{"gene":"RNF10","run_date":"2026-06-10T06:43:37","timeline":{"discoveries":[{"year":2021,"finding":"RNF10 is the E3 ubiquitin ligase responsible for site-specific monoubiquitylation of 40S ribosomal proteins uS3 (RPS3) and uS5 (RPS2) during ribosome-associated quality control (RQC); USP10 is the opposing deubiquitylase. Prolonged uS3/uS5 ubiquitylation leads to selective 40S (but not 60S) ribosomal protein degradation independent of canonical autophagy. This pathway, termed initiation RQC (iRQC), is triggered by blockade of scanning or elongating ribosomes at the start codon.","method":"Genetic screen with ubiquitylation assays, ribosome fractionation, RNF10/USP10 knockout/knockdown, autophagy inhibitors","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal loss-of-function and gain-of-function, multiple orthogonal methods, replicated in companion paper (PMID:34348161)","pmids":["34469731"],"is_preprint":false},{"year":2021,"finding":"RNF10 is the RING-domain E3 ligase that specifically monoubiquitinates RPS2/uS5 and RPS3/uS3 on ribosomes compromised in translation. RNF10-mediated ubiquitination occurs both downstream of ZNF598-dependent sensing of collided ribosomes and independently upon ZNF598-independent impairment of translation initiation and elongation. PAR-CLIP showed RNF10 crosslinks to mRNAs, tRNAs, and 18S rRNA, indicating physical recruitment to stalled ribosomes. Overexpression of RNF10 increases 40S subunit degradation similarly to USP10 knockout.","method":"Overexpression/knockout, ribosome sedimentation, PAR-CLIP, ubiquitylation assays, ZNF598 genetic epistasis","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (PAR-CLIP, genetic epistasis, ribosome fractionation), replicated by PMID:34469731","pmids":["34348161"],"is_preprint":false},{"year":2025,"finding":"Mammalian 18S nonfunctional rRNA decay (18S NRD) is initiated through the integrated stress response via GCN2. GCN2 activation limits translation initiation, attenuating collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. RNF10-mediated ubiquitination of 40S ribosomal proteins promotes 18S NRD and 40S ribosomal protein turnover. RIOK3 subsequently binds ubiquitylated 40S subunits to facilitate 18S rRNA decay, establishing a GCN2–RNF10–RIOK3 axis for ribosome surveillance at translation initiation.","method":"Genome-wide CRISPR genetic interaction screens, ribosome profiling, biochemical fractionation, ubiquitylation assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — genome-wide CRISPR screens combined with biochemical validation, mechanistic pathway defined with multiple orthogonal approaches, replicated by companion paper PMID:39947183","pmids":["39947182"],"is_preprint":false},{"year":2025,"finding":"Starvation induces selective depletion of 40S ribosomes through RNF10-mediated ubiquitylation. RIOK3 specifically recognizes ubiquitylated 40S ribosomes via a unique ubiquitin-interacting motif (visualized by cryo-EM). RIOK3 then induces progressive 18S rRNA degradation beginning at the 3' end, as revealed by cryo-EM structures of degradation intermediates.","method":"cryo-EM structure determination, ubiquitylation assays, ribosome fractionation, RIOK3 mutant analysis","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structures of degradation intermediates plus functional mutagenesis, replicated by companion paper PMID:39947182","pmids":["39947183"],"is_preprint":false},{"year":2025,"finding":"RNF10-mediated RPS3/uS3 monoubiquitination antagonizes ribosomal half-mer formation by promoting dissociation of 40S subunits stalled during translation elongation and aberrant translation initiation. RNF10 protein levels are tightly coupled to 40S subunit abundance: knockdown of RPS proteins leads to proteasomal degradation of RNF10, whereas knockdown of RPL proteins increases 40S stalling, elevates RNF10 levels, and enhances RPS3 monoubiquitination.","method":"Polysome/half-mer analysis, RNF10 knockdown/overexpression, ribosome fractionation, immunoblotting","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (polysome profiling, genetic depletion, protein-level readouts), single lab but convergent evidence","pmids":["39609413"],"is_preprint":false},{"year":2025,"finding":"Disruption of 60S biogenesis (altered 60S:40S stoichiometry) triggers iRQC activation and RNF10-dependent 40S decay. Depletion of the scanning helicase eIF4A1 impairs 40S ubiquitylation and degradation, indicating that mRNA engagement is required for iRQC. Amino acid starvation also stimulates iRQC-dependent 40S decay. RIOK3 is required for iRQC and interacts with ubiquitylated 40S subunits. RNF10 and RIOK3 protein levels increase upon iRQC activation, establishing a feedforward mechanism.","method":"Genetic knockdown/knockout, ribosome fractionation, ubiquitylation assays, eIF4A1 depletion","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple genetic perturbations with convergent phenotypic readouts, mechanistic epistasis established","pmids":["40022732"],"is_preprint":false},{"year":2025,"finding":"The E3 ubiquitin ligase LTN1 suppresses RNF10 expression in a manner dependent on the RING domain of LTN1, revealing regulatory crosstalk between ribosome quality control E3 ligases.","method":"Knockout mouse and human cell lines, immunoblotting, LTN1 RING domain mutant analysis","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic knockouts and domain mutants, single lab, mechanism partially defined","pmids":["41451945"],"is_preprint":false},{"year":2025,"finding":"RNF10 negatively regulates Rbpjk expression during vascular calcification in a transcriptional (non-ubiquitin ligase) capacity. Nuclear RNF10 expression increases in calcified VSMCs; pharmacological inhibition of the ubiquitin-proteasome system did not impair RNF10's anticalcific activity. Rbpjk overexpression partially reversed the protective effects of RNF10, and Rbpjk knockdown reduced osteogenic marker expression.","method":"RNA-seq, ChIP-seq, ChIP-qPCR, luciferase reporter assays, RNF10 knock-in rats, siRNA knockdown, gain/loss-of-function in vivo and in vitro","journal":"Arteriosclerosis, thrombosis, and vascular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple genomic and biochemical methods in one study, mechanistic model partially defined; single lab","pmids":["41988714"],"is_preprint":false},{"year":2016,"finding":"RNF10 functions as a synaptonuclear protein messenger in hippocampal