{"gene":"ZNF350","run_date":"2026-06-11T09:02:07","timeline":{"discoveries":[{"year":2000,"finding":"ZBRK1 (ZNF350) directly interacts with BRCA1 both in vitro and in vivo, binds the specific DNA sequence GGGxxxCAGxxxTTT within GADD45 intron 3, and represses GADD45 transcription in a BRCA1-dependent manner, revealing a corepressor function for BRCA1.","method":"In vitro binding assay, co-immunoprecipitation, DNA binding/EMSA, transcriptional reporter assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (in vitro interaction, co-IP, DNA binding, reporter assay) in a foundational study, widely replicated by subsequent work","pmids":["11090615"],"is_preprint":false},{"year":2003,"finding":"Upon DNA damage (UV or MMS), ZBRK1 is rapidly degraded via the ubiquitin-proteasome pathway; a 44-amino-acid element between the N-terminal KRAB domain and the eight zinc fingers is sufficient for DNA damage-induced degradation; this degradation is independent of BRCA1 E3 ligase activity and is required for derepression of GADD45a.","method":"Proteasome inhibitor treatment, detection of polyubiquitinated ZBRK1, deletion mutant analysis, cell survival and GADD45a derepression assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods including biochemical detection of ubiquitinated forms, domain mapping by mutant analysis, and functional rescue experiments in a single rigorous study","pmids":["14517299"],"is_preprint":false},{"year":2003,"finding":"ZBRK1 contains a portable BRCA1-dependent C-terminal transcriptional repression domain (CTRD) composed of zinc fingers 5-8 plus the unique C-terminus; this CTRD functions in a BRCA1-, histone deacetylase-, and promoter-specific manner, distinguishable from the N-terminal KRAB repression domain which is BRCA1-independent and broadly active; the CTRD also modulates sequence-specific DNA binding activity.","method":"Domain deletion and point mutant analysis, transcriptional reporter assay, HDAC inhibitor treatment","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — systematic mutagenesis combined with functional transcription assays and pharmacological inhibition, multiple orthogonal methods","pmids":["14660588"],"is_preprint":false},{"year":2004,"finding":"ZBRK1 homo-oligomerizes as a tetramer in solution through its C-terminal repression domain (CTRD); oligomerization facilitates ZBRK1-directed transcriptional repression via ZBRK1 response elements; the KRAB and CTRD domains but not DNA-binding activity are required for oligomerization-dependent repression.","method":"Protein cross-linking, gel filtration chromatography, in vitro and in vivo protein interaction assays, transcriptional reporter assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — biochemical reconstitution with gel filtration and cross-linking, combined with functional transcription assays and domain mapping","pmids":["15496401"],"is_preprint":false},{"year":2005,"finding":"ZBRK1 interacts with the EBV replication protein BBLF2/3 and with the corepressor KAP-1; ZBRK1 binds a specific site in the EBV oriLyt enhancer; ZBRK1, KAP-1, and BRCA1 localize to EBV replication compartments and associate with oriLyt DNA; exogenous ZBRK1 increases oriLyt replication efficiency, and deletion of the ZBRK1 binding site impairs replication.","method":"Yeast two-hybrid, co-immunoprecipitation, EMSA, indirect immunofluorescence, chromatin immunoprecipitation, oriLyt replication assay","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (Y2H, Co-IP, EMSA, ChIP, functional replication assay) in a single study","pmids":["15596820"],"is_preprint":false},{"year":2006,"finding":"BRCA1, CtIP, and ZBRK1 form a trimeric repressor complex that represses angiopoietin-1 (ANG1) expression via a ZBRK1 recognition site in the ANG1 promoter; impairment of this complex upregulates ANG1, stabilizes endothelial cells and promotes angiogenesis; Brca1-deficient mouse mammary tumors show accelerated growth, vascularization, and ANG1 overexpression.","method":"Microarray analysis, co-immunoprecipitation, chromatin immunoprecipitation, RNA interference, in vitro angiogenesis assay, mouse mammary tumor model","journal":"Cancer cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, ChIP, RNAi with functional phenotype, in vivo mouse model; multiple orthogonal approaches","pmids":["16843262"],"is_preprint":false},{"year":2009,"finding":"ZBRK1 directly represses MMP9 transcription in cervical cancer cells; enforced ZBRK1 expression inhibits invasion and metastasis in vitro and in vivo; ZBRK1 and MMP9 levels are inversely correlated in tumor tissues.","method":"Enforced expression, shRNA knockdown, invasion assay, in vivo xenograft assay, ChIP/reporter assay","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss- and gain-of-function experiments with defined phenotypic readout and transcriptional target, single lab","pmids":["19996286"],"is_preprint":false},{"year":2009,"finding":"ZBRK1, BRCA1, and CtIP form a repressor complex that coordinately represses HMGA2 expression via a ZBRK1 recognition site in the HMGA2 promoter; depletion of any component activates HMGA2, increases colony formation and causes abnormal acinar morphology in mammary epithelial cells.","method":"Microarray, adenoviral RNAi, chromatin immunoprecipitation, soft agar assay, 3D acinar morphogenesis assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — ChIP confirms direct binding, multiple RNAi experiments with orthogonal phenotypic readouts, consistent with in vivo mouse tumor data","pmids":["20007691"],"is_preprint":false},{"year":2010,"finding":"ZBRK1 activates SCA2 (ataxin-2) gene transcription through direct interaction with its gene product ataxin-2; elevated ZBRK1 increases ataxin-2 levels; ZBRK1-binding sites are present in the SCA2 promoter and validated by ChIP; ataxin-2 acts as the first identified ZBRK1 co-activator.","method":"Yeast two-hybrid, co-immunoprecipitation, chromatin immunoprecipitation, luciferase promoter assay, siRNA knockdown","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Y2H, Co-IP, ChIP, reporter assay), single lab","pmids":["20926453"],"is_preprint":false},{"year":2010,"finding":"The RB·E2F1/CtIP/CtBP complex represses ZBRK1 transcription by binding an E2F recognition sequence in the ZBRK1 promoter; loss of RB increases ZBRK1 transcript levels and sensitizes cells to UV- and MMS-induced DNA damage.","method":"Chromatin immunoprecipitation, reporter assay, RNAi, cell survival assay after DNA damage","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and reporter assays demonstrate direct regulation, functional consequence shown, single lab","pmids":["20713352"],"is_preprint":false},{"year":2012,"finding":"ZBRK1 represses HIV-1 LTR-mediated transcription; this repressor activity requires TRIM28 (KAP-1) binding; ZBRK1 is found bound to the HIV-1 LTR in vivo by ChIP.","method":"Ectopic expression, siRNA knockdown, luciferase reporter assay, chromatin immunoprecipitation","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reporter assay, ChIP, and requirement for KAP-1 demonstrated, single lab","pmids":["22975076"],"is_preprint":false},{"year":2013,"finding":"Loss of ZBRK1 leads to increased KAP1 expression, which enhances migration and invasion of cervical