{"gene":"ZNF598","run_date":"2026-06-11T09:02:07","timeline":{"discoveries":[{"year":2017,"finding":"ZNF598 is an E3 ubiquitin ligase that mediates regulatory ubiquitylation of ribosomal proteins RPS10 and RPS20 on stalled ribosomes to initiate ribosome-associated quality control (RQC) of poly(A)-induced stalled ribosomes; loss of ZNF598 function or mutations blocking RPS10/RPS20 ubiquitylation result in defective resolution of stalled ribosomes and readthrough of poly(A)-containing stall sequences.","method":"Gain/loss-of-function experiments, ubiquitylation site mutagenesis, poly(A)-stall readthrough reporter assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (mutagenesis, loss-of-function, reporter assays), replicated across two independent 2017 studies","pmids":["28132843"],"is_preprint":false},{"year":2017,"finding":"ZNF598 cross-links to tRNAs, mRNAs, and rRNAs on translating ribosomes (PAR-CLIP), is enriched on AAA-decoding tRNALys(UUU), triggers ubiquitination of multiple ribosomal proteins in response to translated poly(AAA) sequences, and requires the E2 ubiquitin ligase UBE2D3 to initiate RQC.","method":"PAR-CLIP, ribosomal protein ubiquitination assays, E2 ligase co-dependency experiments","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — PAR-CLIP with mass spectrometry plus functional ubiquitination assays in a single rigorous study","pmids":["28685749"],"is_preprint":false},{"year":2017,"finding":"In yeast, Hel2 (ZNF598 ortholog) and Asc1 are required for RQC-mediated modification (ubiquitination/targeting) of nascent chains on arrested ribosomes; ribosome stalling itself still occurs in their absence, placing Hel2/Asc1 downstream of arrest but upstream of RQC engagement.","method":"Genetic epistasis analysis in S. cerevisiae, nascent chain modification assays","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with multiple deletion combinations, replicated across RQC pathway studies","pmids":["28223409"],"is_preprint":false},{"year":2017,"finding":"In yeast, Hel2 E3 ligase mediates mono-ubiquitination of Rps3 (the yeast equivalent of regulatory ribosomal ubiquitination), and this is reversed by the deubiquitinase Ubp3; in mammalian cells the analogous pair is RNF123 (E3) and USP10 (DUB).","method":"Ubiquitination assays, deubiquitinase activity assays, co-fractionation","journal":"Experimental & molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal enzymatic assays in yeast and mammalian cells, single lab","pmids":["29147007"],"is_preprint":false},{"year":2019,"finding":"In yeast, the C-terminal region of Hel2 is an RNA-binding domain that contacts 18S rRNA and translated mRNAs; this 18S rRNA interaction is required for Hel2 polysome association and for its function in both RQC and no-go decay (NGD). Asc1 acts upstream of Hel2 and is required for Hel2 binding to 18S rRNA.","method":"In vivo UV-crosslinking/mass spectrometry (CRAC), C-terminal truncation mutants, polysome fractionation, genetic epistasis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vivo crosslinking + mass spectrometry + deletion mutagenesis + genetic epistasis, multiple orthogonal methods in one study","pmids":["30718516"],"is_preprint":false},{"year":2019,"finding":"ZNF598 functions as an RNA-binding protein with three proline-rich motifs that bind the GYF domain of GIGYF1, linking ZNF598 to the 4EHP-GIGYF1/2 translational repression complex; ZNF598 binds IL-8 mRNA and is required for regulation of TTP target mRNAs including IL-8 and CSF2.","method":"RNA sequencing (loss-of-function), protein interaction assays (GYF domain binding), RNA immunoprecipitation","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — protein interaction assays and RNA-seq with KO, single lab, two orthogonal methods","pmids":["30917308"],"is_preprint":false},{"year":2019,"finding":"ZNF598 binds directly to RIG-I and promotes FAT10 (a ubiquitin-like protein) binding to RIG-I, thereby inhibiting RIG-I polyubiquitination required for downstream type I IFN signaling; ZNF598 ubiquitin ligase activity is dispensable for this suppression, and the effect is abrogated by FAT10 knockout.","method":"Co-immunoprecipitation, FAT10 knockout, IFN signaling assays, ubiquitination assays with E3-dead mutant","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, KO rescue, catalytic mutant analysis in one study, single lab","pmids":["31433974"],"is_preprint":false},{"year":2020,"finding":"Arsenite directly binds ZNF598 in cells and reduces ubiquitination of RPS10 (K138/K139) and RPS20 (K8), leading to augmented readthrough of poly(A)-containing stall sequences; this readthrough defect is abolished in ZNF598 knockout cells, placing ZNF598 as the arsenite target mediating proteostatic stress.","method":"Chemical biology (arsenite-protein interaction), ubiquitination site-specific MS, poly(A) stall-readthrough reporter in ZNF598 KO cells","journal":"Chemical research in toxicology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding assay, site-specific ubiquitination quantification, KO validation, single lab","pmids":["32324387"],"is_preprint":false},{"year":2021,"finding":"ZNF598 co-translationally titrates expression of C9ORF72-derived poly(GR) protein; ZNF598 and listerin 1 promote poly(GR) degradation via the ubiquitin-proteasome pathway. An ALS-associated ZNF598 R69C mutant displays loss-of-function on poly(GR) expression and general RQC. Lentiviral ZNF598 overexpression in C9-ALS patient neurons reduces poly(GR) and suppresses caspase-3 activation.","method":"Reporter assays, ZNF598 KO/overexpression, Drosophila genetic screen, patient-derived neurons, lentiviral overexpression, ubiquitin-proteasome pathway assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Drosophila genetics, human cell KO/OE, patient neurons, ALS mutant), replicated across model systems","pmids":["34551427"],"is_preprint":false},{"year":2021,"finding":"In yeast, Hel2 preferentially binds pre-engaged secretory ribosome-nascent chain complexes (RNCs) that translate upstream of signal sequences; Hel2 recruitment to secretory RNCs is elevated under SRP-deficient conditions, and hel2 deletion enhances mitochondrial mistargeting of secretory proteins.","method":"Selective ribosome profiling (genome-wide), SRP-deficient strains, mitochondrial import assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ribosome profiling plus functional genetic assay, single lab","pmids":["33761353"],"is_preprint":false},{"year":2022,"finding":"ZNF598 mediates ubiquitination and destabilization of Nrf2; 4-octyl itaconate inhibits ZNF598-dependent ubiquitination of