neurons. It associates with the GluN2A subunit of NMDA receptors at excitatory synapses and translocates from dendritic spines to the nucleus in an importin-dependent manner upon activation of synaptic GluN2A-containing NMDARs and LTP induction. RNF10 silencing prevents LTP maintenance and LTP-dependent structural modifications of dendritic spines.","method":"Co-immunoprecipitation, live-cell imaging, importin inhibition, siRNA knockdown, LTP electrophysiology, spine morphology analysis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, live imaging with importin inhibition, LTP and structural readouts, multiple orthogonal methods in single rigorous study","pmids":["26977767"],"is_preprint":false},{"year":2019,"finding":"PKC-dependent phosphorylation of RNF10 at Ser31 is required for RNF10 detachment from the NMDA receptor GluN2A subunit and subsequent nuclear translocation. Preventing Ser31 phosphorylation decreases spine density, neuronal branching, and CREB signaling; mimicking stable Ser31 phosphorylation produces opposite effects.","method":"Phospho-specific antibodies, phosphomimetic and phospho-dead mutants, spine density quantification, CREB reporter assays, imaging","journal":"Molecular neurobiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — site-specific mutagenesis with multiple morphological and signaling readouts, single lab","pmids":["31069631"],"is_preprint":false},{"year":2008,"finding":"RNF10 acts as a transcriptional activator of the myelin-associated glycoprotein (MAG) gene in Schwann cells by binding a cis-acting element 160 bp upstream of the MAG transcription start site. RNF10 overexpression enhanced MAG promoter activity; RNF10 siRNA knockdown reduced MAG mRNA and protein expression and inhibited myelin formation in Schwann cell–DRG neuron co-cultures.","method":"Yeast one-hybrid screen, luciferase reporter assay, siRNA knockdown, retroviral expression, Schwann cell–DRG co-culture myelination assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast one-hybrid plus functional reporter and co-culture myelination assay, single lab but multiple orthogonal methods","pmids":["18941509"],"is_preprint":false},{"year":2005,"finding":"RNF10 physically binds to the transcription factor MEOX2. In vitro pull-down and co-immunoprecipitation in mammalian cells confirmed the interaction. The minimal MEOX2 binding region maps to amino acids 101–185 (between the HQ-rich domain and homeodomain), while the N-terminal RING finger domain of RNF10 is not required for MEOX2 binding. RNF10 co-expression enhanced MEOX2 activation of the p21WAF1 promoter.","method":"Yeast two-hybrid, in vitro pull-down, co-immunoprecipitation, deletion mapping, p21WAF1 luciferase reporter assay","journal":"Molecular and cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal binding assays (pull-down + co-IP) plus functional promoter reporter, single lab","pmids":["16335786"],"is_preprint":false},{"year":2013,"finding":"RNF10 is required for retinoic acid-induced neuronal differentiation and cell cycle exit in P19 embryonic carcinoma cells. Rnf10 knockdown impairs neuronal marker expression and prevents G1 arrest after RA treatment. RNF10 acts via upregulation of the cyclin-dependent kinase inhibitor p21 (but not p27 or p57); ectopic p21 expression partially rescues the differentiation defect caused by Rnf10 depletion.","method":"siRNA knockdown, BrdU incorporation, flow cytometry, immunoblotting, p21/p27/p57 protein analysis, p21 rescue experiment","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — rescue experiment plus multiple readouts in single lab, pathway placement via p21 established","pmids":["23526782"],"is_preprint":false},{"year":2013,"finding":"RNF10 is one of eight E3 ubiquitin ligases identified as substrates for S-nitrosylation, suggesting that nitric oxide modulates RNF10 activity via S-nitrosylation of cysteine residues.","method":"High-density protein microarray (16,368 proteins), affinity capture of S-nitrosylated proteins, mass spectrometry identification of modified cysteine residues","journal":"Molecular & cellular proteomics : MCP","confidence":"Low","confidence_rationale":"Tier 3 / Weak — proteome-scale screen, RNF10 identified as one of many hits; no functional follow-up specific to RNF10","pmids":["24105792"],"is_preprint":false},{"year":2021,"finding":"RNF10 expression is reduced in aged mouse macrophages. Knockdown of RNF10 in macrophages enhances both NF-κB and IRF3 signaling pathways, increasing proinflammatory cytokines and type I interferons and promoting Listeria monocytogenes clearance, indicating that RNF10 negatively regulates innate immune signaling in macrophages.","method":"siRNA knockdown in primary macrophages, NF-κB/IRF3 reporter/signaling assays, cytokine measurement, bacterial clearance assay","journal":"FEBS open bio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct loss-of-function with defined pathway readouts (NF-κB, IRF3), single lab","pmids":["33249776"],"is_preprint":false},{"year":2024,"finding":"In Drosophila, the E3 ligases CNOT4 and RNF10 function upstream of the deubiquitinase OTUD6 to regulate RPS7 ubiquitination and alkylation stress response on the free 40S ribosome. OTUD6 acts on the free 40S (not on 43S/48S or translating ribosomes), and its loss results in RPS7 hyperubiquitination.","method":"Co-immunoprecipitation, enrichment of monoubiquitinated proteins from catalytically inactive OTUD6 flies, genetic epistasis in Drosophila","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis and co-IP in Drosophila ortholog system; RNF10's specific role partially defined upstream of OTUD6","pmids":["39127721"],"is_preprint":false},{"year":2007,"finding":"RNF10 interacts with the tumor suppressor RASSF1C in a nuclear protein interactome; the interaction was confirmed in vitro by pull-down of bacterially expressed proteins.","method":"Yeast two-hybrid screen, in vitro pull-down with bacterially expressed proteins","journal":"Biochemical and biophysical research communications","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single pull-down in a pan-interactome screen; no functional follow-up for RNF10 specifically","pmids":["17335777"],"is_preprint":false},{"year":2024,"finding":"Mammalian 18S NRD acts through GCN2 and RNF10-mediated ribosomal protein ubiquitination. CRISPR genetic interaction screens identified RNF10 as essential for nonfunctional 18S rRNA and 40S