cancer cells; the N-terminal KRAB domain of ZBRK1 is specifically required for inhibiting metastasis and invasion by modulating KAP1 function in a transcriptionally dependent manner.","method":"Domain deletion analysis, shRNA knockdown, overexpression, in vitro migration/invasion assays, in vivo xenograft assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain dissection combined with functional assays in vitro and in vivo, single lab","pmids":["23991171"],"is_preprint":false},{"year":2014,"finding":"LCoR (ligand-dependent corepressor) interacts with KAP-1, and together with ZBRK1 forms a trimeric complex on GADD45A intron and a novel FGF2 gene site; chromatin at these sites is enriched for SETDB1 and H3K9me3; depletion of ZBRK1, KAP-1, or LCoR elevates GADD45A and FGF2 expression and causes apoptotic cell death in breast epithelial cells.","method":"Co-immunoprecipitation, chromatin immunoprecipitation, siRNA knockdown, gene expression analysis, cell viability assay","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP confirms complex, ChIP confirms chromatin association, RNAi provides functional phenotype; single lab","pmids":["24829459"],"is_preprint":false},{"year":2014,"finding":"The purified ZBRK1 DNA-binding domain forms a homotetramer in solution and binds cognate DNA (5'GGGXXXCAGXXXTTT3') even in the absence of zinc ions; zinc ions increase protein stability; ZBRK1-DNA complex adopts a secondary structure significantly different from standard B-DNA.","method":"Recombinant protein purification, gel filtration, cross-linking, CD spectroscopy, pulldown assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biophysical reconstitution with multiple methods but single lab, not replicated independently","pmids":["24924633"],"is_preprint":false},{"year":2015,"finding":"ZBRK1 activates VHL gene transcription via a ZBRK1-binding site in the VHL promoter; VHL protein serves as a bridge between ZBRK1 and p300, facilitating increased ZBRK1 transcriptional activity at the VHL promoter; ZBRK1 suppresses VEGF transcription through the VHL/HIF pathway.","method":"Yeast two-hybrid, co-immunoprecipitation, reporter assay, shRNA knockdown, in vitro and in vivo tumor assays","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Y2H, Co-IP, reporter assays with RNAi; single lab","pmids":["25749518"],"is_preprint":false},{"year":2018,"finding":"ZNF121 physically interacts with ZBRK1 and BRCA1 (confirmed by yeast two-hybrid and co-immunoprecipitation) and suppresses expression of ANG1 and HMGA2, two established downstream targets of the ZBRK1/BRCA1/CtIP repressor complex; ZNF121 also regulates BRCA1 and ZBRK1 expression levels.","method":"Yeast two-hybrid, co-immunoprecipitation, gene expression analysis","journal":"FEBS open bio","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Y2H and single Co-IP with limited mechanistic follow-up, single lab","pmids":["30524945"],"is_preprint":false},{"year":2018,"finding":"Hypermethylation of the ZNF350 proximal promoter silences ZNF350 expression and accelerates colon cancer cell migration; ZNF350 knockdown accelerates migration while overexpression impairs it; three hyper-methylated CpG sites in the -268 to +49 bp region are responsible for basal promoter activity.","method":"5-azacytidine treatment, global transcriptome analysis, global methylation analysis, siRNA knockdown, ZNF350 overexpression, migration assay, pyrosequencing, luciferase promoter assay","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — methylation-dependent promoter silencing confirmed by multiple methods (bisulfite, reporter assay), gain- and loss-of-function phenotype, single lab","pmids":["30613364"],"is_preprint":false},{"year":2019,"finding":"BRCA1 and ZBRK1 form a co-repressor complex that directly represses GOT2 (glutamate-oxaloacetate transaminase 2) transcription via a ZBRK1 recognition element in the GOT2 promoter; impairment of this complex upregulates GOT2, increases aspartate and alpha-ketoglutarate production, and accelerates breast cancer cell proliferation.","method":"Co-immunoprecipitation, chromatin immunoprecipitation, reporter assay, shRNA knockdown, metabolite measurement, cell proliferation assay","journal":"Molecular oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ChIP, and reporter confirm direct complex and binding; metabolic and proliferation phenotype, single lab","pmids":["30714292"],"is_preprint":false},{"year":2002,"finding":"ZBRK1 and the hematopoietic KRAB-ZFP SZF1 recognize overlapping DNA consensus sequences (both bind GGGxxxCAGxxxTTT-like sites); SZF1 KRAB domain directly binds KAP-1 corepressor; full-length SZF1 represses a promoter containing ZBRK1 recognition sequences.","method":"PCR-based binding site selection, EMSA, in vitro binding assay, reporter assay","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — in vitro binding site selection and EMSA with functional reporter assay; primarily characterizes SZF1 but directly defines ZBRK1 binding specificity","pmids":["12097288"],"is_preprint":false},{"year":2018,"finding":"ZNF350 missense variants L66P (rs2278420) and S501R (rs2278415) weaken the capability of ZNF350-mediated transcriptional repression of GADD45α, providing a functional mechanism for observed breast cancer risk associations.","method":"Luciferase reporter assay with variant ZNF350 constructs","journal":"DNA and cell biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single reporter assay, single lab, limited mechanistic depth","pmids":["29653063"],"is_preprint":false}],"current_model":"ZNF350/ZBRK1 is a KRAB-domain, eight-zinc-finger transcriptional repressor that binds the DNA consensus GGGxxxCAGxxxTTT and assembles a nuclear co-repressor complex minimally containing BRCA1 and KAP-1/TRIM28 to silence target genes (GADD45A, ANG1, HMGA2, MMP9, GOT2, FGF2, VHL); it forms homotetramers through its C-terminal repression domain, is degraded via the ubiquitin-proteasome pathway in response to DNA damage through a discrete 44-aa degron element (thereby de-repressing damage-response genes), is itself transcriptionally controlled by the RB·E2F1/CtIP/CtBP complex, and additionally interacts with ataxin-2 (acting as a transcriptional activator of SCA2), with the EBV helicase-linker protein BBLF2/3 to facilitate viral oriLyt replication, and with LCoR, CtIP, and ZNF121 as further co-regulatory partners."