved proline P588 (in the C-terminal linker between zinc finger 3 and the DNA-binding extension) is required for efficient Kaiso-DNA binding. Substitution of P588 to alanine negatively affects DNA binding; molecular dynamics simulations show allosteric effects on the entire zinc finger domain. The cis-conformation of P588 is important for DNA-binding affinity.","method":"Site-directed mutagenesis, in vitro DNA binding assays, molecular dynamics simulation","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 1-3 / Moderate — mutagenesis with in vitro binding assays validated by MD simulation; single lab","pmids":["36555132"],"is_preprint":false},{"year":2024,"finding":"In vivo ChIP-seq in Caki-1 renal carcinoma cells (using Kaiso-deficient cells as negative control) revealed that the principal binding motifs for Kaiso are CGCG and CTGCNAT, with 60% of binding sites containing both sequences. Kaiso is present at CpG islands with a preference for methylated ones. An E535A mutant (unable to bind methylated DNA in vitro) can still bind CTGCNA sequences in vivo, confirming the dual-binding mode in cells.","method":"ChIP-seq with Kaiso-KO cells as negative control, E535A mutant ChIP-seq, bisulfite sequencing, gene expression analysis","journal":"Epigenetics & chromatin","confidence":"High","confidence_rationale":"Tier 2 / Strong — ChIP-seq with rigorous KO negative control plus structure-guided mutant analysis; multiple cell lines tested; definitively maps in vivo binding","pmids":["39702290"],"is_preprint":false},{"year":2016,"finding":"RhoH forms a multi-protein complex with Kaiso and p120-catenin that co-localizes at chemokine-induced actin-containing cell protrusion sites in Jurkat T cells. RhoH knockdown disrupts Kaiso localization to protrusion sites and to the nucleus after chemokine stimulation. Kaiso downregulation alters cell migration and actin polymerization in chemokine-stimulated T cells.","method":"In vivo biotinylation/mass spectrometry, co-immunoprecipitation, immunofluorescence, RhoH knockdown, migration/actin assays","journal":"Small GTPases","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — MS identification confirmed by Co-IP, co-localization, knockdown with functional readout; single lab","pmids":["27574848"],"is_preprint":false},{"year":2015,"finding":"Kaiso directly binds to the E-cadherin promoter in a methylation-dependent manner (confirmed by ChIP in PC-3 cells). Kaiso inhibition results in increased E-cadherin expression, re-establishment of cell-cell contacts, and reversal of mesenchymal markers N-cadherin and fibronectin in prostate cancer cells. EGF receptor signaling causes nuclear localization of Kaiso.","method":"ChIP for Kaiso at E-cadherin promoter, shRNA knockdown, immunofluorescence, Western blot","journal":"The American journal of pathology","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — ChIP at E-cadherin promoter, shRNA with functional phenotype; single lab","pmids":["22974583"],"is_preprint":false},{"year":2015,"finding":"KAISO directly binds and transcriptionally activates APAF1 only in cells expressing WT p53, by augmenting p53 binding to the APAF1 promoter distal p53RE#1. A nearby NF-κB response element mediates APAF1 repression; ectopic RelA/p65 sequesters KAISO in the cytoplasm, preventing nuclear KAISO-p53 interaction and thus blocking APAF1 activation.","method":"Reporter assays, ChIP, co-immunoprecipitation, ectopic p65 expression with cytoplasmic fractionation","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — ChIP and Co-IP with functional reporter; single lab, complementary to PNAS 2014 Koh paper","pmids":["26183023"],"is_preprint":false},{"year":2016,"finding":"Kaiso binds directly to the miR-31 promoter in a methylation-dependent manner (ChIP). Kaiso represses miR-31 expression, promoting prostate cancer cell migration and invasiveness. miR-31 overexpression decreases these malignant phenotypes, while anti-miR-31 restores them in Kaiso-depleted cells.","method":"ChIP, miRNA array, siRNA/shRNA depletion, cell migration/invasion assays","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — ChIP demonstrates methylation-dependent promoter binding, functional knockdown/rescue; single lab","pmids":["26734997"],"is_preprint":false},{"year":2013,"finding":"Kaiso overexpression in intestinal-specific transgenic mice (driven by villin promoter) causes crypt expansion, increased differentiation into secretory cell lineages (goblet, Paneth, enteroendocrine cells), reduced proliferation, and decreased Notch signaling target HES-1. p120ctn is recruited to the nucleus in transgenic mice intestinal cells, suggesting Kaiso antagonizes p120ctn's anti-inflammatory function.","method":"Transgenic mouse model with intestinal-specific Kaiso overexpression, histology, immunohistochemistry, immunofluorescence","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — transgenic mouse with defined intestinal phenotype; in vivo localization data; single lab","pmids":["24040197"],"is_preprint":false},{"year":2017,"finding":"Kaiso directly associates with the DLL1 and JAG1 promoter regions in a methylation-dependent manner in colon cancer cells (ChIP). In Kaiso transgenic mice, Notch1 and Dll-1 expression are reduced while Jagged-1 is increased. Kaiso promotes secretory cell hyperplasia independently of Kaiso-induced inflammation, acting through differential regulation of Notch ligands.","method":"ChIP in three colon cancer cell lines, transgenic mouse intestine analysis, real-time PCR, immunohistochemistry","journal":"Cell communication and signaling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP in multiple cell lines, in vivo transgenic mouse phenotype; single lab","pmids":["28637464"],"is_preprint":false},{"year":2019,"finding":"p53 transcriptionally activates KAISO/ZBTB33 by binding to p53RE1 (5'-upstream, -4326 to -4227) and p53RE3 (exon 2, +2929 to +2959). ATM/ATR kinase-mediated p53 phosphorylation at Ser-15 or Ser-37 activates KAISO transcription during early DNA damage response (DDR). Acetylated p53 activates KAISO transcription at p53RE1 during later DDR phase.","method":"Reporter assays with various p53RE constructs, ChIP, oligonucleotide pulldown, phospho-specific mutants","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and pulldown assays confirm p53 binding sites, phospho-mutants tested, multiple p53RE reporters; single lab","pmids":["31296660"],"is_preprint":false},{"year":2016,"finding":"Kaiso directly binds to the methylated THBS1 promoter and represses its expression. Kaiso depletion results in decreased expression of CD47 and its ligand SIRPA, promoting macrophage polarization towards M1 phenotype. Kaiso-depleted xenograft tissues showed higher phagocytosis and increased M1 macrophage infiltration.","method":"ChIP for Kaiso at THBS1 promoter, siRNA depletion, in vivo xenograft with immunohistochemistry","journal":"Cancers","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — ChIP establishes direct methylation-dependent binding, functional knockdown with in vivo phenotype; single lab","pmids":["37190208"],"is_preprint":false},{"year":2016,"finding":"Kaiso binds unmethylated KBS in the human ICR1 (imprinting control region of H19/IGF2), and Kaiso depletion or CRISPR/Cas9 deletion of the ICR1-KBS results in reduced methylation of the paternal ICR1. Kaiso also affects transcription of the lncRNA H19 via ICR1.","method":"ChIP, EMSA, lentiviral Kaiso knockdown, CRISPR/Cas9 editing of KBS, bisulfite sequencing","journal":"Clinical epigenetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and EMSA confirm binding, CRISPR editing of binding site with methylation readout; single lab","pmids":["27152123"],"is_preprint":false},{"year":2021,"finding":"Kaiso regulates osteoblast differentiation and mineralization through the Itga10/PI3K/AKT signaling pathway. Itga10 (integrin subunit α10) is identified as a direct transcriptional target of Kaiso by ChIP and luciferase reporter assays. Kaiso is downregulated during osteoblast differentiation; gain- and loss-of-function modulate osteoblast differentiation in vitro and in vivo.","method":"ChIP, luciferase reporter assays, gain/loss-of-function in MC3T3-E1 cells, in vivo mouse experiments, pathway analysis","journal":"International journal of molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and reporter confirm direct Itga10 targeting, in vitro and in vivo phenotype; single lab","pmids":["33576467"],"is_preprint":false},{"year":2021,"finding":"Kaiso protects human endothelial cells against apoptosis by differentially regulating BCL2 family member expression: Kaiso overexpression increases BCL2 and reduces BAX and BIK expression through differential regulation of gene promoter activity. Both methylated DNA and KBS-dependent mechanisms contribute to Kaiso's gene regulatory activity in endothelial cells. p120ctn cooperates with Kaiso in this transcriptional regulation.","method":"Kaiso overexpression/knockdown, cell viability assay, promoter reporter assay, Western blot, co-immunoprecipitation","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — reporter assays with promoter analysis, OE/KD phenotype, Co-IP; single lab","pmids":["28769046"],"is_preprint":false},{"year":2013,"finding":"Kaiso is a key regulator of spleen germinal center formation. Kaiso represses Bcl6 expression (confirmed by ChIP and transcription assays). In Kaiso-KO mice, derepressed Bcl6 increases cell proliferation by suppressing p27, p21, and Gadd45a while upregulating c-Myc.","method":"ChIP, reporter assays, KO mouse analysis, immunohistochemistry, B lymphocyte ectopic expression","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and reporter confirm Bcl6 as direct target, KO mouse phenotype; single lab","pmids":["24269670"],"is_preprint":false}],"current_model":"ZBTB33/Kaiso is a dual-specificity BTB/POZ-ZF transcriptional repressor that binds methylated CpG dinucleotides (via CH···O hydrogen bonds mediated by E535 across zinc fingers 1-3 plus C-terminal extension) and an unmethylated sequence-specific consensus (TCCTGCNA/KBS), recruits corepressor complexes (N-CoR/HDAC, MTG16, SMRT) to silence target genes (MTA2, cyclin D1, matrilysin/MMP-7, Wnt11, Siamois, CDKN2A, Bcl6, miR-31, miR-200c, TRIM25), and is regulated by its binding partner p120-catenin (which, upon nuclear translocation, relieves Kaiso DNA binding and repression), by SUMOylation at K42 (switching Kaiso from repressor to activator), by TRIM28-mediated SUMOylation, by Wnt/CK1ε-mediated p120-catenin phosphorylation, and by interaction with the p53-p300 complex during DNA damage responses; Kaiso also localizes to the mitotic spindle/pericentriolar material and its mutations confer a competitive advantage to hematopoietic stem cells associated with increased intron retention."},"narrative":{"mechanistic_narrative":"ZBTB33/Kaiso is a dual-specificity BTB/POZ-zinc finger transcription factor that controls gene silencing programs in development, cell-cycle progression, and cancer by reading both methylated CpG DNA and a sequence-specific consensus [PMID:11445535, PMID:12087177, PMID:39702290]. Its three zinc fingers, together with N- and C-terminal extensions, recognize a methylated CpG (5'CGCG) site and the unmethylated KBS consensus (TCCTGCNA); high-affinity binding requires all three fingers plus flanking regions and a conserved C-terminal extension that folds upon DNA contact [PMID:12087177, PMID:22949637, PMID:22300642]. At atomic resolution, glutamate E535 in zinc finger 1 discriminates methylated from unmethylated CpG (~100-fold) through CH···O hydrogen bonds to 5-methylcytosine and acts as a conformational switch that also screens KBS flanking sequence [PMID:22949637, PMID:29546986, PMID:32352758]; in vivo, Kaiso occupies CGCG and CTGCNAT motifs with preference for methylated CpG islands, and an E535A mutant retains sequence-specific KBS binding in cells [PMID:39702290]. Through its zinc fingers and POZ domain, Kaiso tethers corepressor machinery—the N-CoR/HDAC complex, MTG16, and SMRT—to target promoters, producing histone hypoacetylation and H3K9 methylation and silencing genes including MTA2, cyclin D1, matrilysin/MMP-7, and CDKN2A [PMID:14527417, PMID:23226276, PMID:23251453, PMID:22521691]. Kaiso function is gated by its binding partner p120-catenin: nuclear translocation of p120-catenin, driven by Wnt/CK1ε-mediated phosphorylation, relieves Kaiso DNA binding and repression of targets such as Wnt11, Siamois, and MMP-7 [PMID:10207085, PMID:15138284, PMID:15817151, PMID:21670201]. In Xenopus, Kaiso maintains transcriptional silencing of methylated genes before the mid-blastula transition and intersects the canonical Wnt/β-catenin–TCF axis [PMID:15548582, PMID:15935774]. SUMOylation at K42, enhanced by TRIM28, converts Kaiso from a repressor into an activator on methylated promoters and is reversed by hyperosmotic stress [PMID:29472715, PMID:36252888]. Kaiso participates in the DNA-damage response by joining the p53–p300 complex to direct p53 acetylation and activate CDKN1A and apoptotic genes [PMID:25288747]. Kaiso-null mice are viable but show delayed Apc(Min/+)-driven intestinal tumorigenesis, and Kaiso modulates de novo DNA methylation via association with DNMT3a/3b [PMID:16354691, PMID:34299205].","teleology":[{"year":1999,"claim":"Established