{"gene":"CNOT10","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2012,"finding":"CNOT10 and CNOT11 (C2ORF29) form a distinct module of the human CCR4-NOT complex that interacts with the N-terminal region of CNOT1. CNOT11 interacts with the first amino acids of CNOT1 and with CNOT10, and is required for the association of CNOT10 with the CCR4-NOT complex.","method":"Co-immunoprecipitation, affinity purification, interaction mapping","journal":"RNA biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP and biochemical purification, replicated across two papers (PMID:23232451, PMID:36586408) with orthogonal structural validation in later work","pmids":["23232451"],"is_preprint":false},{"year":2012,"finding":"In trypanosomes, TbCNOT10 is essential for growth and stabilizes the interaction between the deadenylase TbCAF1 and the NOT complex scaffold TbNOT1; depletion of TbCNOT10 causes decreased TbNOT1 levels, detachment of TbCAF1 from the complex, and pronounced stabilization of most trypanosome mRNAs.","method":"RNAi depletion, co-immunoprecipitation, yeast two-hybrid, mRNA stability assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus yeast two-hybrid plus functional mRNA stability readout in a single study","pmids":["23221646"],"is_preprint":false},{"year":2012,"finding":"Depletion of CNOT10 from human embryonic kidney cells did NOT affect the association of CAF1 with the NOT complex (negative finding contrasting with the trypanosome result).","method":"siRNA knockdown, co-immunoprecipitation","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, single method (Co-IP after KD), explicitly reported as negative result","pmids":["23221646"],"is_preprint":false},{"year":2022,"finding":"High-resolution structural analysis revealed that the human N-terminal module of CCR4-NOT is composed of CNOT1, CNOT10, and CNOT11, where two helical domains of CNOT1 sandwich CNOT10 and CNOT11, and the most conserved domain of CNOT11 protrudes as a solvent-exposed 'antenna'. The module functions as a protein-protein interaction platform, with GGNBP2 identified as a conserved interacting partner of the CNOT11 antenna domain via structural and biochemical analyses.","method":"Cryo-EM/X-ray crystallography structural determination, biochemical interaction assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution structural determination combined with biochemical validation, multiple orthogonal methods in one study","pmids":["36586408"],"is_preprint":false},{"year":2020,"finding":"RNF219 interacts with the CCR4-NOT deadenylase complex; CNOT10 depletion in mouse embryonic stem cells upregulates a subset of genes (2-cell-specific and neuronal genes) that overlap with those downregulated by RNF219 knockdown, placing CNOT10 in the same regulatory axis for these transcripts during ES cell biology.","method":"siRNA knockdown, RNA-seq, in vitro deadenylation assay","journal":"Journal of molecular cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — RNA-seq functional readout after KD in a single lab, pathway placement inferred by overlap analysis","pmids":["33104214"],"is_preprint":false},{"year":2025,"finding":"siRNA knockdown of CNOT10 (and CNOT11) impairs tubulin autoregulation and basal tubulin mRNA stability, identifying CNOT10 as a central effector of CCR4-NOT-mediated tubulin mRNA degradation in response to elevated soluble tubulin levels.","method":"siRNA knockdown, Roadblock-qPCR kinetic measurements of mRNA decay","journal":"microPublication biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — quantitative kinetic mRNA decay measurements after specific KD, validates prior work independently","pmids":["41426964"],"is_preprint":false},{"year":2026,"finding":"CNOT10, identified as a TTP-proximal factor by proximity labeling, together with tryptophan residues in the TTP N-terminus, is involved in the reduction of ARE-containing mRNA levels during the early (transcriptional) phase of gene expression but is NOT involved in steady-state mRNA decay.","method":"Proximity labeling (BioID/APEX), cell-based luciferase reporter assay with tetracycline-responsive promoter, siRNA knockdown","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — proximity labeling plus reporter assay, single lab, two complementary methods","pmids":["42049461"],"is_preprint":false},{"year":2024,"finding":"GGNBP2, CNOT10, and CNOT11 interact and collectively regulate sensing of unedited cellular dsRNA by MDA5; loss of CNOT10/CNOT11 (identified in a genome-wide CRISPR screen) modifies the response to unedited dsRNA downstream of transcription but upstream of cytoplasmic MDA5 sensing.","method":"Genome-wide