{"gene":"SKIC8","run_date":"2026-06-10T07:46:32","timeline":{"discoveries":[{"year":2016,"finding":"SKIC8 (Ski8) is a core subunit of the Ski2-Ski3-Ski8 helicase complex that directly associates with 80S ribosomes presenting a short mRNA 3' overhang; cryo-EM structure shows that ribosome binding displaces the autoinhibitory domain of Ski2, positioning it near the ribosomal mRNA entry tunnel so that the mRNA 3' overhang is threaded directly from the small ribosomal subunit into the Ski2 helicase channel for exosome-mediated 3'–5' degradation.","method":"Cryo-electron microscopy of endogenous ribosome–Ski complex at ~4–10 Å resolution","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure of endogenous complex with local resolution reaching 4 Å, combined with structural interpretation of conformational change; single study but multiple orthogonal structural observations","pmids":["27980209"],"is_preprint":false},{"year":2004,"finding":"SKIC8 (Ski8) plays a direct role in meiotic double-strand break (DSB) formation as a physical partner of Spo11: Ski8 relocalizes from the cytoplasm to the nucleus and associates with meiotic chromosomes specifically during meiosis; this relocalization and DSB formation require the Ski8–Spo11 interaction; obligate RNA-metabolism partners of Ski8 are dispensable for recombination; Ski8 acts as a scaffold to recruit other DSB proteins to meiotic chromosomes.","method":"Two-hybrid interaction mapping, chromosome spreading/immunolocalization, genetic epistasis (deletion of RNA-metabolism partners), Ski8 relocalization assay","journal":"Molecular Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal two-hybrid, direct localization experiment with functional consequence, genetic epistasis with multiple deletion combinations in a single rigorous study","pmids":["14992724"],"is_preprint":false},{"year":1993,"finding":"SKIC8 (SKI8) encodes a 397-amino-acid WD-repeat protein containing two copies of the ~31-amino-acid beta-transducin repeat, establishing it as a WD-repeat scaffold protein; it is essential for repressing M double-stranded RNA virus replication in yeast.","method":"DNA sequencing, sequence analysis, and genetic disruption","journal":"Yeast","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — sequence characterization plus genetic knockout phenotype, single lab, two complementary approaches","pmids":["8442386","3029964"],"is_preprint":false},{"year":1997,"finding":"S. pombe Rec14, the ortholog of S. cerevisiae Ski8/SKIC8, is essential for meiotic recombination (reducing recombination up to 1000-fold in tested intervals) but has no detectable effect on mitotic recombination, establishing a conserved meiotic recombination function for this WD-repeat protein.","method":"Genetic disruption/deletion, recombination frequency assays across multiple chromosomal intervals, complementation cloning","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic loss-of-function with quantitative recombination readout, single lab, ortholog context","pmids":["9258671"],"is_preprint":false},{"year":2012,"finding":"The Arabidopsis SKI8 homolog VIP3 localizes to both nucleus and cytoplasm and associates biochemically with the SKI complex, supporting a role in cytoplasmic mRNA turnover; its nuclear role is in the Paf1 complex (Paf1c) for mRNA synthesis. Human SKIC8 (unlike yeast Ski8) also associates with Paf1c, indicating a context-dependent dual nuclear/cytoplasmic role for SKI8 homologs.","method":"GFP-fusion live imaging/subcellular localization, biochemical fractionation/co-purification, RNA sequencing of mutants, complementation with ScSKI8","journal":"PLoS Genetics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — localization by fluorescence plus biochemical association with SKI complex, single lab, multiple orthogonal methods; claim about human SKIC8–Paf1c association noted but not independently replicated here","pmids":["22511887"],"is_preprint":false},{"year":2024,"finding":"The antiviral compound UMB18 directly binds to SKIC8 of the SKI complex; this binding triggers SREBP/SCAP-dependent upregulation of the mevalonate pathway, increasing total cellular cholesterol, which in turn inhibits viral replication; siRNA depletion of SREBPs or SCAP, or cholesterol extraction, attenuates UMB18 antiviral activity.","method":"Direct binding assay (UMB18 to SKIC8), transcriptomic analysis of treated A549 cells, siRNA knockdown of SREBPs/SCAP, cholesterol extraction with methyl-β-cyclodextrin, antiviral assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding demonstrated, multiple genetic/pharmacological interventions to validate mechanism, single lab, preprint not yet peer-reviewed","pmids":["bio_10.1101_2024.12.03.626536"],"is_preprint":true},{"year":2024,"finding":"WDR61 (SKIC8) interacts with R-loops in breast tumor cells; loss of WDR61 leads to R-loop accumulation, causing DNA damage and inhibiting cell proliferation, demonstrating that WDR61 normally suppresses R-loop formation to maintain genomic stability.","method":"Tamoxifen-induced conditional knockout in mouse tumor model, siRNA knockdown in breast tumor cell lines, R-loop interaction assays, DNA damage assays, proliferation/colony-formation assays","journal":"The FEBS Journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with mechanistic readout (R-loop accumulation and DNA damage), in vivo and in vitro approaches, single lab","pmids":["38708718"],"is_preprint":false}],"current_model":"SKIC8 (Ski8/WDR61) is a WD-repeat scaffold protein that functions in at least two mechanistically distinct contexts: in the cytoplasm it is a core subunit of the Ski2–Ski3–Ski8 helicase complex that docks onto 80S ribosomes and threads mRNA 3' overhangs into the Ski2 helicase channel for exosome-mediated 3'–5' mRNA degradation, while in the nucleus during meiosis it physically associates with Spo11 to recruit additional DSB proteins and scaffold assembly of the multiprotein complex required for meiotic double-strand break formation; additionally, nuclear SKIC8 associates with the Paf1 transcription elongation complex, and its loss leads to R-loop accumulation and DNA damage, and it is the direct binding target of the broad-spectrum antiviral compound UMB18 whose activity depends on SREBP/SCAP-driven cholesterol upregulation."},"narrative":{"mechanistic_narrative":"SKIC8 (Ski8/WDR61) is a WD-repeat scaffold protein that operates in mechanistically distinct cytoplasmic and nuclear contexts to support RNA turnover, genome stability, and meiotic recombination [PMID:27980209, PMID:14992724, PMID:8442386, PMID:3029964]. In the cytoplasm it is a core subunit of the Ski2–Ski3–Ski8 helicase complex: docking of this complex onto 80S ribosomes displaces the autoinhibitory domain of Ski2 and positions the helicase channel at the ribosomal mRNA entry tunnel so that an mRNA 3' overhang is threaded directly from the small subunit into Ski2 for exosome-mediated 3'–5' degradation [PMID:27980209]. Consistent with this role in RNA metabolism, the protein is essential for repressing M double-stranded RNA virus replication in yeast [PMID:8442386, PMID:3029964]. During meiosis SKIC8 relocalizes from cytoplasm to nucleus and physically associates with Spo11 on meiotic chromosomes, acting as a scaffold that recruits additional double-strand break proteins; this meiotic function is independent of its RNA-metabolism partners and is conserved in the fission yeast ortholog Rec14 [PMID:14992724, PMID:9258671]. In a nuclear context distinct from RNA decay, the protein associates with the Paf1 transcription elongation complex, and loss of WDR61 causes R-loop accumulation, DNA damage, and impaired proliferation, defining a role in maintaining genomic stability [PMID:22511887, PMID:38708718].","teleology":[{"year":1993,"claim":"Established the molecular nature of the gene product, defining SKI8 as a WD-repeat scaffold protein and linking it to control of an RNA virus.","evidence":"DNA sequencing, sequence analysis, and genetic disruption in yeast","pmids":["8442386","3029964"],"confidence":"Medium","gaps":["Did not resolve the biochemical mechanism of viral repression","No direct partners or complex membership identified"]},{"year":1997,"claim":"Resolved whether the protein's recombination role is meiosis-specific by showing the fission yeast ortholog Rec14 is required for meiotic but not mitotic recombination.","evidence":"Genetic deletion and quantitative recombination assays across multiple intervals in S. pombe, with complementation cloning","pmids":["9258671"],"confidence":"Medium","gaps":["Did not identify the molecular partner mediating the recombination function","Mechanistic link between this WD-repeat protein and DSB machinery undefined"]},{"year":2004,"claim":"Connected the meiotic recombination defect to a direct physical and scaffolding role, showing Ski8 partners with Spo11 and relocalizes to recruit DSB proteins independently of its RNA-metabolism functions.","evidence":"Two-hybrid mapping, chromosome