Kaiso as a BTB/POZ zinc finger protein physically linked to the cell-adhesion regulator p120-catenin, framing it as the nuclear effector of a catenin signaling arm.","evidence":"Yeast two-hybrid screen and reciprocal Co-IP with domain mapping in mammalian cells","pmids":["10207085"],"confidence":"High","gaps":["No DNA target or transcriptional activity defined yet","Functional consequence of p120 binding unknown"]},{"year":2001,"claim":"Answered what DNA Kaiso recognizes by showing it is a methyl-CpG-dependent repressor requiring symmetric methylated CpGs, placing it among methyl-DNA readers.","evidence":"Biochemical purification (MeCP1 fractionation) and transient transfection reporter assays","pmids":["11445535"],"confidence":"High","gaps":["Corepressor machinery not identified","In vivo target genes not defined"]},{"year":2002,"claim":"Resolved that Kaiso is dual-specificity, binding both a sequence-specific KBS consensus and methylated CpG, and that p120-catenin inhibits both binding modes.","evidence":"EMSA with GST-Kaiso fusions, zinc finger deletion analysis, SELEX-type assays","pmids":["12087177"],"confidence":"High","gaps":["Structural basis of dual recognition unresolved","Relative in vivo usage of the two modes unknown"]},{"year":2003,"claim":"Connected Kaiso DNA binding to a silencing mechanism by showing it recruits the N-CoR/HDAC complex to a methylated promoter, producing repressive chromatin marks.","evidence":"Co-IP, in vitro binding, ChIP and RNAi at the MTA2 locus","pmids":["14527417"],"confidence":"High","gaps":["Generality across promoters not established","Other corepressors not yet mapped"]},{"year":2004,"claim":"Demonstrated a physiological role as a global repressor of methylated genes in early development, conserved between Xenopus and human Kaiso.","evidence":"Morpholino depletion with human Kaiso mRNA rescue and expression profiling in Xenopus","pmids":["15548582"],"confidence":"High","gaps":["Specific developmental target genes only partly defined","Methylation-independent contributions not separated"]},{"year":2004,"claim":"Defined the nuclear import and partner-regulation logic: Kaiso uses an importin-alpha2-dependent NLS, and nuclear (not cytoplasmic) p120-catenin is required to relieve repression.","evidence":"NLS mutagenesis, importin Co-IP, fractionation and minimal-promoter reporter assays","pmids":["15564377","15138284"],"confidence":"High","gaps":["Signals driving p120 nuclear entry not yet identified","Stoichiometry of p120-Kaiso regulation unclear"]},{"year":2005,"claim":"Integrated Kaiso into the Wnt pathway by establishing direct repression of canonical and non-canonical Wnt targets and physical association with TCF and β-catenin.","evidence":"Xenopus epistasis/rescue, Co-IP of Kaiso-TCF, ChIP and reporter assays; ChIP at the matrilysin promoter with KBS mutagenesis","pmids":["15543138","15935774","15817151"],"confidence":"High","gaps":["How Kaiso/p120 and β-catenin/TCF arms are coordinated mechanistically unresolved","Direct vs indirect target distinctions incomplete"]},{"year":2006,"claim":"Provided in vivo cancer relevance: Kaiso loss delays intestinal tumorigenesis, indicating a tumor-promoting role downstream of Apc.","evidence":"Kaiso knockout mouse crossed to Apc(Min/+) with tumor quantification and IHC","pmids":["16354691"],"confidence":"High","gaps":["Lack of overt knockout phenotype leaves baseline function unclear","Tumor-promoting target genes not pinned down"]},{"year":2008,"claim":"Linked Kaiso to epigenetic silencing of tumor suppressors, showing methylation-dependent CDKN2A binding whose loss sensitizes cancer cells to arrest and death.","evidence":"ChIP, siRNA depletion, RT-PCR and cell-cycle/apoptosis assays in colon cancer cells","pmids":["18794111"],"confidence":"High","gaps":["Kaiso does not alter methylation itself, leaving reader-vs-writer role open","Other silenced suppressors not enumerated"]},{"year":2012,"claim":"Defined the atomic basis of dual recognition: crystal structures with KBS and methylated DNA show zinc-finger major-groove contacts and a disordered-to-folded C-terminal extension required for affinity, while corepressor and target repertoire expanded to MTG16, SMRT, and cyclin D1.","evidence":"X-ray crystallography of two DNA-bound complexes; systematic deletion/ITC binding; Co-IP, ChIP and reporter assays","pmids":["22949637","22300642","23226276","23251453","22521691"],"confidence":"High","gaps":["Single-residue determinant of methyl preference not yet isolated","Corepressor selection rules among N-CoR/SMRT/MTG16 unclear"]},{"year":2012,"claim":"Challenged the methyl-dependent model with genome-wide data showing Kaiso preferentially occupies unmethylated, active, acetylated regions in cells, raising the question of context-dependent binding.","evidence":"Kaiso ChIP-seq integrated with genome-wide methylation analysis","pmids":["23693142"],"confidence":"Medium","gaps":["Discrepancy with in vitro methyl-binding not reconciled in this study","Antibody/cell-context dependence not excluded"]},{"year":2014,"claim":"Revealed a non-repressive function in the DNA-damage response: Kaiso joins the p53-p300 complex to reshape p53 acetylation and drive CDKN1A and apoptotic transcription.","evidence":"Co-IP, p53 acetylation mapping, ChIP and KO MEF reporter assays","pmids":["25288747"],"confidence":"High","gaps":["How DNA-damage signals recruit Kaiso to p53 unclear","Relationship to its repressor activity not integrated"]},{"year":2018,"claim":"Pinpointed E535 as the methyl-discrimination residue via CH···O hydrogen bonds and showed SUMOylation at K42 acts as a repressor-to-activator switch, adding a post-translational control layer.","evidence":"X-ray/NMR with E535 mutants and binding assays; K42R mutagenesis, CRISPR editing, reporter assays and salt-diet KO mice","pmids":["29546986","29472715"],"confidence":"High","gaps":["Genome-wide consequences of the SUMO switch incompletely mapped","Coupling of E535 readout to corepressor recruitment unresolved"]},{"year":2020,"claim":"Explained how one residue achieves dual specificity by showing E535 functions as a conformational switch that directly reads mCpG but indirectly screens KBS flanking sequence.","evidence":"X-ray crystallography of mutant complexes with nucleotide substitutions and binding assays","pmids":["32352758"],"confidence":"High","gaps":["In vivo relevance of flexibility-based selectivity not directly tested","Linker/proline contributions only later addressed"]},{"year":2021,"claim":"Tied Kaiso to genome methylation maintenance and to hematopoietic disease by showing it recruits de novo DNMT3a/3b and that ZBTB33 mutations give HSCs a competitive advantage with altered splicing.","evidence":"CRISPR-KO renal cells with whole-genome methylation and DNMT Co-IP; CRISPR-edited mouse HSPC transplantation with RNA-seq","pmids":["34299205","34568833"],"confidence":"Medium","gaps":["Mechanism linking methylation reading to intron retention unestablished","Direct DNMT recruitment to chromatin not shown in vivo"]},{"year":2022,"claim":"Clarified SUMO-switch regulation and DNA-binding fine structure by mapping TRIM28-mediated mutual SUMOylation and a conserved linker proline required for binding.","evidence":"Co-IP/domain mapping and SUMOylation assays; P588 mutagenesis with binding assays and MD simulation","pmids":["36252888","36555132"],"confidence":"Medium","gaps":["Physiological triggers of TRIM28-Kaiso SUMOylation unclear","Allosteric model from MD not validated structurally"]},{"year":2024,"claim":"Definitively resolved the in vivo binding mode, showing Kaiso occupies CGCG and CTGCNAT motifs (often both), prefers methylated CpG islands, and that E535A retains KBS binding in cells.","evidence":"ChIP-seq with Kaiso-KO negative control, E535A mutant ChIP-seq, bisulfite sequencing across cell lines","pmids":["39702290"],"confidence":"High","gaps":["Direct corepressor occupancy genome-wide not co-mapped","Reconciliation with earlier unmethylated-site ChIP-seq partial"]},{"year":null,"claim":"How Kaiso's dual reader activity, SUMO-controlled repressor/activator switch, and association with de novo methyltransferases and the splicing machinery are mechanistically integrated into a single regulatory output remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model coupling methyl-reading to splicing changes","Rules selecting repression vs activation at a given locus undefined","Corepressor-versus-DNMT recruitment hierarchy unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,3,31,50]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[1,2,20,38]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,5]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[3,24,38]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[18]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[3,22,38]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[3,34]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[9,19]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[22,29]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[12,14]}],"complexes":["N-CoR/HDAC corepressor complex","SMRT corepressor complex","MeCP1","pericentriolar material"],"partners":["CTNND1","TRIM28","CTCF","ZNF131","MTG16","NCOR2","TP53","EP300"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86T24","full_name":"Transcriptional regulator Kaiso","aliases":["Zinc finger and BTB domain-containing protein 33"],"length_aa":672,"mass_kda":74.5,"function":"Transcriptional regulator with bimodal DNA-binding specificity. Binds to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' and also binds to the non-methylated consensus sequence 5'-CTGCNA-3' also known as the consensus kaiso binding site (KBS). Recruits the N-CoR repressor complex to promote histone deacetylation and the formation of repressive chromatin structures in target gene promoters. May contribute to the repression of target genes of the Wnt signaling pathway. May also activate transcription of a subset of target genes by the recruitment of CTNND2. Represses expression of MMP7 in conjunction with transcriptional corepressors CBFA2T3, CBFA2T2 and RUNX1T1 (PubMed:23251453)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q86T24/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ZBTB33","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPZB","stoichiometry":0.2},{"gene":"MIF","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/ZBTB33","total_profiled":1310},"omim":[{"mim_id":"612218","title":"ZINC FINGER- AND BTB DOMAIN-CONTAINING PROTEIN 38; ZBTB38","url":"https://www.omim.org/entry/612218"},{"mim_id":"601592","title":"RECEPTOR-ASSOCIATED PROTEIN OF THE SYNAPSE, 43-KD; RAPSN","url":"https://www.omim.org/entry/601592"},{"mim_id":"300354","title":"INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC, CABEZAS TYPE; MRXSC","url":"https://www.omim.org/entry/300354"},{"mim_id":"300329","title":"ZINC FINGER- AND BTB DOMAIN-CONTAINING PROTEIN 33; ZBTB33","url":"https://www.omim.org/entry/300329"},{"mim_id":"300304","title":"CULLIN 4B; CUL4B","url":"https://www.omim.org/entry/300304"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"},{"location":"Plasma membrane","reliability":"Enhanced"},{"location":"Cytosol","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ZBTB33"},"hgnc":{"alias_symbol":["ZNF-kaiso","kaiso","WUGSC:H_DJ525N14.1","KAISO","ZNF348"],"prev_symbol":[]},"alphafold":{"accession":"Q86T24","domains":[{"cath_id":"3.30.710.10","chopping":"14-119","consensus_level":"high","plddt":89.5545,"start":14,"end":119},{"cath_id":"3.30.160.60","chopping":"484-518","consensus_level":"medium","plddt":90.414,"start":484,"end":518},{"cath_id":"3.30.160.60","chopping":"523-597","consensus_level":"medium","plddt":90.7656,"start":523,"end":597}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86T24","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86T24-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86T24-F1-predicted_aligned_error_v6.png","plddt_mean":54.78},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZBTB33","jax_strain_url":"https://www.jax.org/strain/search?query=ZBTB33"},"sequence":{"accession":"Q86T24","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86T24.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86T24/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86T24"}},"corpus_meta":[{"pmid":"11445535","id":"PMC_11445535","title":"The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor.","date":"2001","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/11445535","citation_count":372,"is_preprint":false},{"pmid":"10207085","id":"PMC_10207085","title":"The catenin p120(ctn) interacts with Kaiso, a novel BTB/POZ domain zinc finger transcription factor.