ribosomal protein turnover, with ribosome profiling showing translational arrest at start sites as the initiating event. (Preprint version of PMID:39947182.)","method":"Genome-wide CRISPR genetic interaction screens, selective ribosome profiling, biochemical fractionation","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide CRISPR screen plus ribosome profiling; preprint superseded by peer-reviewed PMID:39947182","pmids":["39211161"],"is_preprint":true}],"current_model":"RNF10 is a RING-domain E3 ubiquitin ligase that primarily functions in ribosome quality control: it monoubiquitinates 40S ribosomal proteins uS3/RPS3 and uS5/RPS2 on ribosomes stalled during translation initiation (iRQC) or elongation, tagging them for selective 40S subunit degradation—a process opposed by the deubiquitylase USP10 and executed downstream by RIOK3; in neurons, RNF10 additionally acts as a synaptonuclear messenger that associates with GluN2A-containing NMDA receptors, undergoes PKC-dependent Ser31 phosphorylation to detach and translocate importin-dependently to the nucleus, where it modulates gene transcription required for LTP maintenance and dendritic architecture; and in other cellular contexts RNF10 regulates transcription (MAG gene in Schwann cells, p21 in neuronal differentiation, Rbpjk in VSMCs) and innate immune signaling via NF-κB/IRF3 suppression in macrophages."},"narrative":{"mechanistic_narrative":"RNF10 is a RING-domain E3 ubiquitin ligase that serves as the central sensor and effector of ribosome surveillance at the small (40S) subunit [PMID:34469731, PMID:34348161]. It site-specifically monoubiquitinates the 40S ribosomal proteins uS3/RPS3 and uS5/RPS2 on ribosomes compromised during translation, acting both downstream of ZNF598-dependent sensing of collided ribosomes and independently upon impairment of translation initiation or elongation; this modification is reversed by the deubiquitylase USP10 [PMID:34469731, PMID:34348161]. Prolonged ubiquitylation drives selective degradation of the 40S subunit and its 18S rRNA via a quality-control pathway termed initiation RQC (iRQC), with RIOK3 recognizing ubiquitylated 40S subunits through a ubiquitin-interacting motif and executing progressive 3'-to-5' 18S rRNA decay [PMID:34469731, PMID:39947183]. This GCN2–RNF10–RIOK3 axis is triggered by physiological cues including amino-acid starvation, disrupted 60S:40S stoichiometry, and nonfunctional 18S rRNA, and RNF10 abundance is itself coupled to 40S levels through proteasomal turnover and feedforward induction [PMID:39947182, PMID:39609413, PMID:40022732]. Independently of its ligase activity, RNF10 acts as a transcriptional regulator: in hippocampal neurons it is a synaptonuclear messenger that associates with GluN2A-containing NMDA receptors, detaches following PKC-dependent Ser31 phosphorylation, and translocates importin-dependently to the nucleus to support LTP maintenance and dendritic spine architecture [PMID:26977767, PMID:31069631]. In other contexts it controls gene expression programs—activating the MAG gene in Schwann cells during myelination, driving p21-dependent neuronal differentiation and cell-cycle exit, and repressing Rbpjk during vascular calcification—and negatively regulates NF-κB/IRF3 innate immune signaling in macrophages [PMID:18941509, PMID:23526782, PMID:41988714, PMID:33249776].","teleology":[{"year":2005,"claim":"Before any catalytic role was assigned, RNF10 was placed in a transcriptional context by identifying a direct partner, establishing it as more than an orphan RING protein.","evidence":"Yeast two-hybrid, reciprocal pull-down/co-IP, deletion mapping and p21WAF1 reporter showing RNF10 binds MEOX2 and enhances p21 promoter activation","pmids":["16335786"],"confidence":"Medium","gaps":["Did not establish whether the interaction depends on RNF10 catalytic activity","No in vivo relevance demonstrated"]},{"year":2008,"claim":"Extended the transcriptional role by showing RNF10 directly drives a tissue-specific gene program, demonstrating sequence-specific promoter engagement.","evidence":"Yeast one-hybrid, luciferase reporter, siRNA knockdown, and Schwann cell–DRG myelination co-culture showing RNF10 activates the MAG gene via an upstream cis-element","pmids":["18941509"],"confidence":"Medium","gaps":["Mechanism of DNA-element recognition unresolved","Whether RNF10 binds DNA directly or via cofactors unclear"]},{"year":2013,"claim":"Connected RNF10 to cell-fate decisions by placing it upstream of a cyclin-dependent kinase inhibitor, defining a differentiation pathway.","evidence":"siRNA knockdown, BrdU/flow cytometry, and p21 rescue in retinoic acid-treated P19 cells showing RNF10 drives differentiation and G1 arrest via p21","pmids":["23526782"],"confidence":"Medium","gaps":["Mechanism of p21 upregulation (direct vs indirect) not defined","Restricted to one carcinoma model"]},{"year":2016,"claim":"Revealed an unanticipated synaptonuclear signaling role, showing RNF10 carries activity-dependent information from synapse to nucleus.","evidence":"Reciprocal co-IP, live-cell imaging with importin inhibition, LTP electrophysiology, and spine morphology in hippocampal neurons","pmids":["26977767"],"confidence":"High","gaps":["Nuclear transcriptional targets in neurons not identified","Whether ligase activity is needed for synaptonuclear function unresolved"]},{"year":2019,"claim":"Defined the molecular switch governing RNF10 nuclear trafficking, identifying the post-translational trigger for receptor detachment.","evidence":"Phospho-specific antibodies, Ser31 phosphomimetic/phospho-dead mutants, spine density and CREB reporter assays","pmids":["31069631"],"confidence":"Medium","gaps":["Which PKC isoform phosphorylates Ser31 not specified","Nuclear effectors downstream of CREB not mapped"]},{"year":2021,"claim":"Established the defining catalytic function: RNF10 is the E3 ligase that site-specifically monoubiquitinates 40S proteins to mark stalled small subunits for degradation, opposed by USP10.","evidence":"Two companion studies using genetic screens, RNF10/USP10 knockout/knockdown, ribosome fractionation, PAR-CLIP, and ZNF598 epistasis defining iRQC","pmids":["34469731","34348161"],"confidence":"High","gaps":["Downstream degradation machinery not yet identified in these studies","Determinants of uS3/uS5 site selectivity unresolved"]},{"year":2021,"claim":"Showed RNF10 acts as a brake on innate immunity, extending