},"narrative":{"mechanistic_narrative":"ZNF350 (ZBRK1) is a KRAB-domain, eight-zinc-finger sequence-specific transcriptional repressor that nucleates a BRCA1-containing co-repressor complex to silence damage-response, angiogenic, and metabolic target genes [PMID:11090615, PMID:16843262]. It binds the consensus GGGxxxCAGxxxTTT through its zinc-finger DNA-binding domain, which forms a homotetramer and engages cognate DNA even in the absence of zinc [PMID:24924633, PMID:12097288], and represses transcription through two separable modules: an N-terminal KRAB domain that acts broadly and BRCA1-independently, and a C-terminal repression domain (zinc fingers 5–8 plus the unique C-terminus) that confers BRCA1-, HDAC-, and promoter-specific repression and mediates oligomerization-dependent silencing [PMID:14660588, PMID:15496401]. Acting with BRCA1, CtIP, and the corepressor KAP-1/TRIM28 (and additionally LCoR, which recruits SETDB1 and H3K9me3 chromatin marks), ZBRK1 directly represses GADD45A, ANG1, HMGA2, MMP9, and the metabolic gene GOT2, thereby restraining angiogenesis, invasion/metastasis, and tumor cell proliferation [PMID:16843262, PMID:19996286, PMID:20007691, PMID:24829459, PMID:30714292]. Repression is reversed by DNA damage: UV or MMS triggers ubiquitin-proteasome degradation of ZBRK1 via a discrete 44-amino-acid degron between the KRAB and zinc-finger regions, derepressing GADD45A [PMID:14517299]. ZBRK1 levels are themselves transcriptionally controlled by the RB·E2F1/CtIP/CtBP complex [PMID:20713352], and it can act outside the repressive mode, activating SCA2/ataxin-2 and VHL transcription [PMID:20926453, PMID:25749518] and being co-opted by Epstein–Barr virus, where it binds the oriLyt enhancer to promote lytic viral replication [PMID:15596820]. Functional ZNF350 missense variants that weaken GADD45A repression provide a mechanistic link to breast cancer risk [PMID:29653063], and promoter hypermethylation that silences ZNF350 accelerates colon cancer cell migration [PMID:30613364].","teleology":[{"year":2000,"claim":"Established ZBRK1 as a sequence-specific repressor and identified BRCA1 as its essential corepressor, defining a transcriptional arm of BRCA1 function.","evidence":"In vitro binding, co-IP, EMSA, and reporter assays on the GADD45 intron 3 element","pmids":["11090615"],"confidence":"High","gaps":["Did not map the repression domains responsible","Mechanism of BRCA1 recruitment to chromatin unresolved","Scope of target genes beyond GADD45 unknown"]},{"year":2002,"claim":"Defined the ZBRK1 DNA recognition consensus by comparison with the related KRAB-ZFP SZF1, anchoring the GGGxxxCAGxxxTTT motif and KAP-1 corepressor linkage.","evidence":"PCR binding-site selection, EMSA, and reporter assays (study primarily of SZF1)","pmids":["12097288"],"confidence":"Medium","gaps":["Direct ZBRK1–KAP-1 binding not demonstrated here","Genome-wide occupancy not assessed"]},{"year":2003,"claim":"Resolved how ZBRK1 repression is relieved after genotoxic stress, mapping a discrete 44-aa degron that drives proteasomal degradation and GADD45a derepression.","evidence":"Proteasome inhibition, polyubiquitin detection, deletion mutants, and derepression assays","pmids":["14517299"],"confidence":"High","gaps":["E3 ligase responsible not identified","Signaling kinases linking damage to degron unknown"]},{"year":2003,"claim":"Dissected ZBRK1 into two functionally distinct repression modules, explaining how BRCA1-dependent and BRCA1-independent silencing coexist in one protein.","evidence":"Systematic mutagenesis, reporter assays, HDAC inhibition","pmids":["14660588"],"confidence":"High","gaps":["Structural basis of CTRD–BRCA1 contact undefined","Identity of HDAC partner not specified"]},{"year":2004,"claim":"Showed ZBRK1 self-assembles into tetramers via the CTRD and that oligomerization, not DNA binding alone, drives efficient repression.","evidence":"Cross-linking, gel filtration, protein interaction and reporter assays","pmids":["15496401"],"confidence":"High","gaps":["Stoichiometry on chromatin in vivo unresolved","No high-resolution oligomer structure"]},{"year":2005,"claim":"Revealed that EBV hijacks ZBRK1: it binds the oriLyt enhancer with KAP-1 and BRCA1 to enhance lytic viral replication, a non-repressive role.","evidence":"Y2H, co-IP, EMSA, immunofluorescence, ChIP, oriLyt replication assay","pmids":["15596820"],"confidence":"High","gaps":["Mechanism by which ZBRK1 stimulates replication unclear","Whether host gene repression contributes not addressed"]},{"year":2006,"claim":"Demonstrated the BRCA1/CtIP/ZBRK1 trimeric complex restrains angiogenesis by repressing ANG1, connecting the complex to tumor vascularization in vivo.","evidence":"Microarray, reciprocal co-IP, ChIP, RNAi, angiogenesis assay, Brca1-deficient mouse tumors","pmids":["16843262"],"confidence":"High","gaps":["CtIP's biochemical contribution to repression undefined","Direct relevance to human tumors not tested here"]},{"year":2009,"claim":"Extended the repressor complex to HMGA2 and MMP9, linking ZBRK1 loss to colony formation, abnormal acinar morphology, and invasion/metastasis.","evidence":"Microarray, RNAi, ChIP, soft agar, 3D morphogenesis, invasion and xenograft assays","pmids":["20007691","19996286"],"confidence":"Medium","gaps":["MMP9 repression confirmed in a single tumor context","Whether targets share co-regulation in vivo unclear"]},{"year":2010,"claim":"Identified an upstream regulatory loop in which RB·E2F1/CtIP/CtBP transcriptionally represses ZBRK1, tying ZBRK1 levels to RB status and DNA-damage sensitivity.","evidence":"ChIP, reporter assays, RNAi, survival assays after UV/MMS","pmids":["20713352"],"confidence":"Medium","gaps":["Physiological conditions activating this loop unclear","Single-lab observation"]},{"year":2010,"claim":"Uncovered a transcriptional-activator mode of ZBRK1, with ataxin-2 as its first co-activator upregulating SCA2.","evidence":"Y2H, co-IP, ChIP, luciferase, siRNA","pmids":["20926453"],"confidence":"Medium","gaps":["Switch between repressor and activator states unexplained","Single-lab observation"]},{"year":2012,"claim":"Showed ZBRK1 represses the HIV-1 LTR in a KAP-1/TRIM28-dependent manner, broadening its viral-promoter repertoire.","evidence":"Ectopic expression, siRNA, reporter assay, ChIP","pmids":["22975076"],"confidence":"Medium","gaps":["Effect on authentic proviral transcription not tested","Single-lab observation"]},{"year":2014,"claim":"Defined the chromatin-modifying machinery of the complex, placing LCoR–KAP-1–ZBRK1 at GADD45A and FGF2 with SETDB1 and H3K9me3, with depletion causing apoptosis.","evidence":"Co-IP, ChIP, siRNA, expression and viability assays","pmids":["24829459"],"confidence":"Medium","gaps":["Order of factor assembly on chromatin unresolved","Direct SETDB1–ZBRK1 contact not shown"]},{"year":2014,"claim":"Characterized the isolated DNA-binding domain biophysically, showing zinc-independent tetrameric DNA binding and a non-B-DNA complex conformation.","evidence":"Recombinant protein purification, gel filtration, cross-linking, CD spectroscopy, pulldown","pmids":["24924633"],"confidence":"Medium","gaps":["No crystal/cryo-EM structure of the complex","In vitro findings not validated in cells"]},{"year":2015,"claim":"Demonstrated a second activator role at VHL, where VHL bridges ZBRK1 to p300 and ZBRK1 suppresses VEGF via the VHL/HIF axis.","evidence":"Y2H, co-IP, reporter, shRNA, tumor assays","pmids":["25749518"],"confidence":"Medium","gaps":["How p300 recruitment overrides repressor activity unclear","Single-lab observation"]},{"year":2017,"claim":"Connected the complex to cancer metabolism, showing BRCA1/ZBRK1 repress GOT2 to limit aspartate/α-ketoglutarate production and proliferation.","evidence":"Co-IP, ChIP, reporter, shRNA, metabolite and proliferation assays","pmids":["30714292"],"confidence":"Medium","gaps":["CtIP/KAP-1 involvement at GOT2 not tested","Single-lab observation"]},{"year":2018,"claim":"Provided disease and regulatory context: cancer-risk missense variants weaken GADD45A repression, promoter hypermethylation silences ZNF350 to drive migration, and