CRISPR knockout screen, genetic epistasis, functional assays for IFN induction","journal":"Science immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide CRISPR screen with functional validation, CNOT10 role defined by epistasis relative to GGNBP2 and MDA5","pmids":["39576872"],"is_preprint":false},{"year":2025,"finding":"CRISPRi knockdown screen in human iPSC-derived microglia identified CNOT10 as a regulator of the Interferon-Responsive Microglia (IRM) state, with a non-canonical role in IRM activation independent of its traditional CCR4-NOT deadenylase function.","method":"Genome-wide CRISPRi screen, IFIT1 reporter readout in iPSC-derived microglia","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, screen hit with limited mechanistic follow-up described in abstract; non-canonical role asserted but molecular basis not detailed","pmids":["bio_10.1101_2025.06.05.658176"],"is_preprint":true}],"current_model":"CNOT10 is a conserved subunit of the CCR4-NOT deadenylase complex that, together with CNOT11, forms a structurally defined N-terminal module bound by two helical domains of the scaffold CNOT1; this module acts as a protein-protein interaction platform (recruiting partners such as GGNBP2), is required for complex integrity and global mRNA deadenylation in trypanosomes, mediates tubulin mRNA autoregulation and ARE-containing mRNA metabolism in human cells (in the early phase of gene expression via cooperation with TTP/ZFP36), and participates in regulating innate immune dsRNA sensing and interferon-responsive microglial activation."},"narrative":{"mechanistic_narrative":"CNOT10 is a conserved subunit of the CCR4-NOT deadenylase complex that anchors mRNA turnover and post-transcriptional gene regulation [PMID:23232451, PMID:36586408]. Together with CNOT11, it forms a structurally defined N-terminal module in which two helical domains of the scaffold CNOT1 sandwich CNOT10 and CNOT11, while a conserved CNOT11 'antenna' domain protrudes to recruit the partner GGNBP2; CNOT11 bridges CNOT10 to CNOT1 and is required for CNOT10 association with the complex [PMID:23232451, PMID:36586408]. This module operates as a protein-protein interaction platform that determines complex composition and integrity: in trypanosomes TbCNOT10 is essential for viability, stabilizes the TbCAF1-TbNOT1 association, and is required for global mRNA turnover, with depletion stabilizing most mRNAs [PMID:23221646]. In human cells CNOT10 directs specific decay programs, mediating tubulin mRNA autoregulation and basal tubulin mRNA stability [PMID:41426964], acting in the early phase of ARE-containing mRNA reduction as a TTP/ZFP36-proximal factor without contributing to steady-state decay [PMID:42049461], and shaping ES-cell transcript programs within the RNF219 regulatory axis [PMID:33104214]. Beyond canonical deadenylation, CNOT10—together with CNOT11 and GGNBP2—regulates innate sensing of unedited cellular dsRNA upstream of cytoplasmic MDA5 [PMID:39576872].","teleology":[{"year":2012,"claim":"Established that CNOT10 is not a peripheral associate but part of a defined N-terminal module of CCR4-NOT, answering how it docks onto the complex.","evidence":"Co-immunoprecipitation, affinity purification, and interaction mapping in human cells","pmids":["23232451"],"confidence":"High","gaps":["Functional consequence of the module for deadenylation not addressed in this study","Structural basis of the CNOT1-CNOT10-CNOT11 interface not yet resolved at this stage"]},{"year":2012,"claim":"Showed in trypanosomes that CNOT10 is essential and required for complex integrity and global mRNA turnover, but the parallel human experiment revealed species-specific differences in how it controls catalytic-subunit association.","evidence":"RNAi/siRNA depletion, Co-IP, yeast two-hybrid, and mRNA stability assays in trypanosomes and human HEK cells","pmids":["23221646"],"confidence":"High","gaps":["Why human CNOT10 depletion does not detach CAF1 while trypanosome depletion does is unexplained","Specific mRNA targets in human cells not defined here"]},{"year":2020,"claim":"Placed CNOT10 in a defined regulatory axis with RNF219 controlling 2-cell-specific and neuronal transcripts, moving from generic deadenylase subunit to a transcript-program regulator in stem cells.","evidence":"siRNA knockdown, RNA-seq, and in vitro deadenylation assay in mouse ES cells","pmids":["33104214"],"confidence":"Medium","gaps":["Pathway placement inferred from gene-set overlap rather than direct mechanism","Direct interaction between CNOT10 and RNF219 not demonstrated"]},{"year":2022,"claim":"Resolved the high-resolution architecture