{"gene":"ZNF263","run_date":"2026-04-28T23:00:24","timeline":{"discoveries":[{"year":2020,"finding":"ZNF263 binds to the core promoter region of SIX3 and recruits the KAP1/HATS/DNMT corepressor complex to induce transcriptional silencing of SIX3 through H3K27me3 and DNA methylation. ERK, when activated by EGFR-MAPK signaling, binds ZNF263 and abrogates its ubiquitination, leading to ZNF263 stabilization.","method":"Co-immunoprecipitation, ChIP, promoter assays, mutagenesis, siRNA knockdown, gain-of-function experiments in glioblastoma cells","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Co-IP, ChIP, promoter assays, functional rescue) in single study with clear mechanistic chain","pmids":["32051553"],"is_preprint":false},{"year":2020,"finding":"ZNF263 acts as a transcriptional repressor of heparan sulfate biosynthesis genes, including HS3ST1 and HS3ST3A1. CRISPR knockout or siRNA knockdown of ZNF263 dramatically increases expression of these enzymes, enhancing 3-O-sulfation, antithrombin binding, Factor Xa inhibition, and neuropilin-1 binding.","method":"CRISPR-mediated knockout, siRNA knockdown, transcriptomics, ChIP-seq (motif analysis), functional heparin anticoagulant assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — CRISPR KO and siRNA KD with multiple orthogonal functional readouts; replicated in mammalian cell lines and primary human cells","pmids":["32277030"],"is_preprint":false},{"year":2024,"finding":"ZNF263 binds the EGFR gene promoter and recruits DNMT1 to suppress EGFR transcription via DNA hypermethylation. ZNF263 also interacts with nuclear EGFR protein, impairing the EGFR-STAT5 interaction to enhance AURKA expression, thereby sensitizing lung adenocarcinoma cells to EGFR-targeted therapy.","method":"ChIP, Co-IP, promoter methylation assays, luciferase reporter assays, overexpression/knockdown, xenograft animal models","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (ChIP, Co-IP, methylation assays, in vivo xenograft) establishing distinct mechanisms","pmids":["38335093"],"is_preprint":false},{"year":2023,"finding":"OGT O-GlcNAcylates ZNF263 at Ser662, which is responsible for ZNF263's chromatin association at candidate gene promoters. This OGT-ZNF263 cooperation activates downstream transcription and drives HCC malignant progression.","method":"ChIP-seq, Co-IP, mass spectrometry for PTM site identification, mutagenesis of Ser662, in vitro and in vivo functional assays","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1-2 — PTM site identified by MS, validated by mutagenesis, ChIP-seq genome-wide occupancy, and functional rescue","pmids":["37353617"],"is_preprint":false},{"year":2024,"finding":"ZNF263 binds the promoter of CPT1B to activate its transcription, thereby enhancing fatty acid β-oxidation and promoting cisplatin resistance in lung adenocarcinoma cells.","method":"Dual-luciferase reporter assay, chromatin immunoprecipitation (ChIP), qRT-PCR, western blot, IC50 assays, FAO rate measurement","journal":"The pharmacogenomics journal","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP and luciferase reporter with functional metabolic readout, but single lab","pmids":["39500874"],"is_preprint":false},{"year":2024,"finding":"ZNF263 acts as a transcriptional activator of RNF126 by binding its promoter. ZNF263 interacts with ZNF31 to co-regulate RNF126 transcription, which promotes ubiquitination-mediated degradation of PTEN, activating AKT/Cyclin D1 and AKT/GSK-3β/β-catenin signaling to drive EMT and drug resistance in pancreatic cancer.","method":"ChIP, Co-IP, luciferase reporter assay, siRNA knockdown, overexpression, in vivo xenograft and metastasis models","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP, Co-IP, luciferase reporter with in vivo validation; single lab","pmids":["38515383"],"is_preprint":false},{"year":2025,"finding":"ZNF263 directly initiates expression of early differentiation genes and dampens the core pluripotency circuitry in human embryonic stem cells, promoting pluripotency priming and lineage commitment. ZNF263 deficiency impairs pluripotency dissolution and multi-lineage differentiation, particularly toward ectoderm.","method":"Genetic knockout, functional differentiation assays, single-cell transcriptomics (scRNA-seq), ChIP, chromatin accessibility assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — genetic KO with scRNA-seq, ChIP, and multiple orthogonal functional differentiation assays","pmids":["41193435"],"is_preprint":false},{"year":2021,"finding":"ZNF263 transcriptionally induces circFOXP1 expression in renal cell carcinoma cells, contributing to the ZNF263/circFOXP1/miR-423-5p/U2AF2 regulatory axis that promotes tumor