ZNF121 modulates the ZBRK1/BRCA1 axis.","evidence":"Variant reporter assays; 5-aza, bisulfite/pyrosequencing, RNAi, migration assays; Y2H and co-IP","pmids":["29653063","30613364","30524945"],"confidence":"Low","gaps":["Variant effects shown only by reporter assay","ZNF121 interaction rests on single co-IP without reciprocal validation","Causal contribution to clinical phenotypes not established"]},{"year":null,"claim":"The structural basis of the BRCA1/CtIP/KAP-1 co-repressor assembly on chromatin and the molecular switch governing ZBRK1's transition between repressor and activator at different promoters remain undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structure of the assembled complex on DNA","Determinants of activator vs repressor mode unknown","Identity of the DNA-damage-responsive E3 ligase for the degron unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,2,8,14]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,13,18]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,12]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,4,5]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,2,5,7]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[12]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[1,9]}],"complexes":["ZBRK1/BRCA1/CtIP repressor complex","ZBRK1/KAP-1/LCoR repressor complex"],"partners":["BRCA1","CTIP","TRIM28","LCOR","ATXN2","VHL","ZNF121","BBLF2/3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9GZX5","full_name":"Zinc finger protein 350","aliases":["KRAB zinc finger protein ZFQR","Zinc finger and BRCA1-interacting protein with a KRAB domain 1","Zinc finger protein ZBRK1"],"length_aa":532,"mass_kda":60.0,"function":"Transcriptional repressor. Binds to a specific sequence, 5'-GGGxxxCAGxxxTTT-3', within GADD45 intron 3","subcellular_location":"Nucleus; Nucleus matrix","url":"https://www.uniprot.org/uniprotkb/Q9GZX5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ZNF350","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ZNF350","total_profiled":1310},"omim":[{"mim_id":"616702","title":"ZINC FINGER PROTEIN 589; ZNF589","url":"https://www.omim.org/entry/616702"},{"mim_id":"612598","title":"RING FINGER PROTEIN 11; RNF11","url":"https://www.omim.org/entry/612598"},{"mim_id":"605422","title":"ZINC FINGER PROTEIN 350; ZNF350","url":"https://www.omim.org/entry/605422"},{"mim_id":"604588","title":"NIMA-RELATED KINASE 1; NEK1","url":"https://www.omim.org/entry/604588"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ZNF350"},"hgnc":{"alias_symbol":["ZBRK1","ZFQR"],"prev_symbol":[]},"alphafold":{"accession":"Q9GZX5","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9GZX5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9GZX5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9GZX5-F1-predicted_aligned_error_v6.png","plddt_mean":59.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZNF350","jax_strain_url":"https://www.jax.org/strain/search?query=ZNF350"},"sequence":{"accession":"Q9GZX5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9GZX5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9GZX5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9GZX5"}},"corpus_meta":[{"pmid":"11090615","id":"PMC_11090615","title":"Sequence-specific transcriptional corepressor function for BRCA1 through a novel zinc finger protein, ZBRK1.","date":"2000","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/11090615","citation_count":203,"is_preprint":false},{"pmid":"16843262","id":"PMC_16843262","title":"Removal of BRCA1/CtIP/ZBRK1 repressor complex on ANG1 promoter leads to accelerated mammary tumor growth contributed by prominent vasculature.","date":"2006","source":"Cancer cell","url":"https://pubmed.ncbi.nlm.nih.gov/16843262","citation_count":87,"is_preprint":false},{"pmid":"12872252","id":"PMC_12872252","title":"Mutational analysis of the BRCA1-interacting genes ZNF350/ZBRK1 and BRIP1/BACH1 among BRCA1 and BRCA2-negative probands from breast-ovarian cancer families and among early-onset breast cancer cases and reference individuals.","date":"2003","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/12872252","citation_count":46,"is_preprint":false},{"pmid":"14517299","id":"PMC_14517299","title":"Degradation of transcription repressor ZBRK1 through the ubiquitin-proteasome pathway relieves repression of Gadd45a upon DNA damage.","date":"2003","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/14517299","citation_count":45,"is_preprint":false},{"pmid":"19996286","id":"PMC_19996286","title":"ZBRK1 acts as a metastatic suppressor by directly regulating MMP9 in cervical cancer.","date":"2009","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/19996286","citation_count":44,"is_preprint":false},{"pmid":"20007691","id":"PMC_20007691","title":"Derepression of HMGA2 via removal of ZBRK1/BRCA1/CtIP complex enhances mammary tumorigenesis.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20007691","citation_count":42,"is_preprint":false},{"pmid":"30714292","id":"PMC_30714292","title":"Preventing BRCA1/ZBRK1 repressor complex binding to the GOT2 promoter results in accelerated aspartate biosynthesis and promotion of cell proliferation.","date":"2019","source":"Molecular oncology","url":"https://pubmed.ncbi.nlm.nih.gov/30714292","citation_count":41,"is_preprint":false},{"pmid":"15596820","id":"PMC_15596820","title":"The Epstein-Barr virus replication protein BBLF2/3 provides an origin-tethering function through interaction with the zinc finger DNA binding protein ZBRK1 and the KAP-1 corepressor.","date":"2005","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/15596820","citation_count":38,"is_preprint":false},{"pmid":"23991171","id":"PMC_23991171","title":"Loss of ZBRK1 contributes to the increase of KAP1 and promotes KAP1-mediated metastasis and invasion in cervical cancer.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23991171","citation_count":38,"is_preprint":false},{"pmid":"14660588","id":"PMC_14660588","title":"Functional dissection of transcription factor ZBRK1 reveals zinc fingers with dual roles in DNA-binding and BRCA1-dependent transcriptional repression.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/14660588","citation_count":35,"is_preprint":false},{"pmid":"20926453","id":"PMC_20926453","title":"The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2.","date":"2010","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/20926453","citation_count":33,"is_preprint":false},{"pmid":"12097288","id":"PMC_12097288","title":"A common DNA-binding site for SZF1 and the BRCA1-associated zinc finger protein, ZBRK1.","date":"2002","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/12097288","citation_count":29,"is_preprint":false},{"pmid":"22975076","id":"PMC_22975076","title":"ZBRK1 represses HIV-1 LTR-mediated transcription.","date":"2012","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/22975076","citation_count":28,"is_preprint":false},{"pmid":"15772983","id":"PMC_15772983","title":"The GADD45, ZBRK1 and BRCA1 pathway: quantitative analysis of mRNA expression in colon carcinomas.","date":"2005","source":"The Journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/15772983","citation_count":22,"is_preprint":false},{"pmid":"25749518","id":"PMC_25749518","title":"ZBRK1, a