{"gene":"ZNF644","run_date":"2026-06-11T09:02:07","timeline":{"discoveries":[{"year":2015,"finding":"ZNF644 is a core subunit of the G9a/GLP histone methyltransferase complex; it interacts with the transcription activation domain of G9a and contains multiple zinc finger motifs that recognize consensus DNA sequences, thereby targeting G9a to chromatin and mediating G9a/GLP complex-dependent H3K9 mono- and dimethylation and gene repression.","method":"Unbiased protein affinity purification, co-immunoprecipitation, chromatin targeting assays, H3K9 methylation assays","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, affinity purification identifying complex subunits, functional chromatin targeting and methylation assays with mechanistic follow-up, all in one rigorous study","pmids":["25789554"],"is_preprint":false},{"year":2015,"finding":"ZNF644 interacts specifically with the transcription activation domain of G9a (not GLP), while the paralog WIZ interacts with GLP, establishing distinct targeting mechanisms within the same complex.","method":"Protein affinity purification and co-immunoprecipitation mapping of interaction domains","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mapping by co-IP in single study, two orthogonal binding methods","pmids":["25789554"],"is_preprint":false},{"year":2018,"finding":"ZNF644 is targeted by miR-362 in porcine immature Sertoli cells; miR-362 binds the 3'UTR of ZNF644 mRNA and suppresses its expression. Knockdown of ZNF644 arrests cells in G1/G2 phases, inhibits proliferation, and enhances apoptosis, indicating ZNF644 is required for normal cell cycle progression and survival in Sertoli cells.","method":"Dual luciferase reporter assay (3'UTR), miR-362 mimic/inhibitor transfection, flow cytometry (cell cycle/apoptosis), CCK8 and EdU proliferation assays, qRT-PCR","journal":"Yi chuan = Hereditas","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal functional assays in a single lab, porcine (non-human) model; direct mechanistic link established","pmids":["30021720"],"is_preprint":false},{"year":2011,"finding":"ZNF644 is expressed in human retina and retinal pigment epithelium (RPE), consistent with a role in ocular development; loss-of-function mutations in ZNF644 co-segregate with autosomal dominant high myopia in affected families.","method":"Exome sequencing, Sanger sequencing validation, expression analysis in retinal/RPE tissue","journal":"PLoS genetics","confidence":"Low","confidence_rationale":"Tier 3 / Moderate — expression localization established but no functional mechanism demonstrated; genetic co-segregation supports disease relevance but does not define molecular mechanism","pmids":["21695231"],"is_preprint":false}],"current_model":"ZNF644 is a zinc finger transcription factor that functions as a core subunit of the G9a/GLP histone H3K9 methyltransferase complex, where it interacts with the activation domain of G9a, uses its zinc finger motifs to recognize specific DNA sequences, recruits the complex to chromatin, and thereby mediates H3K9 mono/dimethylation and transcriptional repression at target loci; it is also expressed in retinal/RPE tissue and is required for normal cell cycle progression, with mutations linked to autosomal dominant high myopia."},"narrative":{"mechanistic_narrative":"ZNF644 is a zinc finger transcription factor that operates as a DNA-targeting subunit of the G9a/GLP histone H3K9 methyltransferase complex, coupling sequence-specific chromatin recognition to repressive H3K9 mono- and dimethylation [PMID:25789554]. Within the complex, ZNF644 engages the transcription activation domain of G9a specifically—distinct from its paralog WIZ, which binds GLP—establishing parallel, non-redundant targeting routes for the two enzymatic subunits [PMID:25789554]. Through its multiple zinc finger motifs, ZNF644 recognizes consensus DNA sequences and thereby recruits the methyltransferase complex to chromatin to silence target loci [PMID:25789554]. Beyond this chromatin role, ZNF644 supports cell cycle progression and survival: its depletion arrests cells in G1/G2, reduces proliferation, and increases apoptosis [PMID:30021720]. The gene is expressed in human retina and retinal pigment epithelium, and loss-of-function mutations co-segregate with autosomal dominant high myopia [PMID:21695231].","teleology":[{"year":2011,"claim":"Before any molecular function was known, it was unclear whether ZNF644 had a role in the eye; linking it to a disease and tissue established it as a candidate ocular gene.","evidence":"Exome and Sanger sequencing in high-myopia families with expression analysis in retina/RPE","pmids":["21695231"],"confidence":"Low","gaps":["No molecular mechanism connecting ZNF644 to myopia demonstrated","Genetic co-segregation does not