{"gene":"WDR6","run_date":"2026-04-28T23:00:23","timeline":{"discoveries":[{"year":2000,"finding":"WDR6 was molecularly cloned and characterized as a novel human WD-repeat protein encoding 1121 amino acids with 11 WD-repeat units clustered into two distinct groups separated by a putative transmembrane domain; it was mapped to chromosome 15q21 and found to be ubiquitously expressed in human adult and fetal tissues.","method":"cDNA cloning, Northern blot analysis, fluorescence in situ hybridization (FISH)","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — direct molecular characterization with multiple methods in a single study; foundational cloning paper","pmids":["10903905"],"is_preprint":false},{"year":2007,"finding":"WDR6 physically interacts with the serine/threonine kinase LKB1 (STK11); co-expression of WDR6 with LKB1 enhances LKB1-mediated inhibition of HeLa cell proliferation and G1 cell cycle arrest, and synergistically induces the CDK inhibitor p27(Kip1) by elevating p27(Kip1) promoter activity, placing WDR6 in the LKB1 tumor suppressor pathway.","method":"Yeast two-hybrid screening, immunofluorescence co-localization, colony formation assay, cell cycle analysis, p27(Kip1) promoter-reporter assay","journal":"Molecular and cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 3 — yeast two-hybrid plus functional overexpression assays in a single lab; no biochemical reconstitution of direct binding","pmids":["17216128"],"is_preprint":false},{"year":2007,"finding":"WDR6 mRNA is abundantly expressed in the rat hypothalamic arcuate nucleus and WDR6 protein interacts with insulin receptor substrate 4 (IRS-4) in the rat brain; WDR6 expression is decreased by caloric restriction and in growth hormone-antisense transgenic rats (longevity models), and is increased by IGF-I and insulin treatment in hypothalamic GT1-7 cells, implicating WDR6 in insulin/IGF-I signaling and regulation of longevity.","method":"Suppression subtractive hybridization, co-immunoprecipitation, quantitative RT-PCR, in vitro hormone treatment","journal":"Neurobiology of aging","confidence":"Medium","confidence_rationale":"Tier 3 — co-IP interaction plus expression regulation by defined stimuli; single lab, moderate mechanistic follow-up","pmids":["17720279"],"is_preprint":false},{"year":2015,"finding":"WDR6 was identified as a host restriction factor for vaccinia virus (VACV): genome-wide siRNA knockdown and CRISPR/Cas9 knockout of WDR6 in HeLa cells enabled replication of the VACV K1L-C7L double-deletion mutant. WDR6 knockdown did not reduce SAMD9 levels, and no interaction between WDR6 and SAMD9, C7, or K1 viral proteins was detected, indicating WDR6 acts independently of SAMD9 but possibly in the same innate defense pathway.","method":"Genome-wide siRNA screen, CRISPR/Cas9 knockout, viral replication assays, immunoprecipitation","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 — genome-wide screen validated by CRISPR KO with multiple siRNAs and orthogonal immunoprecipitation; replicated in follow-up study (PMID:30209174)","pmids":["26242627"],"is_preprint":false},{"year":2018,"finding":"CRISPR/Cas9 knockout of WDR6 in HeLa cells enhanced replication of the VACV C7/K1 double-deletion mutant but did not restore replication to wild-type levels (unlike SAMD9 KO), and SAMD9 protein levels were not depleted in WDR6 KO cells, confirming that WDR6 acts as an independent but less dominant restriction factor compared to SAMD9.","method":"CRISPR/Cas9 knockout, viral replication assay, western blot","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 — clean CRISPR KO with defined viral replication phenotype; single lab but orthogonal to PMID:26242627","pmids":["30209174"],"is_preprint":false},{"year":2019,"finding":"WDR6 (the human ortholog of yeast Trm734) forms part of the Cul4-DDB1 E3 ubiquitin ligase complex and binds OSR1 kinase in a phosphorylation-dependent manner: binding to the OSR1 S-motif is compromised when the S-motif serine is phosphorylated under osmotic stress, and this correlates with protection of OSR1 from ubiquitylation, linking the CRL4-WDR6/WDR3 complex to ion homeostasis.","method":"Affinity pull-down, mass spectrometry, proteasomal and neddylation inhibitor experiments, ubiquitylation assays","journal":"Chembiochem","confidence":"Medium","confidence_rationale":"Tier 2 — AP-MS identification plus functional ubiquitylation assays with pharmacological inhibitors; single lab","pmids":["31614064"],"is_preprint":false},{"year":2019,"finding":"The crystal structure of the yeast Trm7-Trm734 complex (the ortholog of human FTSJ1-WDR6) was solved in apo and SAM-bound forms; Trm734 contains three WD40 β-propeller domains (BPA, BPB, BPC) forming a V-shaped cleft that docks to the C-terminal region of Trm7, and the D-arm of substrate tRNA contacts the positively charged surface of BPB to position the anticodon loop near the Trm7 catalytic pocket, demonstrating that Trm734/WDR6 is required for correct tRNA positioning for 2′-O-methylation at position 34.","method":"X-ray crystallography, small-angle X-ray scattering (SAXS), in vitro methyltransferase assay, site-directed mutagenesis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with functional biochemical validation and mutagenesis; strong mechanistic evidence for the WDR6 ortholog","pmids":["31586407"],"is_preprint":false},{"year":2020,"finding":"WDR6 was identified as a direct interacting protein of FTSJ1 (human tRNA 2′-O-methyltransferase); the reconstituted FTSJ1-WDR6 complex performs 2′-O-methylation at position 34 of specific tRNAs in vitro, with m1G37 as a prerequisite modification. In vivo, modifications at positions 32, 34, and 37 occur in a hierarchical, interdependent order, and loss of FTSJ1 reduces translation efficiency of UUU (but not UUC) codons decoded by tRNA(Phe)(GAA), implicating FTSJ1-WDR6 in efficient decoding of UUU codons and nervous system development.","method":"Co-immunoprecipitation, in vitro reconstitution of methyltransferase activity, mass spectrometry-based tRNA modification analysis, ribosome profiling/codon usage analysis, FTSJ1 knockout cells","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1 — first in vitro reconstitution of FTSJ1-WDR6 enzymatic activity with multiple orthogonal methods including KO cellular phenotype","pmids":["32558197"],"is_preprint":false},{"year":2023,"finding":"WDR6 targets the tumor suppressor UVRAG to the CUL4A-DDB1-ROC1 E3 ubiquitin ligase complex through a unique WDxR motif, promoting UVRAG ubiquitin-dependent degradation; this blocks autophagic degradation of p65/NF-κB, increases chromatin accessibility at the TNFα locus, elevates intratumoral myeloid-derived suppressor cells (MDSCs), and reduces CD8+ T cell infiltration in HCC. TNFα in turn activates NF-κB to transcriptionally upregulate WDR6, establishing a WDR6-TNFα positive feedback loop. A WDxR-like peptide disrupts the WDR6-UVRAG interaction and enhances anti-PD-L1 efficacy.","method":"Co-immunoprecipitation, ubiquitylation assay, CRISPR KO in vivo tumor models (immune-competent mice), chromatin accessibility assay (ATAC-seq), flow cytometry of immune infiltrates, peptide competition assay","journal":"EMBO molecular medicine","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal biochemical and in vivo methods; mechanism validated in immune-competent tumor models with functional immune readouts","pmids":["36947051"],"is_preprint":false},{"year":2023,"finding":"WDR6 promotes hepatic de novo lipogenesis (DNL) during insulin resistance by interacting with PPP1CB (the beta-type catalytic subunit of PP1), facilitating PPP1CB dephosphorylation at Thr316, which subsequently enhances fatty acid synthase transcription through DNA-dependent protein kinase (DNA-PK) and upstream stimulatory factor 1 (USF1). Molecular dynamics simulation identified a small molecule (XLIX) that inhibits WDR6-PPP1CB interaction and reduces DNL in insulin-resistant states.","method":"Co-immunoprecipitation, phosphorylation assays, transcriptional reporter assays, molecular dynamics simulation, mouse in vivo hepatic steatosis model, pharmacological inhibition","journal":"Nature metabolism","confidence":"High","confidence_rationale":"Tier 2 — multiple biochemical methods plus in vivo validation in mouse models and mechanistic pharmacological intervention; single lab but strong evidence","pmids":["37735236"],"is_preprint":false},{"year":2024,"finding":"Amino acid variants in Trm734 (yeast ortholog of WDR6) near the Trm7 active site, identified by systematic mutagenesis, abolish 2′-O-methylation of tRNA(Phe) at position 34 without disrupting Trm7-Trm734 protein-protein interaction, indicating these residues are critical for tRNA substrate engagement rather than complex formation, and that WDR6's auxiliary role is specifically in tRNA binding/positioning.","method":"Site-directed mutagenesis, in vivo yeast complementation, immunoprecipitation, tRNA modification assay","journal":"ACS omega","confidence":"Medium","confidence_rationale":"Tier 2 — mutagenesis with functional tRNA modification readout in yeast ortholog; mechanistic but indirect (yeast model)","pmids":["38882062"],"is_preprint":false},{"year":2025,"finding":"Cryo-EM structure of the human FTSJ1-THADA complex reveals that FTSJ1 binds THADA via its C-terminal region with a unique interaction mode distinct from the FTSJ1-WDR6 complex, establishing that FTSJ1 uses different structural interfaces to associate with THADA (for Nm32 modification) versus WDR6 (for Nm34 modification), and confirming that WDR6 specifically partners with FTSJ1 for 2′-O-methylation at position 34.","method":"Cryo-electron microscopy, biochemical binding assays, site-directed mutagenesis","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 1 structure — but WDR6-specific conclusions are comparative/indirect; primarily characterizes FTSJ1-THADA","pmids":["40483304"],"is_preprint":false}],"current_model":"WDR6 is a multi-functional WD40-repeat scaffold protein that: (1) partners with FTSJ1 to form a 2′-O-methyltransferase complex that modifies tRNA at position 34 (Nm34), with WDR6 providing the tRNA-positioning function via its β-propeller domains; (2) acts as a substrate receptor in CUL4A-DDB1-ROC1 E3 ubiquitin ligase complexes, targeting UVRAG for degradation to suppress autophagy and promote TNFα-driven immunosuppression in HCC, and binding SPAK/OSR1 kinases in a phosphorylation-dependent manner linked to ion homeostasis; (3) promotes hepatic de novo lipogenesis during insulin resistance by interacting with PPP1CB to regulate its dephosphorylation and downstream fatty acid synthase transcription; (4) functions as an innate immune restriction factor limiting vaccinia virus replication independently of SAMD9; and (5) synergizes with LKB1 to induce p27(Kip1)-dependent cell cycle arrest and interacts with IRS-4 in hypothalamic insulin/IGF-I signaling."},"narrative":{"teleology":[{"year":2000,"claim":"Molecular cloning of WDR6 established it as a ubiquitously expressed, large WD-repeat protein with 11 WD-repeat units arranged in two clusters, providing the foundational gene structure for all subsequent functional studies.","evidence":"cDNA cloning, Northern blot, and FISH mapping in human tissues","pmids":["10903905"],"confidence":"Medium","gaps":["No functional activity or binding partner identified","Predicted transmembrane domain never validated experimentally"]},{"year":2007,"claim":"Identification of WDR6 as an interactor of both LKB1 (enhancing p27Kip1-dependent cell cycle arrest) and IRS-4 in hypothalamic neurons (regulated by insulin/IGF-I) placed WDR6 at the intersection of growth-suppressive and metabolic signaling pathways, though the direct biochemical mechanisms remained undefined.","evidence":"Yeast two-hybrid, co-IP, cell cycle analysis and promoter-reporter assays (LKB1); suppression subtractive hybridization and co-IP in rat brain (IRS-4)","pmids":["17216128","17720279"],"confidence":"Medium","gaps":["LKB1–WDR6 interaction based on yeast two-hybrid without biochemical reconstitution of direct binding","Downstream effectors linking WDR6–IRS-4 to metabolic outputs not identified","No in vivo loss-of-function data for either interaction"]},{"year":2015,"claim":"A genome-wide siRNA screen identified WDR6 as a host restriction factor for vaccinia virus, acting independently of the known restriction factor SAMD9, thereby revealing an unexpected innate immune function for a WD-repeat scaffold protein.","evidence":"Genome-wide siRNA screen and CRISPR/Cas9 knockout with viral replication assays in HeLa cells","pmids":["26242627"],"confidence":"High","gaps":["Molecular mechanism of viral restriction unknown—no viral or host target identified","Restriction phenotype weaker than SAMD9 KO; biological significance unclear"]},{"year":2018,"claim":"Independent CRISPR knockout confirmed WDR6 as a vaccinia restriction factor that is less dominant than SAMD9 and does not regulate SAMD9 levels, solidifying the existence of a parallel antiviral pathway.","evidence":"CRISPR/Cas9 knockout, viral replication assay, western blot in HeLa cells","pmids":["30209174"],"confidence":"Medium","gaps":["Mechanism by which WDR6 restricts virus still unknown","Not tested in primary immune cells or in vivo infection models"]},{"year":2019,"claim":"Crystal structures of the yeast Trm7–Trm734 complex revealed that WDR6's ortholog forms a three-β-propeller V-shaped cleft that docks the catalytic methyltransferase and positions the tRNA D-arm for 2′-O-methylation at position 34, providing the first atomic-resolution mechanism for WDR6's role in tRNA modification.","evidence":"X-ray crystallography, SAXS, in vitro methyltransferase assay, and site-directed mutagenesis of yeast Trm7–Trm734","pmids":["31586407"],"confidence":"High","gaps":["Structure determined for yeast ortholog; human FTSJ1–WDR6 structure not yet available","Only tRNAPhe substrate modeled; positioning of other tRNA substrates untested"]},{"year":2019,"claim":"Discovery that WDR6 integrates into CUL4–DDB1 E3 ligase complexes and binds OSR1 kinase in a phosphorylation-dependent manner established WDR6 as a bona fide substrate receptor for cullin-RING ligases, linking it to ubiquitin-dependent regulation of ion homeostasis.","evidence":"Affinity pull-down, mass spectrometry, proteasomal/neddylation inhibitor experiments, and ubiquitylation assays","pmids":["31614064"],"confidence":"Medium","gaps":["In vivo ubiquitylation of OSR1 by CRL4–WDR6 not demonstrated","Functional impact on ion transport not directly measured","Overlap between WDR6 and WDR3 substrate-receptor roles not delineated"]},{"year":2020,"claim":"In vitro reconstitution of the human FTSJ1–WDR6 complex demonstrated Nm34 methyltransferase activity dependent on prior m1G37 modification, and ribosome profiling showed that loss of this modification selectively impairs UUU codon decoding, connecting WDR6 to translational fidelity and nervous system development.","evidence":"Co-IP, reconstituted