immunolocalization, relocalization assay, and genetic epistasis with RNA-metabolism partner deletions","pmids":["14992724"],"confidence":"High","gaps":["Structural basis of the Ski8–Spo11 interaction not resolved","Full set of recruited DSB proteins and order of assembly not defined"]},{"year":2012,"claim":"Demonstrated dual subcellular partitioning of SKI8 homologs, separating a cytoplasmic SKI-complex role from a nuclear Paf1 complex association and extending the latter to human SKIC8.","evidence":"GFP localization, biochemical co-purification, RNA-seq of mutants, and complementation in Arabidopsis VIP3, with note of human SKIC8–Paf1c association","pmids":["22511887"],"confidence":"Medium","gaps":["Human SKIC8–Paf1c association not independently replicated in this study","Functional consequence of nuclear Paf1c association in animals not established"]},{"year":2016,"claim":"Defined how the Ski complex physically couples to translation, showing SKIC8 is part of a complex that docks on 80S ribosomes and channels mRNA 3' overhangs into the Ski2 helicase for exosome degradation.","evidence":"Cryo-EM of an endogenous ribosome–Ski complex at ~4–10 Å resolution","pmids":["27980209"],"confidence":"High","gaps":["Specific SKIC8 contacts within the ribosome-bound complex not delineated at high resolution","Regulation of complex recruitment to ribosomes undefined"]},{"year":2024,"claim":"Assigned a genome-stability function to human WDR61, showing it suppresses R-loop accumulation to prevent DNA damage and sustain proliferation.","evidence":"Conditional knockout in a mouse tumor model, siRNA knockdown, R-loop interaction and DNA damage assays in breast tumor cells","pmids":["38708718"],"confidence":"Medium","gaps":["Mechanism linking WDR61 to R-loop resolution not defined","Relationship between R-loop suppression and Paf1c association not established"]},{"year":2024,"claim":"Identified SKIC8 as the direct target of the antiviral compound UMB18, linking compound binding to SREBP/SCAP-driven cholesterol upregulation that restricts viral replication.","evidence":"Direct binding assay, transcriptomics in A549 cells, siRNA knockdown of SREBPs/SCAP, and cholesterol extraction (preprint)","pmids":["bio_10.1101_2024.12.03.626536"],"confidence":"Medium","gaps":["Preprint not yet peer-reviewed","How UMB18 binding to SKIC8 mechanistically triggers the mevalonate pathway is unresolved","Binding site on SKIC8 not mapped"]},{"year":null,"claim":"How a single WD-repeat scaffold is partitioned among the cytoplasmic SKI/ribosome complex, the meiotic Spo11 DSB machinery, and the nuclear Paf1c/R-loop functions remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of SKIC8 within Paf1c","Regulatory switch controlling cytoplasmic vs nuclear deployment unknown","Whether R-loop suppression depends on Paf1c association untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,2]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,4]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,4]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[1,3]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[6]}],"complexes":["Ski2–Ski3–Ski8 (SKI) complex","Paf1 complex"],"partners":["SKIV2L","TTC37","SPO11","PAF1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9GZS3","full_name":"Superkiller complex protein 8","aliases":["Meiotic recombination REC14 protein homolog","WD repeat-containing protein 61"],"length_aa":305,"mass_kda":33.6,"function":"Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency (PubMed:16307923, PubMed:19952111, PubMed:20178742). PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both independently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1 (PubMed:16307923, PubMed:19952111, PubMed:20178742). PAF1C is required for transcription of Hox and Wnt target genes (PubMed:16307923, PubMed:19952111, PubMed:20178742). PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL (PubMed:16307923, PubMed:19952111, PubMed:20178742). PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3) (PubMed:16307923, PubMed:19952111, PubMed:20178742). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription (PubMed:16307923, PubMed:19952111, PubMed:20178742). PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors (PubMed:16307923, PubMed:19952111, PubMed:20178742). In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription (PubMed:16307923, PubMed:19952111, PubMed:20178742). Required for mono- and trimethylation on histone H3 'Lys-4' (H3K4me3), dimethylation on histone H3 'Lys-79' (H3K4me3). Required for Hox gene transcription (PubMed:16307923, PubMed:19952111, PubMed:20178742). Also acts as a component of the SKI complex, a multiprotein complex that assists the RNA-degrading exosome during the mRNA decay and quality-control pathways (PubMed:16024656, PubMed:32006463, PubMed:35120588). The SKI complex catalyzes mRNA extraction from 80S ribosomal complexes in the 3'-5' direction and channels mRNA to the cytosolic exosome for degradation (PubMed:32006463, PubMed:35120588). SKI-mediated extraction of mRNA from stalled ribosomes allow binding of the Pelota-HBS1L complex and subsequent ribosome disassembly by ABCE1 for ribosome recycling (PubMed:32006463)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9GZS3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SKIC8","classification":"Common Essential","n_dependent_lines":991,"n_total_lines":1208,"dependency_fraction":0.820364238410596},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"SF3B1","stoichiometry":10.0},{"gene":"SF3B6","stoichiometry":10.0},{"gene":"SF3A2","stoichiometry":4.0},{"gene":"SF3B3","stoichiometry":4.0},{"gene":"SF3B5","stoichiometry":4.0},{"gene":"SSRP1","stoichiometry":4.0},{"gene":"TOP1","stoichiometry":4.0},{"gene":"G3BP2","stoichiometry":0.2},{"gene":"RAN","stoichiometry":0.2},{"gene":"SF3A1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/SKIC8","total_profiled":1310},"omim":[{"mim_id":"609540","title":"SKI8 SUBUNIT OF SUPERKILLER COMPLEX; SKIC8","url":"https://www.omim.org/entry/609540"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"},{"location":"Cytosol","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SKIC8"},"hgnc":{"alias_symbol":["REC14","SKI8"],"prev_symbol":["WDR61"]},"alphafold":{"accession":"Q9GZS3","domains":[{"cath_id":"2.130.10.10","chopping":"5-301","consensus_level":"high","plddt":97.1222,"start":5,"end":301}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9GZS3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9GZS3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9GZS3-F1-predicted_aligned_error_v6.png","plddt_mean":96.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SKIC8","jax_strain_url":"https://www.jax.org/strain/search?query=SKIC8"},"sequence":{"accession":"Q9GZS3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9GZS3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9GZS3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9GZS3"}},"corpus_meta":[{"pmid":"14992724","id":"PMC_14992724","title":"Antiviral protein Ski8 is a direct partner of Spo11 in meiotic DNA break formation, independent of its cytoplasmic role in RNA metabolism.","date":"2004","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/14992724","citation_count":141,"is_preprint":false},{"pmid":"27980209","id":"PMC_27980209","title":"The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex.","date":"2016","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/27980209","citation_count":95,"is_preprint":false},{"pmid":"9258671","id":"PMC_9258671","title":"A WD repeat protein, Rec14, essential for meiotic recombination in Schizosaccharomyces pombe.","date":"1997","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/9258671","citation_count":40,"is_preprint":false},{"pmid":"8442386","id":"PMC_8442386","title":"A yeast antiviral protein, SKI8, shares a repeated amino acid sequence pattern with beta-subunits of G proteins and several other proteins.","date":"1993","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/8442386","citation_count":30,"is_preprint":false},{"pmid":"22511887","id":"PMC_22511887","title":"Context-dependent dual role of SKI8 homologs in mRNA synthesis and turnover.","date":"2012","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22511887","citation_count":29,"is_preprint":false},{"pmid":"3029964","id":"PMC_3029964","title":"Gene disruption indicates that the only essential function of the SKI8 chromosomal gene is to protect Saccharomyces cerevisiae from viral cytopathology.","date":"1987","source":"Virology","url":"https://pubmed.ncbi.nlm.nih.gov/3029964","citation_count":21,"is_preprint":false},{"pmid":"38708718","id":"PMC_38708718","title":"WDR61 ablation triggers R-loop accumulation and suppresses breast cancer progression.","date":"2024","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/38708718","citation_count":8,"is_preprint":false},{"pmid":"20490547","id":"PMC_20490547","title":"Gerbu adjuvant modulates the immune response and thus