Nrf2, thereby increasing Nrf2 protein levels.","method":"Western blotting, immunoprecipitation ubiquitination assay","journal":"Osteoarthritis and cartilage","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/ubiquitination assay, single lab, no mutagenesis or reconstitution","pmids":["36270478"],"is_preprint":false},{"year":2024,"finding":"Using in vitro reconstitution, ribosomal collision is not a strict prerequisite for ZNF598-mediated K63-polyubiquitination of uS10 (RPS10) or for ASCC-mediated ribosome dissociation; ASCC efficiently dissociates polysomes, monosomes, and reconstituted 80S elongation complexes following ZNF598 ubiquitination, provided ≥30-35 nt of mRNA extend downstream of the P site and sufficiently long ubiquitin chains are present.","method":"In vitro reconstitution, cell-free ubiquitination assays, ribosome dissociation assays with defined substrates","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — rigorous in vitro reconstitution with defined components, systematic variation of substrates, single lab","pmids":["38366554"],"is_preprint":false},{"year":2024,"finding":"ZNF598 undergoes regulatory K63-linked ubiquitination in a CNOT4-dependent manner and is upregulated upon mitochondrial stress; this ZNF598 ubiquitination is required for resolution of stalled ribosomes and protection against mitochondrial stress in mammalian cells and Drosophila.","method":"Ubiquitination assays, CNOT4 KO/KD, Drosophila models, mitochondrial stress assays","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ubiquitination assays with KO validation and Drosophila models, two orthogonal systems, single lab","pmids":["38388640"],"is_preprint":false},{"year":2024,"finding":"In zebrafish, Znf598 down-regulates mRNAs encoding C2H2-type zinc finger domains during the maternal-to-zygotic transition; ribosomes stall and collide while translating tandem C2H2-ZF sequences, triggering Znf598-dependent mRNA degradation via no-go decay.","method":"RNA-Seq of znf598 mutant embryos, reporter assays, disome profiling","journal":"PLoS biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic mutant + ribosome profiling + reporter assay, single lab","pmids":["39636823"],"is_preprint":false},{"year":2023,"finding":"During zebrafish development, Znf598 ubiquitinates ribosomal protein Rps10/eS10, and Rps10 ubiquitination-site mutations reduce the overall ubiquitination pattern of the ribosome; ribosome ubiquitination by Znf598 is dynamically regulated across developmental stages.","method":"Affinity purification of FLAG-tagged ribosomes, immunoblotting, ubiquitination-site mutant zebrafish","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — endogenous tagging, site mutants, developmental time-course, single lab","pmids":["37751929"],"is_preprint":false},{"year":2025,"finding":"In yeast, Hel2 occupancy on ribosomes increases progressively from monosomes to disomes to trisomes; Hel2 translates the duration of ribosome stalling into polyubiquitin chain length on Rps20/uS10 (mono/di-ubiquitinated disomes resolve independently of Slh1; tri/tetra-ubiquitinated ones do not), allowing distinction of transient from long-term stalling. Ubp2/Ubp3 deubiquitinases remove Hel2-dependent ubiquitin chains upon translational run-off.","method":"Quantitative in vivo analysis of Hel2-ribosome complexes, polysome fractionation, ubiquitination chain-length analysis, Slh1/Ubp2/Ubp3 genetic epistasis","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — quantitative in vivo ribosome association and ubiquitination dynamics with multiple genetic backgrounds, single lab","pmids":["39875504"],"is_preprint":false},{"year":2025,"finding":"Single-protein/mRNA imaging shows that multiple ZNF598 molecules engage a single RQC reporter mRNA simultaneously (not just the leading collided ribosome); ZNF598 overexpression increases ribosomal clearance rate, establishing ZNF598 as a rate-limiting factor for RQC. Under global UV-induced RNA damage, ZNF598 recruitment to RQC reporter mRNA diminishes, consistent with ZNF598 being a limiting resource.","method":"Single-molecule live-cell imaging (HaloTag endogenous tagging), ZNF598 overexpression ribosome clearance assay","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single-molecule imaging with endogenous tag plus functional overexpression assay, single lab","pmids":["40750700"],"is_preprint":false},{"year":2025,"finding":"In human iPSCs, ZNF598 is required to resolve a novel class of ribosome collisions at translation start sites on endogenous mRNAs with highly efficient initiation; CRISPRi screens show ZNF598 is selectively essential in stem cells compared to differentiated neural/cardiac cells.","method":"Comparative CRISPRi screens in hiPSC vs. differentiated cells","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — CRISPRi screen with cell-type essentiality readout, preprint, no direct biochemical reconstitution","pmids":[],"is_preprint":true}],"current_model":"ZNF598 is an E3 ubiquitin ligase (with E2 partner UBE2D3) and RNA-binding protein that acts as the primary sensor of stalled/collided ribosomes in mammalian ribosome-associated quality control (RQC): it recognizes collided 40S subunits and catalyzes K63-linked polyubiquitination of ribosomal proteins uS10/RPS10 and uS20/RPS20, which primes stalled ribosomes for disassembly by the ASCC complex and downstream degradation of aberrant nascent chains via the ubiquitin-proteasome pathway; ZNF598 is itself regulated by CNOT4-mediated K63-ubiquitination in response to mitochondrial stress, is titrated as a rate-limiting factor during widespread ribosome collisions, and additionally functions outside canonical RQC by binding GIGYF1/2 to repress cytokine mRNAs and by promoting FAT10-mediated suppression of RIG-I innate immune signaling."