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10207085","citation_count":346,"is_preprint":false},{"pmid":"14527417","id":"PMC_14527417","title":"N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso.","date":"2003","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/14527417","citation_count":288,"is_preprint":false},{"pmid":"12087177","id":"PMC_12087177","title":"The p120(ctn)-binding partner Kaiso is a bi-modal DNA-binding protein that recognizes both a sequence-specific consensus and methylated CpG dinucleotides.","date":"2002","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/12087177","citation_count":208,"is_preprint":false},{"pmid":"15935774","id":"PMC_15935774","title":"Kaiso/p120-catenin and TCF/beta-catenin complexes coordinately regulate canonical Wnt gene targets.","date":"2005","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/15935774","citation_count":190,"is_preprint":false},{"pmid":"15543138","id":"PMC_15543138","title":"Non-canonical Wnt signals are modulated by the Kaiso transcriptional repressor and p120-catenin.","date":"2004","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/15543138","citation_count":139,"is_preprint":false},{"pmid":"16354691","id":"PMC_16354691","title":"Kaiso-deficient mice show resistance to intestinal cancer.","date":"2006","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16354691","citation_count":128,"is_preprint":false},{"pmid":"16294216","id":"PMC_16294216","title":"A role for Kaiso-p120ctn complexes in cancer?","date":"2005","source":"Nature reviews. Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/16294216","citation_count":103,"is_preprint":false},{"pmid":"15817151","id":"PMC_15817151","title":"The catenin p120ctn inhibits Kaiso-mediated transcriptional repression of the beta-catenin/TCF target gene matrilysin.","date":"2005","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/15817151","citation_count":101,"is_preprint":false},{"pmid":"22949637","id":"PMC_22949637","title":"Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso.","date":"2012","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/22949637","citation_count":99,"is_preprint":false},{"pmid":"17050009","id":"PMC_17050009","title":"Dancing in and out of the nucleus: p120(ctn) and the transcription factor Kaiso.","date":"2006","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/17050009","citation_count":97,"is_preprint":false},{"pmid":"15548582","id":"PMC_15548582","title":"Kaiso is a genome-wide repressor of transcription that is essential for amphibian development.","date":"2004","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/15548582","citation_count":96,"is_preprint":false},{"pmid":"15282317","id":"PMC_15282317","title":"Regulation of the rapsyn promoter by kaiso and delta-catenin.","date":"2004","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/15282317","citation_count":92,"is_preprint":false},{"pmid":"15138284","id":"PMC_15138284","title":"NLS-dependent nuclear localization of p120ctn is necessary to relieve Kaiso-mediated transcriptional repression.","date":"2004","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/15138284","citation_count":89,"is_preprint":false},{"pmid":"18794111","id":"PMC_18794111","title":"Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer cell lines.","date":"2008","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/18794111","citation_count":86,"is_preprint":false},{"pmid":"17084360","id":"PMC_17084360","title":"Frodo links Dishevelled to the p120-catenin/Kaiso pathway: distinct catenin subfamilies promote Wnt signals.","date":"2006","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/17084360","citation_count":84,"is_preprint":false},{"pmid":"22521691","id":"PMC_22521691","title":"Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO.","date":"2012","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/22521691","citation_count":74,"is_preprint":false},{"pmid":"16230345","id":"PMC_16230345","title":"The human enhancer blocker CTC-binding factor interacts with the transcription factor Kaiso.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16230345","citation_count":70,"is_preprint":false},{"pmid":"18653469","id":"PMC_18653469","title":"p120 and Kaiso regulate Helicobacter pylori-induced expression of matrix metalloproteinase-7.","date":"2008","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/18653469","citation_count":60,"is_preprint":false},{"pmid":"19177165","id":"PMC_19177165","title":"The methyl-CpG binding proteins Mecp2, Mbd2 and Kaiso are dispensable for mouse embryogenesis, but play a redundant function in neural differentiation.","date":"2009","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/19177165","citation_count":55,"is_preprint":false},{"pmid":"23693142","id":"PMC_23693142","title":"ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes.","date":"2013","source":"Epigenetics & chromatin","url":"https://pubmed.ncbi.nlm.nih.gov/23693142","citation_count":54,"is_preprint":false},{"pmid":"15781635","id":"PMC_15781635","title":"Expression and nuclear location of the transcriptional repressor Kaiso is regulated by the tumor microenvironment.","date":"2005","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/15781635","citation_count":53,"is_preprint":false},{"pmid":"22974583","id":"PMC_22974583","title":"Nuclear Kaiso indicates aggressive prostate cancers and promotes migration and invasiveness of prostate cancer cells.","date":"2012","source":"The American journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/22974583","citation_count":51,"is_preprint":false},{"pmid":"22662240","id":"PMC_22662240","title":"Nuclear Kaiso expression is associated with high grade and triple-negative invasive breast cancer.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22662240","citation_count":45,"is_preprint":false},{"pmid":"25288747","id":"PMC_25288747","title":"KAISO, a critical regulator of p53-mediated transcription of CDKN1A and apoptotic genes.","date":"2014","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/25288747","citation_count":45,"is_preprint":false},{"pmid":"23226276","id":"PMC_23226276","title":"Kaiso represses the cell cycle gene cyclin D1 via sequence-specific and methyl-CpG-dependent mechanisms.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23226276","citation_count":44,"is_preprint":false},{"pmid":"15564377","id":"PMC_15564377","title":"Nuclear import of the BTB/POZ transcriptional regulator Kaiso.","date":"2004","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/15564377","citation_count":44,"is_preprint":false},{"pmid":"19158185","id":"PMC_19158185","title":"The non-methylated DNA-binding function of Kaiso is not required in early Xenopus laevis development.","date":"2009","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/19158185","citation_count":43,"is_preprint":false},{"pmid":"21670201","id":"PMC_21670201","title":"Wnt controls the transcriptional activity of Kaiso through CK1ε-dependent phosphorylation of p120-catenin.","date":"2011","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/21670201","citation_count":43,"is_preprint":false},{"pmid":"26734997","id":"PMC_26734997","title":"Kaiso, a transcriptional repressor, promotes cell migration and invasion of prostate cancer cells through regulation of miR-31 expression.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/26734997","citation_count":39,"is_preprint":false},{"pmid":"22389395","id":"PMC_22389395","title":"Down's-syndrome-related kinase Dyrk1A modulates the p120-catenin-Kaiso trajectory of the Wnt signaling pathway.","date":"2012","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/22389395","citation_count":39,"is_preprint":false},{"pmid":"22276175","id":"PMC_22276175","title":"P120-catenin isoforms 1 and 3 regulate proliferation and cell cycle of lung cancer cells via β-catenin and Kaiso respectively.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22276175","citation_count":39,"is_preprint":false},{"pmid":"24570268","id":"PMC_24570268","title":"Nuclear localization of Kaiso promotes the poorly differentiated phenotype and EMT in infiltrating ductal carcinomas.","date":"2014","source":"Clinical & experimental metastasis","url":"https://pubmed.ncbi.nlm.nih.gov/24570268","citation_count":36,"is_preprint":false},{"pmid":"27694442","id":"PMC_27694442","title":"Cell-specific Kaiso (ZBTB33) Regulation of Cell Cycle through Cyclin D1 and Cyclin E1.","date":"2016","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/27694442","citation_count":35,"is_preprint":false},{"pmid":"34568833","id":"PMC_34568833","title":"ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing.","date":"2021","source":"Blood cancer discovery","url":"https://pubmed.ncbi.nlm.nih.gov/34568833","citation_count":34,"is_preprint":false},{"pmid":"26999717","id":"PMC_26999717","title":"Kaiso depletion attenuates transforming growth factor-β signaling and metastatic activity of triple-negative breast cancer cells.","date":"2016","source":"Oncogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/26999717","citation_count":34,"is_preprint":false},{"pmid":"25713299","id":"PMC_25713299","title":"Nuclear p120-catenin regulates the anoikis resistance of mouse lobular breast cancer cells through Kaiso-dependent Wnt11 expression.","date":"2015","source":"Disease models & mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/25713299","citation_count":33,"is_preprint":false},{"pmid":"30419310","id":"PMC_30419310","title":"Dancing from bottoms up - Roles of the POZ-ZF transcription factor Kaiso in Cancer.","date":"2018","source":"Biochimica et biophysica acta. Reviews on cancer","url":"https://pubmed.ncbi.nlm.nih.gov/30419310","citation_count":29,"is_preprint":false},{"pmid":"19166851","id":"PMC_19166851","title":"Kaiso is a bimodal modulator for Wnt/beta-catenin signaling.","date":"2009","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/19166851","citation_count":29,"is_preprint":false},{"pmid":"21468542","id":"PMC_21468542","title":"p120-catenin isoform 3 regulates subcellular localization of Kaiso and promotes invasion in lung cancer cells via a phosphorylation-dependent mechanism.","date":"2011","source":"International journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/21468542","citation_count":29,"is_preprint":false},{"pmid":"26073433","id":"PMC_26073433","title":"Kaiso overexpression promotes intestinal inflammation and potentiates intestinal tumorigenesis in Apc(Min/+) mice.","date":"2015","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/26073433","citation_count":27,"is_preprint":false},{"pmid":"28887687","id":"PMC_28887687","title":"Kaiso is highly expressed in TNBC tissues of women of African ancestry compared to Caucasian women.","date":"2017","source":"Cancer causes & control : CCC","url":"https://pubmed.ncbi.nlm.nih.gov/28887687","citation_count":26,"is_preprint":false},{"pmid":"20169156","id":"PMC_20169156","title":"The transcriptional repressor Kaiso localizes at the mitotic spindle and is a constituent of the pericentriolar material.","date":"2010","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/20169156","citation_count":24,"is_preprint":false},{"pmid":"24474278","id":"PMC_24474278","title":"Knockdown of both p120 catenin and Kaiso promotes expansion of human corneal endothelial monolayers via RhoA-ROCK-noncanonical BMP-NFκB pathway.","date":"2014","source":"Investigative ophthalmology & visual science","url":"https://pubmed.ncbi.nlm.nih.gov/24474278","citation_count":24,"is_preprint":false},{"pmid":"34299205","id":"PMC_34299205","title":"Kaiso Regulates DNA Methylation Homeostasis.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34299205","citation_count":23,"is_preprint":false},{"pmid":"19615783","id":"PMC_19615783","title":"Kaiso is expressed in lung cancer: its expression and localization is affected by p120ctn.","date":"2009","source":"Lung cancer (Amsterdam, Netherlands)","url":"https://pubmed.ncbi.nlm.nih.gov/19615783","citation_count":23,"is_preprint":false},{"pmid":"28333150","id":"PMC_28333150","title":"Kaiso depletion attenuates the growth and survival of triple negative breast cancer cells.","date":"2017","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/28333150","citation_count":23,"is_preprint":false},{"pmid":"29546986","id":"PMC_29546986","title":"CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso.","date":"2018","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29546986","citation_count":23,"is_preprint":false},{"pmid":"29751044","id":"PMC_29751044","title":"Transcriptional repressor Kaiso promotes epithelial to mesenchymal transition and metastasis in prostate cancer through direct regulation of miR-200c.","date":"2018","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/29751044","citation_count":22,"is_preprint":false},{"pmid":"20303951","id":"PMC_20303951","title":"Kaiso regulates Znf131-mediated transcriptional activation.","date":"2010","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/20303951","citation_count":21,"is_preprint":false},{"pmid":"29472715","id":"PMC_29472715","title":"DeSUMOylation switches Kaiso from activator to repressor upon hyperosmotic stress.","date":"2018","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/29472715","citation_count":21,"is_preprint":false},{"pmid":"22709531","id":"PMC_22709531","title":"Knock-down of Kaiso induces proliferation and blocks granulocytic differentiation in blast crisis of chronic myeloid leukemia.","date":"2012","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/22709531","citation_count":21,"is_preprint":false},{"pmid":"23251453","id":"PMC_23251453","title":"Kaiso directs the transcriptional corepressor MTG16 to the Kaiso binding site in target promoters.