in vitro methyltransferase assay, mass spectrometry-based tRNA modification analysis, ribosome profiling in FTSJ1 KO cells","pmids":["32558197"],"confidence":"High","gaps":["WDR6-specific knockout phenotype on tRNA modification and codon decoding not tested","Contribution to neurodevelopment inferred from FTSJ1 mutations, not WDR6 patient data"]},{"year":2023,"claim":"WDR6 was shown to recruit UVRAG to the CUL4A–DDB1–ROC1 complex via its WDxR motif for ubiquitin-dependent degradation, suppressing autophagy-mediated p65 turnover and establishing a WDR6–TNFα positive feedback loop that drives immunosuppression in hepatocellular carcinoma—directly linking WDR6's E3 ligase adaptor function to tumor immune evasion.","evidence":"Co-IP, ubiquitylation assay, CRISPR KO in immune-competent mouse tumor models, ATAC-seq, flow cytometry, peptide competition","pmids":["36947051"],"confidence":"High","gaps":["Applicability beyond HCC not tested","Structural basis of WDR6–UVRAG interface not resolved"]},{"year":2023,"claim":"WDR6 was found to promote hepatic de novo lipogenesis by scaffolding PPP1CB dephosphorylation at Thr316, activating a DNA-PK/USF1 cascade that drives fatty acid synthase transcription during insulin resistance, revealing a metabolic adaptor role distinct from its E3 ligase and tRNA functions.","evidence":"Co-IP, phosphorylation assays, transcriptional reporters, molecular dynamics simulation, mouse hepatic steatosis model, pharmacological inhibition","pmids":["37735236"],"confidence":"High","gaps":["Whether WDR6 acts as a PP1 regulatory subunit or an indirect scaffold not resolved","No genetic loss-of-function in human hepatocytes"]},{"year":2024,"claim":"Systematic mutagenesis of Trm734 residues near the Trm7 active site separated the tRNA-positioning function from complex formation, demonstrating that WDR6's catalytic contribution is specifically in substrate engagement, not in stabilizing the heterodimer.","evidence":"Site-directed mutagenesis, yeast complementation, immunoprecipitation, tRNA modification assay","pmids":["38882062"],"confidence":"Medium","gaps":["Mutagenesis performed in yeast; equivalent mutations not tested in human WDR6","Only tRNAPhe substrate examined"]},{"year":2025,"claim":"Cryo-EM of the FTSJ1–THADA complex confirmed that FTSJ1 uses structurally distinct interfaces to engage THADA (for Nm32) versus WDR6 (for Nm34), establishing the specificity determinants that partition substrate selection between the two modification complexes.","evidence":"Cryo-EM, biochemical binding assays, site-directed mutagenesis","pmids":["40483304"],"confidence":"Medium","gaps":["WDR6-specific structural conclusions are inferred by comparison; no cryo-EM structure of human FTSJ1–WDR6 complex itself","Whether WDR6 and THADA compete or are temporally regulated is unknown"]},{"year":null,"claim":"A high-resolution structure of the human FTSJ1–WDR6–tRNA ternary complex, the molecular mechanism of WDR6-mediated vaccinia virus restriction, and the integration of WDR6's E3 ligase, tRNA modification, and lipogenic scaffolding functions within a unified cellular regulatory framework remain to be determined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No human FTSJ1–WDR6 atomic structure available","Mechanism of antiviral restriction entirely unknown at the molecular level","Whether the three major WDR6 functions (tRNA modification, CRL4 substrate adaptor, PPP1CB scaffold) involve the same or distinct WDR6 pools/domains is unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[5,6,7,8,9,10]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[6,7,10]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[7,8]}],"pathway":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,6,7,8,9,10]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[6,7,10,11]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[5,8]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[8]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,4]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[9]}],"complexes":["FTSJ1–WDR6 tRNA 2′-O-methyltransferase complex","CUL4A–DDB1–ROC1–WDR6 E3 ubiquitin ligase complex"],"partners":["FTSJ1","DDB1","CUL4A","UVRAG","PPP1CB","OSR1","LKB1","IRS4"],"other_free_text":[]},"mechanistic_narrative":"WDR6 is a large WD40-repeat scaffold protein that functions in tRNA modification, ubiquitin-dependent protein degradation, and metabolic signaling. As the obligate partner of the 2′-O-methyltransferase FTSJ1, WDR6 uses its three β-propeller domains to position tRNA substrates for 2′-O-methylation at the anticodon wobble position (Nm34), with residues near the active site critical for tRNA engagement rather than complex integrity [PMID:31586407, PMID:32558197, PMID:38882062]. WDR6 also serves as a substrate receptor in CUL4A–DDB1–ROC1 E3 ubiquitin ligase complexes, targeting UVRAG for degradation to suppress autophagy and amplify TNFα/NF-κB signaling in hepatocellular carcinoma, and binding SPAK/OSR1 kinases in a phosphorylation-dependent manner linked to ion homeostasis [PMID:36947051, PMID:31614064]. Additionally, WDR6 promotes hepatic de novo lipogenesis during insulin resistance by facilitating PPP1CB dephosphorylation and downstream fatty acid synthase transcription, and acts as a host restriction factor limiting vaccinia virus replication independently of SAMD9 [PMID:37735236, PMID:26242627]."},"prefetch_data":{"uniprot":{"accession":"Q9NNW5","full_name":"tRNA (34-2'-O)-methyltransferase regulator WDR6","aliases":["WD repeat-containing protein 6"],"length_aa":1121,"mass_kda":121.7,"function":"Together with methyltransferase FTSJ1, methylates the 2'-O-ribose of nucleotides at position 34 of the tRNA anticodon loop of substrate tRNAs (PubMed:32558197, PubMed:33771871). Required for the correct positioning of the substrate tRNA for methylation (PubMed:32558197). Required to suppress amino acid starvation-induced autophagy (PubMed:22354037). Enhances the STK11/LKB1-induced cell growth suppression activity (PubMed:17216128)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9NNW5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/WDR6","classification":"Not Classified","n_dependent_lines":13,"n_total_lines":1208,"dependency_fraction":0.01076158940397351},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PIK3R1","stoichiometry":4.0},{"gene":"PIK3R2","stoichiometry":4.0},{"gene":"CLNS1A","stoichiometry":0.2},{"gene":"FKBP5","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2},{"gene":"SSB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/WDR6","total_profiled":1310},"omim":[{"mim_id":"606031","title":"WD REPEAT-CONTAINING PROTEIN 6; WDR6","url":"https://www.omim.org/entry/606031"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/WDR6"},"hgnc":{"alias_symbol":["Trm734"],"prev_symbol":[]},"alphafold":{"accession":"Q9NNW5","domains":[{"cath_id":"2.130.10.10","chopping":"979-1020_1027-1121","consensus_level":"medium","plddt":89.7851,"start":979,"end":1121},{"cath_id":"2.40.128","chopping":"17-115","consensus_level":"medium","plddt":87.2729,"start":17,"end":115},{"cath_id":"2.40.10","chopping":"621-690","consensus_level":"medium","plddt":84.4439,"start":621,"end":690}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NNW5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NNW5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NNW5-F1-predicted_aligned_error_v6.png","plddt_mean":85.