},"narrative":{"mechanistic_narrative":"ZNF598 is the primary E3 ubiquitin ligase that initiates ribosome-associated quality control (RQC) by sensing aberrant translation and marking stalled ribosomes for resolution [PMID:28132843, PMID:28685749]. Acting with the E2 enzyme UBE2D3, it catalyzes regulatory ubiquitination of the small-subunit ribosomal proteins RPS10/uS10 (at K138/K139) and RPS20/uS20 (at K8) in response to ribosome stalling on poly(A) and other problematic sequences, and loss of this activity causes readthrough of stall sequences and defective stall resolution [PMID:28132843, PMID:28685749, PMID:32324387]. ZNF598 is an RNA-binding protein that cross-links to tRNAs, mRNAs, and rRNA on translating ribosomes, with its yeast ortholog Hel2 using a C-terminal RNA-binding region to contact 18S rRNA in an Asc1-dependent manner required for polysome association and RQC/no-go decay function [PMID:28685749, PMID:30718516]. The ubiquitin chains it deposits are read out quantitatively: chain length scales with stalling duration to distinguish transient from persistent stalls, and sufficiently long K63-linked chains on uS10 prime ribosomes for ASCC-mediated subunit dissociation, after which aberrant nascent chains are degraded by the ubiquitin-proteasome pathway [PMID:38366554, PMID:39875504, PMID:34551427]. ZNF598 activity is itself regulated, being upregulated and K63-ubiquitinated in a CNOT4-dependent manner upon mitochondrial stress, and it behaves as a rate-limiting RQC factor whose recruitment to a stalled mRNA can be titrated during widespread collisions [PMID:38388640, PMID:40750700]. Beyond canonical RQC, ZNF598 binds the GYF domain of GIGYF1 to link to the 4EHP–GIGYF translational repression complex and regulate cytokine mRNAs such as IL-8 and CSF2, and it binds RIG-I to promote FAT10-mediated suppression of type I interferon signaling independently of its ligase activity [PMID:30917308, PMID:31433974]. An ALS-associated R69C variant is a loss-of-function mutation that impairs RQC and clearance of C9ORF72-derived poly(GR), and ZNF598 overexpression reduces poly(GR) and caspase-3 activation in patient neurons [PMID:34551427].","teleology":[{"year":2017,"claim":"Established ZNF598 as the E3 ligase that initiates mammalian RQC, defining the enzymatic event that converts a stalled ribosome into a quality-control substrate.","evidence":"Gain/loss-of-function, ubiquitylation site mutagenesis, and poly(A) stall-readthrough reporters; parallel PAR-CLIP and E2 co-dependency in a second study","pmids":["28132843","28685749"],"confidence":"High","gaps":["Did not define ubiquitin chain linkage type or length requirements","Did not identify downstream disassembly machinery","Mechanism of collided-ribosome recognition not structurally resolved"]},{"year":2017,"claim":"Genetic epistasis in yeast placed Hel2/Asc1 downstream of ribosome arrest but upstream of nascent-chain RQC engagement, ordering the pathway.","evidence":"Genetic epistasis with deletion combinations and nascent chain modification assays in S. cerevisiae","pmids":["28223409"],"confidence":"High","gaps":["Did not map the molecular signal Hel2 recognizes on arrested ribosomes","Relationship to mammalian factors inferred by orthology"]},{"year":2017,"claim":"Defined the reversibility of regulatory ribosomal ubiquitination by identifying opposing deubiquitinases, framing RQC ubiquitination as a dynamic switch.","evidence":"Ubiquitination and DUB activity assays in yeast (Hel2/Ubp3) and mammalian cells","pmids":["29147007"],"confidence":"Medium","gaps":["Mammalian E3/DUB assignment based on single-lab assays","In vivo physiological trigger for deubiquitination not established here"]},{"year":2019,"claim":"Mapped the RNA-binding determinant of the ortholog Hel2 to a C-terminal region contacting 18S rRNA, explaining how the ligase docks onto translating ribosomes.","evidence":"In vivo CRAC crosslinking/MS, C-terminal truncation mutants, polysome fractionation, and Asc1 epistasis in yeast","pmids":["30718516"],"confidence":"High","gaps":["Structural basis of 18S contact unresolved","Whether the mammalian protein uses an identical RNA-binding mode not tested"]},{"year":2019,"claim":"Revealed a non-canonical role linking ZNF598 to translational repression of cytokine mRNAs via the GIGYF/4EHP complex, expanding its function beyond RQC.","evidence":"GYF-domain interaction assays, RNA-seq in KO cells, and RNA immunoprecipitation of IL-8/CSF2 mRNAs","pmids":["30917308"],"confidence":"Medium","gaps":["Whether ligase activity is required for cytokine mRNA repression unclear","Mechanistic link between repression and stalling not defined","Single-lab, two-method support"]},{"year":2019,"claim":"Identified a ligase-independent innate-immunity function in which ZNF598 promotes FAT10 binding to RIG-I to dampen type I IFN signaling.","evidence":"Reciprocal Co-IP, FAT10 KO rescue, and E3-dead mutant IFN signaling assays","pmids":["31433974"],"confidence":"Medium","gaps":["Structural basis of ZNF598–RIG-I–FAT10 assembly unknown","Physiological context distinguishing this from RQC role unclear"]},{"year":2020,"claim":"Showed ZNF598 is a direct chemical target of arsenite, providing a mechanistic link between an environmental proteostatic stressor and RQC inhibition.","evidence":"Direct arsenite-binding assay, site-specific ubiquitination MS, and poly(A) readthrough reporters in ZNF598 KO cells","pmids":["32324387"],"confidence":"Medium","gaps":["Arsenite binding site on ZNF598 not mapped","Single-lab study"]},{"year":2021,"claim":"Connected ZNF598 to neurodegeneration by demonstrating co-translational titration and degradation of C9ORF72 poly(GR) and an ALS-associated loss-of-function variant.","evidence":"Reporter assays, KO/overexpression, Drosophila screen, ALS R69C mutant, and lentiviral rescue in patient-derived neurons","pmids":["34551427"],"confidence":"High","gaps":["Causal genetic link of R69C to ALS in patient cohorts not established here","How poly(GR) translation triggers ZNF598 engagement unresolved"]},{"year":2021,"claim":"Demonstrated that Hel2 surveils secretory ribosome-nascent chain complexes and protects against organelle mistargeting, broadening the substrate range of the sensor.","evidence":"Selective ribosome profiling, SRP-deficient strains, and mitochondrial import assays in yeast","pmids":["33761353"],"confidence":"Medium","gaps":["Whether mammalian ZNF598 performs equivalent secretory surveillance untested","Single-lab study"]},{"year":2024,"claim":"In vitro reconstitution refined the mechanism, showing collision is not strictly required for ZNF598 ubiquitination or ASCC dissociation given adequate downstream mRNA and ubiquitin chain length.","evidence":"Cell-free ubiquitination and ribosome dissociation assays with defined substrates","pmids":["38366554"],"confidence":"High","gaps":["Reconciliation with in-cell collision-dependence not fully resolved","Minimal recognition determinant on the 40S not defined"]},{"year":2024,"claim":"Identified CNOT4-dependent K63-ubiquitination as an upstream regulatory layer that activates ZNF598 during mitochondrial stress.","evidence":"Ubiquitination assays, CNOT4 KO/KD, and Drosophila mitochondrial stress models","pmids":["38388640"],"confidence":"Medium","gaps":["Ubiquitination sites on ZNF598 and their mechanistic consequence not mapped","Single-lab study"]},{"year":2025,"claim":"Established