establish causal biochemical pathway","Ocular cell-type-specific function not defined"]},{"year":2015,"claim":"The biochemical function of ZNF644 was unknown; identifying it as a core G9a/GLP subunit that recognizes DNA and targets the complex to chromatin defined it as the sequence-specific recruiter for H3K9 methylation-mediated repression.","evidence":"Unbiased affinity purification, reciprocal co-IP, chromatin targeting and H3K9 methylation assays","pmids":["25789554"],"confidence":"High","gaps":["Genome-wide repertoire of ZNF644 target loci not mapped","DNA consensus specificity per zinc finger not resolved","Link between this chromatin role and the myopia phenotype not established"]},{"year":2015,"claim":"It was unclear how the two enzymatic subunits of the complex are independently targeted; mapping ZNF644 to the G9a activation domain and WIZ to GLP revealed parallel, subunit-specific recruitment.","evidence":"Affinity purification and co-IP interaction-domain mapping","pmids":["25789554"],"confidence":"Medium","gaps":["Structural basis of the ZNF644-G9a interaction not determined","Functional consequence of losing one targeting route versus the other not tested","Single-study domain mapping"]},{"year":2018,"claim":"Whether ZNF644 has cellular roles beyond chromatin repression was open; showing it is miR-362-regulated and required for cell cycle progression and survival in Sertoli cells extended its role to proliferation control.","evidence":"Luciferase 3'UTR reporter, miR-362 mimic/inhibitor, flow cytometry, proliferation assays in porcine Sertoli cells","pmids":["30021720"],"confidence":"Medium","gaps":["Demonstrated in porcine, not human, cells","Mechanistic link between cell-cycle role and H3K9 methyltransferase function not established","Downstream cell-cycle targets unidentified"]},{"year":null,"claim":"How ZNF644's chromatin-targeting function mechanistically produces the high-myopia phenotype, and which target loci it represses in retinal tissue, remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No genome-wide target map in retinal/RPE cells","No animal model linking H3K9 methylation defects to myopia","Disease mutations not functionally connected to complex assembly or methylation"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA 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WIZ","url":"https://www.omim.org/entry/619715"},{"mim_id":"615431","title":"MYOPIA 23, AUTOSOMAL RECESSIVE; MYP23","url":"https://www.omim.org/entry/615431"},{"mim_id":"614167","title":"MYOPIA 21, AUTOSOMAL DOMINANT; MYP21","url":"https://www.omim.org/entry/614167"},{"mim_id":"614159","title":"ZINC FINGER PROTEIN 644; ZNF644","url":"https://www.omim.org/entry/614159"},{"mim_id":"607001","title":"EUCHROMATIC HISTONE METHYLTRANSFERASE 1; EHMT1","url":"https://www.omim.org/entry/607001"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Uncertain","locations":[{"location":"Vesicles","reliability":"Uncertain"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ZNF644"},"hgnc":{"alias_symbol":["KIAA1221","BM-005","MGC60165","MGC70410"],"prev_symbol":[]},"alphafold":{"accession":"Q9H582","domains":[{"cath_id":"3.30.160","chopping":"489-552","consensus_level":"medium","plddt":76.1142,"start":489,"end":552},{"cath_id":"-","chopping":"1038-1085","consensus_level":"medium","plddt":82.6496,"start":1038,"end":1085},{"cath_id":"-","chopping":"1263-1287","consensus_level":"medium","plddt":88.6532,"start":1263,"end":1287}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H582","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H582-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H582-F1-predicted_aligned_error_v6.png","plddt_mean":45.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZNF644","jax_strain_url":"https://www.jax.org/strain/search?query=ZNF644"},"sequence":{"accession":"Q9H582","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H582.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H582/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H582"}},"corpus_meta":[{"pmid":"21695231","id":"PMC_21695231","title":"Exome sequencing identifies ZNF644 mutations in high myopia.","date":"2011","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/21695231","citation_count":161,"is_preprint":false},{"pmid":"25525168","id":"PMC_25525168","title":"Detection of mutations in LRPAP1, CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2 in 298 families with early-onset high myopia by exome sequencing.","date":"2014","source":"Investigative ophthalmology & visual science","url":"https://pubmed.ncbi.nlm.nih.gov/25525168","citation_count":94,"is_preprint":false},{"pmid":"25789554","id":"PMC_25789554","title":"The zinc finger proteins ZNF644 and WIZ regulate the G9a/GLP complex for gene