of the CNOT1-CNOT10-CNOT11 module and identified the CNOT11 antenna as a recruitment surface for GGNBP2, establishing the module as a protein-protein interaction platform.","evidence":"Cryo-EM/X-ray structural determination with biochemical interaction validation","pmids":["36586408"],"confidence":"High","gaps":["Functional output of GGNBP2 recruitment to mRNA decay not established here","Whether other partners use the same antenna surface is unknown"]},{"year":2024,"claim":"Demonstrated a non-deadenylase-centric role: CNOT10/CNOT11 with GGNBP2 control innate sensing of unedited cellular dsRNA, positioned downstream of transcription but upstream of MDA5.","evidence":"Genome-wide CRISPR knockout screen with genetic epistasis and IFN-induction assays","pmids":["39576872"],"confidence":"Medium","gaps":["Molecular step by which CNOT10 influences dsRNA sensing not defined","Whether this requires the deadenylase activity of CCR4-NOT is unresolved"]},{"year":2025,"claim":"Confirmed CNOT10 as a central effector of CCR4-NOT-mediated tubulin mRNA autoregulation, linking it to a specific decay program responsive to soluble tubulin.","evidence":"siRNA knockdown with Roadblock-qPCR kinetic measurement of mRNA decay in human cells","pmids":["41426964"],"confidence":"Medium","gaps":["Mechanism coupling soluble tubulin sensing to CNOT10 not detailed","Whether tubulin mRNA is a direct substrate of the module unaddressed"]},{"year":2025,"claim":"Implicated CNOT10 in the interferon-responsive microglia state via a non-canonical role independent of its deadenylase function, extending its reach into innate-immune cell-state control.","evidence":"Genome-wide CRISPRi screen with IFIT1 reporter in iPSC-derived microglia (preprint)","pmids":["bio_10.1101_2025.06.05.658176"],"confidence":"Low","gaps":["Preprint screen hit with limited mechanistic follow-up; molecular basis of the non-canonical role not detailed","Independence from CCR4-NOT function asserted but not biochemically demonstrated"]},{"year":2026,"claim":"Defined CNOT10 as a TTP-proximal factor acting in the early transcriptional phase of ARE-mRNA reduction, distinguishing its contribution from steady-state decay.","evidence":"Proximity labeling, tetracycline-responsive luciferase reporter assay, and siRNA knockdown in human cells","pmids":["42049461"],"confidence":"Medium","gaps":["Direct physical interaction between CNOT10 and TTP not biochemically confirmed","Mechanism distinguishing early-phase from steady-state action unresolved"]},{"year":null,"claim":"How CNOT10 switches between canonical CCR4-NOT deadenylation and its non-canonical roles in dsRNA sensing and microglial interferon responses remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No mechanism links module assembly to selection between deadenylase-dependent and -independent functions","Direct substrate or RNA-binding contribution of CNOT10 itself not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,3]}],"localization":[],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,5,6]}],"complexes":["CCR4-NOT"],"partners":["CNOT11","CNOT1","GGNBP2","CAF1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H9A5","full_name":"CCR4-NOT transcription complex subunit 10","aliases":[],"length_aa":744,"mass_kda":82.3,"function":"Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Is not required for association of CNOT7 to the CCR4-NOT complex","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9H9A5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CNOT10","classification":"Not Classified","n_dependent_lines":41,"n_total_lines":1208,"dependency_fraction":0.03394039735099338},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPZB","stoichiometry":0.2},{"gene":"CTTN","stoichiometry":0.2},{"gene":"G3BP2","stoichiometry":0.2},{"gene":"NPM1","stoichiometry":0.2},{"gene":"PTGES3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CNOT10","total_profiled":1310},"omim":[{"mim_id":"620509","title":"CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 11; CNOT11","url":"https://www.omim.org/entry/620509"},{"mim_id":"620508","title":"CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 10; CNOT10","url":"https://www.omim.org/entry/620508"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Centrosome","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CNOT10"},"hgnc":{"alias_symbol":["FLJ12890","FLJ13165"],"prev_symbol":[]},"alphafold":{"accession":"Q9H9A5","domains":[{"cath_id":"1.25.40","chopping":"521-605","consensus_level":"medium","plddt":95.052,"start":521,"end":605}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H9A5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H9A5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H9A5-F1-predicted_aligned_error_v6.png","plddt_mean":79.