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=WDR6","jax_strain_url":"https://www.jax.org/strain/search?query=WDR6"},"sequence":{"accession":"Q9NNW5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NNW5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NNW5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NNW5"}},"corpus_meta":[{"pmid":"33523105","id":"PMC_33523105","title":"Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets.","date":"2021","source":"JAMA neurology","url":"https://pubmed.ncbi.nlm.nih.gov/33523105","citation_count":153,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26310293","id":"PMC_26310293","title":"Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1.","date":"2015","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/26310293","citation_count":117,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25625329","id":"PMC_25625329","title":"Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification.","date":"2014","source":"RNA biology","url":"https://pubmed.ncbi.nlm.nih.gov/25625329","citation_count":92,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25404562","id":"PMC_25404562","title":"Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes.","date":"2014","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/25404562","citation_count":65,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26242627","id":"PMC_26242627","title":"Identification of Restriction Factors by Human Genome-Wide RNA Interference Screening of Viral Host Range Mutants Exemplified by Discovery of SAMD9 and WDR6 as Inhibitors of the Vaccinia Virus K1L-C7L- Mutant.","date":"2015","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/26242627","citation_count":63,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"32558197","id":"PMC_32558197","title":"Intellectual disability-associated gene ftsj1 is responsible for 2'-O-methylation of specific tRNAs.","date":"2020","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/32558197","citation_count":48,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19906709","id":"PMC_19906709","title":"Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.","date":"2009","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/19906709","citation_count":45,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17216128","id":"PMC_17216128","title":"Association of LKB1 with a WD-repeat protein WDR6 is implicated in cell growth arrest and p27(Kip1) induction.","date":"2007","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17216128","citation_count":32,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"37735236","id":"PMC_37735236","title":"Upregulation of WDR6 drives hepatic de novo lipogenesis in insulin resistance in mice.","date":"2023","source":"Nature metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/37735236","citation_count":29,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"40360802","id":"PMC_40360802","title":"Genome-wide analyses identify 30 loci associated with obsessive-compulsive disorder.","date":"2025","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40360802","citation_count":29,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30209174","id":"PMC_30209174","title":"Human Host Range Restriction of the Vaccinia Virus C7/K1 Double Deletion Mutant Is Mediated by an Atypical Mode of Translation Inhibition.","date":"2018","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/30209174","citation_count":23,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31586407","id":"PMC_31586407","title":"Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/31586407","citation_count":21,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17720279","id":"PMC_17720279","title":"Identification and characterization of an insulin receptor substrate 4-interacting protein in rat brain: implications for longevity.","date":"2007","source":"Neurobiology of aging","url":"https://pubmed.ncbi.nlm.nih.gov/17720279","citation_count":20,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23968726","id":"PMC_23968726","title":"Global DNA methylation screening of liver in piperonyl butoxide-treated mice in a two-stage hepatocarcinogenesis model.","date":"2013","source":"Toxicology letters","url":"https://pubmed.ncbi.nlm.nih.gov/23968726","citation_count":20,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"36947051","id":"PMC_36947051","title":"Targeting WDxR motif reprograms immune microenvironment and inhibits hepatocellular carcinoma progression.","date":"2023","source":"EMBO molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/36947051","citation_count":16,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"36803885","id":"PMC_36803885","title":"Multiomic prioritisation of risk genes for anorexia nervosa.","date":"2023","source":"Psychological medicine","url":"https://pubmed.ncbi.nlm.nih.gov/36803885","citation_count":16,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"38712091","id":"PMC_38712091","title":"Genome-wide analyses identify 30 loci associated with obsessive-compulsive disorder.","date":"2025","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38712091","citation_count":15,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27692106","id":"PMC_27692106","title":"Whole-exome sequencing analysis in twin sibling males with an anterior cruciate ligament rupture.","date":"2016","source":"Injury","url":"https://pubmed.ncbi.nlm.nih.gov/27692106","citation_count":14,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10903905","id":"PMC_10903905","title":"Molecular cloning, expression analysis, and chromosome mapping of WDR6, a novel human WD-repeat gene.","date":"2000","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/10903905","citation_count":13,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28468585","id":"PMC_28468585","title":"Suppression subtractive hybridization identified differentially expressed genes in colorectal cancer: microRNA-451a as a novel colorectal cancer-related gene.","date":"2017","source":"Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/28468585","citation_count":12,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31614064","id":"PMC_31614064","title":"The Cul4-DDB1-WDR3/WDR6 Complex Binds SPAK and OSR1 Kinases in a Phosphorylation-Dependent Manner.","date":"2019","source":"Chembiochem : a European journal of chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/31614064","citation_count":10,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"35559166","id":"PMC_35559166","title":"Identification of a Trm732 Motif Required for 2'-O-methylation of the tRNA Anticodon Loop by Trm7.","date":"2022","source":"ACS omega","url":"https://pubmed.ncbi.nlm.nih.gov/35559166","citation_count":7,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"38158471","id":"PMC_38158471","title":"PABPN1 functions as a predictive biomarker in colorectal carcinoma.","date":"2023","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/38158471","citation_count":2,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"40483304","id":"PMC_40483304","title":"Structural insights into tRNA recognition of the human FTSJ1-THADA complex.","date":"2025","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/40483304","citation_count":1,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"38882062","id":"PMC_38882062","title":"Identification of Amino Acids in Trm734 Required for 2'-O-Methylation of the tRNAPhe Wobble Residue.","date":"2024","source":"ACS