progression.","method":"siRNA knockdown, overexpression, luciferase reporter assay, qRT-PCR","journal":"Journal of immunology research","confidence":"Low","confidence_rationale":"Tier 3 — single lab, limited mechanistic validation of direct ZNF263 binding to circFOXP1 locus","pmids":["34514002"],"is_preprint":false},{"year":2021,"finding":"ZNF263 binding at a CpG site (cg11797365) in an intron of COL4A3 is associated with regulation of COL4A3 expression in bronchial epithelium; ZNF263 silencing by siRNA affects COL4A3 expression levels.","method":"ChIP-seq with qPCR, siRNA knockdown, DNA methylation bead arrays, RNA-seq in bronchial biopsies","journal":"ERJ open research","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP-seq and siRNA KD with gene expression readout; mechanistic link to methylation inferred","pmids":["34109240"],"is_preprint":false},{"year":2012,"finding":"ZNF263 binds to a 24-nucleotide DNA motif that differs from the motif predicted by the zinc finger code in several positions, as determined by de novo ChIP-based motif discovery.","method":"ChIP-seq, de novo motif discovery (ChIPMotifs/MEME/Weeder), bootstrap re-sampling","journal":"Methods in molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP-based high-throughput data with computational motif analysis; characterizes DNA binding specificity","pmids":["22130890"],"is_preprint":false},{"year":2019,"finding":"ZNF263 functions as a transcriptional activator of the bovine TORC2 gene promoter, binding within the core promoter region (-314 to -69 bp upstream of TSS), as confirmed by EMSA with nuclear extracts and luciferase reporter assays with mutated binding sites.","method":"Luciferase reporter assay with serial deletions and site-directed mutagenesis, EMSA, siRNA knockdown","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 — EMSA and functional reporter assays confirm direct binding and activation; bovine ortholog context","pmids":["31487963"],"is_preprint":false},{"year":2024,"finding":"ZNF263 regulates the expression of LINC00599 via a super-enhancer mechanism in pulmonary arterial smooth muscle cells, contributing to pulmonary hypertension progression.","method":"Super-enhancer analysis, transcription factor binding assays (details in preprint)","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 — preprint with limited mechanistic detail on ZNF263-specific binding validation","pmids":[],"is_preprint":true},{"year":2026,"finding":"ZNF263 acts as a transcriptional activator of GPSM2 by binding its promoter, activating the cell cycle pathway in a GPSM2-dependent manner to drive invasion, migration, and proliferation in colorectal cancer cells.","method":"ChIP, luciferase reporter assay, siRNA knockdown, overexpression, cell invasion/migration assays","journal":"Acta biochimica et biophysica Sinica","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP and luciferase reporter with functional cellular phenotype; single lab","pmids":["41772960"],"is_preprint":false}],"current_model":"ZNF263 is a C2H2 zinc finger transcription factor that functions primarily as a transcriptional repressor or activator depending on context: it binds specific DNA promoter motifs (a characterized 24-nt consensus), recruits corepressor complexes (KAP1/HATS/DNMT) to silence target genes via H3K27me3 and DNA methylation, or directly activates target gene transcription; its chromatin association is regulated by O-GlcNAcylation at Ser662 (written by OGT), and its protein stability is controlled by ERK-mediated inhibition of ubiquitination; downstream targets include heparan sulfate biosynthesis enzymes (HS3ST1, HS3ST3A1), SIX3, EGFR, CPT1B, RNF126, GPSM2, and COL4A3, placing ZNF263 at the intersection of epigenetic regulation, metabolic control, and lineage commitment in human cells."},"narrative":{"teleology":[{"year":2012,"claim":"Defining ZNF263's DNA-binding specificity resolved its 24-nt consensus motif, establishing that its in vivo binding preference diverges from zinc finger code predictions and enabling downstream target identification.","evidence":"ChIP-seq with de novo motif discovery (ChIPMotifs/MEME/Weeder) and bootstrap resampling","pmids":["22130890"],"confidence":"Medium","gaps":["Motif computationally derived without systematic biochemical validation of individual zinc finger–base contacts","No functional consequence of motif binding assessed"]},{"year":2019,"claim":"Demonstrating that ZNF263 can function as a transcriptional activator (on the bovine TORC2 promoter) established that ZNF263 is not exclusively a repressor, foreshadowing its context-dependent dual role.","evidence":"EMSA, luciferase reporter assays with serial deletions and site-directed mutagenesis, siRNA