repression.","date":"2015","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/25789554","citation_count":52,"is_preprint":false},{"pmid":"22539872","id":"PMC_22539872","title":"Study of a US cohort supports the role of ZNF644 and high-grade myopia susceptibility.","date":"2012","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/22539872","citation_count":28,"is_preprint":false},{"pmid":"24991186","id":"PMC_24991186","title":"New ZNF644 mutations identified in patients with high myopia.","date":"2014","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/24991186","citation_count":14,"is_preprint":false},{"pmid":"36052886","id":"PMC_36052886","title":"Downregulation of circ-ZNF644 alleviates LPS-induced HK2 cell injury via miR-335-5p/HIPK1 axis.","date":"2022","source":"Environmental toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/36052886","citation_count":9,"is_preprint":false},{"pmid":"35002215","id":"PMC_35002215","title":"Mutational screening of AGRN, SLC39A5, SCO2, P4HA2, BSG, ZNF644, and CPSF1 in a Chinese cohort of 103 patients with nonsyndromic high myopia.","date":"2021","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/35002215","citation_count":8,"is_preprint":false},{"pmid":"25142846","id":"PMC_25142846","title":"[Association of ZNF644, GRM6 and CTNND2 genes polymorphisms with high myopia].","date":"2014","source":"Zhonghua yi xue za zhi","url":"https://pubmed.ncbi.nlm.nih.gov/25142846","citation_count":4,"is_preprint":false},{"pmid":"30021720","id":"PMC_30021720","title":"[miR-362 regulates the proliferation and apoptosis of porcine immature Sertoli cells through targeting the ZNF644 gene].","date":"2018","source":"Yi chuan = Hereditas","url":"https://pubmed.ncbi.nlm.nih.gov/30021720","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7561,"output_tokens":1040,"usd":0.019141,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7565,"output_tokens":1857,"usd":0.042125,"stage2_stop_reason":"end_turn"},"total_usd":0.061266,"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\": 2015,\n      \"finding\": \"ZNF644 is a core subunit of the G9a/GLP histone methyltransferase complex; it interacts with the transcription activation domain of G9a and contains multiple zinc finger motifs that recognize consensus DNA sequences, thereby targeting G9a to chromatin and mediating G9a/GLP complex-dependent H3K9 mono- and dimethylation and gene repression.\",\n      \"method\": \"Unbiased protein affinity purification, co-immunoprecipitation, chromatin targeting assays, H3K9 methylation assays\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, affinity purification identifying complex subunits, functional chromatin targeting and methylation assays with mechanistic follow-up, all in one rigorous study\",\n      \"pmids\": [\"25789554\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"ZNF644 interacts specifically with the transcription activation domain of G9a (not GLP), while the paralog WIZ interacts with GLP, establishing distinct targeting mechanisms within the same complex.\",\n      \"method\": \"Protein affinity purification and co-immunoprecipitation mapping of interaction domains\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mapping by co-IP in single study, two orthogonal binding methods\",\n      \"pmids\": [\"25789554\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ZNF644 is targeted by miR-362 in porcine immature Sertoli cells; miR-362 binds the 3'UTR of ZNF644 mRNA and suppresses its expression. Knockdown of ZNF644 arrests cells in G1/G2 phases, inhibits proliferation, and enhances apoptosis, indicating ZNF644 is required for normal cell cycle progression and survival in Sertoli cells.\",\n      \"method\": \"Dual luciferase reporter assay (3'UTR), miR-362 mimic/inhibitor transfection, flow cytometry (cell cycle/apoptosis), CCK8 and EdU proliferation assays, qRT-PCR\",\n      \"journal\": \"Yi chuan = Hereditas\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal functional assays in a single lab, porcine (non-human) model; direct mechanistic link established\",\n      \"pmids\": [\"30021720\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"ZNF644 is expressed in human retina and retinal pigment epithelium (RPE), consistent with a role in ocular development; loss-of-function mutations in ZNF644 co-segregate with autosomal dominant high myopia in affected families.