omega","url":"https://pubmed.ncbi.nlm.nih.gov/38882062","citation_count":0,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"41595424","id":"PMC_41595424","title":"Machine Learning Reveals Common Regulatory Mechanisms Mediated by Autophagy-Related Genes in the Development of Inflammatory Bowel Disease and Major Depressive Disorder.","date":"2025","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/41595424","citation_count":0,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16189514","id":"PMC_16189514","title":"Towards a proteome-scale map of the human protein-protein interaction network.","date":"2005","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/16189514","citation_count":2090,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"22658674","id":"PMC_22658674","title":"Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.","date":"2012","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/22658674","citation_count":1718,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12477932","id":"PMC_12477932","title":"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.","date":"2002","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/12477932","citation_count":1479,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"16751776","id":"PMC_16751776","title":"A germline-specific class of small RNAs binds mammalian Piwi proteins.","date":"2006","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/16751776","citation_count":1362,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"28514442","id":"PMC_28514442","title":"Architecture of the human interactome defines protein communities and disease networks.","date":"2017","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/28514442","citation_count":1085,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26496610","id":"PMC_26496610","title":"A human interactome in three quantitative dimensions organized by stoichiometries and abundances.","date":"2015","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/26496610","citation_count":1015,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"25416956","id":"PMC_25416956","title":"A proteome-scale map of the human interactome network.","date":"2014","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/25416956","citation_count":977,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"32296183","id":"PMC_32296183","title":"A reference map of the human binary protein interactome.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/32296183","citation_count":849,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"14702039","id":"PMC_14702039","title":"Complete sequencing and characterization of 21,243 full-length human cDNAs.","date":"2003","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/14702039","citation_count":754,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"33961781","id":"PMC_33961781","title":"Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.","date":"2021","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/33961781","citation_count":705,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"22939629","id":"PMC_22939629","title":"A census of human soluble protein complexes.","date":"2012","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/22939629","citation_count":689,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21873635","id":"PMC_21873635","title":"Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.","date":"2011","source":"Briefings in bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/21873635","citation_count":656,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"29395067","id":"PMC_29395067","title":"High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/29395067","citation_count":580,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"8125298","id":"PMC_8125298","title":"Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides.","date":"1994","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/8125298","citation_count":492,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"25231870","id":"PMC_25231870","title":"Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.","date":"2014","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/25231870","citation_count":445,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"15489334","id":"PMC_15489334","title":"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).","date":"2004","source":"Genome research","url":"https://pubmed.ncbi.nlm.nih.gov/15489334","citation_count":438,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26638075","id":"PMC_26638075","title":"A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface.","date":"2015","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/26638075","citation_count":433,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"35271311","id":"PMC_35271311","title":"OpenCell: Endogenous tagging for the cartography of human cellular organization.","date":"2022","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/35271311","citation_count":432,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26344197","id":"PMC_26344197","title":"Panorama of ancient metazoan macromolecular complexes.","date":"2015","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/26344197","citation_count":407,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"11814058","id":"PMC_11814058","title":"WD-repeat proteins: structure characteristics, biological function, and their involvement in human diseases.","date":"2001","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/11814058","citation_count":404,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"34079125","id":"PMC_34079125","title":"A proximity-dependent biotinylation map of a human cell.","date":"2021","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/34079125","citation_count":339,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"25036637","id":"PMC_25036637","title":"A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.","date":"2014","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/25036637","citation_count":325,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21145461","id":"PMC_21145461","title":"Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics.","date":"2010","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/21145461","citation_count":318,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"29568061","id":"PMC_29568061","title":"An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29568061","citation_count":201,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"32203420","id":"PMC_32203420","title":"Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions.","date":"2020","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/32203420","citation_count":194,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"23022380","id":"PMC_23022380","title":"NOTCH1 nuclear interactome reveals key regulators of its transcriptional activity and oncogenic function.","date":"2012","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/23022380","citation_count":174,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"23602568","id":"PMC_23602568","title":"The protein interaction landscape of the human CMGC kinase group.","date":"2013","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/23602568","citation_count":174,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21706016","id":"PMC_21706016","title":"Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor.","date":"2011","source":"Nature biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/21706016","citation_count":172,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"23455922","id":"PMC_23455922","title":"Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS.","date":"2013","source":"Nature methods","url":"https://pubmed.ncbi.nlm.nih.gov/23455922","citation_count":170,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"32807901","id":"PMC_32807901","title":"UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination.","date":"2020","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/32807901","citation_count":168,"is_preprint":false,"source_track":"gene2pubmed"}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14587,"output_tokens":2574,"usd":0.041185},"stage2":{"model":"claude-opus-4-6","input_tokens":5889,"output_tokens":2507,"usd":0.13818},"total_usd":0.433868,"stage1_batch_id":"msgbatch_01BparvgRZ9S2LMidvaoo86K","stage2_batch_id":"msgbatch_01NkBfv9SVZWthhS7j6mU6G3","note":"batch pricing = 50% of standard","round2_stage1":{"model":"claude-sonnet-4-6","input_tokens":25689,"output_tokens":4473,"usd":0.072081},"round2_rules_fired":"R3","round2_stage2":{"model":"claude-opus-4-6","input_tokens":7318,"output_tokens":3401,"usd":0.182422}},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"WDR6 interacts with LKB1 (STK11) serine/threonine kinase, as identified by yeast two-hybrid screening and co-localization in cytoplasm; coexpression of WDR6 with LKB1 enhances LKB1-mediated inhibition of HeLa cell proliferation, synergizes in G1 cell cycle arrest, and elevates p27(Kip1) expression by increasing LKB1-stimulated p27(Kip1) promoter activity.\",\n      \"method\": \"Yeast two-hybrid, immunofluorescence co-localization, colony formation assay, cell cycle analysis, p27(Kip1) promoter reporter assay\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab, multiple functional readouts but no reciprocal Co-IP or in vitro reconstitution\",\n      \"pmids\": [\"17216128\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"WDR6 interacts with insulin receptor substrate 4 (IRS-4) in rat brain hypothalamus, identified by suppression subtractive hybridization and interaction studies; WDR6 mRNA is enriched in the hypothalamic arcuate nucleus and regulated by caloric restriction and IGF-I/insulin signaling, implicating WDR6 in the insulin/IGF-I signaling pathway.\",\n      \"method\": \"Suppression subtractive hybridization, interaction studies, RT-PCR expression analysis\",\n      \"journal\": \"Neurobiology of aging\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, single interaction method without reciprocal validation\",\n      \"pmids\": [\"17720279\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"WDR6 functions as a host restriction factor that inhibits vaccinia virus K1L-C7L double deletion mutant replication in human HeLa cells; siRNA knockdown or CRISPR/Cas9 knockout of WDR6 enables viral replication, and this restriction acts independently of SAMD9 (no interaction between WDR6 and SAMD9, C7, or K1 proteins detected), suggesting WDR6 acts in the same innate defense pathway but through a distinct mechanism.\",\n      \"method\": \"Genome-wide siRNA screen, CRISPR/Cas9 knockout, immunoprecipitation (negative result for WDR6-SAMD9 interaction), viral replication assay\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (genome-wide siRNA screen, CRISPR KO, replicated with independent siRNAs), replicated in follow-up study\",\n      \"pmids\": [\"26242627\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"WDR6 CRISPR/Cas9 knockout HeLa cells show enhanced (though not wild-type level) replication of vaccinia virus C7/K1 deletion mutant, confirming WDR6 as a restriction factor; SAMD9 levels are not reduced in WDR6 KO cells, confirming independent mechanisms of restriction.\",\n      \"method\": \"CRISPR/Cas9 knockout, viral replication assay, western blot\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined phenotype, single lab but corroborates prior screen\",\n      \"pmids\": [\"30209174\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"WDR6 is a component of the CUL4-DDB1 E3 ubiquitin ligase complex that binds OSR1 kinase in a phosphorylation-dependent manner at its S-motif; this binding is disrupted by osmotic stress-induced S-motif phosphorylation, and OSR1 ubiquitylation is abolished under osmotic stress, linking WDR6-containing CRL4 complex to ion homeostasis regulation.\",\n      \"method\": \"Affinity pulldown, mass spectrometry, proteasomal and neddylation inhibitor assays, ubiquitylation assay\",\n      \"journal\": \"Chembiochem\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — affinity pulldown plus MS identification plus functional ubiquitylation assay, single lab\",\n      \"pmids\": [\"31614064\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"WDR6 physically interacts with FTSJ1 (human tRNA 2'-O-methyltransferase) and is required for its catalytic activity; the reconstituted FTSJ1-WDR6 complex performs 2'-O-methylation at position 34 (Gm34) of specific tRNAs in vitro, with m1G37 as a prerequisite modification, establishing WDR6 as the auxiliary subunit for FTSJ1-mediated Gm34 modification of tRNAs including tRNAPhe.\",\n      \"method\": \"Co-immunoprecipitation, in vitro reconstitution of 2'-O-methyltransferase activity, tRNA modification analysis\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — first in vitro reconstitution of FTSJ1-WDR6 enzymatic activity with substrate specificity and prerequisite modification established\",\n      \"pmids\": [\"32558197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"WDR6 promotes hepatic de novo lipogenesis during insulin resistance by interacting with PPP1CB (PP1β catalytic subunit) to facilitate PPP1CB dephosphorylation at Thr316, which subsequently enhances fatty acid synthase transcription through DNA-dependent protein kinase and upstream stimulatory factor 1; a small compound (XLIX) that inhibits WDR6-PPP1CB interaction reduces de novo lipogenesis.\",\n      \"method\": \"Co-immunoprecipitation, phosphorylation assays, molecular dynamics simulation, transcription reporter assays, mouse liver metabolic models\",\n      \"journal\": \"Nature metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including Co-IP, mechanistic phosphorylation assays, and in vivo mouse models with defined molecular pathway\",\n      \"pmids\": [\"37735236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"WDR6 targets tumor suppressor UVRAG to the CUL4A-DDB1-ROC1 E3 ubiquitin ligase complex via a unique WDxR motif, promoting UVRAG ubiquitin-mediated degradation; this upregulates chromatin accessibility at the TNFα locus by blocking autophagic degradation of p65/NF-κB, elevates intratumoral MDSCs, reduces CD8+ T cell infiltration, and promotes HCC progression; TNFα feeds back to activate WDR6 transcription via NF-κB, forming a WDR6-TNFα loop.\",\n      \"method\": \"Loss-of-function and gain-of-function experiments, orthotopic tumor implantation, ubiquitination assay, chromatin accessibility assay, flow cytometry (immune cell infiltration), co-immunoprecipitation, peptide inhibitor competition\",\n      \"journal\": \"EMBO molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (ubiquitination assay, Co-IP, chromatin assay, in vivo tumor model) from single lab with mechanistic loop validation\",\n      \"pmids\": [\"36947051\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-electron microscopy structure of the human FTSJ1-THADA complex (with and without tRNA substrate) reveals that FTSJ1 interacts with THADA via its C-terminal region in a distinct mode from the FTSJ1-WDR6 complex; tRNA substrate is anchored inside THADA, and key THADA residues for tRNA interaction were validated biochemically, establishing structural basis for complex-dependent substrate specificity (FTSJ1-THADA for Nm32, FTSJ1-WDR6 for Nm34).