that ubiquitin chain length on uS10/uS20 encodes stalling duration, allowing ZNF598 to discriminate transient from persistent stalls.","evidence":"Quantitative in vivo Hel2-ribosome association, chain-length analysis, and Slh1/Ubp2/Ubp3 epistasis in yeast","pmids":["39875504"],"confidence":"Medium","gaps":["Mechanism by which chain length is read by downstream machinery in mammals unclear","Single-lab study"]},{"year":2025,"claim":"Single-molecule imaging established ZNF598 as a rate-limiting RQC factor that multiple copies engage per stalled mRNA and that is titrated during widespread collisions.","evidence":"Single-molecule live-cell imaging with endogenous HaloTag and overexpression ribosome-clearance assays","pmids":["40750700"],"confidence":"Medium","gaps":["Quantitative cellular abundance limits not defined across cell types","Single-lab study"]},{"year":2024,"claim":"Demonstrated a developmental gene-regulatory role in which Znf598 targets C2H2-zinc-finger mRNAs for no-go decay during the maternal-to-zygotic transition.","evidence":"RNA-seq of mutant embryos, disome profiling, and reporter assays in zebrafish","pmids":["39636823"],"confidence":"Medium","gaps":["Whether this developmental program is conserved in mammals untested","Link between tandem C2H2 translation and collision not structurally defined"]},{"year":null,"claim":"How ZNF598 selectively recognizes the collided/40S interface at the structural level, and how cell-type-specific demand (e.g., stem cell essentiality, start-site collisions) is met by a limiting amount of the protein, remain open.","evidence":"Comparative CRISPRi screens in hiPSC vs differentiated cells point to context-dependent essentiality (preprint)","pmids":[],"confidence":"Low","gaps":["No structure of ZNF598 engaging collided ribosomes in the corpus","Cell-type essentiality data is from a preprint without biochemical reconstitution","Determinants of start-site collision recognition undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,11]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,11]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1,4,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,15]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[1,4,14]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,16]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,11,13]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,8,11]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[5,6]}],"complexes":[],"partners":["UBE2D3","GIGYF1","RIG-I","FAT10","CNOT4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86UK7","full_name":"E3 ubiquitin-protein ligase ZNF598","aliases":["Zinc finger protein 598"],"length_aa":904,"mass_kda":98.6,"function":"E3 ubiquitin-protein ligase that plays a key role in the ribosome quality control (RQC), a pathway that takes place when a ribosome has stalled during translation, leading to degradation of nascent peptide chains (PubMed:28065601, PubMed:28132843, PubMed:28685749, PubMed:32099016, PubMed:32579943, PubMed:33581075). ZNF598 is activated when ribosomes are stalled within an mRNA following translation of prematurely polyadenylated mRNAs (PubMed:28065601, PubMed:28132843, PubMed:28685749). Acts as a ribosome collision sensor: specifically recognizes and binds collided di-ribosome, which arises when a trailing ribosome encounters a slower leading ribosome, leading to terminally arrest translation (PubMed:28065601, PubMed:28132843, PubMed:28685749, PubMed:30293783). Following binding to colliding ribosomes, mediates monoubiquitination of 40S ribosomal proteins RPS10/eS10 and RPS3/uS3, and 'Lys-63'-linked polyubiquitination of RPS20/uS10 (PubMed:28065601, PubMed:28132843, PubMed:28685749). Polyubiquitination of RPS20/uS10 promotes recruitment of the RQT (ribosome quality control trigger) complex, which drives the disassembly of stalled ribosomes, followed by degradation of nascent peptides (PubMed:32099016, PubMed:32579943, PubMed:36302773). E3 ubiquitin-protein ligase activity is dependent on the E2 ubiquitin-conjugating enzyme UBE2D3 (PubMed:28685749). Also acts as an adapter that recruits the 4EHP-GYF2 complex to mRNAs (PubMed:22751931, PubMed:32726578). Independently of its role in RQC, may also act as a negative regulator of interferon-stimulated gene (ISG) expression (PubMed:29719242) (Microbial infection) Required for poxvirus protein synthesis by mediating ubiquitination of RPS10/eS10 and RPS20/uS10 (PubMed:29719242). Poxvirus encoding mRNAs contain unusual 5' poly(A) leaders and ZNF598 is required for their translational efficiency, possibly via its ability to suppress readthrough or sliding on shorter poly(A) tracts (PubMed:29719242)","subcellular_location":"Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/Q86UK7/entry"},"depmap":{"release":"DepMap","has_data":false,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ZNF598"},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000167962","cell_line_id":"CID001824","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"er","grade":1}],"interactors":[{"gene":"EIF3B","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"RACK1","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001824","total_profiled":1310},"omim":[{"mim_id":"617508","title":"ZINC FINGER PROTEIN 598; ZNF598","url":"https://www.omim.org/entry/617508"},{"mim_id":"612003","title":"GRB10-INTERACTING GYF PROTEIN 2; GIGYF2","url":"https://www.omim.org/entry/612003"},{"mim_id":"605895","title":"EUKARYOTIC TRANSLATION INITIATION FACTOR 4E FAMILY, MEMBER 2; EIF4E2","url":"https://www.omim.org/entry/605895"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ZNF598"},"hgnc":{"alias_symbol":["FLJ00086","HEL2"],"prev_symbol":[]},"alphafold":{"accession":"Q86UK7","domains":[{"cath_id":"-","chopping":"21-160","consensus_level":"medium","plddt":90.3866,"start":21,"end":160},{"cath_id":"-","chopping":"754-836_861-894","consensus_level":"medium","plddt":87.6256,"start":754,"end":894}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86UK7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86UK7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86UK7-F1-predicted_aligned_error_v6.png","plddt_mean":62.