novel tumor suppressor, activates VHL gene transcription through formation of a complex with VHL and p300 in renal cancer.","date":"2015","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/25749518","citation_count":22,"is_preprint":false},{"pmid":"14743505","id":"PMC_14743505","title":"Altered expression of the ZBRK1 gene in human breast carcinomas.","date":"2004","source":"The Journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/14743505","citation_count":20,"is_preprint":false},{"pmid":"24829459","id":"PMC_24829459","title":"Ligand-dependent corepressor contributes to transcriptional repression by C2H2 zinc-finger transcription factor ZBRK1 through association with KRAB-associated protein-1.","date":"2014","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/24829459","citation_count":20,"is_preprint":false},{"pmid":"27586871","id":"PMC_27586871","title":"Functional SNP in 3'-UTR MicroRNA-Binding Site of ZNF350 Confers Risk for Age-Related Cataract.","date":"2016","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/27586871","citation_count":19,"is_preprint":false},{"pmid":"20713352","id":"PMC_20713352","title":"RB·E2F1 complex mediates DNA damage responses through transcriptional regulation of ZBRK1.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20713352","citation_count":18,"is_preprint":false},{"pmid":"17764113","id":"PMC_17764113","title":"Genetic variants and haplotype analyses of the ZBRK1/ZNF350 gene in high-risk non BRCA1/2 French Canadian breast and ovarian cancer families.","date":"2008","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/17764113","citation_count":17,"is_preprint":false},{"pmid":"15496401","id":"PMC_15496401","title":"Tetrameric oligomerization mediates transcriptional repression by the BRCA1-dependent Kruppel-associated box-zinc finger protein ZBRK1.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15496401","citation_count":15,"is_preprint":false},{"pmid":"30613364","id":"PMC_30613364","title":"ZNF350 promoter methylation accelerates colon cancer cell migration.","date":"2018","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/30613364","citation_count":12,"is_preprint":false},{"pmid":"30524945","id":"PMC_30524945","title":"ZNF121 interacts with ZBRK1 and BRCA1 to regulate their target genes in mammary epithelial cells.","date":"2018","source":"FEBS open bio","url":"https://pubmed.ncbi.nlm.nih.gov/30524945","citation_count":7,"is_preprint":false},{"pmid":"23151675","id":"PMC_23151675","title":"Analysis of ZNF350/ZBRK1 promoter variants and breast cancer susceptibility in non-BRCA1/2 French Canadian breast cancer families.","date":"2012","source":"Journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23151675","citation_count":5,"is_preprint":false},{"pmid":"33407485","id":"PMC_33407485","title":"Correlation between ZBRK1/ZNF350 gene polymorphism and breast cancer.","date":"2021","source":"BMC medical genomics","url":"https://pubmed.ncbi.nlm.nih.gov/33407485","citation_count":4,"is_preprint":false},{"pmid":"29653063","id":"PMC_29653063","title":"Functional Evaluation of ZNF350 Missense Genetic Variants Associated with Breast Cancer Susceptibility.","date":"2018","source":"DNA and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/29653063","citation_count":3,"is_preprint":false},{"pmid":"39575240","id":"PMC_39575240","title":"ZNF350 gene polymorphisms promote the response to Peg-IFNα therapy through JAK-STAT signaling pathway in patients with chronic hepatitis B.","date":"2024","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/39575240","citation_count":2,"is_preprint":false},{"pmid":"24924633","id":"PMC_24924633","title":"Tetrameric ZBRK1 DNA binding domain has affinity towards cognate DNA in absence of zinc ions.","date":"2014","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/24924633","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15652,"output_tokens":4943,"usd":0.060551,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13098,"output_tokens":4682,"usd":0.09127,"stage2_stop_reason":"end_turn"},"total_usd":0.151821,"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\": 2000,\n      \"finding\": \"ZBRK1 (ZNF350) directly interacts with BRCA1 both in vitro and in vivo, binds the specific DNA sequence GGGxxxCAGxxxTTT within GADD45 intron 3, and represses GADD45 transcription in a BRCA1-dependent manner, revealing a corepressor function for BRCA1.\",\n      \"method\": \"In vitro binding assay, co-immunoprecipitation, DNA binding/EMSA, transcriptional reporter assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (in vitro interaction, co-IP, DNA binding, reporter assay) in a foundational study, widely replicated by subsequent work\",\n      \"pmids\": [\"11090615\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Upon DNA damage (UV or MMS), ZBRK1 is rapidly degraded via the ubiquitin-proteasome pathway; a 44-amino-acid element between the N-terminal KRAB domain and the eight zinc fingers is sufficient for DNA damage-induced degradation; this degradation is independent of BRCA1 E3 ligase activity and is required for derepression of GADD45a.\",\n      \"method\": \"Proteasome inhibitor treatment, detection of polyubiquitinated ZBRK1, deletion mutant analysis, cell survival and GADD45a derepression assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods including biochemical detection of ubiquitinated forms, domain mapping by mutant analysis, and functional rescue experiments in a single rigorous study\",\n      \"pmids\": [\"14517299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"ZBRK1 contains a portable BRCA1-dependent C-terminal transcriptional repression domain (CTRD) composed of zinc fingers 5-8 plus the unique C-terminus; this CTRD functions in a BRCA1-, histone deacetylase-, and promoter-specific manner, distinguishable from the N-terminal KRAB repression domain which is BRCA1-independent and broadly active; the CTRD also modulates sequence-specific DNA binding activity.\",\n      \"method\": \"Domain deletion and point mutant analysis, transcriptional reporter assay, HDAC inhibitor treatment\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — systematic mutagenesis combined with functional transcription assays and pharmacological inhibition, multiple orthogonal methods\",\n      \"pmids\": [\"14660588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"ZBRK1 homo-oligomerizes as a tetramer in solution through its C-terminal repression domain (CTRD); oligomerization facilitates ZBRK1-directed transcriptional repression via ZBRK1 response elements; the KRAB and CTRD domains but not DNA-binding activity are required for oligomerization-dependent repression.\",\n      \"method\": \"Protein cross-linking, gel filtration chromatography, in vitro and in vivo protein interaction assays, transcriptional reporter assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — biochemical reconstitution with gel filtration and cross-linking, combined with functional transcription assays and domain mapping\",\n      \"pmids\": [\"15496401\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"ZBRK1 interacts with the EBV replication protein BBLF2/3 and with the corepressor KAP-1; ZBRK1 binds a specific site in the EBV oriLyt enhancer; ZBRK1, KAP-1, and BRCA1 localize to EBV replication compartments and associate with oriLyt DNA; exogenous ZBRK1 increases oriLyt replication efficiency, and deletion of the ZBRK1 binding site impairs replication.