\",\n      \"method\": \"Cryo-electron microscopy, structural analysis, site-directed mutagenesis, biochemical modification assays\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure with mutagenesis and biochemical validation, distinguishes WDR6 vs. THADA complex architecture\",\n      \"pmids\": [\"40483304\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"WDR6 is a multifunctional WD40-repeat scaffold protein that: (1) serves as the auxiliary subunit of the FTSJ1 tRNA 2'-O-methyltransferase complex, enabling Gm34 modification of specific tRNAs (including tRNAPhe) required for accurate translation; (2) acts as a subunit of the CUL4A-DDB1-ROC1 E3 ubiquitin ligase complex, targeting substrates such as UVRAG for proteasomal degradation to modulate immune microenvironment and autophagy; (3) interacts with PPP1CB to promote hepatic de novo lipogenesis during insulin resistance; (4) functions as an innate immune restriction factor against vaccinia virus; and (5) synergizes with LKB1 to promote p27(Kip1)-mediated cell cycle G1 arrest.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\nI'll classify each paper first, then extract discoveries only from KEEP papers.\n\n**Classification:**\n\n- [1] GWAS/expression association → EXCLUDE (no mechanism)\n- [2] About FTSJ1/TRM7, mentions WDR6 only tangentially → EXCLUDE (not about WDR6 protein mechanism)\n- [3] About Trm7 two-subunit enzymes, WDR6 not mentioned → EXCLUDE\n- [4] About Trm7/Trm732/Trm734 conservation; mentions human FTSJ1/THADA but not WDR6 → EXCLUDE\n- [5] WDR6 identified as vaccinia virus restriction factor by genome-wide siRNA screen + CRISPR KO → KEEP\n- [6] WDR6 identified as interacting protein of FTSJ1; FTSJ1-WDR6 complex reconstituted in vitro → KEEP\n- [7] CASGP bioinformatics; WDR6 mentioned in genomic context only → EXCLUDE\n- [8] WDR6 interaction with LKB1 via yeast two-hybrid; functional studies → KEEP\n- [9] WDR6 promotes hepatic DNL via PPP1CB interaction → KEEP\n- [10] GWAS for OCD → EXCLUDE\n- [11] SAMD9/WDR6 as vaccinia restriction factors; CRISPR KO mechanistic follow-up → KEEP\n- [12] Structure of Trm7-Trm734 (yeast orthologs); WDR6 is human ortholog of Trm734 → KEEP\n- [13] WDR6 interacts with IRS-4 in rat brain → KEEP\n- [14] Epigenetic/expression study → EXCLUDE\n- [15] WDR6 targets UVRAG to CUL4A-DDB1-ROC1 E3 ligase via WDxR motif → KEEP\n- [16] GWAS/expression association → EXCLUDE\n- [17] GWAS preprint → EXCLUDE\n- [18] WES genetic study → EXCLUDE\n- [19] Cloning and characterization of WDR6 gene → KEEP\n- [20] Expression correlation study → EXCLUDE\n- [21] CUL4-DDB1-WDR6 complex binds SPAK/OSR1 → KEEP\n- [22] tRNA modification motif in Trm732 (THADA); about THADA not WDR6 → EXCLUDE\n- [23] PABPN1 biomarker study; WDR6 mentioned as interactor only → EXCLUDE\n- [24] Structure of FTSJ1-THADA complex; mentions FTSJ1-WDR6 structural context → KEEP (partially relevant)\n- [25] Trm734 amino acids for modification; yeast ortholog of WDR6 → KEEP\n- [26] MDD/IBD autophagy; WDR6 mentioned as Mendelian randomization result only → EXCLUDE\n\n**Gene2pubmed curated papers:** Most are large-scale interactome/proteomics studies. None describe specific WDR6 mechanisms beyond detection in screens → EXCLUDE all (no specific WDR6 mechanism extracted).\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"WDR6 was molecularly cloned and characterized as a novel human WD-repeat protein encoding 1121 amino acids with 11 WD-repeat units clustered into two distinct groups separated by a putative transmembrane domain; it was mapped to chromosome 15q21 and found to be ubiquitously expressed in human adult and fetal tissues.\",\n      \"method\": \"cDNA cloning, Northern blot analysis, fluorescence in situ hybridization (FISH)\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct molecular characterization with multiple methods in a single study; foundational cloning paper\",\n      \"pmids\": [\"10903905\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"WDR6 physically interacts with the serine/threonine kinase LKB1 (STK11); co-expression of WDR6 with LKB1 enhances LKB1-mediated inhibition of HeLa cell proliferation and G1 cell cycle arrest, and synergistically induces the CDK inhibitor p27(Kip1) by elevating p27(Kip1) promoter activity, placing WDR6 in the LKB1 tumor suppressor pathway.\",\n      \"method\": \"Yeast two-hybrid screening, immunofluorescence co-localization, colony formation assay, cell cycle analysis, p27(Kip1) promoter-reporter assay\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — yeast two-hybrid plus functional overexpression assays in a single lab; no biochemical reconstitution of direct binding\",\n      \"pmids\": [\"17216128\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"WDR6 mRNA is abundantly expressed in the rat hypothalamic arcuate nucleus and WDR6 protein interacts with insulin receptor substrate 4 (IRS-4) in the rat brain; WDR6 expression is decreased by caloric restriction and in growth hormone-antisense transgenic rats (longevity models), and is increased by IGF-I and insulin treatment in hypothalamic GT1-7 cells, implicating WDR6 in insulin/IGF-I signaling and regulation of longevity.\",\n      \"method\": \"Suppression subtractive hybridization, co-immunoprecipitation, quantitative RT-PCR, in vitro hormone treatment\",\n      \"journal\": \"Neurobiology of aging\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — co-IP interaction plus expression regulation by defined stimuli; single lab, moderate mechanistic follow-up\",\n      \"pmids\": [\"17720279\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"WDR6 was identified as a host restriction factor for vaccinia virus (VACV): genome-wide siRNA knockdown and CRISPR/Cas9 knockout of WDR6 in HeLa cells enabled replication of the VACV K1L-C7L double-deletion mutant. WDR6 knockdown did not reduce SAMD9 levels, and no interaction between WDR6 and SAMD9, C7, or K1 viral proteins was detected, indicating WDR6 acts independently of SAMD9 but possibly in the same innate defense pathway.\",\n      \"method\": \"Genome-wide siRNA screen, CRISPR/Cas9 knockout, viral replication assays, immunoprecipitation\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide screen validated by CRISPR KO with multiple siRNAs and orthogonal immunoprecipitation; replicated in follow-up study (PMID:30209174)\",\n      \"pmids\": [\"26242627\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CRISPR/Cas9 knockout of WDR6 in HeLa cells enhanced replication of the VACV C7/K1 double-deletion mutant but did not restore replication to wild-type levels (unlike SAMD9 KO), and SAMD9 protein levels were not depleted in WDR6 KO cells, confirming that WDR6 acts as an independent but less dominant restriction factor compared to SAMD9.\",\n      \"method\": \"CRISPR/Cas9 knockout, viral replication assay, western blot\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean CRISPR KO with defined viral replication phenotype; single lab but orthogonal to PMID:26242627\",\n      \"pmids\": [\"30209174\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"WDR6 (the human ortholog of yeast Trm734) forms part of the Cul4-DDB1 E3 ubiquitin ligase complex and binds OSR1 kinase in a phosphorylation-dependent manner: binding to the OSR1 S-motif is compromised when the S-motif serine is phosphorylated under osmotic stress, and this correlates with protection of OSR1 from ubiquitylation, linking the CRL4-WDR6/WDR3 complex to ion homeostasis.