its functional repertoire to inflammation and aging.","evidence":"siRNA knockdown in primary macrophages with NF-κB/IRF3 signaling, cytokine, and Listeria clearance readouts","pmids":["33249776"],"confidence":"Medium","gaps":["Molecular substrate/mechanism of NF-κB/IRF3 suppression not defined","Link to its ribosomal or transcriptional activities unclear"]},{"year":2025,"claim":"Resolved the executioner of RNF10-tagged ribosomes, defining the GCN2–RNF10–RIOK3 axis and the structural basis of 18S rRNA decay.","evidence":"Genome-wide CRISPR interaction screens, ribosome profiling, and cryo-EM of degradation intermediates showing RIOK3 recognizes ubiquitylated 40S and degrades 18S rRNA from the 3' end","pmids":["39947182","39947183"],"confidence":"High","gaps":["Nuclease responsible for 18S cleavage not fully defined","How GCN2 activation is coupled to RNF10 recruitment incompletely resolved"]},{"year":2025,"claim":"Clarified the physiological triggers and homeostatic regulation of iRQC, including RNF10's coupling to 40S abundance and a feedforward loop.","evidence":"Polysome/half-mer analysis, eIF4A1 depletion, RPS/RPL knockdown, and ubiquitylation assays across multiple studies","pmids":["39609413","40022732"],"confidence":"High","gaps":["Sensing mechanism linking 60S:40S imbalance to RNF10 activation not fully defined","Physiological consequences of half-mer resolution in vivo unclear"]},{"year":2025,"claim":"Demonstrated regulatory crosstalk among RQC ligases, showing RNF10 levels are controlled by a second E3 ligase.","evidence":"Knockout mouse/human cell lines and LTN1 RING-domain mutant analysis showing LTN1 suppresses RNF10 expression","pmids":["41451945"],"confidence":"Medium","gaps":["Whether LTN1 directly ubiquitinates RNF10 not established","Mechanism of RING-dependent suppression undefined"]},{"year":2025,"claim":"Extended the ligase-independent transcriptional role to vascular disease, showing RNF10 represses an osteogenic transcription factor.","evidence":"RNA-seq, ChIP-seq/qPCR, luciferase reporters, RNF10 knock-in rats, and siRNA in VSMCs showing proteasome-independent repression of Rbpjk","pmids":["41988714"],"confidence":"Medium","gaps":["How nuclear RNF10 represses Rbpjk transcription mechanistically unresolved","Relationship to synaptonuclear nuclear function unexplored"]},{"year":2024,"claim":"Tested conservation and pathway architecture of 40S quality control in an invertebrate model, placing RNF10 in a ligase–DUB circuit.","evidence":"Co-IP, ubiquitinated-protein enrichment, and genetic epistasis in Drosophila showing CNOT4/RNF10 act upstream of OTUD6 on the free 40S","pmids":["39127721"],"confidence":"Medium","gaps":["Whether mammalian RNF10 acts in the same OTUD6 circuit unknown","RPS7 as a mammalian RNF10 substrate not confirmed"]},{"year":null,"claim":"It remains unresolved how RNF10's distinct activities—40S ubiquitylation in the cytoplasm versus ligase-independent transcriptional regulation in the nucleus—are coordinated within a single cell or whether they share regulatory inputs.","evidence":"No timeline study reconciles the catalytic RQC role with the nuclear transcriptional/synaptonuclear functions","pmids":[],"confidence":"Low","gaps":["No unified model linking cytoplasmic ligase and nuclear transcriptional roles","Tissue-specific determinants of which RNF10 function dominates unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,4]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,4]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[10,7,11]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[8,7,10]},{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,2,3]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[10,7,12]},{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[8,9]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[14]}],"complexes":[],"partners":["RPS3","RPS2","USP10","RIOK3","GLUN2A","MEOX2","LTN1","RASSF1C"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8N5U6","full_name":"E3 ubiquitin-protein ligase RNF10","aliases":["RING finger protein 10"],"length_aa":811,"mass_kda":89.9,"function":"E3 ubiquitin-protein ligase that catalyzes monoubiquitination of 40S ribosomal proteins RPS2/us5 and RPS3/us3 in response to ribosome stalling (PubMed:34348161, PubMed:34469731, PubMed:39609413, PubMed:39947182, PubMed:39947183, PubMed:40022732). Part of a ribosome quality control that takes place when ribosomes have stalled during translation initiation (iRQC) or elongation (PubMed:34348161, PubMed:34469731, PubMed:39609413, PubMed:39947182, PubMed:39947183, PubMed:40022732). The ribosome quality control is activated in response to ribosome subunit imbalance, amino acid starvation or downstream the EIF2AK4/GCN2-mediated integrated stress response (ISR) (PubMed:39609413, PubMed:39947182, PubMed:39947183, PubMed:40022732). RNF10 acts by mediating monoubiquitination of RPS2/us5 and RPS3/us3: monoubiquitinated RPS2/us5 and RPS3/us3 are then recognized by RIOK3 kinase, leading to 18S non-functional rRNA decay and degradation of the 40S ribosomal subunit (PubMed:34348161, PubMed:34469731, PubMed:39609413, PubMed:39947182, PubMed:39947183, PubMed:40022732). The action of RNF10 in iRQC is counteracted by USP10 (PubMed:34469731)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q8N5U6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RNF10","classification":"Not Classified","n_dependent_lines":4,"n_total_lines":1208,"dependency_fraction":0.0033112582781456954},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DDOST","stoichiometry":0.2},{"gene":"OST4","stoichiometry":0.2},{"gene":"STT3B","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RNF10","total_profiled":1310},"omim":[{"mim_id":"616388","title":"UBIQUITIN DOMAIN-CONTAINING PROTEIN 1; UBTD1","url":"https://www.omim.org/entry/616388"},{"mim_id":"615998","title":"RING FINGER PROTEIN 10; RNF10","url":"https://www.omim.org/entry/615998"},{"mim_id":"600535","title":"MESENCHYME HOMEOBOX 2; MEOX2","url":"https://www.omim.org/entry/600535"},{"mim_id":"159460","title":"MYELIN-ASSOCIATED GLYCOPROTEIN; MAG","url":"https://www.omim.org/entry/159460"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Mitochondria","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RNF10"},"hgnc":{"alias_symbol":["KIAA0262","RIE2"],"prev_symbol":[]},"alphafold":{"accession":"Q8N5U6","domains":[{"cath_id":"3.30.40.10","chopping":"177-291_316-386","consensus_level":"medium","plddt":91.3092,"start":177,"end":386},{"cath_id":"-","chopping":"505-625","consensus_level":"medium","plddt":94.1603,"start":505,"end":625}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N5U6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N5U6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N5U6-F1-predicted_aligned_error_v6.png","plddt_mean":64.