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, EMSA, indirect immunofluorescence, chromatin immunoprecipitation, oriLyt replication assay\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (Y2H, Co-IP, EMSA, ChIP, functional replication assay) in a single study\",\n      \"pmids\": [\"15596820\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"BRCA1, CtIP, and ZBRK1 form a trimeric repressor complex that represses angiopoietin-1 (ANG1) expression via a ZBRK1 recognition site in the ANG1 promoter; impairment of this complex upregulates ANG1, stabilizes endothelial cells and promotes angiogenesis; Brca1-deficient mouse mammary tumors show accelerated growth, vascularization, and ANG1 overexpression.\",\n      \"method\": \"Microarray analysis, co-immunoprecipitation, chromatin immunoprecipitation, RNA interference, in vitro angiogenesis assay, mouse mammary tumor model\",\n      \"journal\": \"Cancer cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, ChIP, RNAi with functional phenotype, in vivo mouse model; multiple orthogonal approaches\",\n      \"pmids\": [\"16843262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"ZBRK1 directly represses MMP9 transcription in cervical cancer cells; enforced ZBRK1 expression inhibits invasion and metastasis in vitro and in vivo; ZBRK1 and MMP9 levels are inversely correlated in tumor tissues.\",\n      \"method\": \"Enforced expression, shRNA knockdown, invasion assay, in vivo xenograft assay, ChIP/reporter assay\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss- and gain-of-function experiments with defined phenotypic readout and transcriptional target, single lab\",\n      \"pmids\": [\"19996286\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"ZBRK1, BRCA1, and CtIP form a repressor complex that coordinately represses HMGA2 expression via a ZBRK1 recognition site in the HMGA2 promoter; depletion of any component activates HMGA2, increases colony formation and causes abnormal acinar morphology in mammary epithelial cells.\",\n      \"method\": \"Microarray, adenoviral RNAi, chromatin immunoprecipitation, soft agar assay, 3D acinar morphogenesis assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ChIP confirms direct binding, multiple RNAi experiments with orthogonal phenotypic readouts, consistent with in vivo mouse tumor data\",\n      \"pmids\": [\"20007691\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"ZBRK1 activates SCA2 (ataxin-2) gene transcription through direct interaction with its gene product ataxin-2; elevated ZBRK1 increases ataxin-2 levels; ZBRK1-binding sites are present in the SCA2 promoter and validated by ChIP; ataxin-2 acts as the first identified ZBRK1 co-activator.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, chromatin immunoprecipitation, luciferase promoter assay, siRNA knockdown\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Y2H, Co-IP, ChIP, reporter assay), single lab\",\n      \"pmids\": [\"20926453\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The RB·E2F1/CtIP/CtBP complex represses ZBRK1 transcription by binding an E2F recognition sequence in the ZBRK1 promoter; loss of RB increases ZBRK1 transcript levels and sensitizes cells to UV- and MMS-induced DNA damage.\",\n      \"method\": \"Chromatin immunoprecipitation, reporter assay, RNAi, cell survival assay after DNA damage\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and reporter assays demonstrate direct regulation, functional consequence shown, single lab\",\n      \"pmids\": [\"20713352\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"ZBRK1 represses HIV-1 LTR-mediated transcription; this repressor activity requires TRIM28 (KAP-1) binding; ZBRK1 is found bound to the HIV-1 LTR in vivo by ChIP.\",\n      \"method\": \"Ectopic expression, siRNA knockdown, luciferase reporter assay, chromatin immunoprecipitation\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reporter assay, ChIP, and requirement for KAP-1 demonstrated, single lab\",\n      \"pmids\": [\"22975076\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Loss of ZBRK1 leads to increased KAP1 expression, which enhances migration and invasion of cervical cancer cells; the N-terminal KRAB domain of ZBRK1 is specifically required for inhibiting metastasis and invasion by modulating KAP1 function in a transcriptionally dependent manner.\",\n      \"method\": \"Domain deletion analysis, shRNA knockdown, overexpression, in vitro migration/invasion assays, in vivo xenograft assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain dissection combined with functional assays in vitro and in vivo, single lab\",\n      \"pmids\": [\"23991171\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"LCoR (ligand-dependent corepressor) interacts with KAP-1, and together with ZBRK1 forms a trimeric complex on GADD45A intron and a novel FGF2 gene site; chromatin at these sites is enriched for SETDB1 and H3K9me3; depletion of ZBRK1, KAP-1, or LCoR elevates GADD45A and FGF2 expression and causes apoptotic cell death in breast epithelial cells.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation, siRNA knockdown, gene expression analysis, cell viability assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP confirms complex, ChIP confirms chromatin association, RNAi provides functional phenotype; single lab\",\n      \"pmids\": [\"24829459\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The purified ZBRK1 DNA-binding domain forms a homotetramer in solution and binds cognate DNA (5'GGGXXXCAGXXXTTT3') even in the absence of zinc ions; zinc ions increase protein stability; ZBRK1-DNA complex adopts a secondary structure significantly different from standard B-DNA.\",\n      \"method\": \"Recombinant protein purification, gel filtration, cross-linking, CD spectroscopy, pulldown assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biophysical reconstitution with multiple methods but single lab, not replicated independently\",\n      \"pmids\": [\"24924633\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"ZBRK1 activates VHL gene transcription via a ZBRK1-binding site in the VHL promoter; VHL protein serves as a bridge between ZBRK1 and p300, facilitating increased ZBRK1 transcriptional activity at the VHL promoter; ZBRK1 suppresses VEGF transcription through the VHL/HIF pathway.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, reporter assay, shRNA knockdown, in vitro and in vivo tumor assays\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Y2H, Co-IP, reporter assays with RNAi; single lab\",\n      \"pmids\": [\"25749518\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ZNF121 physically interacts with ZBRK1 and BRCA1 (confirmed by yeast two-hybrid and co-immunoprecipitation) and suppresses expression of ANG1 and HMGA2, two established downstream targets of the ZBRK1/BRCA1/CtIP repressor complex; ZNF121 also regulates BRCA1 and ZBRK1 expression levels.