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZNF598","jax_strain_url":"https://www.jax.org/strain/search?query=ZNF598"},"sequence":{"accession":"Q86UK7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86UK7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86UK7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86UK7"}},"corpus_meta":[{"pmid":"28132843","id":"PMC_28132843","title":"ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation.","date":"2017","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/28132843","citation_count":308,"is_preprint":false},{"pmid":"28685749","id":"PMC_28685749","title":"The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs.","date":"2017","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/28685749","citation_count":177,"is_preprint":false},{"pmid":"28223409","id":"PMC_28223409","title":"Asc1, Hel2, and Slh1 couple translation arrest to nascent chain degradation.","date":"2017","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/28223409","citation_count":120,"is_preprint":false},{"pmid":"30917308","id":"PMC_30917308","title":"GIGYF1/2-Driven Cooperation between ZNF598 and TTP in Posttranscriptional Regulation of Inflammatory Signaling.","date":"2019","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/30917308","citation_count":48,"is_preprint":false},{"pmid":"29147007","id":"PMC_29147007","title":"Modulating cellular balance of Rps3 mono-ubiquitination by both Hel2 E3 ligase and Ubp3 deubiquitinase regulates protein quality control.","date":"2017","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/29147007","citation_count":42,"is_preprint":false},{"pmid":"30718516","id":"PMC_30718516","title":"Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/30718516","citation_count":34,"is_preprint":false},{"pmid":"34551427","id":"PMC_34551427","title":"ZNF598 co-translationally titrates poly(GR) protein implicated in the pathogenesis of C9ORF72-associated ALS/FTD.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/34551427","citation_count":32,"is_preprint":false},{"pmid":"31433974","id":"PMC_31433974","title":"Attenuation of the Innate Immune Response against Viral Infection Due to ZNF598-Promoted Binding of FAT10 to RIG-I.","date":"2019","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/31433974","citation_count":31,"is_preprint":false},{"pmid":"36270478","id":"PMC_36270478","title":"Activation of Nrf2 signaling by 4-octyl itaconate attenuates the cartilaginous endplate degeneration by inhibiting E3 ubiquitin ligase ZNF598.","date":"2022","source":"Osteoarthritis and cartilage","url":"https://pubmed.ncbi.nlm.nih.gov/36270478","citation_count":21,"is_preprint":false},{"pmid":"33761353","id":"PMC_33761353","title":"The ribosome collision sensor Hel2 functions as preventive quality control in the secretory pathway.","date":"2021","source":"Cell 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regulatory ubiquitylation of ribosomal proteins RPS10 and RPS20 on stalled ribosomes to initiate ribosome-associated quality control (RQC) of poly(A)-induced stalled ribosomes; loss of ZNF598 function or mutations blocking RPS10/RPS20 ubiquitylation result in defective resolution of stalled ribosomes and readthrough of poly(A)-containing stall sequences.\",\n      \"method\": \"Gain/loss-of-function experiments, ubiquitylation site mutagenesis, poly(A)-stall readthrough reporter assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (mutagenesis, loss-of-function, reporter assays), replicated across two independent 2017 studies\",\n      \"pmids\": [\"28132843\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ZNF598 cross-links to tRNAs, mRNAs, and rRNAs on translating ribosomes (PAR-CLIP), is enriched on AAA-decoding tRNALys(UUU), triggers ubiquitination of multiple ribosomal proteins in response to translated poly(AAA) sequences, and requires the E2 ubiquitin ligase UBE2D3 to initiate RQC.\",\n      \"method\": \"PAR-CLIP, ribosomal protein ubiquitination assays, E2 ligase co-dependency experiments\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — PAR-CLIP with mass spectrometry plus functional ubiquitination assays in a single rigorous study\",\n      \"pmids\": [\"28685749\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In yeast, Hel2 (ZNF598 ortholog) and Asc1 are required for RQC-mediated modification (ubiquitination/targeting) of nascent chains on arrested ribosomes; ribosome stalling itself still occurs in their absence, placing Hel2/Asc1 downstream of arrest but upstream of RQC engagement.\",\n      \"method\": \"Genetic epistasis analysis in S. cerevisiae, nascent chain modification assays\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with multiple deletion combinations, replicated across RQC pathway studies\",\n      \"pmids\": [\"28223409\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In yeast, Hel2 E3 ligase mediates mono-ubiquitination of Rps3 (the yeast equivalent of regulatory ribosomal ubiquitination), and this is reversed by the deubiquitinase Ubp3; in mammalian cells the analogous pair is RNF123 (E3) and USP10 (DUB).\",\n      \"method\": \"Ubiquitination assays, deubiquitinase activity assays, co-fractionation\",\n      \"journal\": \"Experimental & molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal enzymatic assays in yeast and mammalian cells, single lab\",\n      \"pmids\": [\"29147007\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In yeast, the C-terminal region of Hel2 is an RNA-binding domain that contacts 18S rRNA and translated mRNAs; this 18S rRNA interaction is required for Hel2 polysome association and for its function in both RQC and no-go decay (NGD). Asc1 acts upstream of Hel2 and is required for Hel2 binding to 18S rRNA.\",\n      \"method\": \"In vivo UV-crosslinking/mass spectrometry (CRAC), C-terminal truncation mutants, polysome fractionation, genetic epistasis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vivo crosslinking + mass spectrometry + deletion mutagenesis + genetic epistasis, multiple orthogonal methods in one study\",\n      \"pmids\": [\"30718516\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ZNF598 functions as an RNA-binding protein with three proline-rich motifs that bind the GYF domain of GIGYF1, linking ZNF598 to the 4EHP-GIGYF1/2 translational repression complex; ZNF598 binds IL-8 mRNA and is required for regulation of TTP target mRNAs including IL-8 and CSF2.\",\n      \"method\": \"RNA sequencing (loss-of-function), protein interaction assays (GYF domain binding), RNA immunoprecipitation\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — protein interaction assays and RNA-seq with KO, single lab, two orthogonal methods\",\n      \"pmids\": [\"30917308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ZNF598 binds directly to RIG-I and promotes FAT10 (a ubiquitin-like protein) binding to RIG-I, thereby inhibiting RIG-I polyubiquitination required for downstream type I IFN signaling; ZNF598 ubiquitin ligase activity is dispensable for this suppression, and the effect is abrogated by FAT10 knockout.