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23251453","citation_count":21,"is_preprint":false},{"pmid":"11461664","id":"PMC_11461664","title":"Monoclonal antibodies to Kaiso: a novel transcription factor and p120ctn-binding protein.","date":"2001","source":"Hybridoma","url":"https://pubmed.ncbi.nlm.nih.gov/11461664","citation_count":20,"is_preprint":false},{"pmid":"30036882","id":"PMC_30036882","title":"Kaiso (ZBTB33) Downregulation by Mirna-181a Inhibits Cell Proliferation, Invasion, and the Epithelial-Mesenchymal Transition in Glioma Cells.","date":"2018","source":"Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/30036882","citation_count":19,"is_preprint":false},{"pmid":"24498333","id":"PMC_24498333","title":"Kaiso interacts with p120-catenin to regulate β-catenin expression at the transcriptional level.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24498333","citation_count":19,"is_preprint":false},{"pmid":"26454239","id":"PMC_26454239","title":"Knockout Zbtb33 gene results in an increased locomotion, exploration and pre-pulse inhibition in mice.","date":"2015","source":"Behavioural brain research","url":"https://pubmed.ncbi.nlm.nih.gov/26454239","citation_count":18,"is_preprint":false},{"pmid":"24040197","id":"PMC_24040197","title":"The POZ-ZF transcription factor Kaiso (ZBTB33) induces inflammation and progenitor cell differentiation in the murine intestine.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24040197","citation_count":18,"is_preprint":false},{"pmid":"22300642","id":"PMC_22300642","title":"Kaiso uses all three zinc fingers and adjacent sequence motifs for high affinity binding to sequence-specific and methyl-CpG DNA targets.","date":"2012","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/22300642","citation_count":18,"is_preprint":false},{"pmid":"27424525","id":"PMC_27424525","title":"African Americans with pancreatic ductal adenocarcinoma exhibit gender differences in Kaiso expression.","date":"2016","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/27424525","citation_count":17,"is_preprint":false},{"pmid":"27152123","id":"PMC_27152123","title":"Kaiso mediates human ICR1 methylation maintenance and H19 transcriptional fine regulation.","date":"2016","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/27152123","citation_count":15,"is_preprint":false},{"pmid":"26183023","id":"PMC_26183023","title":"Transcriptional activation of APAF1 by KAISO (ZBTB33) and p53 is attenuated by RelA/p65.","date":"2015","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/26183023","citation_count":13,"is_preprint":false},{"pmid":"28637464","id":"PMC_28637464","title":"Kaiso differentially regulates components of the Notch signaling pathway in intestinal cells.","date":"2017","source":"Cell communication and signaling : CCS","url":"https://pubmed.ncbi.nlm.nih.gov/28637464","citation_count":13,"is_preprint":false},{"pmid":"27574848","id":"PMC_27574848","title":"RhoH participates in a multi-protein complex with the zinc finger protein kaiso that regulates both cytoskeletal structures and chemokine-induced T cells.","date":"2016","source":"Small GTPases","url":"https://pubmed.ncbi.nlm.nih.gov/27574848","citation_count":13,"is_preprint":false},{"pmid":"29735970","id":"PMC_29735970","title":"Jinfu'an Decoction Inhibits Invasion and Metastasis in Human Lung Cancer Cells (H1650) via p120ctn-Mediated Induction and Kaiso.","date":"2018","source":"Medical science monitor : international medical journal of experimental and clinical research","url":"https://pubmed.ncbi.nlm.nih.gov/29735970","citation_count":13,"is_preprint":false},{"pmid":"28800784","id":"PMC_28800784","title":"Upregulation of MicroRNA-4262 Targets Kaiso (ZBTB33) to Inhibit the Proliferation and EMT of Cervical Cancer Cells.","date":"2017","source":"Oncology research","url":"https://pubmed.ncbi.nlm.nih.gov/28800784","citation_count":12,"is_preprint":false},{"pmid":"32352758","id":"PMC_32352758","title":"A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.","date":"2020","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32352758","citation_count":12,"is_preprint":false},{"pmid":"38450773","id":"PMC_38450773","title":"High-Frequency Spinal Stimulation Suppresses Microglial Kaiso-P2X7 Receptor Axis-Induced Inflammation to Alleviate Neuropathic Pain in Rats.","date":"2024","source":"Annals of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/38450773","citation_count":12,"is_preprint":false},{"pmid":"31729179","id":"PMC_31729179","title":"Alu-mediated Xq24 deletion encompassing CUL4B, LAMP2, ATP1B4, TMEM255A, and ZBTB33 genes causes Danon disease in a female patient.","date":"2019","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/31729179","citation_count":12,"is_preprint":false},{"pmid":"25937776","id":"PMC_25937776","title":"Kaiso mainly locates in the nucleus in vivo and binds to methylated, but not hydroxymethylated DNA.","date":"2015","source":"Chinese journal of cancer research = Chung-kuo yen cheng yen chiu","url":"https://pubmed.ncbi.nlm.nih.gov/25937776","citation_count":11,"is_preprint":false},{"pmid":"20382170","id":"PMC_20382170","title":"P120 catenin represses transcriptional activity through Kaiso in endothelial cells.","date":"2010","source":"Microvascular research","url":"https://pubmed.ncbi.nlm.nih.gov/20382170","citation_count":11,"is_preprint":false},{"pmid":"36252888","id":"PMC_36252888","title":"TRIM28 regulates transcriptional activity of methyl-DNA binding protein Kaiso by SUMOylation.","date":"2022","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/36252888","citation_count":10,"is_preprint":false},{"pmid":"30858547","id":"PMC_30858547","title":"Kaiso is required for MTG16-dependent effects on colitis-associated carcinoma.","date":"2019","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/30858547","citation_count":10,"is_preprint":false},{"pmid":"33576467","id":"PMC_33576467","title":"Kaiso regulates osteoblast differentiation and mineralization via the Itga10/PI3K/AKT signaling pathway.","date":"2021","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/33576467","citation_count":10,"is_preprint":false},{"pmid":"31221066","id":"PMC_31221066","title":"Kaiso Gene Knockout Promotes Somatic Cell Reprogramming.","date":"2019","source":"Biochemistry. Biokhimiia","url":"https://pubmed.ncbi.nlm.nih.gov/31221066","citation_count":9,"is_preprint":false},{"pmid":"28769046","id":"PMC_28769046","title":"Kaiso protects human umbilical vein endothelial cells against apoptosis by differentially regulating the expression of B-cell CLL/lymphoma 2 family members.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28769046","citation_count":9,"is_preprint":false},{"pmid":"27765636","id":"PMC_27765636","title":"Cigarette Smoke Mediates Nuclear to Cytoplasmic Trafficking of Transcriptional Inhibitor Kaiso through MUC1 and P120-Catenin.","date":"2016","source":"The American journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/27765636","citation_count":9,"is_preprint":false},{"pmid":"25297569","id":"PMC_25297569","title":"KAISO inhibition: an atomic insight.","date":"2014","source":"Journal of biomolecular structure & dynamics","url":"https://pubmed.ncbi.nlm.nih.gov/25297569","citation_count":9,"is_preprint":false},{"pmid":"31199830","id":"PMC_31199830","title":"Kaiso-induced intestinal inflammation is preceded by diminished E-cadherin expression and intestinal integrity.","date":"2019","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/31199830","citation_count":8,"is_preprint":false},{"pmid":"28882591","id":"PMC_28882591","title":"The POZ-ZF transcription factor Znf131 is implicated as a regulator of Kaiso-mediated biological processes.","date":"2017","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/28882591","citation_count":8,"is_preprint":false},{"pmid":"28880889","id":"PMC_28880889","title":"Loss of Kaiso expression in breast cancer cells prevents intra-vascular invasion in the lung and secondary metastasis.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28880889","citation_count":8,"is_preprint":false},{"pmid":"22833212","id":"PMC_22833212","title":"Expression of P120 catenin, Kaiso, and metastasis tumor antigen-2 in thymomas.","date":"2012","source":"Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/22833212","citation_count":7,"is_preprint":false},{"pmid":"26424557","id":"PMC_26424557","title":"Kaiso represses the expression of glucocorticoid receptor via a methylation-dependent mechanism and attenuates the anti-apoptotic activity of glucocorticoids in breast cancer cells.","date":"2016","source":"BMB reports","url":"https://pubmed.ncbi.nlm.nih.gov/26424557","citation_count":7,"is_preprint":false},{"pmid":"16530985","id":"PMC_16530985","title":"The X-linked methyl binding protein gene Kaiso is highly expressed in brain but is not mutated in Rett syndrome patients.","date":"2006","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/16530985","citation_count":7,"is_preprint":false},{"pmid":"25182933","id":"PMC_25182933","title":"Distribution of Kaiso protein in mouse tissues.","date":"2014","source":"Histochemistry and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/25182933","citation_count":6,"is_preprint":false},{"pmid":"37190208","id":"PMC_37190208","title":"Immune Profile of Exosomes in African American Breast Cancer Patients Is Mediated by Kaiso/THBS1/CD47 Signaling.","date":"2023","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/37190208","citation_count":6,"is_preprint":false},{"pmid":"24269670","id":"PMC_24269670","title":"Kaiso is a key regulator of spleen germinal center formation by repressing Bcl6 expression in splenocytes.","date":"2013","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/24269670","citation_count":6,"is_preprint":false},{"pmid":"30552232","id":"PMC_30552232","title":"Epigenetic Regulation of Dlg1, via Kaiso, Alters Mitotic Spindle Polarity and Promotes Intestinal Tumorigenesis.","date":"2018","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/30552232","citation_count":6,"is_preprint":false},{"pmid":"31296660","id":"PMC_31296660","title":"Temporal and differential regulation of KAISO-controlled transcription by phosphorylated and acetylated p53 highlights a crucial regulatory role of apoptosis.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31296660","citation_count":5,"is_preprint":false},{"pmid":"17767857","id":"PMC_17767857","title":"[Methylation specific binding activity of zinc finger protein Kaiso].","date":"2007","source":"Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]","url":"https://pubmed.ncbi.nlm.nih.gov/17767857","citation_count":5,"is_preprint":false},{"pmid":"36115941","id":"PMC_36115941","title":"Expressional variations of Kaiso: an association with pathological characteristics and field cancerization of OSCC.","date":"2022","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/36115941","citation_count":4,"is_preprint":false},{"pmid":"37737015","id":"PMC_37737015","title":"Canonical Kaiso target genes define a functional signature that associates with breast cancer survival and the invasive lobular carcinoma histological type.","date":"2023","source":"The Journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/37737015","citation_count":4,"is_preprint":false},{"pmid":"11517759","id":"PMC_11517759","title":"[KAISO--a new member of the BTB/POZ family specifically bindsto methylated DNA sequences].","date":"2001","source":"Genetika","url":"https://pubmed.ncbi.nlm.nih.gov/11517759","citation_count":4,"is_preprint":false},{"pmid":"29086688","id":"PMC_29086688","title":"Kaiso Protein in the Regulation of Brain and Behavior.","date":"2018","source":"Current protein & peptide science","url":"https://pubmed.ncbi.nlm.nih.gov/29086688","citation_count":3,"is_preprint":false},{"pmid":"36563044","id":"PMC_36563044","title":"A 5'-Flanking C/G Pair at the Core Region Enhances the Recognition and Binding of Kaiso to Methylated DNA.","date":"2022","source":"Journal of chemical information and modeling","url":"https://pubmed.ncbi.nlm.nih.gov/36563044","citation_count":3,"is_preprint":false},{"pmid":"38840164","id":"PMC_38840164","title":"Imprinted DNA methylation of the H19 ICR is established and maintained in vivo in the absence of Kaiso.","date":"2024","source":"Epigenetics & chromatin","url":"https://pubmed.ncbi.nlm.nih.gov/38840164","citation_count":3,"is_preprint":false},{"pmid":"36555132","id":"PMC_36555132","title":"The Essential Role of Prolines and Their Conformation in Allosteric Regulation of Kaiso Zinc Finger DNA-Binding Activity by the Adjacent C-Terminal Loop.