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CNOT10","jax_strain_url":"https://www.jax.org/strain/search?query=CNOT10"},"sequence":{"accession":"Q9H9A5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H9A5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H9A5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H9A5"}},"corpus_meta":[{"pmid":"23232451","id":"PMC_23232451","title":"C2ORF29/CNOT11 and CNOT10 form a new module of the CCR4-NOT complex.","date":"2012","source":"RNA biology","url":"https://pubmed.ncbi.nlm.nih.gov/23232451","citation_count":61,"is_preprint":false},{"pmid":"23221646","id":"PMC_23221646","title":"Trypanosome CNOT10 is essential for the integrity of the NOT deadenylase complex and for degradation of many mRNAs.","date":"2012","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/23221646","citation_count":27,"is_preprint":false},{"pmid":"36586408","id":"PMC_36586408","title":"The human CNOT1-CNOT10-CNOT11 complex forms a structural platform for protein-protein interactions.","date":"2022","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/36586408","citation_count":21,"is_preprint":false},{"pmid":"33104214","id":"PMC_33104214","title":"RNF219 interacts with CCR4-NOT in regulating stem cell differentiation.","date":"2020","source":"Journal of molecular cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/33104214","citation_count":15,"is_preprint":false},{"pmid":"32664164","id":"PMC_32664164","title":"Identification of Target Genes in Hypertension and Left Ventricular Remodeling.","date":"2020","source":"Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32664164","citation_count":15,"is_preprint":false},{"pmid":"29434669","id":"PMC_29434669","title":"Copy number variation and regions of homozygosity analysis in patients with MÜLLERIAN aplasia.","date":"2018","source":"Molecular cytogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/29434669","citation_count":14,"is_preprint":false},{"pmid":"36869404","id":"PMC_36869404","title":"Epigenome-wide association study in Chinese monozygotic twins identifies DNA methylation loci associated with blood pressure.","date":"2023","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/36869404","citation_count":13,"is_preprint":false},{"pmid":"27478502","id":"PMC_27478502","title":"A balanced chromosomal translocation involving chromosomes 3 and 16 in a patient with Mayer-Rokitansky-Kuster-Hauser syndrome reveals new candidate genes at 3p22.3 and 16p13.3.","date":"2016","source":"Molecular cytogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/27478502","citation_count":10,"is_preprint":false},{"pmid":"39576872","id":"PMC_39576872","title":"GGNBP2 regulates MDA5 sensing triggered by self double-stranded RNA following loss of ADAR1 editing.","date":"2024","source":"Science immunology","url":"https://pubmed.ncbi.nlm.nih.gov/39576872","citation_count":5,"is_preprint":false},{"pmid":"38326779","id":"PMC_38326779","title":"Sex-biased genetic regulation of inflammatory proteins in the Dutch population.","date":"2024","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/38326779","citation_count":4,"is_preprint":false},{"pmid":"37995439","id":"PMC_37995439","title":"Differential transcript usage across mammalian oocytes at the germinal vesicle and metaphase II stages.","date":"2023","source":"Theriogenology","url":"https://pubmed.ncbi.nlm.nih.gov/37995439","citation_count":1,"is_preprint":false},{"pmid":"41426964","id":"PMC_41426964","title":"The CCR4-NOT deadenylase complex mediates tubulin autoregulation via specific adapters CNOT10 and CNOT11.","date":"2025","source":"microPublication biology","url":"https://pubmed.ncbi.nlm.nih.gov/41426964","citation_count":0,"is_preprint":false},{"pmid":"41542502","id":"PMC_41542502","title":"CNOT10 is involved in TTP-mediated AU-rich element containing mRNA metabolism, independent of mRNA decay regulation.","date":"2026","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41542502","citation_count":0,"is_preprint":false},{"pmid":"42049461","id":"PMC_42049461","title":"CNOT10 is involved in TTP-mediated AU-rich element containing mRNA metabolism, independent of mRNA decay regulation.","date":"2026","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/42049461","citation_count":0,"is_preprint":false},{"pmid":"41774989","id":"PMC_41774989","title":"A natural product-hybridization approach toward anticancer drug discovery: synthesis and antitumor evaluation of CTBC6, designed from sulforaphane and