knockdown in bovine cells","pmids":["31487963"],"confidence":"Medium","gaps":["Bovine ortholog context; generalizability to human ZNF263 not directly tested","Co-activator partners not identified"]},{"year":2020,"claim":"Two studies simultaneously established ZNF263 as a transcriptional repressor that recruits the KAP1/HATS/DNMT corepressor complex to silence target genes (SIX3 and heparan sulfate biosynthesis enzymes), and revealed that ERK-mediated inhibition of ZNF263 ubiquitination stabilizes the protein, linking EGFR-MAPK signaling to ZNF263 activity.","evidence":"Co-IP, ChIP, promoter assays, mutagenesis, siRNA/CRISPR KO, functional anticoagulant assays in glioblastoma and mammalian cell lines","pmids":["32051553","32277030"],"confidence":"High","gaps":["E3 ubiquitin ligase responsible for ZNF263 turnover not identified","Structural basis for KAP1/DNMT recruitment unknown","Whether ERK directly phosphorylates ZNF263 or acts indirectly not resolved"]},{"year":2023,"claim":"Identification of OGT-mediated O-GlcNAcylation at Ser662 as a requirement for ZNF263 chromatin association revealed a metabolic-sensing mechanism controlling its transcription factor activity.","evidence":"Mass spectrometry PTM site identification, Ser662 mutagenesis, ChIP-seq, Co-IP, in vitro and in vivo functional assays in hepatocellular carcinoma","pmids":["37353617"],"confidence":"High","gaps":["Whether O-GlcNAcylation and ERK-dependent stabilization act on the same or distinct ZNF263 pools is unknown","Genome-wide targets specifically dependent on Ser662 modification not fully delineated"]},{"year":2024,"claim":"Multiple studies expanded ZNF263's direct target repertoire to include EGFR (repressed via DNMT1-mediated methylation), CPT1B (activated to drive fatty acid oxidation), and RNF126 (co-activated with ZNF31), demonstrating its dual repressor/activator function across diverse cancer contexts.","evidence":"ChIP, Co-IP, luciferase reporters, promoter methylation assays, xenograft models, FAO rate measurements in lung adenocarcinoma and pancreatic cancer cells","pmids":["38335093","39500874","38515383"],"confidence":"High","gaps":["Determinants that switch ZNF263 between activator and repressor modes at different promoters remain unclear","ZNF31 interaction interface not mapped","Whether CPT1B activation requires the same cofactors as repression targets is untested"]},{"year":2025,"claim":"Establishing ZNF263 as a regulator of pluripotency exit in human embryonic stem cells showed it directly activates early differentiation genes and dampens the core pluripotency circuitry, placing it in normal developmental biology beyond cancer.","evidence":"Genetic knockout, scRNA-seq, ChIP, chromatin accessibility assays, multi-lineage differentiation assays in hESCs","pmids":["41193435"],"confidence":"High","gaps":["Upstream signals triggering ZNF263 activity during differentiation not identified","Whether OGT-dependent O-GlcNAcylation regulates ZNF263 in stem cell context is unknown"]},{"year":null,"claim":"The molecular logic governing ZNF263's switch between activator and repressor modes — including which cofactors, post-translational modifications, or chromatin features determine the outcome at a given locus — remains the central unresolved question.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural information on ZNF263 or its cofactor complexes","The E3 ligase mediating ZNF263 ubiquitination is unidentified","Genome-wide classification of activator vs. repressor targets with matched cofactor occupancy has not been performed"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,1,2,3,4,5,6,9,10,12]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,1,2,3,4,5,6,10,12]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,2,3,6]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[3,6]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,1,2,3,4,5,6,10,12]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,2,3]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[6]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,2,5]}],"complexes":["KAP1/HATS/DNMT corepressor complex"],"partners":["KAP1","DNMT1","OGT","ERK","EGFR","ZNF31"],"other_free_text":[]},"mechanistic_narrative":"ZNF263 is a C2H2 zinc finger transcription factor that functions as both a transcriptional repressor and activator depending on promoter context and cofactor recruitment, operating at the intersection of epigenetic silencing, metabolic regulation, and lineage commitment. As a repressor, ZNF263 binds target promoters and recruits the KAP1/HATS/DNMT corepressor complex to silence genes such as SIX3, EGFR, and heparan sulfate biosynthesis enzymes (HS3ST1, HS3ST3A1) through