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RNF10","jax_strain_url":"https://www.jax.org/strain/search?query=RNF10"},"sequence":{"accession":"Q8N5U6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N5U6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N5U6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N5U6"}},"corpus_meta":[{"pmid":"34469731","id":"PMC_34469731","title":"iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/34469731","citation_count":59,"is_preprint":false},{"pmid":"32457162","id":"PMC_32457162","title":"Putative regulators for the continuum of erythroid differentiation revealed by single-cell transcriptome of human BM and UCB cells.","date":"2020","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/32457162","citation_count":52,"is_preprint":false},{"pmid":"24105792","id":"PMC_24105792","title":"Protein microarray characterization of the S-nitrosoproteome.","date":"2013","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/24105792","citation_count":50,"is_preprint":false},{"pmid":"34348161","id":"PMC_34348161","title":"The E3 ubiquitin ligase RNF10 modifies 40S ribosomal subunits of ribosomes compromised in 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Prolonged uS3/uS5 ubiquitylation leads to selective 40S (but not 60S) ribosomal protein degradation independent of canonical autophagy. This pathway, termed initiation RQC (iRQC), is triggered by blockade of scanning or elongating ribosomes at the start codon.\",\n      \"method\": \"Genetic screen with ubiquitylation assays, ribosome fractionation, RNF10/USP10 knockout/knockdown, autophagy inhibitors\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal loss-of-function and gain-of-function, multiple orthogonal methods, replicated in companion paper (PMID:34348161)\",\n      \"pmids\": [\"34469731\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RNF10 is the RING-domain E3 ligase that specifically monoubiquitinates RPS2/uS5 and RPS3/uS3 on ribosomes compromised in translation. RNF10-mediated ubiquitination occurs both downstream of ZNF598-dependent sensing of collided ribosomes and independently upon ZNF598-independent impairment of translation initiation and elongation. PAR-CLIP showed RNF10 crosslinks to mRNAs, tRNAs, and 18S rRNA, indicating physical recruitment to stalled ribosomes. Overexpression of RNF10 increases 40S subunit degradation similarly to USP10 knockout.\",\n      \"method\": \"Overexpression/knockout, ribosome sedimentation, PAR-CLIP, ubiquitylation assays, ZNF598 genetic epistasis\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (PAR-CLIP, genetic epistasis, ribosome fractionation), replicated by PMID:34469731\",\n      \"pmids\": [\"34348161\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Mammalian 18S nonfunctional rRNA decay (18S NRD) is initiated through the integrated stress response via GCN2. GCN2 activation limits translation initiation, attenuating collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. RNF10-mediated ubiquitination of 40S ribosomal proteins promotes 18S NRD and 40S ribosomal protein turnover. RIOK3 subsequently binds ubiquitylated 40S subunits to facilitate 18S rRNA decay, establishing a GCN2–RNF10–RIOK3 axis for ribosome surveillance at translation initiation.\",\n      \"method\": \"Genome-wide CRISPR genetic interaction screens, ribosome profiling, biochemical fractionation, ubiquitylation assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genome-wide CRISPR screens combined with biochemical validation, mechanistic pathway defined with multiple orthogonal approaches, replicated by companion paper PMID:39947183\",\n      \"pmids\": [\"39947182\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Starvation induces selective depletion of 40S ribosomes through RNF10-mediated ubiquitylation. RIOK3 specifically recognizes ubiquitylated 40S ribosomes via a unique ubiquitin-interacting motif (visualized by cryo-EM). RIOK3 then induces progressive 18S rRNA degradation beginning at the 3' end, as revealed by cryo-EM structures of degradation intermediates.\",\n      \"method\": \"cryo-EM structure determination, ubiquitylation assays, ribosome fractionation, RIOK3 mutant analysis\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structures of degradation intermediates plus functional mutagenesis, replicated by companion paper PMID:39947182\",\n      \"pmids\": [\"39947183\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RNF10-mediated RPS3/uS3 monoubiquitination antagonizes ribosomal half-mer formation by promoting dissociation of 40S subunits stalled during translation elongation and aberrant translation initiation. RNF10 protein levels are tightly coupled to 40S subunit abundance: knockdown of RPS proteins leads to proteasomal degradation of RNF10, whereas knockdown of RPL proteins increases 40S stalling, elevates RNF10 levels, and enhances RPS3 monoubiquitination.\",\n      \"method\": \"Polysome/half-mer analysis, RNF10 knockdown/overexpression, ribosome fractionation, immunoblotting\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (polysome profiling, genetic depletion, protein-level readouts), single lab but convergent evidence\",\n      \"pmids\": [\"39609413\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Disruption of 60S biogenesis (altered 60S:40S stoichiometry) triggers iRQC activation and RNF10-dependent 40S decay. Depletion of the scanning helicase eIF4A1 impairs 40S ubiquitylation and degradation, indicating that mRNA engagement is required for iRQC. Amino acid starvation also stimulates iRQC-dependent 40S decay. RIOK3 is required for iRQC and interacts with ubiquitylated 40S subunits. RNF10 and RIOK3 protein levels increase upon iRQC activation, establishing a feedforward mechanism.\",\n      \"method\": \"Genetic knockdown/knockout, ribosome fractionation, ubiquitylation assays, eIF4A1 depletion\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple genetic perturbations with convergent phenotypic readouts, mechanistic epistasis established\",\n      \"pmids\": [\"40022732\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The E3 ubiquitin ligase LTN1 suppresses RNF10 expression in a manner dependent on the RING domain of LTN1, revealing regulatory crosstalk between ribosome quality control E3 ligases.