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36555132","citation_count":3,"is_preprint":false},{"pmid":"34983288","id":"PMC_34983288","title":"Deletion of murine Rhoh leads to de-repression of Bcl-6 via decreased KAISO levels and accelerates a malignancy phenotype in a murine model of lymphoma.","date":"2022","source":"Small GTPases","url":"https://pubmed.ncbi.nlm.nih.gov/34983288","citation_count":3,"is_preprint":false},{"pmid":"39702290","id":"PMC_39702290","title":"Dissecting the Kaiso binding profile in clear renal cancer cells.","date":"2024","source":"Epigenetics & chromatin","url":"https://pubmed.ncbi.nlm.nih.gov/39702290","citation_count":2,"is_preprint":false},{"pmid":"36852243","id":"PMC_36852243","title":"Association of Kaiso and partner proteins in oral squamous cell carcinoma.","date":"2022","source":"Journal of Taibah University Medical Sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36852243","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":49971,"output_tokens":13209,"usd":0.174024,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":25239,"output_tokens":5489,"usd":0.13171,"stage2_stop_reason":"end_turn"},"total_usd":0.305734,"stage1_batch_id":"msgbatch_01UT1AahFPCAyn2uVweS7A9z","stage2_batch_id":"msgbatch_01HuKWtKNT4Pqj1bc8eEP5RV","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"Kaiso was identified as a novel BTB/POZ zinc finger transcription factor that directly interacts with p120-catenin (p120ctn). Yeast two-hybrid screening identified Kaiso as a p120ctn-binding partner; the interaction was confirmed by co-immunoprecipitation with p120ctn-specific antibodies. Mapping studies showed the interaction involves Arm repeats 1-7 of p120ctn and the C-terminal 200 amino acids of Kaiso. Kaiso homodimerizes via its POZ domain but does not heterodimerize with BCL-6. Kaiso localizes to the nucleus and nuclear dots.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation, immunolocalization, domain mapping\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP confirmed by multiple p120-specific antibodies, domain mapping, and replicated in subsequent studies\",\n      \"pmids\": [\"10207085\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Kaiso is a methylation-dependent transcriptional repressor that requires at least two symmetrically methylated CpG dinucleotides (preferably within 5'CGCG) for DNA binding. Kaiso is a constituent of one of two methyl-CpG binding complexes originally designated as MeCP1. The zinc finger motifs are responsible for DNA binding. Kaiso behaves as a methylation-dependent transcriptional repressor in transient transfection assays.\",\n      \"method\": \"Biochemical purification, transient transfection reporter assays, complex fractionation (MeCP1)\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro binding assays, reporter assays, biochemical fractionation; foundational paper replicated across many subsequent studies\",\n      \"pmids\": [\"11445535\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Kaiso is a dual-specificity DNA-binding protein that recognizes both a sequence-specific consensus (TCCTGCNA, minimal core CTGCNA) and methylated CpG dinucleotides via its zinc fingers. Zinc fingers 2 and 3 are necessary and sufficient for sequence-specific DNA binding. p120ctn inhibits Kaiso DNA binding at both recognition sites. Kaiso has higher affinity for the TCCTGCNA consensus than for methylated CpG sites.\",\n      \"method\": \"EMSA with GST-Kaiso fusion proteins, domain deletion analysis, SELEX-type binding assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with purified fusion proteins, mutagenesis of zinc finger domains, replicated across multiple studies\",\n      \"pmids\": [\"12087177\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Kaiso is a component of the human N-CoR corepressor complex. The Kaiso/N-CoR complex binds specific CpG-rich sequences in a methylation-dependent manner in vitro. In vivo, Kaiso recruits the N-CoR complex to the MTA2 gene promoter in a methylation-dependent manner, resulting in histone hypoacetylation and H3 lysine 9 methylation at the MTA2 locus. Kaiso is required for transcriptional repression of the methylated MTA2 locus, and this repression requires a functional N-CoR deacetylase complex.\",\n      \"method\": \"Co-immunoprecipitation, in vitro binding assays, chromatin immunoprecipitation (ChIP), reporter assays, RNAi depletion\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (Co-IP, ChIP, in vitro binding, RNAi with defined phenotype), single rigorous study\",\n      \"pmids\": [\"14527417\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Kaiso is required to maintain transcriptional silencing during early Xenopus laevis development. xKaiso depletion causes premature zygotic gene expression before the mid-blastula transition (MBT), phenocopying hypomethylated embryos. Wild-type human Kaiso mRNA rescues the xKaiso depletion phenotype, establishing functional conservation. xKaiso acts as a global repressor of methylated genes.\",\n      \"method\": \"Morpholino antisense depletion in Xenopus, mRNA rescue, gene expression profiling\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with defined phenotype, rescue by human Kaiso ortholog, replicated in multiple Xenopus studies\",\n      \"pmids\": [\"15548582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Kaiso contains a functional nuclear localization signal (NLS) that mediates interaction with importin-alpha2 for nuclear import. Mutation of a key lysine in the NLS significantly inhibits nuclear localization. Wild-type but not NLS-defective Kaiso interacts with importin-alpha2 both in vitro and in vivo. The NLS is required for Kaiso-mediated transcriptional repression.\",\n      \"method\": \"NLS identification, beta-gal/GFP fusion reporter localization, Co-IP with importin-alpha2, minimal promoter reporter assays, site-directed mutagenesis\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — multiple orthogonal methods including mutagenesis, in vitro and in vivo importin binding, functional reporter assay in single study\",\n      \"pmids\": [\"15564377\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Nuclear localization of p120ctn is necessary to relieve Kaiso-mediated transcriptional repression. An NLS in p120ctn was identified; mutation of key lysines in the NLS inhibited p120ctn nuclear localization. Using minimal promoter assays, p120ctn's regulatory effect on Kaiso transcriptional activity requires nuclear translocation of p120ctn, not cytoplasmic sequestration of Kaiso.\",\n      \"method\": \"NLS mutagenesis, heterologous reporter (beta-gal/GFP), minimal promoter reporter assays, nuclear fractionation\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — NLS mutagenesis with functional consequence, reporter assay validation, mechanistic follow-up of p120ctn-Kaiso pathway\",\n      \"pmids\": [\"15138284\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Kaiso represses the non-canonical Wnt ligand xWnt11 in Xenopus, and xWnt11 is a direct gene target of xKaiso. p120-catenin association relieves xKaiso repression of xWnt11 in vivo. xKaiso knockdown results in increased xWnt11 expression contributing to gastrulation defects.\",\n      \"method\": \"Morpholino depletion, mRNA rescue, dominant-negative Wnt11, reporter assays in Xenopus\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis in Xenopus with rescue experiments, direct target established, replicated across Wnt/Kaiso studies\",\n      \"pmids\": [\"15543138\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Rapsyn gene is a direct sequence-specific transcriptional target of Kaiso. Kaiso associates with the rapsyn promoter in vivo (ChIP). Delta-catenin (a brain-specific p120 subfamily member) forms a complex with Kaiso. In C2C12 myocytes, Kaiso and delta-catenin activate the rapsyn promoter in a muscle-specific manner.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), co-immunoprecipitation, minimal promoter reporter assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and Co-IP combined with reporter assay; multiple orthogonal methods in single study\",\n      \"pmids\": [\"15282317\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Kaiso directly represses canonical Wnt gene targets (Siamois, c-Fos, Cyclin-D1, c-Myc) in Xenopus in conjunction with TCF/LEF. Kaiso and TCF coassociate. p120-catenin relieves Kaiso-mediated repression of Siamois. Kaiso suppresses beta-catenin-induced axis duplication and TCF-3 rescues Kaiso depletion phenotypes, establishing functional interdependency between Kaiso/p120ctn and beta-catenin/TCF pathways.\",\n      \"method\": \"Xenopus embryo microinjection, co-immunoprecipitation (Kaiso-TCF), beta-catenin ChIP on Siamois promoter, reporter assays, epistasis experiments\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis in Xenopus with rescue, Co-IP of Kaiso-TCF complex, ChIP, replicated by multiple labs\",\n      \"pmids\": [\"15935774\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Kaiso associates with the matrilysin promoter in vivo via the Kaiso binding site (KBS). Kaiso specifically represses transcription of the matrilysin promoter; mutation of KBS or siRNA depletion of Kaiso abrogates this repression. Kaiso blocks beta-catenin-mediated activation of matrilysin. p120ctn overexpression inhibits Kaiso-DNA binding and repression, but only when p120ctn can translocate to the nucleus (NLS-dependent).\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), minimal promoter reporter assays, KBS mutagenesis, siRNA depletion, p120ctn nuclear localization mutant\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — ChIP, reporter assay with mutagenesis, siRNA knockdown, NLS mutant rescue; multiple orthogonal methods\",\n      \"pmids\": [\"15817151\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"CTCF (enhancer blocker) interacts with Kaiso as a binding partner. The interaction occurs through the C-terminal region of CTCF and the POZ domain of Kaiso. CTCF was specifically co-immunoprecipitated by Kaiso monoclonal antibodies from nuclear lysates. A Kaiso binding site near the CTCF binding site in the 5' beta-globin insulator reduces the enhancer-blocking activity of CTCF.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation from nuclear lysates, insulation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP confirmed interaction, functional insulation assay; single lab, POZ-domain interaction confirmed by two methods\",\n      \"pmids\": [\"16230345\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Kaiso-null mice are viable and fertile with no detectable developmental abnormalities, but display delayed onset of intestinal tumorigenesis when crossed with Apc(Min/+) mice. Kaiso is upregulated in murine intestinal tumors and expressed in human colon cancers, indicating a role in intestinal cancer promotion.\",\n      \"method\": \"Gene knockout mouse, Apc(Min/+) cross, tumor quantification, immunohistochemistry\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean knockout with defined tumor phenotype, genetic cross epistasis, replicated in subsequent mouse studies\",\n      \"pmids\": [\"16354691\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Frodo mediates stabilization of p120-catenin in response to Wnt signals, which in turn promotes Kaiso nuclear sequestration or removal. p120-catenin binds Frodo, and Frodo interacts with Dishevelled (Dsh). Wnt signals thus act through Dsh-Frodo-p120ctn to regulate the p120ctn/Kaiso signaling pathway.\",\n      \"method\": \"Co-immunoprecipitation, Xenopus embryo epistasis, protein stability assays\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP of Frodo-p120ctn, Xenopus epistasis; single lab study placing Dsh upstream of p120ctn-Kaiso\",\n      \"pmids\": [\"17084360\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer. Kaiso binds the CDKN2A promoter in a methylation-dependent manner. Kaiso depletion induces tumor suppressor gene expression without affecting DNA methylation levels, sensitizing colon cancer cells to cell cycle arrest and cell death.\",\n      \"method\": \"ChIP, siRNA depletion, RT-PCR, cell cycle and apoptosis assays\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP demonstrating methylation-dependent promoter binding, RNAi with defined cellular phenotype, multiple orthogonal approaches\",\n      \"pmids\": [\"18794111\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"H. pylori cag(+) strains induce translocation of p120-catenin to the nucleus, which relieves Kaiso-mediated transcriptional repression of mmp-7 (matrix metalloproteinase-7). This mechanism is cag- and p120-dependent and results in increased MMP-7 mRNA and protein levels.\",\n      \"method\": \"siRNA knockdown, nuclear fractionation, ex vivo gastric gland culture, RT-PCR\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — p120 knockdown, nuclear fractionation showing translocation, siRNA confirming Kaiso-dependence; single lab\",\n      \"pmids\": [\"18653469\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The non-methylated DNA-binding function of Kaiso (CTGCNA) is not evolutionarily conserved in frogs, fish, or chicken. In Xenopus, phenotypic abnormalities of xKaiso depletion are independent of the CTGCNA-dependent DNA-binding function. xKaiso does not regulate xWnt11 or Siamois; instead, the major phenotypic defects are premature transcription activation and activation of a p53-dependent cell-death pathway.\",\n      \"method\": \"Comparative species analysis of Kaiso DNA-binding, morpholino depletion, reporter assays, mutant Kaiso rescue experiments\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple independent experimental lines in Xenopus; contradicts some earlier findings about CTGCNA function of xKaiso\",\n      \"pmids\": [\"19158185\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Kaiso interacts with the POZ-ZF protein Znf131 via POZ-POZ domain interaction. GST pull-down and co-immunoprecipitation confirmed the Kaiso-Znf131 in vivo interaction. Znf131 is a transcriptional activator (activates artificial promoter containing ZBE). Kaiso overexpression significantly inhibits Znf131-mediated transcriptional activation, and co-expression of p120ctn relieves this Kaiso inhibition.