\",\n      \"method\": \"Co-immunoprecipitation, FAT10 knockout, IFN signaling assays, ubiquitination assays with E3-dead mutant\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, KO rescue, catalytic mutant analysis in one study, single lab\",\n      \"pmids\": [\"31433974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Arsenite directly binds ZNF598 in cells and reduces ubiquitination of RPS10 (K138/K139) and RPS20 (K8), leading to augmented readthrough of poly(A)-containing stall sequences; this readthrough defect is abolished in ZNF598 knockout cells, placing ZNF598 as the arsenite target mediating proteostatic stress.\",\n      \"method\": \"Chemical biology (arsenite-protein interaction), ubiquitination site-specific MS, poly(A) stall-readthrough reporter in ZNF598 KO cells\",\n      \"journal\": \"Chemical research in toxicology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding assay, site-specific ubiquitination quantification, KO validation, single lab\",\n      \"pmids\": [\"32324387\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ZNF598 co-translationally titrates expression of C9ORF72-derived poly(GR) protein; ZNF598 and listerin 1 promote poly(GR) degradation via the ubiquitin-proteasome pathway. An ALS-associated ZNF598 R69C mutant displays loss-of-function on poly(GR) expression and general RQC. Lentiviral ZNF598 overexpression in C9-ALS patient neurons reduces poly(GR) and suppresses caspase-3 activation.\",\n      \"method\": \"Reporter assays, ZNF598 KO/overexpression, Drosophila genetic screen, patient-derived neurons, lentiviral overexpression, ubiquitin-proteasome pathway assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Drosophila genetics, human cell KO/OE, patient neurons, ALS mutant), replicated across model systems\",\n      \"pmids\": [\"34551427\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In yeast, Hel2 preferentially binds pre-engaged secretory ribosome-nascent chain complexes (RNCs) that translate upstream of signal sequences; Hel2 recruitment to secretory RNCs is elevated under SRP-deficient conditions, and hel2 deletion enhances mitochondrial mistargeting of secretory proteins.\",\n      \"method\": \"Selective ribosome profiling (genome-wide), SRP-deficient strains, mitochondrial import assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ribosome profiling plus functional genetic assay, single lab\",\n      \"pmids\": [\"33761353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ZNF598 mediates ubiquitination and destabilization of Nrf2; 4-octyl itaconate inhibits ZNF598-dependent ubiquitination of Nrf2, thereby increasing Nrf2 protein levels.\",\n      \"method\": \"Western blotting, immunoprecipitation ubiquitination assay\",\n      \"journal\": \"Osteoarthritis and cartilage\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/ubiquitination assay, single lab, no mutagenesis or reconstitution\",\n      \"pmids\": [\"36270478\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Using in vitro reconstitution, ribosomal collision is not a strict prerequisite for ZNF598-mediated K63-polyubiquitination of uS10 (RPS10) or for ASCC-mediated ribosome dissociation; ASCC efficiently dissociates polysomes, monosomes, and reconstituted 80S elongation complexes following ZNF598 ubiquitination, provided ≥30-35 nt of mRNA extend downstream of the P site and sufficiently long ubiquitin chains are present.\",\n      \"method\": \"In vitro reconstitution, cell-free ubiquitination assays, ribosome dissociation assays with defined substrates\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — rigorous in vitro reconstitution with defined components, systematic variation of substrates, single lab\",\n      \"pmids\": [\"38366554\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZNF598 undergoes regulatory K63-linked ubiquitination in a CNOT4-dependent manner and is upregulated upon mitochondrial stress; this ZNF598 ubiquitination is required for resolution of stalled ribosomes and protection against mitochondrial stress in mammalian cells and Drosophila.\",\n      \"method\": \"Ubiquitination assays, CNOT4 KO/KD, Drosophila models, mitochondrial stress assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ubiquitination assays with KO validation and Drosophila models, two orthogonal systems, single lab\",\n      \"pmids\": [\"38388640\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In zebrafish, Znf598 down-regulates mRNAs encoding C2H2-type zinc finger domains during the maternal-to-zygotic transition; ribosomes stall and collide while translating tandem C2H2-ZF sequences, triggering Znf598-dependent mRNA degradation via no-go decay.\",\n      \"method\": \"RNA-Seq of znf598 mutant embryos, reporter assays, disome profiling\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic mutant + ribosome profiling + reporter assay, single lab\",\n      \"pmids\": [\"39636823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"During zebrafish development, Znf598 ubiquitinates ribosomal protein Rps10/eS10, and Rps10 ubiquitination-site mutations reduce the overall ubiquitination pattern of the ribosome; ribosome ubiquitination by Znf598 is dynamically regulated across developmental stages.\",\n      \"method\": \"Affinity purification of FLAG-tagged ribosomes, immunoblotting, ubiquitination-site mutant zebrafish\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — endogenous tagging, site mutants, developmental time-course, single lab\",\n      \"pmids\": [\"37751929\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In yeast, Hel2 occupancy on ribosomes increases progressively from monosomes to disomes to trisomes; Hel2 translates the duration of ribosome stalling into polyubiquitin chain length on Rps20/uS10 (mono/di-ubiquitinated disomes resolve independently of Slh1; tri/tetra-ubiquitinated ones do not), allowing distinction of transient from long-term stalling. Ubp2/Ubp3 deubiquitinases remove Hel2-dependent ubiquitin chains upon translational run-off.\",\n      \"method\": \"Quantitative in vivo analysis of Hel2-ribosome complexes, polysome fractionation, ubiquitination chain-length analysis, Slh1/Ubp2/Ubp3 genetic epistasis\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — quantitative in vivo ribosome association and ubiquitination dynamics with multiple genetic backgrounds, single lab\",\n      \"pmids\": [\"39875504\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Single-protein/mRNA imaging shows that multiple ZNF598 molecules engage a single RQC reporter mRNA simultaneously (not just the leading collided ribosome); ZNF598 overexpression increases ribosomal clearance rate, establishing ZNF598 as a rate-limiting factor for RQC. Under global UV-induced RNA damage, ZNF598 recruitment to RQC reporter mRNA diminishes, consistent with ZNF598 being a limiting resource.