\",\n      \"method\": \"Knockout mouse and human cell lines, immunoblotting, LTN1 RING domain mutant analysis\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic knockouts and domain mutants, single lab, mechanism partially defined\",\n      \"pmids\": [\"41451945\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RNF10 negatively regulates Rbpjk expression during vascular calcification in a transcriptional (non-ubiquitin ligase) capacity. Nuclear RNF10 expression increases in calcified VSMCs; pharmacological inhibition of the ubiquitin-proteasome system did not impair RNF10's anticalcific activity. Rbpjk overexpression partially reversed the protective effects of RNF10, and Rbpjk knockdown reduced osteogenic marker expression.\",\n      \"method\": \"RNA-seq, ChIP-seq, ChIP-qPCR, luciferase reporter assays, RNF10 knock-in rats, siRNA knockdown, gain/loss-of-function in vivo and in vitro\",\n      \"journal\": \"Arteriosclerosis, thrombosis, and vascular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple genomic and biochemical methods in one study, mechanistic model partially defined; single lab\",\n      \"pmids\": [\"41988714\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RNF10 functions as a synaptonuclear protein messenger in hippocampal neurons. It associates with the GluN2A subunit of NMDA receptors at excitatory synapses and translocates from dendritic spines to the nucleus in an importin-dependent manner upon activation of synaptic GluN2A-containing NMDARs and LTP induction. RNF10 silencing prevents LTP maintenance and LTP-dependent structural modifications of dendritic spines.\",\n      \"method\": \"Co-immunoprecipitation, live-cell imaging, importin inhibition, siRNA knockdown, LTP electrophysiology, spine morphology analysis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, live imaging with importin inhibition, LTP and structural readouts, multiple orthogonal methods in single rigorous study\",\n      \"pmids\": [\"26977767\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PKC-dependent phosphorylation of RNF10 at Ser31 is required for RNF10 detachment from the NMDA receptor GluN2A subunit and subsequent nuclear translocation. Preventing Ser31 phosphorylation decreases spine density, neuronal branching, and CREB signaling; mimicking stable Ser31 phosphorylation produces opposite effects.\",\n      \"method\": \"Phospho-specific antibodies, phosphomimetic and phospho-dead mutants, spine density quantification, CREB reporter assays, imaging\",\n      \"journal\": \"Molecular neurobiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — site-specific mutagenesis with multiple morphological and signaling readouts, single lab\",\n      \"pmids\": [\"31069631\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"RNF10 acts as a transcriptional activator of the myelin-associated glycoprotein (MAG) gene in Schwann cells by binding a cis-acting element 160 bp upstream of the MAG transcription start site. RNF10 overexpression enhanced MAG promoter activity; RNF10 siRNA knockdown reduced MAG mRNA and protein expression and inhibited myelin formation in Schwann cell–DRG neuron co-cultures.\",\n      \"method\": \"Yeast one-hybrid screen, luciferase reporter assay, siRNA knockdown, retroviral expression, Schwann cell–DRG co-culture myelination assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast one-hybrid plus functional reporter and co-culture myelination assay, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"18941509\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"RNF10 physically binds to the transcription factor MEOX2. In vitro pull-down and co-immunoprecipitation in mammalian cells confirmed the interaction. The minimal MEOX2 binding region maps to amino acids 101–185 (between the HQ-rich domain and homeodomain), while the N-terminal RING finger domain of RNF10 is not required for MEOX2 binding. RNF10 co-expression enhanced MEOX2 activation of the p21WAF1 promoter.\",\n      \"method\": \"Yeast two-hybrid, in vitro pull-down, co-immunoprecipitation, deletion mapping, p21WAF1 luciferase reporter assay\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding assays (pull-down + co-IP) plus functional promoter reporter, single lab\",\n      \"pmids\": [\"16335786\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"RNF10 is required for retinoic acid-induced neuronal differentiation and cell cycle exit in P19 embryonic carcinoma cells. Rnf10 knockdown impairs neuronal marker expression and prevents G1 arrest after RA treatment. RNF10 acts via upregulation of the cyclin-dependent kinase inhibitor p21 (but not p27 or p57); ectopic p21 expression partially rescues the differentiation defect caused by Rnf10 depletion.\",\n      \"method\": \"siRNA knockdown, BrdU incorporation, flow cytometry, immunoblotting, p21/p27/p57 protein analysis, p21 rescue experiment\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — rescue experiment plus multiple readouts in single lab, pathway placement via p21 established\",\n      \"pmids\": [\"23526782\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"RNF10 is one of eight E3 ubiquitin ligases identified as substrates for S-nitrosylation, suggesting that nitric oxide modulates RNF10 activity via S-nitrosylation of cysteine residues.\",\n      \"method\": \"High-density protein microarray (16,368 proteins), affinity capture of S-nitrosylated proteins, mass spectrometry identification of modified cysteine residues\",\n      \"journal\": \"Molecular & cellular proteomics : MCP\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — proteome-scale screen, RNF10 identified as one of many hits; no functional follow-up specific to RNF10\",\n      \"pmids\": [\"24105792\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RNF10 expression is reduced in aged mouse macrophages. Knockdown of RNF10 in macrophages enhances both NF-κB and IRF3 signaling pathways, increasing proinflammatory cytokines and type I interferons and promoting Listeria monocytogenes clearance, indicating that RNF10 negatively regulates innate immune signaling in macrophages.