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, gene expression analysis\",\n      \"journal\": \"FEBS open bio\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Y2H and single Co-IP with limited mechanistic follow-up, single lab\",\n      \"pmids\": [\"30524945\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Hypermethylation of the ZNF350 proximal promoter silences ZNF350 expression and accelerates colon cancer cell migration; ZNF350 knockdown accelerates migration while overexpression impairs it; three hyper-methylated CpG sites in the -268 to +49 bp region are responsible for basal promoter activity.\",\n      \"method\": \"5-azacytidine treatment, global transcriptome analysis, global methylation analysis, siRNA knockdown, ZNF350 overexpression, migration assay, pyrosequencing, luciferase promoter assay\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — methylation-dependent promoter silencing confirmed by multiple methods (bisulfite, reporter assay), gain- and loss-of-function phenotype, single lab\",\n      \"pmids\": [\"30613364\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"BRCA1 and ZBRK1 form a co-repressor complex that directly represses GOT2 (glutamate-oxaloacetate transaminase 2) transcription via a ZBRK1 recognition element in the GOT2 promoter; impairment of this complex upregulates GOT2, increases aspartate and alpha-ketoglutarate production, and accelerates breast cancer cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation, reporter assay, shRNA knockdown, metabolite measurement, cell proliferation assay\",\n      \"journal\": \"Molecular oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ChIP, and reporter confirm direct complex and binding; metabolic and proliferation phenotype, single lab\",\n      \"pmids\": [\"30714292\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"ZBRK1 and the hematopoietic KRAB-ZFP SZF1 recognize overlapping DNA consensus sequences (both bind GGGxxxCAGxxxTTT-like sites); SZF1 KRAB domain directly binds KAP-1 corepressor; full-length SZF1 represses a promoter containing ZBRK1 recognition sequences.\",\n      \"method\": \"PCR-based binding site selection, EMSA, in vitro binding assay, reporter assay\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro binding site selection and EMSA with functional reporter assay; primarily characterizes SZF1 but directly defines ZBRK1 binding specificity\",\n      \"pmids\": [\"12097288\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ZNF350 missense variants L66P (rs2278420) and S501R (rs2278415) weaken the capability of ZNF350-mediated transcriptional repression of GADD45α, providing a functional mechanism for observed breast cancer risk associations.\",\n      \"method\": \"Luciferase reporter assay with variant ZNF350 constructs\",\n      \"journal\": \"DNA and cell biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single reporter assay, single lab, limited mechanistic depth\",\n      \"pmids\": [\"29653063\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ZNF350/ZBRK1 is a KRAB-domain, eight-zinc-finger transcriptional repressor that binds the DNA consensus GGGxxxCAGxxxTTT and assembles a nuclear co-repressor complex minimally containing BRCA1 and KAP-1/TRIM28 to silence target genes (GADD45A, ANG1, HMGA2, MMP9, GOT2, FGF2, VHL); it forms homotetramers through its C-terminal repression domain, is degraded via the ubiquitin-proteasome pathway in response to DNA damage through a discrete 44-aa degron element (thereby de-repressing damage-response genes), is itself transcriptionally controlled by the RB·E2F1/CtIP/CtBP complex, and additionally interacts with ataxin-2 (acting as a transcriptional activator of SCA2), with the EBV helicase-linker protein BBLF2/3 to facilitate viral oriLyt replication, and with LCoR, CtIP, and ZNF121 as further co-regulatory partners.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ZNF350 (ZBRK1) is a KRAB-domain, eight-zinc-finger sequence-specific transcriptional repressor that nucleates a BRCA1-containing co-repressor complex to silence damage-response, angiogenic, and metabolic target genes [#0, #5]. It binds the consensus GGGxxxCAGxxxTTT through its zinc-finger DNA-binding domain, which forms a homotetramer and engages cognate DNA even in the absence of zinc [#13, #18], and represses transcription through two separable modules: an N-terminal KRAB domain that acts broadly and BRCA1-independently, and a C-terminal repression domain (zinc fingers 5–8 plus the unique C-terminus) that confers BRCA1-, HDAC-, and promoter-specific repression and mediates oligomerization-dependent silencing [#2, #3]. Acting with BRCA1, CtIP, and the corepressor KAP-1/TRIM28 (and additionally LCoR, which recruits SETDB1 and H3K9me3 chromatin marks), ZBRK1 directly represses GADD45A, ANG1, HMGA2, MMP9, and the metabolic gene GOT2, thereby restraining angiogenesis, invasion/metastasis, and tumor cell proliferation [#5, #6, #7, #12, #17]. Repression is reversed by DNA damage: UV or MMS triggers ubiquitin-proteasome degradation of ZBRK1 via a discrete 44-amino-acid degron between the KRAB and zinc-finger regions, derepressing GADD45A [#1]. ZBRK1 levels are themselves transcriptionally controlled by the RB·E2F1/CtIP/CtBP complex [#9], and it can act outside the repressive mode, activating SCA2/ataxin-2 and VHL transcription [#8, #14] and being co-opted by Epstein–Barr virus, where it binds the oriLyt enhancer to promote lytic viral replication [#4]. Functional ZNF350 missense variants that weaken GADD45A repression provide a mechanistic link to breast cancer risk [#19], and promoter hypermethylation that silences ZNF350 accelerates colon cancer cell migration [#16].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established ZBRK1 as a sequence-specific repressor and identified BRCA1 as its essential corepressor, defining a transcriptional arm of BRCA1 function.\",\n      \"evidence\": \"In vitro binding, co-IP, EMSA, and reporter assays on the GADD45 intron 3 element\",\n      \"pmids\": [\"11090615\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not map the repression domains responsible\", \"Mechanism of BRCA1 recruitment to chromatin unresolved\", \"Scope of target genes beyond GADD45 unknown\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Defined the ZBRK1 DNA recognition consensus by comparison with the related KRAB-ZFP SZF1, anchoring the GGGxxxCAGxxxTTT motif and KAP-1 corepressor linkage.\",\n      \"evidence\": \"PCR binding-site selection, EMSA, and reporter assays (study primarily of SZF1)\",\n      \"pmids\": [\"12097288\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ZBRK1–KAP-1 binding not demonstrated here\", \"Genome-wide occupancy not assessed\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Resolved how ZBRK1 repression is relieved after genotoxic stress, mapping a discrete 44-aa degron that drives proteasomal degradation and GADD45a derepression.\",\n      \"evidence\": \"Proteasome inhibition, polyubiquitin detection, deletion mutants, and derepression assays\",\n      \"pmids\": [\"14517299\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"E3 ligase responsible not identified\", \"Signaling kinases linking damage to degron unknown\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Dissected ZBRK1 into two functionally distinct repression modules, explaining how BRCA1-dependent and BRCA1-independent silencing coexist in one protein.