H3K27me3 deposition and DNA methylation [PMID:32051553, PMID:32277030, PMID:38335093]; as an activator, it directly drives transcription of CPT1B, RNF126, and GPSM2, promoting fatty acid oxidation and cell cycle progression [PMID:39500874, PMID:38515383, PMID:41772960]. ZNF263 chromatin occupancy is regulated by OGT-mediated O-GlcNAcylation at Ser662, while its protein stability is controlled by ERK-dependent inhibition of ubiquitination downstream of EGFR-MAPK signaling [PMID:37353617, PMID:32051553]. In human embryonic stem cells, ZNF263 initiates early differentiation gene expression and dampens the core pluripotency network, and its loss impairs pluripotency dissolution and multi-lineage differentiation [PMID:41193435]."},"prefetch_data":{"uniprot":{"accession":"O14978","full_name":"Zinc finger protein 263","aliases":["Zinc finger protein FPM315","Zinc finger protein with KRAB and SCAN domains 12"],"length_aa":683,"mass_kda":77.3,"function":"Transcription factor that binds to the consensus sequence 5'-TCCTCCC-3' and acts as a transcriptional repressor (PubMed:32051553). Binds to the promoter region of SIX3 and recruits other proteins involved in chromatin modification and transcriptional corepression, resulting in methylation of the promoter and transcriptional repression (PubMed:32051553). Acts as a transcriptional repressor of HS3ST1 and HS3ST3A1 via binding to gene promoter regions (PubMed:32277030)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/O14978/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ZNF263","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ZNF263","total_profiled":1310},"omim":[{"mim_id":"608387","title":"ZINC FINGER PROTEIN 213; ZNF213","url":"https://www.omim.org/entry/608387"},{"mim_id":"604191","title":"ZINC FINGER PROTEIN 263; ZNF263","url":"https://www.omim.org/entry/604191"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Mitotic spindle","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ZNF263"},"hgnc":{"alias_symbol":["FPM315","ZKSCAN12","ZSCAN44"],"prev_symbol":[]},"alphafold":{"accession":"O14978","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O14978","model_url":"https://alphafold.ebi.ac.uk/files/AF-O14978-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O14978-F1-predicted_aligned_error_v6.png","plddt_mean":60.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZNF263","jax_strain_url":"https://www.jax.org/strain/search?query=ZNF263"},"sequence":{"accession":"O14978","fasta_url":"https://rest.uniprot.org/uniprotkb/O14978.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O14978/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O14978"}},"corpus_meta":[{"pmid":"31487963","id":"PMC_31487963","title":"Function and Transcriptional Regulation of Bovine TORC2 Gene in Adipocytes: Roles of C/EBP, XBP1, INSM1 and ZNF263.","date":"2019","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/31487963","citation_count":42,"is_preprint":false},{"pmid":"32051553","id":"PMC_32051553","title":"The EGFR-ZNF263 signaling axis silences SIX3 in glioblastoma epigenetically.","date":"2020","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/32051553","citation_count":33,"is_preprint":false},{"pmid":"32277030","id":"PMC_32277030","title":"ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis.","date":"2020","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/32277030","citation_count":32,"is_preprint":false},{"pmid":"32898766","id":"PMC_32898766","title":"A zinc finger family protein, ZNF263, promotes hepatocellular carcinoma resistance to apoptosis via activation of ER stress-dependent autophagy.","date":"2020","source":"Translational oncology","url":"https://pubmed.ncbi.nlm.nih.gov/32898766","citation_count":31,"is_preprint":false},{"pmid":"26339299","id":"PMC_26339299","title":"High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases.","date":"2015","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/26339299","citation_count":31,"is_preprint":false},{"pmid":"38335093","id":"PMC_38335093","title":"Transcription factor ZNF263 enhances EGFR-targeted therapeutic response and reduces residual disease in lung adenocarcinoma.","date":"2024","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/38335093","citation_count":22,"is_preprint":false},{"pmid":"34514002","id":"PMC_34514002","title":"Circular RNA FOXP1 Induced by ZNF263 Upregulates U2AF2 Expression to Accelerate Renal Cell Carcinoma Tumorigenesis and Warburg Effect through Sponging miR-423-5p.","date":"2021","source":"Journal of immunology research","url":"https://pubmed.ncbi.nlm.nih.gov/34514002","citation_count":20,"is_preprint":false},{"pmid":"37353617","id":"PMC_37353617","title":"Chromatin-associated OGT