\",\n      \"method\": \"siRNA knockdown in primary macrophages, NF-κB/IRF3 reporter/signaling assays, cytokine measurement, bacterial clearance assay\",\n      \"journal\": \"FEBS open bio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct loss-of-function with defined pathway readouts (NF-κB, IRF3), single lab\",\n      \"pmids\": [\"33249776\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In Drosophila, the E3 ligases CNOT4 and RNF10 function upstream of the deubiquitinase OTUD6 to regulate RPS7 ubiquitination and alkylation stress response on the free 40S ribosome. OTUD6 acts on the free 40S (not on 43S/48S or translating ribosomes), and its loss results in RPS7 hyperubiquitination.\",\n      \"method\": \"Co-immunoprecipitation, enrichment of monoubiquitinated proteins from catalytically inactive OTUD6 flies, genetic epistasis in Drosophila\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis and co-IP in Drosophila ortholog system; RNF10's specific role partially defined upstream of OTUD6\",\n      \"pmids\": [\"39127721\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"RNF10 interacts with the tumor suppressor RASSF1C in a nuclear protein interactome; the interaction was confirmed in vitro by pull-down of bacterially expressed proteins.\",\n      \"method\": \"Yeast two-hybrid screen, in vitro pull-down with bacterially expressed proteins\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single pull-down in a pan-interactome screen; no functional follow-up for RNF10 specifically\",\n      \"pmids\": [\"17335777\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Mammalian 18S NRD acts through GCN2 and RNF10-mediated ribosomal protein ubiquitination. CRISPR genetic interaction screens identified RNF10 as essential for nonfunctional 18S rRNA and 40S ribosomal protein turnover, with ribosome profiling showing translational arrest at start sites as the initiating event. (Preprint version of PMID:39947182.)\",\n      \"method\": \"Genome-wide CRISPR genetic interaction screens, selective ribosome profiling, biochemical fractionation\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide CRISPR screen plus ribosome profiling; preprint superseded by peer-reviewed PMID:39947182\",\n      \"pmids\": [\"39211161\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"RNF10 is a RING-domain E3 ubiquitin ligase that primarily functions in ribosome quality control: it monoubiquitinates 40S ribosomal proteins uS3/RPS3 and uS5/RPS2 on ribosomes stalled during translation initiation (iRQC) or elongation, tagging them for selective 40S subunit degradation—a process opposed by the deubiquitylase USP10 and executed downstream by RIOK3; in neurons, RNF10 additionally acts as a synaptonuclear messenger that associates with GluN2A-containing NMDA receptors, undergoes PKC-dependent Ser31 phosphorylation to detach and translocate importin-dependently to the nucleus, where it modulates gene transcription required for LTP maintenance and dendritic architecture; and in other cellular contexts RNF10 regulates transcription (MAG gene in Schwann cells, p21 in neuronal differentiation, Rbpjk in VSMCs) and innate immune signaling via NF-κB/IRF3 suppression in macrophages.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RNF10 is a RING-domain E3 ubiquitin ligase that serves as the central sensor and effector of ribosome surveillance at the small (40S) subunit [#0, #1]. It site-specifically monoubiquitinates the 40S ribosomal proteins uS3/RPS3 and uS5/RPS2 on ribosomes compromised during translation, acting both downstream of ZNF598-dependent sensing of collided ribosomes and independently upon impairment of translation initiation or elongation; this modification is reversed by the deubiquitylase USP10 [#0, #1]. Prolonged ubiquitylation drives selective degradation of the 40S subunit and its 18S rRNA via a quality-control pathway termed initiation RQC (iRQC), with RIOK3 recognizing ubiquitylated 40S subunits through a ubiquitin-interacting motif and executing progressive 3'-to-5' 18S rRNA decay [#0, #3]. This GCN2–RNF10–RIOK3 axis is triggered by physiological cues including amino-acid starvation, disrupted 60S:40S stoichiometry, and nonfunctional 18S rRNA, and RNF10 abundance is itself coupled to 40S levels through proteasomal turnover and feedforward induction [#2, #4, #5]. Independently of its ligase activity, RNF10 acts as a transcriptional regulator: in hippocampal neurons it is a synaptonuclear messenger that associates with GluN2A-containing NMDA receptors, detaches following PKC-dependent Ser31 phosphorylation, and translocates importin-dependently to the nucleus to support LTP maintenance and dendritic spine architecture [#8, #9]. In other contexts it controls gene expression programs—activating the MAG gene in Schwann cells during myelination, driving p21-dependent neuronal differentiation and cell-cycle exit, and repressing Rbpjk during vascular calcification—and negatively regulates NF-κB/IRF3 innate immune signaling in macrophages [#10, #12, #7, #14].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Before any catalytic role was assigned, RNF10 was placed in a transcriptional context by identifying a direct partner, establishing it as more than an orphan RING protein.\",\n      \"evidence\": \"Yeast two-hybrid, reciprocal pull-down/co-IP, deletion mapping and p21WAF1 reporter showing RNF10 binds MEOX2 and enhances p21 promoter activation\",\n      \"pmids\": [\"16335786\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not establish whether the interaction depends on RNF10 catalytic activity\", \"No in vivo relevance demonstrated\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Extended the transcriptional role by showing RNF10 directly drives a tissue-specific gene program, demonstrating sequence-specific promoter engagement.\",\n      \"evidence\": \"Yeast one-hybrid, luciferase reporter, siRNA knockdown, and Schwann cell–DRG myelination co-culture showing RNF10 activates the MAG gene via an upstream cis-element\",\n      \"pmids\": [\"18941509\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of DNA-element recognition unresolved\", \"Whether RNF10 binds DNA directly or via cofactors unclear\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Connected RNF10 to cell-fate decisions by placing it upstream of a cyclin-dependent kinase inhibitor, defining a differentiation pathway.