\",\n      \"method\": \"Yeast two-hybrid, GST pull-down, co-immunoprecipitation, EMSA, CAST (SELEX), reporter assay\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — reconstituted interaction by GST pull-down and confirmed by Co-IP, plus EMSA for DNA binding and reporter assay for function; multiple orthogonal methods\",\n      \"pmids\": [\"20303951\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Kaiso localizes at the mitotic spindle and is a constituent of the pericentriolar material (PCM), belonging to a pericentrin molecular complex. During interphase, Kaiso is on microtubular structures and centrosomes; at metaphase, on centrosomes and spindle microtubules; during telophase, at the midbody. Two domains mediate spindle/centrosome targeting: SA1 (spindle-associated domain 1, center of protein) and SA2 (just before zinc fingers). Overexpression of full-length Kaiso causes mitotic cell arrest and cell death; Kaiso knockdown accelerates cell proliferation.\",\n      \"method\": \"GFP-tagged fragment localization, immunofluorescence throughout cell cycle, domain deletion analysis, Kaiso knockdown/overexpression with proliferation readout\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — direct localization experiments with GFP constructs and domain mapping, knockdown/overexpression phenotypes; single lab\",\n      \"pmids\": [\"20169156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Wnt3a-induced phosphorylation of p120-catenin at Ser268 and Ser269 (by CK1ε) enhances its binding to Kaiso, preventing Kaiso-mediated inhibition of the β-catenin-Tcf-4 complex. Kaiso associates with both Tcf-4 and β-catenin. p120-catenin disrupts Tcf-4-Kaiso and β-catenin-Kaiso interactions, freeing Tcf-4 and β-catenin to form their complex and enabling Kaiso to bind methylated CpG islands (e.g., CDKN2A promoter).\",\n      \"method\": \"Co-immunoprecipitation, phospho-site mutagenesis, reporter assays, ChIP, siRNA knockdown\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP showing Kaiso-Tcf4 and Kaiso-β-catenin interaction, phospho-mutants tested, ChIP; single lab\",\n      \"pmids\": [\"21670201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Crystal structures of the Kaiso zinc finger DNA-binding domain in complex with its nonmethylated KBS DNA and with symmetrically methylated E-cadherin promoter-derived DNA were solved. Recognition of specific bases in the major groove of KBS and mCpG sites is mediated by residues in zinc fingers 1 and 2 through classical and methyl CH···O hydrogen-bonding interactions. The C-terminal extension following zinc finger 3 binds in the opposing minor groove and is required for high-affinity binding; this region is disordered in free protein and folds upon DNA binding.\",\n      \"method\": \"X-ray crystallography, structural analysis of protein-DNA complexes\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures of two distinct DNA-bound complexes, structural mechanism defined at atomic level\",\n      \"pmids\": [\"22949637\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Kaiso requires all three zinc fingers plus adjacent protein regions (N-terminal extension for stability and extended C-terminal region for augmented binding) for high-affinity DNA recognition of both methylated and sequence-specific sites. Contrary to prior findings, zinc fingers 2 and 3 alone are not sufficient for high-affinity binding.\",\n      \"method\": \"Systematic domain deletion/mutagenesis, in vitro binding assays (EMSA, ITC)\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — systematic biochemical analysis with purified proteins and multiple binding assays; single lab study\",\n      \"pmids\": [\"22300642\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Kaiso associates with and represses the cyclin D1 promoter via both the KBS consensus site and methylated CpG dinucleotides. The methyl-CpG sites are critical for Kaiso binding to the cyclin D1 promoter, while the KBS stabilizes binding. Kaiso repressed the minimal cyclin D1 promoter-reporter in a dose-dependent, KBS-specific, and methyl-CpG-dependent manner.\",\n      \"method\": \"EMSA, ChIP, minimal promoter reporter assay, KBS mutagenesis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — EMSA in vitro, ChIP in vivo, reporter with KBS mutagenesis; multiple orthogonal methods, single lab\",\n      \"pmids\": [\"23226276\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Kaiso interacts with the transcriptional corepressor MTG16. This interaction is mediated by Kaiso's zinc finger domains. MTG16 family members are required for efficient repression of a reporter construct containing Kaiso binding sites and the known Kaiso target MMP-7/matrilysin. ChIP places MTG16 in a complex occupying the Kaiso binding site on the MMP-7 promoter. MTG16's contribution to repression requires Kaiso binding to its DNA binding site.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, reporter assay, chromatin immunoprecipitation\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ChIP, reporter assay with multiple KBS constructs; domain interaction mapped; single lab with multiple methods\",\n      \"pmids\": [\"23251453\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"In vivo, ZBTB33/Kaiso binds to unmethylated regions of the genome associated with actively expressed genes and highly acetylated histones, rather than methylated DNA as predicted. DNA methylation and nucleosome occupancy restrict Kaiso access to potential binding sites.\",\n      \"method\": \"ChIP-seq for Kaiso, genome-wide DNA methylation analysis, bioinformatic integration\",\n      \"journal\": \"Epigenetics & chromatin\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP-seq with bioinformatic integration; single lab; contradicts in vitro methylation-dependent binding model, creating uncertainty\",\n      \"pmids\": [\"23693142\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"SMRT corepressor is tethered to promoter-proximal regions in preadipocytes primarily via KAISO through the conserved TCTCGCGAGA motif. KAISO, similar to SMRT, functions as an adipogenic repressor that modulates the mitotic clonal expansion phase of adipogenesis; KAISO knockdown increases fat accumulation and accelerates cell cycle.\",\n      \"method\": \"Genome-wide ChIP-seq for SMRT and KAISO, ChIP-seq motif analysis, siRNA knockdown with adipogenesis assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide ChIP-seq plus functional knockdown; single lab, multiple methods\",\n      \"pmids\": [\"22521691\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Dyrk1A kinase is a component of the p120-catenin-Kaiso trajectory of the Wnt pathway. Dyrk1A positively modulates p120-catenin protein levels, impacting p120-catenin and Kaiso gene targets (siamois, wnt11). A consensus Dyrk phosphorylation site in p120-catenin was identified; a phosphomimetic mutant of p120-catenin shows enhanced capacity to promote Wnt-11 and Siamois expression.\",\n      \"method\": \"Xenopus epistasis/rescue, mammalian cell experiments, phosphomimetic mutagenesis, Dyrk1A Co-IP/overexpression\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phosphomimetic mutagenesis plus Xenopus epistasis and rescue; single lab\",\n      \"pmids\": [\"22389395\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"KAISO is induced by DNA damage in p53-expressing cells and interacts with the p53-p300 complex. KAISO increases acetylation of p53 at K320 and K382 residues while decreasing K381 acetylation. This specific p53 acetylation pattern increases p53 DNA binding and potently induces CDKN1A and apoptotic gene transcription. In Kaiso-KO mouse embryonic fibroblasts, p53-promoter binding and upregulation of p21 and apoptosis genes are significantly compromised.\",\n      \"method\": \"Co-immunoprecipitation (KAISO-p53-p300), p53 acetylation assays, ChIP, KO mouse fibroblasts, reporter assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP of KAISO-p53-p300 complex, p53 acetylation mapping, ChIP, KO cell phenotype; multiple orthogonal methods, single lab\",\n      \"pmids\": [\"25288747\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Nuclear p120-catenin relieves Kaiso-mediated transcriptional repression of Wnt11 in anchorage-independent ILC cells. Wnt11 upregulation in anchorage-independent conditions is controlled by nuclear p120 through inhibition of Kaiso repression. Wnt11 promotes RhoA activation causing ILC anoikis resistance.\",\n      \"method\": \"mRNA profiling, nuclear p120 fractionation, siRNA knockdown of Kaiso/Wnt11, RhoA activity assay, anoikis assay\",\n      \"journal\": \"Disease models & mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — nuclear fractionation, siRNA with defined phenotype, RhoA activity assay; single lab\",\n      \"pmids\": [\"25713299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"ZBTB33/Kaiso mediates cell-specific cell cycle regulation through direct occupancy of cyclin D1 and cyclin E1 promoters. In HeLa cells, ZBTB33 occupies and activates cyclin D1 and E1 promoters, promoting RB phosphorylation and E2F transcriptional activity to accelerate G1-to-S transition. In HEK293 cells, ZBTB33 indirectly reduces cyclin E abundance, decreasing RB phosphorylation and decelerating G1 transition.\",\n      \"method\": \"ZBTB33 depletion/overexpression, ChIP, cell cycle analysis (flow cytometry), RB phosphorylation assays, E2F reporter assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP plus knockdown/overexpression with cell cycle readout; cell-type specific effects; single lab\",\n      \"pmids\": [\"27694442\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Glutamate 535 (E535) in Kaiso zinc finger 1 is critical for preferential recognition of methylated CpG (mCpG) over unmethylated CpG, with a ~100-fold difference in affinity. E535 forms multiple direct contacts with mCpG including CH···O hydrogen bonds. NMR and X-ray crystallography with E535 mutants provided first direct experimental evidence for CH···O hydrogen bond formation between Kaiso and 5-methylcytosine.\",\n      \"method\": \"X-ray crystallography, NMR spectroscopy, in vitro protein-DNA binding assays, site-directed mutagenesis of E535\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — X-ray crystallography plus NMR plus binding assays with mutagenesis; mechanistic detail at atomic level validated by multiple structural methods\",\n      \"pmids\": [\"29546986\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Kaiso is SUMOylated at lysine 42 (K42) as a monoSUMOylation under normal physiological conditions in kidney-origin cell lines. SUMOylated Kaiso activates transcription from exogenous methylated promoters, while deSUMOylated Kaiso retains transcriptional repressor activity. Hyperosmotic stress rapidly and reversibly triggers deSUMOylation of Kaiso. Genomic K42R editing (deSUMOylated Kaiso) led to misregulation of ion transport and immune response genes; TRIM25 is a direct transcriptional target of Kaiso.\",\n      \"method\": \"SUMO site mutagenesis (K42R), CRISPR/Cas9 genome editing, reporter assays with methylated promoters, hyperosmotic stress treatment, KO mouse model (salt diet)\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — site-directed SUMO mutagenesis with functional consequence, CRISPR genome editing, in vivo mouse model; multiple orthogonal approaches, single lab\",\n      \"pmids\": [\"29472715\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Kaiso binds to methylated regions of the miR-200c promoter in a methylation-dependent manner (confirmed by ChIP), repressing miR-200c expression. EGFR signaling regulates Kaiso-mediated silencing of miR-200c. miR-200c and Kaiso regulate each other in a feedback loop, with miR-200c overexpression decreasing Kaiso, ZEB1, and EGFR.\",\n      \"method\": \"ChIP assay for Kaiso-miR-200c promoter binding, 5-aza treatment, siRNA knockdown, miR-200c overexpression\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — ChIP confirms direct methylation-dependent binding, siRNA and overexpression functional studies; single lab\",\n      \"pmids\": [\"29751044\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"A conformational switch in Kaiso's E535 residue enables differential readout of methylated (mCpG) and sequence-specific (KBS) DNA. With methylated DNA, multiple direct contacts between E535 and the 5' mCpG site dominate binding, tolerating different flanking sequences. With KBS, E535 acts as an indirect screen for 5' flanking sequence, with tyrosine-DNA interactions stabilizing optimal DNA conformation. Intrinsic variations in DNA flexibility contribute to differential specificity.\",\n      \"method\": \"X-ray crystallography, targeted mutagenesis, in vitro DNA binding assays, nucleotide substitutions\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structures of mutant complexes with mutagenesis and binding assays; atomic-level mechanism; single lab follow-up to prior structural work\",\n      \"pmids\": [\"32352758\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Kaiso deficiency in human renal cancer cells leads to whole-genome hypermethylation at genic regions, enhancers, and regions with low histone modifications, while protecting these regions from demethylation. Kaiso immunoprecipitates with de novo DNA methyltransferases DNMT3a/3b but not with maintenance methyltransferase DNMT1, suggesting Kaiso modulates genome methylation by attracting de novo methyltransferases.