promotes the malignant progression of hepatocellular carcinoma by activating ZNF263.","date":"2023","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/37353617","citation_count":11,"is_preprint":false},{"pmid":"38515383","id":"PMC_38515383","title":"ZNF263 cooperates with ZNF31 to promote the drug resistance and EMT of pancreatic cancer through transactivating RNF126.","date":"2024","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/38515383","citation_count":9,"is_preprint":false},{"pmid":"34109240","id":"PMC_34109240","title":"COL4A3 expression in asthmatic epithelium depends on intronic methylation and ZNF263 binding.","date":"2021","source":"ERJ open research","url":"https://pubmed.ncbi.nlm.nih.gov/34109240","citation_count":8,"is_preprint":false},{"pmid":"22130890","id":"PMC_22130890","title":"Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments.","date":"2012","source":"Methods in molecular biology (Clifton, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/22130890","citation_count":4,"is_preprint":false},{"pmid":"39500874","id":"PMC_39500874","title":"The ZNF263/CPT1B axis regulates fatty acid β-oxidation to affect cisplatin resistance in lung adenocarcinoma.","date":"2024","source":"The pharmacogenomics journal","url":"https://pubmed.ncbi.nlm.nih.gov/39500874","citation_count":4,"is_preprint":false},{"pmid":"37065635","id":"PMC_37065635","title":"Bufei Yishen Formula Inhibits the Cell Senescence in COPD by Up-Regulating the ZNF263 and Klotho Expression.","date":"2023","source":"International journal of chronic obstructive pulmonary disease","url":"https://pubmed.ncbi.nlm.nih.gov/37065635","citation_count":2,"is_preprint":false},{"pmid":"41193435","id":"PMC_41193435","title":"Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and lineage commitment.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41193435","citation_count":0,"is_preprint":false},{"pmid":"37339722","id":"PMC_37339722","title":"The underlying mechanism of transcription factor IRF1, PRDM1, and ZNF263 involved in the regulation of NPPB rs3753581 on pulse pressure hypertension.","date":"2023","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/37339722","citation_count":0,"is_preprint":false},{"pmid":"41772960","id":"PMC_41772960","title":"Transcriptional regulation of GPSM2 by ZNF263 in colorectal cancer: implications for tumor aggressiveness.","date":"2026","source":"Acta biochimica et biophysica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/41772960","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.12.20.629439","title":"LINC00599 Promotes Pulmonary Hypertension via LLPS with G3BP1 and MYH9","date":"2024-12-22","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.20.629439","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10150,"output_tokens":3015,"usd":0.037838},"stage2":{"model":"claude-opus-4-6","input_tokens":6382,"output_tokens":2221,"usd":0.131153},"total_usd":0.168991,"stage1_batch_id":"msgbatch_01BparvgRZ9S2LMidvaoo86K","stage2_batch_id":"msgbatch_01NkBfv9SVZWthhS7j6mU6G3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2020,\n      \"finding\": \"ZNF263 binds to the core promoter region of SIX3 and recruits the KAP1/HATS/DNMT corepressor complex to induce transcriptional silencing of SIX3 through H3K27me3 and DNA methylation. ERK, when activated by EGFR-MAPK signaling, binds ZNF263 and abrogates its ubiquitination, leading to ZNF263 stabilization.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, promoter assays, mutagenesis, siRNA knockdown, gain-of-function experiments in glioblastoma cells\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Co-IP, ChIP, promoter assays, functional rescue) in single study with clear mechanistic chain\",\n      \"pmids\": [\"32051553\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ZNF263 acts as a transcriptional repressor of heparan sulfate biosynthesis genes, including HS3ST1 and HS3ST3A1. CRISPR knockout or siRNA knockdown of ZNF263 dramatically increases expression of these enzymes, enhancing 3-O-sulfation, antithrombin binding, Factor Xa inhibition, and neuropilin-1 binding.\",\n      \"method\": \"CRISPR-mediated knockout, siRNA knockdown, transcriptomics, ChIP-seq (motif analysis), functional heparin anticoagulant assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — CRISPR KO and siRNA KD with multiple orthogonal functional readouts; replicated in mammalian cell lines and primary human cells\",\n      \"pmids\": [\"32277030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZNF263 binds the EGFR gene promoter and recruits DNMT1 to suppress EGFR transcription via DNA hypermethylation. ZNF263 also interacts with nuclear EGFR protein, impairing the EGFR-STAT5 interaction to enhance AURKA expression, thereby sensitizing lung adenocarcinoma cells to EGFR-targeted therapy.