\",\n      \"method\": \"Single-molecule live-cell imaging (HaloTag endogenous tagging), ZNF598 overexpression ribosome clearance assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single-molecule imaging with endogenous tag plus functional overexpression assay, single lab\",\n      \"pmids\": [\"40750700\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In human iPSCs, ZNF598 is required to resolve a novel class of ribosome collisions at translation start sites on endogenous mRNAs with highly efficient initiation; CRISPRi screens show ZNF598 is selectively essential in stem cells compared to differentiated neural/cardiac cells.\",\n      \"method\": \"Comparative CRISPRi screens in hiPSC vs. differentiated cells\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — CRISPRi screen with cell-type essentiality readout, preprint, no direct biochemical reconstitution\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"ZNF598 is an E3 ubiquitin ligase (with E2 partner UBE2D3) and RNA-binding protein that acts as the primary sensor of stalled/collided ribosomes in mammalian ribosome-associated quality control (RQC): it recognizes collided 40S subunits and catalyzes K63-linked polyubiquitination of ribosomal proteins uS10/RPS10 and uS20/RPS20, which primes stalled ribosomes for disassembly by the ASCC complex and downstream degradation of aberrant nascent chains via the ubiquitin-proteasome pathway; ZNF598 is itself regulated by CNOT4-mediated K63-ubiquitination in response to mitochondrial stress, is titrated as a rate-limiting factor during widespread ribosome collisions, and additionally functions outside canonical RQC by binding GIGYF1/2 to repress cytokine mRNAs and by promoting FAT10-mediated suppression of RIG-I innate immune signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ZNF598 is the primary E3 ubiquitin ligase that initiates ribosome-associated quality control (RQC) by sensing aberrant translation and marking stalled ribosomes for resolution [#0, #1]. Acting with the E2 enzyme UBE2D3, it catalyzes regulatory ubiquitination of the small-subunit ribosomal proteins RPS10/uS10 (at K138/K139) and RPS20/uS20 (at K8) in response to ribosome stalling on poly(A) and other problematic sequences, and loss of this activity causes readthrough of stall sequences and defective stall resolution [#0, #1, #7]. ZNF598 is an RNA-binding protein that cross-links to tRNAs, mRNAs, and rRNA on translating ribosomes, with its yeast ortholog Hel2 using a C-terminal RNA-binding region to contact 18S rRNA in an Asc1-dependent manner required for polysome association and RQC/no-go decay function [#1, #4]. The ubiquitin chains it deposits are read out quantitatively: chain length scales with stalling duration to distinguish transient from persistent stalls, and sufficiently long K63-linked chains on uS10 prime ribosomes for ASCC-mediated subunit dissociation, after which aberrant nascent chains are degraded by the ubiquitin-proteasome pathway [#11, #15, #8]. ZNF598 activity is itself regulated, being upregulated and K63-ubiquitinated in a CNOT4-dependent manner upon mitochondrial stress, and it behaves as a rate-limiting RQC factor whose recruitment to a stalled mRNA can be titrated during widespread collisions [#12, #16]. Beyond canonical RQC, ZNF598 binds the GYF domain of GIGYF1 to link to the 4EHP–GIGYF translational repression complex and regulate cytokine mRNAs such as IL-8 and CSF2, and it binds RIG-I to promote FAT10-mediated suppression of type I interferon signaling independently of its ligase activity [#5, #6]. An ALS-associated R69C variant is a loss-of-function mutation that impairs RQC and clearance of C9ORF72-derived poly(GR), and ZNF598 overexpression reduces poly(GR) and caspase-3 activation in patient neurons [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Established ZNF598 as the E3 ligase that initiates mammalian RQC, defining the enzymatic event that converts a stalled ribosome into a quality-control substrate.\",\n      \"evidence\": \"Gain/loss-of-function, ubiquitylation site mutagenesis, and poly(A) stall-readthrough reporters; parallel PAR-CLIP and E2 co-dependency in a second study\",\n      \"pmids\": [\"28132843\", \"28685749\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Did not define ubiquitin chain linkage type or length requirements\",\n        \"Did not identify downstream disassembly machinery\",\n        \"Mechanism of collided-ribosome recognition not structurally resolved\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Genetic epistasis in yeast placed Hel2/Asc1 downstream of ribosome arrest but upstream of nascent-chain RQC engagement, ordering the pathway.\",\n      \"evidence\": \"Genetic epistasis with deletion combinations and nascent chain modification assays in S. cerevisiae\",\n      \"pmids\": [\"28223409\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Did not map the molecular signal Hel2 recognizes on arrested ribosomes\",\n        \"Relationship to mammalian factors inferred by orthology\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined the reversibility of regulatory ribosomal ubiquitination by identifying opposing deubiquitinases, framing RQC ubiquitination as a dynamic switch.\",\n      \"evidence\": \"Ubiquitination and DUB activity assays in yeast (Hel2/Ubp3) and mammalian cells\",\n      \"pmids\": [\"29147007\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mammalian E3/DUB assignment based on single-lab assays\",\n        \"In vivo physiological trigger for deubiquitination not established here\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Mapped the RNA-binding determinant of the ortholog Hel2 to a C-terminal region contacting 18S rRNA, explaining how the ligase docks onto translating ribosomes.\",\n      \"evidence\": \"In vivo CRAC crosslinking/MS, C-terminal truncation mutants, polysome fractionation, and Asc1 epistasis in yeast\",\n      \"pmids\": [\"30718516\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of 18S contact unresolved\",\n        \"Whether the mammalian protein uses an identical RNA-binding mode not tested\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Revealed a non-canonical role linking ZNF598 to translational repression of cytokine mRNAs via the GIGYF/4EHP complex, expanding its function beyond RQC.