\",\n      \"method\": \"CRISPR/Cas9-generated Kaiso-knockout cells, whole-genome methylation analysis, co-immunoprecipitation of Kaiso with DNMT3a/3b\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR KO with genome-wide methylation analysis, Co-IP with DNMTs; single lab, multiple methods\",\n      \"pmids\": [\"34299205\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ZBTB33 mutations in clonal hematopoiesis and MDS confer a competitive advantage to hematopoietic stem cells in vivo. Zbtb33-edited mouse HSPCs show increased genome-wide intron retention, suggesting ZBTB33 mutations potentially link DNA methylation reading and RNA splicing.\",\n      \"method\": \"CRISPR editing of Zbtb33 in mouse HSPCs, competitive transplantation assay, RNA-seq for intron retention\",\n      \"journal\": \"Blood cancer discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo competitive HSPC transplantation, RNA-seq; single study, novel finding linking ZBTB33 to splicing\",\n      \"pmids\": [\"34568833\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM28 enhances SUMOylation of Kaiso, leading to decreased methyl-dependent transcriptional repression. The RBCC domain of TRIM28 interacts with the BTB/POZ domain and zinc fingers of Kaiso; the PHD-bromodomain of TRIM28 is sufficient for interaction with Kaiso zinc fingers. Kaiso also enhances SUMOylation of TRIM28, suggesting mutual self-enhancement of SUMOylation.\",\n      \"method\": \"Co-immunoprecipitation, domain deletion mapping, SUMOylation assays, reporter assays\",\n      \"journal\": \"Biochimie\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP with domain mapping, SUMOylation assay, functional reporter; single lab\",\n      \"pmids\": [\"36252888\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Conserved proline P588 (in the C-terminal linker between zinc finger 3 and the DNA-binding extension) is required for efficient Kaiso-DNA binding. Substitution of P588 to alanine negatively affects DNA binding; molecular dynamics simulations show allosteric effects on the entire zinc finger domain. The cis-conformation of P588 is important for DNA-binding affinity.\",\n      \"method\": \"Site-directed mutagenesis, in vitro DNA binding assays, molecular dynamics simulation\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-3 / Moderate — mutagenesis with in vitro binding assays validated by MD simulation; single lab\",\n      \"pmids\": [\"36555132\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In vivo ChIP-seq in Caki-1 renal carcinoma cells (using Kaiso-deficient cells as negative control) revealed that the principal binding motifs for Kaiso are CGCG and CTGCNAT, with 60% of binding sites containing both sequences. Kaiso is present at CpG islands with a preference for methylated ones. An E535A mutant (unable to bind methylated DNA in vitro) can still bind CTGCNA sequences in vivo, confirming the dual-binding mode in cells.\",\n      \"method\": \"ChIP-seq with Kaiso-KO cells as negative control, E535A mutant ChIP-seq, bisulfite sequencing, gene expression analysis\",\n      \"journal\": \"Epigenetics & chromatin\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ChIP-seq with rigorous KO negative control plus structure-guided mutant analysis; multiple cell lines tested; definitively maps in vivo binding\",\n      \"pmids\": [\"39702290\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RhoH forms a multi-protein complex with Kaiso and p120-catenin that co-localizes at chemokine-induced actin-containing cell protrusion sites in Jurkat T cells. RhoH knockdown disrupts Kaiso localization to protrusion sites and to the nucleus after chemokine stimulation. Kaiso downregulation alters cell migration and actin polymerization in chemokine-stimulated T cells.\",\n      \"method\": \"In vivo biotinylation/mass spectrometry, co-immunoprecipitation, immunofluorescence, RhoH knockdown, migration/actin assays\",\n      \"journal\": \"Small GTPases\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — MS identification confirmed by Co-IP, co-localization, knockdown with functional readout; single lab\",\n      \"pmids\": [\"27574848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Kaiso directly binds to the E-cadherin promoter in a methylation-dependent manner (confirmed by ChIP in PC-3 cells). Kaiso inhibition results in increased E-cadherin expression, re-establishment of cell-cell contacts, and reversal of mesenchymal markers N-cadherin and fibronectin in prostate cancer cells. EGF receptor signaling causes nuclear localization of Kaiso.\",\n      \"method\": \"ChIP for Kaiso at E-cadherin promoter, shRNA knockdown, immunofluorescence, Western blot\",\n      \"journal\": \"The American journal of pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — ChIP at E-cadherin promoter, shRNA with functional phenotype; single lab\",\n      \"pmids\": [\"22974583\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"KAISO directly binds and transcriptionally activates APAF1 only in cells expressing WT p53, by augmenting p53 binding to the APAF1 promoter distal p53RE#1. A nearby NF-κB response element mediates APAF1 repression; ectopic RelA/p65 sequesters KAISO in the cytoplasm, preventing nuclear KAISO-p53 interaction and thus blocking APAF1 activation.\",\n      \"method\": \"Reporter assays, ChIP, co-immunoprecipitation, ectopic p65 expression with cytoplasmic fractionation\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — ChIP and Co-IP with functional reporter; single lab, complementary to PNAS 2014 Koh paper\",\n      \"pmids\": [\"26183023\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Kaiso binds directly to the miR-31 promoter in a methylation-dependent manner (ChIP). Kaiso represses miR-31 expression, promoting prostate cancer cell migration and invasiveness. miR-31 overexpression decreases these malignant phenotypes, while anti-miR-31 restores them in Kaiso-depleted cells.\",\n      \"method\": \"ChIP, miRNA array, siRNA/shRNA depletion, cell migration/invasion assays\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — ChIP demonstrates methylation-dependent promoter binding, functional knockdown/rescue; single lab\",\n      \"pmids\": [\"26734997\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Kaiso overexpression in intestinal-specific transgenic mice (driven by villin promoter) causes crypt expansion, increased differentiation into secretory cell lineages (goblet, Paneth, enteroendocrine cells), reduced proliferation, and decreased Notch signaling target HES-1. p120ctn is recruited to the nucleus in transgenic mice intestinal cells, suggesting Kaiso antagonizes p120ctn's anti-inflammatory function.\",\n      \"method\": \"Transgenic mouse model with intestinal-specific Kaiso overexpression, histology, immunohistochemistry, immunofluorescence\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — transgenic mouse with defined intestinal phenotype; in vivo localization data; single lab\",\n      \"pmids\": [\"24040197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Kaiso directly associates with the DLL1 and JAG1 promoter regions in a methylation-dependent manner in colon cancer cells (ChIP). In Kaiso transgenic mice, Notch1 and Dll-1 expression are reduced while Jagged-1 is increased. Kaiso promotes secretory cell hyperplasia independently of Kaiso-induced inflammation, acting through differential regulation of Notch ligands.\",\n      \"method\": \"ChIP in three colon cancer cell lines, transgenic mouse intestine analysis, real-time PCR, immunohistochemistry\",\n      \"journal\": \"Cell communication and signaling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP in multiple cell lines, in vivo transgenic mouse phenotype; single lab\",\n      \"pmids\": [\"28637464\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"p53 transcriptionally activates KAISO/ZBTB33 by binding to p53RE1 (5'-upstream, -4326 to -4227) and p53RE3 (exon 2, +2929 to +2959). ATM/ATR kinase-mediated p53 phosphorylation at Ser-15 or Ser-37 activates KAISO transcription during early DNA damage response (DDR). Acetylated p53 activates KAISO transcription at p53RE1 during later DDR phase.\",\n      \"method\": \"Reporter assays with various p53RE constructs, ChIP, oligonucleotide pulldown, phospho-specific mutants\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and pulldown assays confirm p53 binding sites, phospho-mutants tested, multiple p53RE reporters; single lab\",\n      \"pmids\": [\"31296660\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Kaiso directly binds to the methylated THBS1 promoter and represses its expression. Kaiso depletion results in decreased expression of CD47 and its ligand SIRPA, promoting macrophage polarization towards M1 phenotype. Kaiso-depleted xenograft tissues showed higher phagocytosis and increased M1 macrophage infiltration.\",\n      \"method\": \"ChIP for Kaiso at THBS1 promoter, siRNA depletion, in vivo xenograft with immunohistochemistry\",\n      \"journal\": \"Cancers\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — ChIP establishes direct methylation-dependent binding, functional knockdown with in vivo phenotype; single lab\",\n      \"pmids\": [\"37190208\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Kaiso binds unmethylated KBS in the human ICR1 (imprinting control region of H19/IGF2), and Kaiso depletion or CRISPR/Cas9 deletion of the ICR1-KBS results in reduced methylation of the paternal ICR1. Kaiso also affects transcription of the lncRNA H19 via ICR1.\",\n      \"method\": \"ChIP, EMSA, lentiviral Kaiso knockdown, CRISPR/Cas9 editing of KBS, bisulfite sequencing\",\n      \"journal\": \"Clinical epigenetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and EMSA confirm binding, CRISPR editing of binding site with methylation readout; single lab\",\n      \"pmids\": [\"27152123\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Kaiso regulates osteoblast differentiation and mineralization through the Itga10/PI3K/AKT signaling pathway. Itga10 (integrin subunit α10) is identified as a direct transcriptional target of Kaiso by ChIP and luciferase reporter assays. Kaiso is downregulated during osteoblast differentiation; gain- and loss-of-function modulate osteoblast differentiation in vitro and in vivo.\",\n      \"method\": \"ChIP, luciferase reporter assays, gain/loss-of-function in MC3T3-E1 cells, in vivo mouse experiments, pathway analysis\",\n      \"journal\": \"International journal of molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and reporter confirm direct Itga10 targeting, in vitro and in vivo phenotype; single lab\",\n      \"pmids\": [\"33576467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Kaiso protects human endothelial cells against apoptosis by differentially regulating BCL2 family member expression: Kaiso overexpression increases BCL2 and reduces BAX and BIK expression through differential regulation of gene promoter activity. Both methylated DNA and KBS-dependent mechanisms contribute to Kaiso's gene regulatory activity in endothelial cells. p120ctn cooperates with Kaiso in this transcriptional regulation.\",\n      \"method\": \"Kaiso overexpression/knockdown, cell viability assay, promoter reporter assay, Western blot, co-immunoprecipitation\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — reporter assays with promoter analysis, OE/KD phenotype, Co-IP; single lab\",\n      \"pmids\": [\"28769046\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Kaiso is a key regulator of spleen germinal center formation. Kaiso represses Bcl6 expression (confirmed by ChIP and transcription assays). In Kaiso-KO mice, derepressed Bcl6 increases cell proliferation by suppressing p27, p21, and Gadd45a while upregulating c-Myc.\",\n      \"method\": \"ChIP, reporter assays, KO mouse analysis, immunohistochemistry, B lymphocyte ectopic expression\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and reporter confirm Bcl6 as direct target, KO mouse phenotype; single lab\",\n      \"pmids\": [\"24269670\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ZBTB33/Kaiso is a dual-specificity BTB/POZ-ZF transcriptional repressor that binds methylated CpG dinucleotides (via CH···O hydrogen bonds mediated by E535 across zinc fingers 1-3 plus C-terminal extension) and an unmethylated sequence-specific consensus (TCCTGCNA/KBS), recruits corepressor complexes (N-CoR/HDAC, MTG16, SMRT) to silence target genes (MTA2, cyclin D1, matrilysin/MMP-7, Wnt11, Siamois, CDKN2A, Bcl6, miR-31, miR-200c, TRIM25), and is regulated by its binding partner p120-catenin (which, upon nuclear translocation, relieves Kaiso DNA binding and repression), by SUMOylation at K42 (switching Kaiso from repressor to activator), by TRIM28-mediated SUMOylation, by Wnt/CK1ε-mediated p120-catenin phosphorylation, and by interaction with the p53-p300 complex during DNA damage responses; Kaiso also localizes to the mitotic spindle/pericentriolar material and its mutations confer a competitive advantage to hematopoietic stem cells associated with increased intron retention.