\",\n      \"method\": \"ChIP, Co-IP, promoter methylation assays, luciferase reporter assays, overexpression/knockdown, xenograft animal models\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (ChIP, Co-IP, methylation assays, in vivo xenograft) establishing distinct mechanisms\",\n      \"pmids\": [\"38335093\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"OGT O-GlcNAcylates ZNF263 at Ser662, which is responsible for ZNF263's chromatin association at candidate gene promoters. This OGT-ZNF263 cooperation activates downstream transcription and drives HCC malignant progression.\",\n      \"method\": \"ChIP-seq, Co-IP, mass spectrometry for PTM site identification, mutagenesis of Ser662, in vitro and in vivo functional assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — PTM site identified by MS, validated by mutagenesis, ChIP-seq genome-wide occupancy, and functional rescue\",\n      \"pmids\": [\"37353617\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZNF263 binds the promoter of CPT1B to activate its transcription, thereby enhancing fatty acid β-oxidation and promoting cisplatin resistance in lung adenocarcinoma cells.\",\n      \"method\": \"Dual-luciferase reporter assay, chromatin immunoprecipitation (ChIP), qRT-PCR, western blot, IC50 assays, FAO rate measurement\",\n      \"journal\": \"The pharmacogenomics journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and luciferase reporter with functional metabolic readout, but single lab\",\n      \"pmids\": [\"39500874\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZNF263 acts as a transcriptional activator of RNF126 by binding its promoter. ZNF263 interacts with ZNF31 to co-regulate RNF126 transcription, which promotes ubiquitination-mediated degradation of PTEN, activating AKT/Cyclin D1 and AKT/GSK-3β/β-catenin signaling to drive EMT and drug resistance in pancreatic cancer.\",\n      \"method\": \"ChIP, Co-IP, luciferase reporter assay, siRNA knockdown, overexpression, in vivo xenograft and metastasis models\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP, Co-IP, luciferase reporter with in vivo validation; single lab\",\n      \"pmids\": [\"38515383\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZNF263 directly initiates expression of early differentiation genes and dampens the core pluripotency circuitry in human embryonic stem cells, promoting pluripotency priming and lineage commitment. ZNF263 deficiency impairs pluripotency dissolution and multi-lineage differentiation, particularly toward ectoderm.\",\n      \"method\": \"Genetic knockout, functional differentiation assays, single-cell transcriptomics (scRNA-seq), ChIP, chromatin accessibility assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO with scRNA-seq, ChIP, and multiple orthogonal functional differentiation assays\",\n      \"pmids\": [\"41193435\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ZNF263 transcriptionally induces circFOXP1 expression in renal cell carcinoma cells, contributing to the ZNF263/circFOXP1/miR-423-5p/U2AF2 regulatory axis that promotes tumor progression.\",\n      \"method\": \"siRNA knockdown, overexpression, luciferase reporter assay, qRT-PCR\",\n      \"journal\": \"Journal of immunology research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, limited mechanistic validation of direct ZNF263 binding to circFOXP1 locus\",\n      \"pmids\": [\"34514002\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ZNF263 binding at a CpG site (cg11797365) in an intron of COL4A3 is associated with regulation of COL4A3 expression in bronchial epithelium; ZNF263 silencing by siRNA affects COL4A3 expression levels.\",\n      \"method\": \"ChIP-seq with qPCR, siRNA knockdown, DNA methylation bead arrays, RNA-seq in bronchial biopsies\",\n      \"journal\": \"ERJ open research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP-seq and siRNA KD with gene expression readout; mechanistic link to methylation inferred\",\n      \"pmids\": [\"34109240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"ZNF263 binds to a 24-nucleotide DNA motif that differs from the motif predicted by the zinc finger code in several positions, as determined by de novo ChIP-based motif discovery.\",\n      \"method\": \"ChIP-seq, de novo motif discovery (ChIPMotifs/MEME/Weeder), bootstrap re-sampling\",\n      \"journal\": \"Methods in molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP-based high-throughput data with computational motif analysis; characterizes DNA binding specificity\",\n      \"pmids\": [\"22130890\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ZNF263 functions as a transcriptional activator of the bovine TORC2 gene promoter, binding within the core promoter region (-314 to -69 bp upstream of TSS), as confirmed by EMSA with nuclear extracts and luciferase reporter assays with mutated binding sites.