\",\n      \"method\": \"Exome sequencing, Sanger sequencing validation, expression analysis in retinal/RPE tissue\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — expression localization established but no functional mechanism demonstrated; genetic co-segregation supports disease relevance but does not define molecular mechanism\",\n      \"pmids\": [\"21695231\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ZNF644 is a zinc finger transcription factor that functions as a core subunit of the G9a/GLP histone H3K9 methyltransferase complex, where it interacts with the activation domain of G9a, uses its zinc finger motifs to recognize specific DNA sequences, recruits the complex to chromatin, and thereby mediates H3K9 mono/dimethylation and transcriptional repression at target loci; it is also expressed in retinal/RPE tissue and is required for normal cell cycle progression, with mutations linked to autosomal dominant high myopia.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ZNF644 is a zinc finger transcription factor that operates as a DNA-targeting subunit of the G9a/GLP histone H3K9 methyltransferase complex, coupling sequence-specific chromatin recognition to repressive H3K9 mono- and dimethylation [#0]. Within the complex, ZNF644 engages the transcription activation domain of G9a specifically—distinct from its paralog WIZ, which binds GLP—establishing parallel, non-redundant targeting routes for the two enzymatic subunits [#1]. Through its multiple zinc finger motifs, ZNF644 recognizes consensus DNA sequences and thereby recruits the methyltransferase complex to chromatin to silence target loci [#0]. Beyond this chromatin role, ZNF644 supports cell cycle progression and survival: its depletion arrests cells in G1/G2, reduces proliferation, and increases apoptosis [#2]. The gene is expressed in human retina and retinal pigment epithelium, and loss-of-function mutations co-segregate with autosomal dominant high myopia [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Before any molecular function was known, it was unclear whether ZNF644 had a role in the eye; linking it to a disease and tissue established it as a candidate ocular gene.\",\n      \"evidence\": \"Exome and Sanger sequencing in high-myopia families with expression analysis in retina/RPE\",\n      \"pmids\": [\"21695231\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No molecular mechanism connecting ZNF644 to myopia demonstrated\", \"Genetic co-segregation does not establish causal biochemical pathway\", \"Ocular cell-type-specific function not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"The biochemical function of ZNF644 was unknown; identifying it as a core G9a/GLP subunit that recognizes DNA and targets the complex to chromatin defined it as the sequence-specific recruiter for H3K9 methylation-mediated repression.\",\n      \"evidence\": \"Unbiased affinity purification, reciprocal co-IP, chromatin targeting and H3K9 methylation assays\",\n      \"pmids\": [\"25789554\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genome-wide repertoire of ZNF644 target loci not mapped\", \"DNA consensus specificity per zinc finger not resolved\", \"Link between this chromatin role and the myopia phenotype not established\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"It was unclear how the two enzymatic subunits of the complex are independently targeted; mapping ZNF644 to the G9a activation domain and WIZ to GLP revealed parallel, subunit-specific recruitment.\",\n      \"evidence\": \"Affinity purification and co-IP interaction-domain mapping\",\n      \"pmids\": [\"25789554\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of the ZNF644-G9a interaction not determined\", \"Functional consequence of losing one targeting route versus the other not tested\", \"Single-study domain mapping\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Whether ZNF644 has cellular roles beyond chromatin repression was open; showing it is miR-362-regulated and required for cell cycle progression and survival in Sertoli cells extended its role to proliferation control.\",\n      \"evidence\": \"Luciferase 3'UTR reporter, miR-362 mimic/inhibitor, flow cytometry, proliferation assays in porcine Sertoli cells\",\n      \"pmids\": [\"30021720\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Demonstrated in porcine, not human, cells\", \"Mechanistic link between cell-cycle role and H3K9 methyltransferase function not established\", \"Downstream cell-cycle targets unidentified\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ZNF644's chromatin-targeting function mechanistically produces the high-myopia phenotype, and which target loci it represses in retinal tissue, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No genome-wide target map in retinal/RPE cells\", \"No animal model linking H3K9 methylation defects to myopia\", \"Disease mutations not functionally connected to complex assembly or methylation\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"G9a/GLP histone methyltransferase complex\"],\n    \"partners\": [\"EHMT2\", \"EHMT1\", \"WIZ\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":5,"faith_total":5,"faith_pct":100.0}}