the course of infection in C56BL/6 mice immunised with Echinococcus multilocularis rec14-3-3 protein.","date":"2010","source":"Parasitology research","url":"https://pubmed.ncbi.nlm.nih.gov/20490547","citation_count":7,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.12.03.626536","title":"The mammalian SKI complex is a broad-spectrum antiviral drug target that upregulates cellular cholesterol to inhibit viral replication","date":"2024-12-04","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.03.626536","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5917,"output_tokens":2018,"usd":0.024011,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9052,"output_tokens":2799,"usd":0.057618,"stage2_stop_reason":"end_turn"},"total_usd":0.081629,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"SKIC8 (Ski8) is a core subunit of the Ski2-Ski3-Ski8 helicase complex that directly associates with 80S ribosomes presenting a short mRNA 3' overhang; cryo-EM structure shows that ribosome binding displaces the autoinhibitory domain of Ski2, positioning it near the ribosomal mRNA entry tunnel so that the mRNA 3' overhang is threaded directly from the small ribosomal subunit into the Ski2 helicase channel for exosome-mediated 3'–5' degradation.\",\n      \"method\": \"Cryo-electron microscopy of endogenous ribosome–Ski complex at ~4–10 Å resolution\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure of endogenous complex with local resolution reaching 4 Å, combined with structural interpretation of conformational change; single study but multiple orthogonal structural observations\",\n      \"pmids\": [\"27980209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"SKIC8 (Ski8) plays a direct role in meiotic double-strand break (DSB) formation as a physical partner of Spo11: Ski8 relocalizes from the cytoplasm to the nucleus and associates with meiotic chromosomes specifically during meiosis; this relocalization and DSB formation require the Ski8–Spo11 interaction; obligate RNA-metabolism partners of Ski8 are dispensable for recombination; Ski8 acts as a scaffold to recruit other DSB proteins to meiotic chromosomes.\",\n      \"method\": \"Two-hybrid interaction mapping, chromosome spreading/immunolocalization, genetic epistasis (deletion of RNA-metabolism partners), Ski8 relocalization assay\",\n      \"journal\": \"Molecular Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal two-hybrid, direct localization experiment with functional consequence, genetic epistasis with multiple deletion combinations in a single rigorous study\",\n      \"pmids\": [\"14992724\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"SKIC8 (SKI8) encodes a 397-amino-acid WD-repeat protein containing two copies of the ~31-amino-acid beta-transducin repeat, establishing it as a WD-repeat scaffold protein; it is essential for repressing M double-stranded RNA virus replication in yeast.\",\n      \"method\": \"DNA sequencing, sequence analysis, and genetic disruption\",\n      \"journal\": \"Yeast\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — sequence characterization plus genetic knockout phenotype, single lab, two complementary approaches\",\n      \"pmids\": [\"8442386\", \"3029964\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"S. pombe Rec14, the ortholog of S. cerevisiae Ski8/SKIC8, is essential for meiotic recombination (reducing recombination up to 1000-fold in tested intervals) but has no detectable effect on mitotic recombination, establishing a conserved meiotic recombination function for this WD-repeat protein.\",\n      \"method\": \"Genetic disruption/deletion, recombination frequency assays across multiple chromosomal intervals, complementation cloning\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic loss-of-function with quantitative recombination readout, single lab, ortholog context\",\n      \"pmids\": [\"9258671\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The Arabidopsis SKI8 homolog VIP3 localizes to both nucleus and cytoplasm and associates biochemically with the SKI complex, supporting a role in cytoplasmic mRNA turnover; its nuclear role is in the Paf1 complex (Paf1c) for mRNA synthesis. Human SKIC8 (unlike yeast Ski8) also associates with Paf1c, indicating a context-dependent dual nuclear/cytoplasmic role for SKI8 homologs.