\",\n      \"method\": \"Luciferase reporter assay with serial deletions and site-directed mutagenesis, EMSA, siRNA knockdown\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — EMSA and functional reporter assays confirm direct binding and activation; bovine ortholog context\",\n      \"pmids\": [\"31487963\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZNF263 regulates the expression of LINC00599 via a super-enhancer mechanism in pulmonary arterial smooth muscle cells, contributing to pulmonary hypertension progression.\",\n      \"method\": \"Super-enhancer analysis, transcription factor binding assays (details in preprint)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — preprint with limited mechanistic detail on ZNF263-specific binding validation\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ZNF263 acts as a transcriptional activator of GPSM2 by binding its promoter, activating the cell cycle pathway in a GPSM2-dependent manner to drive invasion, migration, and proliferation in colorectal cancer cells.\",\n      \"method\": \"ChIP, luciferase reporter assay, siRNA knockdown, overexpression, cell invasion/migration assays\",\n      \"journal\": \"Acta biochimica et biophysica Sinica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and luciferase reporter with functional cellular phenotype; single lab\",\n      \"pmids\": [\"41772960\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ZNF263 is a C2H2 zinc finger transcription factor that functions primarily as a transcriptional repressor or activator depending on context: it binds specific DNA promoter motifs (a characterized 24-nt consensus), recruits corepressor complexes (KAP1/HATS/DNMT) to silence target genes via H3K27me3 and DNA methylation, or directly activates target gene transcription; its chromatin association is regulated by O-GlcNAcylation at Ser662 (written by OGT), and its protein stability is controlled by ERK-mediated inhibition of ubiquitination; downstream targets include heparan sulfate biosynthesis enzymes (HS3ST1, HS3ST3A1), SIX3, EGFR, CPT1B, RNF126, GPSM2, and COL4A3, placing ZNF263 at the intersection of epigenetic regulation, metabolic control, and lineage commitment in human cells.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ZNF263 is a C2H2 zinc finger transcription factor that functions as both a transcriptional repressor and activator depending on promoter context and cofactor recruitment, operating at the intersection of epigenetic silencing, metabolic regulation, and lineage commitment. As a repressor, ZNF263 binds target promoters and recruits the KAP1/HATS/DNMT corepressor complex to silence genes such as SIX3, EGFR, and heparan sulfate biosynthesis enzymes (HS3ST1, HS3ST3A1) through H3K27me3 deposition and DNA methylation [PMID:32051553, PMID:32277030, PMID:38335093]; as an activator, it directly drives transcription of CPT1B, RNF126, and GPSM2, promoting fatty acid oxidation and cell cycle progression [PMID:39500874, PMID:38515383, PMID:41772960]. ZNF263 chromatin occupancy is regulated by OGT-mediated O-GlcNAcylation at Ser662, while its protein stability is controlled by ERK-dependent inhibition of ubiquitination downstream of EGFR-MAPK signaling [PMID:37353617, PMID:32051553]. In human embryonic stem cells, ZNF263 initiates early differentiation gene expression and dampens the core pluripotency network, and its loss impairs pluripotency dissolution and multi-lineage differentiation [PMID:41193435].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Defining ZNF263's DNA-binding specificity resolved its 24-nt consensus motif, establishing that its in vivo binding preference diverges from zinc finger code predictions and enabling downstream target identification.\",\n      \"evidence\": \"ChIP-seq with de novo motif discovery (ChIPMotifs/MEME/Weeder) and bootstrap resampling\",\n      \"pmids\": [\"22130890\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Motif computationally derived without systematic biochemical validation of individual zinc finger–base contacts\", \"No functional consequence of motif binding assessed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrating that ZNF263 can function as a transcriptional activator (on the bovine TORC2 promoter) established that ZNF263 is not exclusively a repressor, foreshadowing its context-dependent dual role.