\",\n      \"evidence\": \"Systematic mutagenesis, reporter assays, HDAC inhibition\",\n      \"pmids\": [\"14660588\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of CTRD–BRCA1 contact undefined\", \"Identity of HDAC partner not specified\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Showed ZBRK1 self-assembles into tetramers via the CTRD and that oligomerization, not DNA binding alone, drives efficient repression.\",\n      \"evidence\": \"Cross-linking, gel filtration, protein interaction and reporter assays\",\n      \"pmids\": [\"15496401\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry on chromatin in vivo unresolved\", \"No high-resolution oligomer structure\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Revealed that EBV hijacks ZBRK1: it binds the oriLyt enhancer with KAP-1 and BRCA1 to enhance lytic viral replication, a non-repressive role.\",\n      \"evidence\": \"Y2H, co-IP, EMSA, immunofluorescence, ChIP, oriLyt replication assay\",\n      \"pmids\": [\"15596820\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which ZBRK1 stimulates replication unclear\", \"Whether host gene repression contributes not addressed\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Demonstrated the BRCA1/CtIP/ZBRK1 trimeric complex restrains angiogenesis by repressing ANG1, connecting the complex to tumor vascularization in vivo.\",\n      \"evidence\": \"Microarray, reciprocal co-IP, ChIP, RNAi, angiogenesis assay, Brca1-deficient mouse tumors\",\n      \"pmids\": [\"16843262\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"CtIP's biochemical contribution to repression undefined\", \"Direct relevance to human tumors not tested here\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Extended the repressor complex to HMGA2 and MMP9, linking ZBRK1 loss to colony formation, abnormal acinar morphology, and invasion/metastasis.\",\n      \"evidence\": \"Microarray, RNAi, ChIP, soft agar, 3D morphogenesis, invasion and xenograft assays\",\n      \"pmids\": [\"20007691\", \"19996286\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"MMP9 repression confirmed in a single tumor context\", \"Whether targets share co-regulation in vivo unclear\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identified an upstream regulatory loop in which RB·E2F1/CtIP/CtBP transcriptionally represses ZBRK1, tying ZBRK1 levels to RB status and DNA-damage sensitivity.\",\n      \"evidence\": \"ChIP, reporter assays, RNAi, survival assays after UV/MMS\",\n      \"pmids\": [\"20713352\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological conditions activating this loop unclear\", \"Single-lab observation\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Uncovered a transcriptional-activator mode of ZBRK1, with ataxin-2 as its first co-activator upregulating SCA2.\",\n      \"evidence\": \"Y2H, co-IP, ChIP, luciferase, siRNA\",\n      \"pmids\": [\"20926453\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Switch between repressor and activator states unexplained\", \"Single-lab observation\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Showed ZBRK1 represses the HIV-1 LTR in a KAP-1/TRIM28-dependent manner, broadening its viral-promoter repertoire.\",\n      \"evidence\": \"Ectopic expression, siRNA, reporter assay, ChIP\",\n      \"pmids\": [\"22975076\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Effect on authentic proviral transcription not tested\", \"Single-lab observation\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defined the chromatin-modifying machinery of the complex, placing LCoR–KAP-1–ZBRK1 at GADD45A and FGF2 with SETDB1 and H3K9me3, with depletion causing apoptosis.\",\n      \"evidence\": \"Co-IP, ChIP, siRNA, expression and viability assays\",\n      \"pmids\": [\"24829459\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Order of factor assembly on chromatin unresolved\", \"Direct SETDB1–ZBRK1 contact not shown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Characterized the isolated DNA-binding domain biophysically, showing zinc-independent tetrameric DNA binding and a non-B-DNA complex conformation.\",\n      \"evidence\": \"Recombinant protein purification, gel filtration, cross-linking, CD spectroscopy, pulldown\",\n      \"pmids\": [\"24924633\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No crystal/cryo-EM structure of the complex\", \"In vitro findings not validated in cells\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrated a second activator role at VHL, where VHL bridges ZBRK1 to p300 and ZBRK1 suppresses VEGF via the VHL/HIF axis.\",\n      \"evidence\": \"Y2H, co-IP, reporter, shRNA, tumor assays\",\n      \"pmids\": [\"25749518\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How p300 recruitment overrides repressor activity unclear\", \"Single-lab observation\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected the complex to cancer metabolism, showing BRCA1/ZBRK1 repress GOT2 to limit aspartate/α-ketoglutarate production and proliferation.\",\n      \"evidence\": \"Co-IP, ChIP, reporter, shRNA, metabolite and proliferation assays\",\n      \"pmids\": [\"30714292\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"CtIP/KAP-1 involvement at GOT2 not tested\", \"Single-lab observation\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Provided disease and regulatory context: cancer-risk missense variants weaken GADD45A repression, promoter hypermethylation silences ZNF350 to drive migration, and ZNF121 modulates the ZBRK1/BRCA1 axis.\",\n      \"evidence\": \"Variant reporter assays; 5-aza, bisulfite/pyrosequencing, RNAi, migration assays; Y2H and co-IP\",\n      \"pmids\": [\"29653063\", \"30613364\", \"30524945\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Variant effects shown only by reporter assay\", \"ZNF121 interaction rests on single co-IP without reciprocal validation\", \"Causal contribution to clinical phenotypes not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis of the BRCA1/CtIP/KAP-1 co-repressor assembly on chromatin and the molecular switch governing ZBRK1's transition between repressor and activator at different promoters remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structure of the assembled complex on DNA\", \"Determinants of activator vs repressor mode unknown\", \"Identity of the DNA-damage-responsive E3 ligase for the degron unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 2, 8, 14]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 13, 18]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5, 12]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 4, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 2, 5, 7]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [12]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [1, 9]}\n    ],\n    \"complexes\": [\n      \"ZBRK1/BRCA1/CtIP repressor complex\",\n      \"ZBRK1/KAP-1/LCoR repressor complex\"\n    ],\n    \"partners\": [\n      \"BRCA1\",\n      \"CtIP\",\n      \"TRIM28\",\n      \"LCoR\",\n      \"ATXN2\",\n      \"VHL\",\n      \"ZNF121\",\n      \"BBLF2/3\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}