\",\n      \"evidence\": \"GYF-domain interaction assays, RNA-seq in KO cells, and RNA immunoprecipitation of IL-8/CSF2 mRNAs\",\n      \"pmids\": [\"30917308\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether ligase activity is required for cytokine mRNA repression unclear\",\n        \"Mechanistic link between repression and stalling not defined\",\n        \"Single-lab, two-method support\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified a ligase-independent innate-immunity function in which ZNF598 promotes FAT10 binding to RIG-I to dampen type I IFN signaling.\",\n      \"evidence\": \"Reciprocal Co-IP, FAT10 KO rescue, and E3-dead mutant IFN signaling assays\",\n      \"pmids\": [\"31433974\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Structural basis of ZNF598–RIG-I–FAT10 assembly unknown\",\n        \"Physiological context distinguishing this from RQC role unclear\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed ZNF598 is a direct chemical target of arsenite, providing a mechanistic link between an environmental proteostatic stressor and RQC inhibition.\",\n      \"evidence\": \"Direct arsenite-binding assay, site-specific ubiquitination MS, and poly(A) readthrough reporters in ZNF598 KO cells\",\n      \"pmids\": [\"32324387\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Arsenite binding site on ZNF598 not mapped\",\n        \"Single-lab study\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Connected ZNF598 to neurodegeneration by demonstrating co-translational titration and degradation of C9ORF72 poly(GR) and an ALS-associated loss-of-function variant.\",\n      \"evidence\": \"Reporter assays, KO/overexpression, Drosophila screen, ALS R69C mutant, and lentiviral rescue in patient-derived neurons\",\n      \"pmids\": [\"34551427\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Causal genetic link of R69C to ALS in patient cohorts not established here\",\n        \"How poly(GR) translation triggers ZNF598 engagement unresolved\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrated that Hel2 surveils secretory ribosome-nascent chain complexes and protects against organelle mistargeting, broadening the substrate range of the sensor.\",\n      \"evidence\": \"Selective ribosome profiling, SRP-deficient strains, and mitochondrial import assays in yeast\",\n      \"pmids\": [\"33761353\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether mammalian ZNF598 performs equivalent secretory surveillance untested\",\n        \"Single-lab study\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"In vitro reconstitution refined the mechanism, showing collision is not strictly required for ZNF598 ubiquitination or ASCC dissociation given adequate downstream mRNA and ubiquitin chain length.\",\n      \"evidence\": \"Cell-free ubiquitination and ribosome dissociation assays with defined substrates\",\n      \"pmids\": [\"38366554\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Reconciliation with in-cell collision-dependence not fully resolved\",\n        \"Minimal recognition determinant on the 40S not defined\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified CNOT4-dependent K63-ubiquitination as an upstream regulatory layer that activates ZNF598 during mitochondrial stress.\",\n      \"evidence\": \"Ubiquitination assays, CNOT4 KO/KD, and Drosophila mitochondrial stress models\",\n      \"pmids\": [\"38388640\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Ubiquitination sites on ZNF598 and their mechanistic consequence not mapped\",\n        \"Single-lab study\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established that ubiquitin chain length on uS10/uS20 encodes stalling duration, allowing ZNF598 to discriminate transient from persistent stalls.\",\n      \"evidence\": \"Quantitative in vivo Hel2-ribosome association, chain-length analysis, and Slh1/Ubp2/Ubp3 epistasis in yeast\",\n      \"pmids\": [\"39875504\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which chain length is read by downstream machinery in mammals unclear\",\n        \"Single-lab study\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Single-molecule imaging established ZNF598 as a rate-limiting RQC factor that multiple copies engage per stalled mRNA and that is titrated during widespread collisions.\",\n      \"evidence\": \"Single-molecule live-cell imaging with endogenous HaloTag and overexpression ribosome-clearance assays\",\n      \"pmids\": [\"40750700\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Quantitative cellular abundance limits not defined across cell types\",\n        \"Single-lab study\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated a developmental gene-regulatory role in which Znf598 targets C2H2-zinc-finger mRNAs for no-go decay during the maternal-to-zygotic transition.\",\n      \"evidence\": \"RNA-seq of mutant embryos, disome profiling, and reporter assays in zebrafish\",\n      \"pmids\": [\"39636823\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether this developmental program is conserved in mammals untested\",\n        \"Link between tandem C2H2 translation and collision not structurally defined\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ZNF598 selectively recognizes the collided/40S interface at the structural level, and how cell-type-specific demand (e.g., stem cell essentiality, start-site collisions) is met by a limiting amount of the protein, remain open.\",\n      \"evidence\": \"Comparative CRISPRi screens in hiPSC vs differentiated cells point to context-dependent essentiality (preprint)\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structure of ZNF598 engaging collided ribosomes in the corpus\",\n        \"Cell-type essentiality data is from a preprint without biochemical reconstitution\",\n        \"Determinants of start-site collision recognition undefined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 11]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 11]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1, 4, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [1, 4, 14]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 16]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 11, 13]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 8, 11]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [5, 6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"UBE2D3\", \"GIGYF1\", \"RIG-I\", \"FAT10\", \"CNOT4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}