\",\n      \"method\": \"GFP-fusion live imaging/subcellular localization, biochemical fractionation/co-purification, RNA sequencing of mutants, complementation with ScSKI8\",\n      \"journal\": \"PLoS Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — localization by fluorescence plus biochemical association with SKI complex, single lab, multiple orthogonal methods; claim about human SKIC8–Paf1c association noted but not independently replicated here\",\n      \"pmids\": [\"22511887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The antiviral compound UMB18 directly binds to SKIC8 of the SKI complex; this binding triggers SREBP/SCAP-dependent upregulation of the mevalonate pathway, increasing total cellular cholesterol, which in turn inhibits viral replication; siRNA depletion of SREBPs or SCAP, or cholesterol extraction, attenuates UMB18 antiviral activity.\",\n      \"method\": \"Direct binding assay (UMB18 to SKIC8), transcriptomic analysis of treated A549 cells, siRNA knockdown of SREBPs/SCAP, cholesterol extraction with methyl-β-cyclodextrin, antiviral assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding demonstrated, multiple genetic/pharmacological interventions to validate mechanism, single lab, preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2024.12.03.626536\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"WDR61 (SKIC8) interacts with R-loops in breast tumor cells; loss of WDR61 leads to R-loop accumulation, causing DNA damage and inhibiting cell proliferation, demonstrating that WDR61 normally suppresses R-loop formation to maintain genomic stability.\",\n      \"method\": \"Tamoxifen-induced conditional knockout in mouse tumor model, siRNA knockdown in breast tumor cell lines, R-loop interaction assays, DNA damage assays, proliferation/colony-formation assays\",\n      \"journal\": \"The FEBS Journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with mechanistic readout (R-loop accumulation and DNA damage), in vivo and in vitro approaches, single lab\",\n      \"pmids\": [\"38708718\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SKIC8 (Ski8/WDR61) is a WD-repeat scaffold protein that functions in at least two mechanistically distinct contexts: in the cytoplasm it is a core subunit of the Ski2–Ski3–Ski8 helicase complex that docks onto 80S ribosomes and threads mRNA 3' overhangs into the Ski2 helicase channel for exosome-mediated 3'–5' mRNA degradation, while in the nucleus during meiosis it physically associates with Spo11 to recruit additional DSB proteins and scaffold assembly of the multiprotein complex required for meiotic double-strand break formation; additionally, nuclear SKIC8 associates with the Paf1 transcription elongation complex, and its loss leads to R-loop accumulation and DNA damage, and it is the direct binding target of the broad-spectrum antiviral compound UMB18 whose activity depends on SREBP/SCAP-driven cholesterol upregulation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SKIC8 (Ski8/WDR61) is a WD-repeat scaffold protein that operates in mechanistically distinct cytoplasmic and nuclear contexts to support RNA turnover, genome stability, and meiotic recombination [#0, #1, #2]. In the cytoplasm it is a core subunit of the Ski2\\u2013Ski3\\u2013Ski8 helicase complex: docking of this complex onto 80S ribosomes displaces the autoinhibitory domain of Ski2 and positions the helicase channel at the ribosomal mRNA entry tunnel so that an mRNA 3' overhang is threaded directly from the small subunit into Ski2 for exosome-mediated 3'\\u20135' degradation [#0]. Consistent with this role in RNA metabolism, the protein is essential for repressing M double-stranded RNA virus replication in yeast [#2]. During meiosis SKIC8 relocalizes from cytoplasm to nucleus and physically associates with Spo11 on meiotic chromosomes, acting as a scaffold that recruits additional double-strand break proteins; this meiotic function is independent of its RNA-metabolism partners and is conserved in the fission yeast ortholog Rec14 [#1, #3]. In a nuclear context distinct from RNA decay, the protein associates with the Paf1 transcription elongation complex, and loss of WDR61 causes R-loop accumulation, DNA damage, and impaired proliferation, defining a role in maintaining genomic stability [#4, #6].\",\n  \"teleology\": [\n    {\n      \"year\": 1993,\n      \"claim\": \"Established the molecular nature of the gene product, defining SKI8 as a WD-repeat scaffold protein and linking it to control of an RNA virus.