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ZBTB33/Kaiso is a dual-specificity BTB/POZ-zinc finger transcription factor that controls gene silencing programs in development, cell-cycle progression, and cancer by reading both methylated CpG DNA and a sequence-specific consensus [#1, #2, #38]. Its three zinc fingers, together with N- and C-terminal extensions, recognize a methylated CpG (5'CGCG) site and the unmethylated KBS consensus (TCCTGCNA); high-affinity binding requires all three fingers plus flanking regions and a conserved C-terminal extension that folds upon DNA contact [#2, #20, #21]. At atomic resolution, glutamate E535 in zinc finger 1 discriminates methylated from unmethylated CpG (~100-fold) through CH\\u00b7\\u00b7\\u00b7O hydrogen bonds to 5-methylcytosine and acts as a conformational switch that also screens KBS flanking sequence [#20, #30, #33]; in vivo, Kaiso occupies CGCG and CTGCNAT motifs with preference for methylated CpG islands, and an E535A mutant retains sequence-specific KBS binding in cells [#38]. Through its zinc fingers and POZ domain, Kaiso tethers corepressor machinery\\u2014the N-CoR/HDAC complex, MTG16, and SMRT\\u2014to target promoters, producing histone hypoacetylation and H3K9 methylation and silencing genes including MTA2, cyclin D1, matrilysin/MMP-7, and CDKN2A [#3, #22, #23, #25]. Kaiso function is gated by its binding partner p120-catenin: nuclear translocation of p120-catenin, driven by Wnt/CK1\\u03b5-mediated phosphorylation, relieves Kaiso DNA binding and repression of targets such as Wnt11, Siamois, and MMP-7 [#0, #6, #10, #19]. In Xenopus, Kaiso maintains transcriptional silencing of methylated genes before the mid-blastula transition and intersects the canonical Wnt/\\u03b2-catenin\\u2013TCF axis [#4, #9]. SUMOylation at K42, enhanced by TRIM28, converts Kaiso from a repressor into an activator on methylated promoters and is reversed by hyperosmotic stress [#31, #36]. Kaiso participates in the DNA-damage response by joining the p53\\u2013p300 complex to direct p53 acetylation and activate CDKN1A and apoptotic genes [#27]. Kaiso-null mice are viable but show delayed Apc(Min/+)-driven intestinal tumorigenesis, and Kaiso modulates de novo DNA methylation via association with DNMT3a/3b [#12, #34].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established Kaiso as a BTB/POZ zinc finger protein physically linked to the cell-adhesion regulator p120-catenin, framing it as the nuclear effector of a catenin signaling arm.\",\n      \"evidence\": \"Yeast two-hybrid screen and reciprocal Co-IP with domain mapping in mammalian cells\",\n      \"pmids\": [\"10207085\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No DNA target or transcriptional activity defined yet\", \"Functional consequence of p120 binding unknown\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Answered what DNA Kaiso recognizes by showing it is a methyl-CpG-dependent repressor requiring symmetric methylated CpGs, placing it among methyl-DNA readers.\",\n      \"evidence\": \"Biochemical purification (MeCP1 fractionation) and transient transfection reporter assays\",\n      \"pmids\": [\"11445535\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Corepressor machinery not identified\", \"In vivo target genes not defined\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Resolved that Kaiso is dual-specificity, binding both a sequence-specific KBS consensus and methylated CpG, and that p120-catenin inhibits both binding modes.\",\n      \"evidence\": \"EMSA with GST-Kaiso fusions, zinc finger deletion analysis, SELEX-type assays\",\n      \"pmids\": [\"12087177\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of dual recognition unresolved\", \"Relative in vivo usage of the two modes unknown\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Connected Kaiso DNA binding to a silencing mechanism by showing it recruits the N-CoR/HDAC complex to a methylated promoter, producing repressive chromatin marks.\",\n      \"evidence\": \"Co-IP, in vitro binding, ChIP and RNAi at the MTA2 locus\",\n      \"pmids\": [\"14527417\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Generality across promoters not established\", \"Other corepressors not yet mapped\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Demonstrated a physiological role as a global repressor of methylated genes in early development, conserved between Xenopus and human Kaiso.\",\n      \"evidence\": \"Morpholino depletion with human Kaiso mRNA rescue and expression profiling in Xenopus\",\n      \"pmids\": [\"15548582\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific developmental target genes only partly defined\", \"Methylation-independent contributions not separated\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Defined the nuclear import and partner-regulation logic: Kaiso uses an importin-alpha2-dependent NLS, and nuclear (not cytoplasmic) p120-catenin is required to relieve repression.\",\n      \"evidence\": \"NLS mutagenesis, importin Co-IP, fractionation and minimal-promoter reporter assays\",\n      \"pmids\": [\"15564377\", \"15138284\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signals driving p120 nuclear entry not yet identified\", \"Stoichiometry of p120-Kaiso regulation unclear\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Integrated Kaiso into the Wnt pathway by establishing direct repression of canonical and non-canonical Wnt targets and physical association with TCF and \\u03b2-catenin.\",\n      \"evidence\": \"Xenopus epistasis/rescue, Co-IP of Kaiso-TCF, ChIP and reporter assays; ChIP at the matrilysin promoter with KBS mutagenesis\",\n      \"pmids\": [\"15543138\", \"15935774\", \"15817151\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How Kaiso/p120 and \\u03b2-catenin/TCF arms are coordinated mechanistically unresolved\", \"Direct vs indirect target distinctions incomplete\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Provided in vivo cancer relevance: Kaiso loss delays intestinal tumorigenesis, indicating a tumor-promoting role downstream of Apc.\",\n      \"evidence\": \"Kaiso knockout mouse crossed to Apc(Min/+) with tumor quantification and IHC\",\n      \"pmids\": [\"16354691\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Lack of overt knockout phenotype leaves baseline function unclear\", \"Tumor-promoting target genes not pinned down\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Linked Kaiso to epigenetic silencing of tumor suppressors, showing methylation-dependent CDKN2A binding whose loss sensitizes cancer cells to arrest and death.\",\n      \"evidence\": \"ChIP, siRNA depletion, RT-PCR and cell-cycle/apoptosis assays in colon cancer cells\",\n      \"pmids\": [\"18794111\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kaiso does not alter methylation itself, leaving reader-vs-writer role open\", \"Other silenced suppressors not enumerated\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined the atomic basis of dual recognition: crystal structures with KBS and methylated DNA show zinc-finger major-groove contacts and a disordered-to-folded C-terminal extension required for affinity, while corepressor and target repertoire expanded to MTG16, SMRT, and cyclin D1.\",\n      \"evidence\": \"X-ray crystallography of two DNA-bound complexes; systematic deletion/ITC binding; Co-IP, ChIP and reporter assays\",\n      \"pmids\": [\"22949637\", \"22300642\", \"23226276\", \"23251453\", \"22521691\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Single-residue determinant of methyl preference not yet isolated\", \"Corepressor selection rules among N-CoR/SMRT/MTG16 unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Challenged the methyl-dependent model with genome-wide data showing Kaiso preferentially occupies unmethylated, active, acetylated regions in cells, raising the question of context-dependent binding.\",\n      \"evidence\": \"Kaiso ChIP-seq integrated with genome-wide methylation analysis\",\n      \"pmids\": [\"23693142\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Discrepancy with in vitro methyl-binding not reconciled in this study\", \"Antibody/cell-context dependence not excluded\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Revealed a non-repressive function in the DNA-damage response: Kaiso joins the p53-p300 complex to reshape p53 acetylation and drive CDKN1A and apoptotic transcription.\",\n      \"evidence\": \"Co-IP, p53 acetylation mapping, ChIP and KO MEF reporter assays\",\n      \"pmids\": [\"25288747\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How DNA-damage signals recruit Kaiso to p53 unclear\", \"Relationship to its repressor activity not integrated\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Pinpointed E535 as the methyl-discrimination residue via CH\\u00b7\\u00b7\\u00b7O hydrogen bonds and showed SUMOylation at K42 acts as a repressor-to-activator switch, adding a post-translational control layer.\",\n      \"evidence\": \"X-ray/NMR with E535 mutants and binding assays; K42R mutagenesis, CRISPR editing, reporter assays and salt-diet KO mice\",\n      \"pmids\": [\"29546986\", \"29472715\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genome-wide consequences of the SUMO switch incompletely mapped\", \"Coupling of E535 readout to corepressor recruitment unresolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Explained how one residue achieves dual specificity by showing E535 functions as a conformational switch that directly reads mCpG but indirectly screens KBS flanking sequence.\",\n      \"evidence\": \"X-ray crystallography of mutant complexes with nucleotide substitutions and binding assays\",\n      \"pmids\": [\"32352758\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of flexibility-based selectivity not directly tested\", \"Linker/proline contributions only later addressed\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Tied Kaiso to genome methylation maintenance and to hematopoietic disease by showing it recruits de novo DNMT3a/3b and that ZBTB33 mutations give HSCs a competitive advantage with altered splicing.\",\n      \"evidence\": \"CRISPR-KO renal cells with whole-genome methylation and DNMT Co-IP; CRISPR-edited mouse HSPC transplantation with RNA-seq\",\n      \"pmids\": [\"34299205\", \"34568833\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking methylation reading to intron retention unestablished\", \"Direct DNMT recruitment to chromatin not shown in vivo\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Clarified SUMO-switch regulation and DNA-binding fine structure by mapping TRIM28-mediated mutual SUMOylation and a conserved linker proline required for binding.\",\n      \"evidence\": \"Co-IP/domain mapping and SUMOylation assays; P588 mutagenesis with binding assays and MD simulation\",\n      \"pmids\": [\"36252888\", \"36555132\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological triggers of TRIM28-Kaiso SUMOylation unclear\", \"Allosteric model from MD not validated structurally\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Definitively resolved the in vivo binding mode, showing Kaiso occupies CGCG and CTGCNAT motifs (often both), prefers methylated CpG islands, and that E535A retains KBS binding in cells.\",\n      \"evidence\": \"ChIP-seq with Kaiso-KO negative control, E535A mutant ChIP-seq, bisulfite sequencing across cell lines\",\n      \"pmids\": [\"39702290\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct corepressor occupancy genome-wide not co-mapped\", \"Reconciliation with earlier unmethylated-site ChIP-seq partial\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How Kaiso's dual reader activity, SUMO-controlled repressor/activator switch, and association with de novo methyltransferases and the splicing machinery are mechanistically integrated into a single regulatory output remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model coupling methyl-reading to splicing changes\", \"Rules selecting repression vs activation at a given locus undefined\", \"Corepressor-versus-DNMT recruitment hierarchy unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 3, 31, 50]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [1, 2, 20, 38]},\n      {\"term_id\": \"GO:0003682\", \"supporting_discovery_ids\": [20]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [3, 24, 38]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [18]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [3, 22, 38]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [3, 34]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [9, 19]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [22, 29]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [12, 14]}\n    ],\n    \"complexes\": [\"N-CoR/HDAC corepressor complex\", \"SMRT corepressor complex\", \"MeCP1\", \"pericentriolar material\"],\n    \"partners\": [\"CTNND1\", \"TRIM28\", \"CTCF\", \"ZNF131\", \"MTG16\", \"NCOR2\", \"TP53\", \"EP300\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":9,"faith_total":9,"faith_pct":100.0}}