magnolol.","date":"2026","source":"Bioorganic chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41774989","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.06.05.658176","title":"Regulators of Interferon-Responsive Microglia Uncovered by Genome-wide CRISPRi Screening","date":"2025-06-06","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.05.658176","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9954,"output_tokens":2147,"usd":0.031033,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9132,"output_tokens":2830,"usd":0.058205,"stage2_stop_reason":"end_turn"},"total_usd":0.089238,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"CNOT10 and CNOT11 (C2ORF29) form a distinct module of the human CCR4-NOT complex that interacts with the N-terminal region of CNOT1. CNOT11 interacts with the first amino acids of CNOT1 and with CNOT10, and is required for the association of CNOT10 with the CCR4-NOT complex.\",\n      \"method\": \"Co-immunoprecipitation, affinity purification, interaction mapping\",\n      \"journal\": \"RNA biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP and biochemical purification, replicated across two papers (PMID:23232451, PMID:36586408) with orthogonal structural validation in later work\",\n      \"pmids\": [\"23232451\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"In trypanosomes, TbCNOT10 is essential for growth and stabilizes the interaction between the deadenylase TbCAF1 and the NOT complex scaffold TbNOT1; depletion of TbCNOT10 causes decreased TbNOT1 levels, detachment of TbCAF1 from the complex, and pronounced stabilization of most trypanosome mRNAs.\",\n      \"method\": \"RNAi depletion, co-immunoprecipitation, yeast two-hybrid, mRNA stability assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus yeast two-hybrid plus functional mRNA stability readout in a single study\",\n      \"pmids\": [\"23221646\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Depletion of CNOT10 from human embryonic kidney cells did NOT affect the association of CAF1 with the NOT complex (negative finding contrasting with the trypanosome result).\",\n      \"method\": \"siRNA knockdown, co-immunoprecipitation\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, single method (Co-IP after KD), explicitly reported as negative result\",\n      \"pmids\": [\"23221646\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"High-resolution structural analysis revealed that the human N-terminal module of CCR4-NOT is composed of CNOT1, CNOT10, and CNOT11, where two helical domains of CNOT1 sandwich CNOT10 and CNOT11, and the most conserved domain of CNOT11 protrudes as a solvent-exposed 'antenna'. The module functions as a protein-protein interaction platform, with GGNBP2 identified as a conserved interacting partner of the CNOT11 antenna domain via structural and biochemical analyses.\",\n      \"method\": \"Cryo-EM/X-ray crystallography structural determination, biochemical interaction assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution structural determination combined with biochemical validation, multiple orthogonal methods in one study\",\n      \"pmids\": [\"36586408\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RNF219 interacts with the CCR4-NOT deadenylase complex; CNOT10 depletion in mouse embryonic stem cells upregulates a subset of genes (2-cell-specific and neuronal genes) that overlap with those downregulated by RNF219 knockdown, placing CNOT10 in the same regulatory axis for these transcripts during ES cell biology.\",\n      \"method\": \"siRNA knockdown, RNA-seq, in vitro deadenylation assay\",\n      \"journal\": \"Journal of molecular cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — RNA-seq functional readout after KD in a single lab, pathway placement inferred by overlap analysis\",\n      \"pmids\": [\"33104214\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"siRNA knockdown of CNOT10 (and CNOT11) impairs tubulin autoregulation and basal tubulin mRNA stability, identifying CNOT10 as a central effector of CCR4-NOT-mediated tubulin mRNA degradation in response to elevated soluble tubulin levels.\",\n      \"method\": \"siRNA knockdown, Roadblock-qPCR kinetic measurements of mRNA decay\",\n      \"journal\": \"microPublication biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — quantitative kinetic mRNA decay measurements after specific KD, validates prior work independently\",\n      \"pmids\": [\"41426964\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CNOT10, identified as a TTP-proximal factor by proximity labeling, together with tryptophan residues in the TTP N-terminus, is involved in the reduction of ARE-containing mRNA levels during the early (transcriptional) phase of gene expression but is NOT involved in steady-state mRNA decay.