\",\n      \"evidence\": \"EMSA, luciferase reporter assays with serial deletions and site-directed mutagenesis, siRNA knockdown in bovine cells\",\n      \"pmids\": [\"31487963\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Bovine ortholog context; generalizability to human ZNF263 not directly tested\", \"Co-activator partners not identified\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Two studies simultaneously established ZNF263 as a transcriptional repressor that recruits the KAP1/HATS/DNMT corepressor complex to silence target genes (SIX3 and heparan sulfate biosynthesis enzymes), and revealed that ERK-mediated inhibition of ZNF263 ubiquitination stabilizes the protein, linking EGFR-MAPK signaling to ZNF263 activity.\",\n      \"evidence\": \"Co-IP, ChIP, promoter assays, mutagenesis, siRNA/CRISPR KO, functional anticoagulant assays in glioblastoma and mammalian cell lines\",\n      \"pmids\": [\"32051553\", \"32277030\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"E3 ubiquitin ligase responsible for ZNF263 turnover not identified\", \"Structural basis for KAP1/DNMT recruitment unknown\", \"Whether ERK directly phosphorylates ZNF263 or acts indirectly not resolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identification of OGT-mediated O-GlcNAcylation at Ser662 as a requirement for ZNF263 chromatin association revealed a metabolic-sensing mechanism controlling its transcription factor activity.\",\n      \"evidence\": \"Mass spectrometry PTM site identification, Ser662 mutagenesis, ChIP-seq, Co-IP, in vitro and in vivo functional assays in hepatocellular carcinoma\",\n      \"pmids\": [\"37353617\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether O-GlcNAcylation and ERK-dependent stabilization act on the same or distinct ZNF263 pools is unknown\", \"Genome-wide targets specifically dependent on Ser662 modification not fully delineated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Multiple studies expanded ZNF263's direct target repertoire to include EGFR (repressed via DNMT1-mediated methylation), CPT1B (activated to drive fatty acid oxidation), and RNF126 (co-activated with ZNF31), demonstrating its dual repressor/activator function across diverse cancer contexts.\",\n      \"evidence\": \"ChIP, Co-IP, luciferase reporters, promoter methylation assays, xenograft models, FAO rate measurements in lung adenocarcinoma and pancreatic cancer cells\",\n      \"pmids\": [\"38335093\", \"39500874\", \"38515383\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Determinants that switch ZNF263 between activator and repressor modes at different promoters remain unclear\", \"ZNF31 interaction interface not mapped\", \"Whether CPT1B activation requires the same cofactors as repression targets is untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Establishing ZNF263 as a regulator of pluripotency exit in human embryonic stem cells showed it directly activates early differentiation genes and dampens the core pluripotency circuitry, placing it in normal developmental biology beyond cancer.\",\n      \"evidence\": \"Genetic knockout, scRNA-seq, ChIP, chromatin accessibility assays, multi-lineage differentiation assays in hESCs\",\n      \"pmids\": [\"41193435\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Upstream signals triggering ZNF263 activity during differentiation not identified\", \"Whether OGT-dependent O-GlcNAcylation regulates ZNF263 in stem cell context is unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular logic governing ZNF263's switch between activator and repressor modes — including which cofactors, post-translational modifications, or chromatin features determine the outcome at a given locus — remains the central unresolved question.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural information on ZNF263 or its cofactor complexes\", \"The E3 ligase mediating ZNF263 ubiquitination is unidentified\", \"Genome-wide classification of activator vs. repressor targets with matched cofactor occupancy has not been performed\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 5, 6, 9, 10, 12]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 5, 6, 10, 12]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 2, 3, 6]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [3, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 5, 6, 10, 12]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 2, 3]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 2, 5]}\n    ],\n    \"complexes\": [\n      \"KAP1/HATS/DNMT corepressor complex\"\n    ],\n    \"partners\": [\n      \"KAP1\",\n      \"DNMT1\",\n      \"OGT\",\n      \"ERK\",\n      \"EGFR\",\n      \"ZNF31\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}