\",\n      \"evidence\": \"DNA sequencing, sequence analysis, and genetic disruption in yeast\",\n      \"pmids\": [\"8442386\", \"3029964\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not resolve the biochemical mechanism of viral repression\", \"No direct partners or complex membership identified\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Resolved whether the protein's recombination role is meiosis-specific by showing the fission yeast ortholog Rec14 is required for meiotic but not mitotic recombination.\",\n      \"evidence\": \"Genetic deletion and quantitative recombination assays across multiple intervals in S. pombe, with complementation cloning\",\n      \"pmids\": [\"9258671\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not identify the molecular partner mediating the recombination function\", \"Mechanistic link between this WD-repeat protein and DSB machinery undefined\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Connected the meiotic recombination defect to a direct physical and scaffolding role, showing Ski8 partners with Spo11 and relocalizes to recruit DSB proteins independently of its RNA-metabolism functions.\",\n      \"evidence\": \"Two-hybrid mapping, chromosome immunolocalization, relocalization assay, and genetic epistasis with RNA-metabolism partner deletions\",\n      \"pmids\": [\"14992724\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the Ski8\\u2013Spo11 interaction not resolved\", \"Full set of recruited DSB proteins and order of assembly not defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrated dual subcellular partitioning of SKI8 homologs, separating a cytoplasmic SKI-complex role from a nuclear Paf1 complex association and extending the latter to human SKIC8.\",\n      \"evidence\": \"GFP localization, biochemical co-purification, RNA-seq of mutants, and complementation in Arabidopsis VIP3, with note of human SKIC8\\u2013Paf1c association\",\n      \"pmids\": [\"22511887\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Human SKIC8\\u2013Paf1c association not independently replicated in this study\", \"Functional consequence of nuclear Paf1c association in animals not established\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined how the Ski complex physically couples to translation, showing SKIC8 is part of a complex that docks on 80S ribosomes and channels mRNA 3' overhangs into the Ski2 helicase for exosome degradation.\",\n      \"evidence\": \"Cryo-EM of an endogenous ribosome\\u2013Ski complex at ~4\\u201310 \\u00c5 resolution\",\n      \"pmids\": [\"27980209\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific SKIC8 contacts within the ribosome-bound complex not delineated at high resolution\", \"Regulation of complex recruitment to ribosomes undefined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Assigned a genome-stability function to human WDR61, showing it suppresses R-loop accumulation to prevent DNA damage and sustain proliferation.\",\n      \"evidence\": \"Conditional knockout in a mouse tumor model, siRNA knockdown, R-loop interaction and DNA damage assays in breast tumor cells\",\n      \"pmids\": [\"38708718\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking WDR61 to R-loop resolution not defined\", \"Relationship between R-loop suppression and Paf1c association not established\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified SKIC8 as the direct target of the antiviral compound UMB18, linking compound binding to SREBP/SCAP-driven cholesterol upregulation that restricts viral replication.\",\n      \"evidence\": \"Direct binding assay, transcriptomics in A549 cells, siRNA knockdown of SREBPs/SCAP, and cholesterol extraction (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.12.03.626536\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint not yet peer-reviewed\", \"How UMB18 binding to SKIC8 mechanistically triggers the mevalonate pathway is unresolved\", \"Binding site on SKIC8 not mapped\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single WD-repeat scaffold is partitioned among the cytoplasmic SKI/ribosome complex, the meiotic Spo11 DSB machinery, and the nuclear Paf1c/R-loop functions remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of SKIC8 within Paf1c\", \"Regulatory switch controlling cytoplasmic vs nuclear deployment unknown\", \"Whether R-loop suppression depends on Paf1c association untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\"Ski2\\u2013Ski3\\u2013Ski8 (SKI) complex\", \"Paf1 complex\"],\n    \"partners\": [\"SKIV2L\", \"TTC37\", \"SPO11\", \"PAF1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}