\",\n      \"method\": \"Proximity labeling (BioID/APEX), cell-based luciferase reporter assay with tetracycline-responsive promoter, siRNA knockdown\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — proximity labeling plus reporter assay, single lab, two complementary methods\",\n      \"pmids\": [\"42049461\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"GGNBP2, CNOT10, and CNOT11 interact and collectively regulate sensing of unedited cellular dsRNA by MDA5; loss of CNOT10/CNOT11 (identified in a genome-wide CRISPR screen) modifies the response to unedited dsRNA downstream of transcription but upstream of cytoplasmic MDA5 sensing.\",\n      \"method\": \"Genome-wide CRISPR knockout screen, genetic epistasis, functional assays for IFN induction\",\n      \"journal\": \"Science immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide CRISPR screen with functional validation, CNOT10 role defined by epistasis relative to GGNBP2 and MDA5\",\n      \"pmids\": [\"39576872\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CRISPRi knockdown screen in human iPSC-derived microglia identified CNOT10 as a regulator of the Interferon-Responsive Microglia (IRM) state, with a non-canonical role in IRM activation independent of its traditional CCR4-NOT deadenylase function.\",\n      \"method\": \"Genome-wide CRISPRi screen, IFIT1 reporter readout in iPSC-derived microglia\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, screen hit with limited mechanistic follow-up described in abstract; non-canonical role asserted but molecular basis not detailed\",\n      \"pmids\": [\"bio_10.1101_2025.06.05.658176\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"CNOT10 is a conserved subunit of the CCR4-NOT deadenylase complex that, together with CNOT11, forms a structurally defined N-terminal module bound by two helical domains of the scaffold CNOT1; this module acts as a protein-protein interaction platform (recruiting partners such as GGNBP2), is required for complex integrity and global mRNA deadenylation in trypanosomes, mediates tubulin mRNA autoregulation and ARE-containing mRNA metabolism in human cells (in the early phase of gene expression via cooperation with TTP/ZFP36), and participates in regulating innate immune dsRNA sensing and interferon-responsive microglial activation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CNOT10 is a conserved subunit of the CCR4-NOT deadenylase complex that anchors mRNA turnover and post-transcriptional gene regulation [#0, #3]. Together with CNOT11, it forms a structurally defined N-terminal module in which two helical domains of the scaffold CNOT1 sandwich CNOT10 and CNOT11, while a conserved CNOT11 'antenna' domain protrudes to recruit the partner GGNBP2; CNOT11 bridges CNOT10 to CNOT1 and is required for CNOT10 association with the complex [#0, #3]. This module operates as a protein-protein interaction platform that determines complex composition and integrity: in trypanosomes TbCNOT10 is essential for viability, stabilizes the TbCAF1-TbNOT1 association, and is required for global mRNA turnover, with depletion stabilizing most mRNAs [#1]. In human cells CNOT10 directs specific decay programs, mediating tubulin mRNA autoregulation and basal tubulin mRNA stability [#5], acting in the early phase of ARE-containing mRNA reduction as a TTP/ZFP36-proximal factor without contributing to steady-state decay [#6], and shaping ES-cell transcript programs within the RNF219 regulatory axis [#4]. Beyond canonical deadenylation, CNOT10—together with CNOT11 and GGNBP2—regulates innate sensing of unedited cellular dsRNA upstream of cytoplasmic MDA5 [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Established that CNOT10 is not a peripheral associate but part of a defined N-terminal module of CCR4-NOT, answering how it docks onto the complex.\",\n      \"evidence\": \"Co-immunoprecipitation, affinity purification, and interaction mapping in human cells\",\n      \"pmids\": [\"23232451\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Functional consequence of the module for deadenylation not addressed in this study\",\n        \"Structural basis of the CNOT1-CNOT10-CNOT11 interface not yet resolved at this stage\"\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Showed in trypanosomes that CNOT10 is essential and required for complex integrity and global mRNA turnover, but the parallel human experiment revealed species-specific differences in how it controls catalytic-subunit association.