\",\n      \"evidence\": \"siRNA knockdown, BrdU/flow cytometry, and p21 rescue in retinoic acid-treated P19 cells showing RNF10 drives differentiation and G1 arrest via p21\",\n      \"pmids\": [\"23526782\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of p21 upregulation (direct vs indirect) not defined\", \"Restricted to one carcinoma model\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Revealed an unanticipated synaptonuclear signaling role, showing RNF10 carries activity-dependent information from synapse to nucleus.\",\n      \"evidence\": \"Reciprocal co-IP, live-cell imaging with importin inhibition, LTP electrophysiology, and spine morphology in hippocampal neurons\",\n      \"pmids\": [\"26977767\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Nuclear transcriptional targets in neurons not identified\", \"Whether ligase activity is needed for synaptonuclear function unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined the molecular switch governing RNF10 nuclear trafficking, identifying the post-translational trigger for receptor detachment.\",\n      \"evidence\": \"Phospho-specific antibodies, Ser31 phosphomimetic/phospho-dead mutants, spine density and CREB reporter assays\",\n      \"pmids\": [\"31069631\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Which PKC isoform phosphorylates Ser31 not specified\", \"Nuclear effectors downstream of CREB not mapped\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Established the defining catalytic function: RNF10 is the E3 ligase that site-specifically monoubiquitinates 40S proteins to mark stalled small subunits for degradation, opposed by USP10.\",\n      \"evidence\": \"Two companion studies using genetic screens, RNF10/USP10 knockout/knockdown, ribosome fractionation, PAR-CLIP, and ZNF598 epistasis defining iRQC\",\n      \"pmids\": [\"34469731\", \"34348161\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream degradation machinery not yet identified in these studies\", \"Determinants of uS3/uS5 site selectivity unresolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed RNF10 acts as a brake on innate immunity, extending its functional repertoire to inflammation and aging.\",\n      \"evidence\": \"siRNA knockdown in primary macrophages with NF-κB/IRF3 signaling, cytokine, and Listeria clearance readouts\",\n      \"pmids\": [\"33249776\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular substrate/mechanism of NF-κB/IRF3 suppression not defined\", \"Link to its ribosomal or transcriptional activities unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Resolved the executioner of RNF10-tagged ribosomes, defining the GCN2–RNF10–RIOK3 axis and the structural basis of 18S rRNA decay.\",\n      \"evidence\": \"Genome-wide CRISPR interaction screens, ribosome profiling, and cryo-EM of degradation intermediates showing RIOK3 recognizes ubiquitylated 40S and degrades 18S rRNA from the 3' end\",\n      \"pmids\": [\"39947182\", \"39947183\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Nuclease responsible for 18S cleavage not fully defined\", \"How GCN2 activation is coupled to RNF10 recruitment incompletely resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Clarified the physiological triggers and homeostatic regulation of iRQC, including RNF10's coupling to 40S abundance and a feedforward loop.\",\n      \"evidence\": \"Polysome/half-mer analysis, eIF4A1 depletion, RPS/RPL knockdown, and ubiquitylation assays across multiple studies\",\n      \"pmids\": [\"39609413\", \"40022732\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Sensing mechanism linking 60S:40S imbalance to RNF10 activation not fully defined\", \"Physiological consequences of half-mer resolution in vivo unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated regulatory crosstalk among RQC ligases, showing RNF10 levels are controlled by a second E3 ligase.\",\n      \"evidence\": \"Knockout mouse/human cell lines and LTN1 RING-domain mutant analysis showing LTN1 suppresses RNF10 expression\",\n      \"pmids\": [\"41451945\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether LTN1 directly ubiquitinates RNF10 not established\", \"Mechanism of RING-dependent suppression undefined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended the ligase-independent transcriptional role to vascular disease, showing RNF10 represses an osteogenic transcription factor.\",\n      \"evidence\": \"RNA-seq, ChIP-seq/qPCR, luciferase reporters, RNF10 knock-in rats, and siRNA in VSMCs showing proteasome-independent repression of Rbpjk\",\n      \"pmids\": [\"41988714\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How nuclear RNF10 represses Rbpjk transcription mechanistically unresolved\", \"Relationship to synaptonuclear nuclear function unexplored\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Tested conservation and pathway architecture of 40S quality control in an invertebrate model, placing RNF10 in a ligase–DUB circuit.\",\n      \"evidence\": \"Co-IP, ubiquitinated-protein enrichment, and genetic epistasis in Drosophila showing CNOT4/RNF10 act upstream of OTUD6 on the free 40S\",\n      \"pmids\": [\"39127721\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether mammalian RNF10 acts in the same OTUD6 circuit unknown\", \"RPS7 as a mammalian RNF10 substrate not confirmed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how RNF10's distinct activities—40S ubiquitylation in the cytoplasm versus ligase-independent transcriptional regulation in the nucleus—are coordinated within a single cell or whether they share regulatory inputs.\",\n      \"evidence\": \"No timeline study reconciles the catalytic RQC role with the nuclear transcriptional/synaptonuclear functions\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified model linking cytoplasmic ligase and nuclear transcriptional roles\", \"Tissue-specific determinants of which RNF10 function dominates unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [10, 7, 11]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [8, 7, 10]},\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 2, 3]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [10, 7, 12]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [8, 9]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [14]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RPS3\", \"RPS2\", \"USP10\", \"RIOK3\", \"GluN2A\", \"MEOX2\", \"LTN1\", \"RASSF1C\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}