\",\n      \"evidence\": \"RNAi/siRNA depletion, Co-IP, yeast two-hybrid, and mRNA stability assays in trypanosomes and human HEK cells\",\n      \"pmids\": [\"23221646\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Why human CNOT10 depletion does not detach CAF1 while trypanosome depletion does is unexplained\",\n        \"Specific mRNA targets in human cells not defined here\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Placed CNOT10 in a defined regulatory axis with RNF219 controlling 2-cell-specific and neuronal transcripts, moving from generic deadenylase subunit to a transcript-program regulator in stem cells.\",\n      \"evidence\": \"siRNA knockdown, RNA-seq, and in vitro deadenylation assay in mouse ES cells\",\n      \"pmids\": [\"33104214\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Pathway placement inferred from gene-set overlap rather than direct mechanism\",\n        \"Direct interaction between CNOT10 and RNF219 not demonstrated\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Resolved the high-resolution architecture of the CNOT1-CNOT10-CNOT11 module and identified the CNOT11 antenna as a recruitment surface for GGNBP2, establishing the module as a protein-protein interaction platform.\",\n      \"evidence\": \"Cryo-EM/X-ray structural determination with biochemical interaction validation\",\n      \"pmids\": [\"36586408\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Functional output of GGNBP2 recruitment to mRNA decay not established here\",\n        \"Whether other partners use the same antenna surface is unknown\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated a non-deadenylase-centric role: CNOT10/CNOT11 with GGNBP2 control innate sensing of unedited cellular dsRNA, positioned downstream of transcription but upstream of MDA5.\",\n      \"evidence\": \"Genome-wide CRISPR knockout screen with genetic epistasis and IFN-induction assays\",\n      \"pmids\": [\"39576872\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Molecular step by which CNOT10 influences dsRNA sensing not defined\",\n        \"Whether this requires the deadenylase activity of CCR4-NOT is unresolved\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Confirmed CNOT10 as a central effector of CCR4-NOT-mediated tubulin mRNA autoregulation, linking it to a specific decay program responsive to soluble tubulin.\",\n      \"evidence\": \"siRNA knockdown with Roadblock-qPCR kinetic measurement of mRNA decay in human cells\",\n      \"pmids\": [\"41426964\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism coupling soluble tubulin sensing to CNOT10 not detailed\",\n        \"Whether tubulin mRNA is a direct substrate of the module unaddressed\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Implicated CNOT10 in the interferon-responsive microglia state via a non-canonical role independent of its deadenylase function, extending its reach into innate-immune cell-state control.\",\n      \"evidence\": \"Genome-wide CRISPRi screen with IFIT1 reporter in iPSC-derived microglia (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.06.05.658176\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Preprint screen hit with limited mechanistic follow-up; molecular basis of the non-canonical role not detailed\",\n        \"Independence from CCR4-NOT function asserted but not biochemically demonstrated\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined CNOT10 as a TTP-proximal factor acting in the early transcriptional phase of ARE-mRNA reduction, distinguishing its contribution from steady-state decay.\",\n      \"evidence\": \"Proximity labeling, tetracycline-responsive luciferase reporter assay, and siRNA knockdown in human cells\",\n      \"pmids\": [\"42049461\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct physical interaction between CNOT10 and TTP not biochemically confirmed\",\n        \"Mechanism distinguishing early-phase from steady-state action unresolved\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CNOT10 switches between canonical CCR4-NOT deadenylation and its non-canonical roles in dsRNA sensing and microglial interferon responses remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No mechanism links module assembly to selection between deadenylase-dependent and -independent functions\",\n        \"Direct substrate or RNA-binding contribution of CNOT10 itself not established\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 5, 6]}\n    ],\n    \"complexes\": [\"CCR4-NOT\"],\n    \"partners\": [\"CNOT11\", \"CNOT1\", \"GGNBP2\", \"CAF1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}