\",\n      \"method\": \"Affinity pull-down, mass spectrometry, proteasomal and neddylation inhibitor experiments, ubiquitylation assays\",\n      \"journal\": \"Chembiochem\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — AP-MS identification plus functional ubiquitylation assays with pharmacological inhibitors; single lab\",\n      \"pmids\": [\"31614064\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The crystal structure of the yeast Trm7-Trm734 complex (the ortholog of human FTSJ1-WDR6) was solved in apo and SAM-bound forms; Trm734 contains three WD40 β-propeller domains (BPA, BPB, BPC) forming a V-shaped cleft that docks to the C-terminal region of Trm7, and the D-arm of substrate tRNA contacts the positively charged surface of BPB to position the anticodon loop near the Trm7 catalytic pocket, demonstrating that Trm734/WDR6 is required for correct tRNA positioning for 2′-O-methylation at position 34.\",\n      \"method\": \"X-ray crystallography, small-angle X-ray scattering (SAXS), in vitro methyltransferase assay, site-directed mutagenesis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with functional biochemical validation and mutagenesis; strong mechanistic evidence for the WDR6 ortholog\",\n      \"pmids\": [\"31586407\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"WDR6 was identified as a direct interacting protein of FTSJ1 (human tRNA 2′-O-methyltransferase); the reconstituted FTSJ1-WDR6 complex performs 2′-O-methylation at position 34 of specific tRNAs in vitro, with m1G37 as a prerequisite modification. In vivo, modifications at positions 32, 34, and 37 occur in a hierarchical, interdependent order, and loss of FTSJ1 reduces translation efficiency of UUU (but not UUC) codons decoded by tRNA(Phe)(GAA), implicating FTSJ1-WDR6 in efficient decoding of UUU codons and nervous system development.\",\n      \"method\": \"Co-immunoprecipitation, in vitro reconstitution of methyltransferase activity, mass spectrometry-based tRNA modification analysis, ribosome profiling/codon usage analysis, FTSJ1 knockout cells\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — first in vitro reconstitution of FTSJ1-WDR6 enzymatic activity with multiple orthogonal methods including KO cellular phenotype\",\n      \"pmids\": [\"32558197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"WDR6 targets the tumor suppressor UVRAG to the CUL4A-DDB1-ROC1 E3 ubiquitin ligase complex through a unique WDxR motif, promoting UVRAG ubiquitin-dependent degradation; this blocks autophagic degradation of p65/NF-κB, increases chromatin accessibility at the TNFα locus, elevates intratumoral myeloid-derived suppressor cells (MDSCs), and reduces CD8+ T cell infiltration in HCC. TNFα in turn activates NF-κB to transcriptionally upregulate WDR6, establishing a WDR6-TNFα positive feedback loop. A WDxR-like peptide disrupts the WDR6-UVRAG interaction and enhances anti-PD-L1 efficacy.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitylation assay, CRISPR KO in vivo tumor models (immune-competent mice), chromatin accessibility assay (ATAC-seq), flow cytometry of immune infiltrates, peptide competition assay\",\n      \"journal\": \"EMBO molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal biochemical and in vivo methods; mechanism validated in immune-competent tumor models with functional immune readouts\",\n      \"pmids\": [\"36947051\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"WDR6 promotes hepatic de novo lipogenesis (DNL) during insulin resistance by interacting with PPP1CB (the beta-type catalytic subunit of PP1), facilitating PPP1CB dephosphorylation at Thr316, which subsequently enhances fatty acid synthase transcription through DNA-dependent protein kinase (DNA-PK) and upstream stimulatory factor 1 (USF1). Molecular dynamics simulation identified a small molecule (XLIX) that inhibits WDR6-PPP1CB interaction and reduces DNL in insulin-resistant states.\",\n      \"method\": \"Co-immunoprecipitation, phosphorylation assays, transcriptional reporter assays, molecular dynamics simulation, mouse in vivo hepatic steatosis model, pharmacological inhibition\",\n      \"journal\": \"Nature metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple biochemical methods plus in vivo validation in mouse models and mechanistic pharmacological intervention; single lab but strong evidence\",\n      \"pmids\": [\"37735236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Amino acid variants in Trm734 (yeast ortholog of WDR6) near the Trm7 active site, identified by systematic mutagenesis, abolish 2′-O-methylation of tRNA(Phe) at position 34 without disrupting Trm7-Trm734 protein-protein interaction, indicating these residues are critical for tRNA substrate engagement rather than complex formation, and that WDR6's auxiliary role is specifically in tRNA binding/positioning.\",\n      \"method\": \"Site-directed mutagenesis, in vivo yeast complementation, immunoprecipitation, tRNA modification assay\",\n      \"journal\": \"ACS omega\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mutagenesis with functional tRNA modification readout in yeast ortholog; mechanistic but indirect (yeast model)\",\n      \"pmids\": [\"38882062\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structure of the human FTSJ1-THADA complex reveals that FTSJ1 binds THADA via its C-terminal region with a unique interaction mode distinct from the FTSJ1-WDR6 complex, establishing that FTSJ1 uses different structural interfaces to associate with THADA (for Nm32 modification) versus WDR6 (for Nm34 modification), and confirming that WDR6 specifically partners with FTSJ1 for 2′-O-methylation at position 34.\",\n      \"method\": \"Cryo-electron microscopy, biochemical binding assays, site-directed mutagenesis\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 structure — but WDR6-specific conclusions are comparative/indirect; primarily characterizes FTSJ1-THADA\",\n      \"pmids\": [\"40483304\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"WDR6 is a multi-functional WD40-repeat scaffold protein that: (1) partners with FTSJ1 to form a 2′-O-methyltransferase complex that modifies tRNA at position 34 (Nm34), with WDR6 providing the tRNA-positioning function via its β-propeller domains; (2) acts as a substrate receptor in CUL4A-DDB1-ROC1 E3 ubiquitin ligase complexes, targeting UVRAG for degradation to suppress autophagy and promote TNFα-driven immunosuppression in HCC, and binding SPAK/OSR1 kinases in a phosphorylation-dependent manner linked to ion homeostasis; (3) promotes hepatic de novo lipogenesis during insulin resistance by interacting with PPP1CB to regulate its dephosphorylation and downstream fatty acid synthase transcription; (4) functions as an innate immune restriction factor limiting vaccinia virus replication independently of SAMD9; and (5) synergizes with LKB1 to induce p27(Kip1)-dependent cell cycle arrest and interacts with IRS-4 in hypothalamic insulin/IGF-I signaling.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"WDR6 is a WD40-repeat scaffold protein that participates in tRNA modification, ubiquitin-dependent protein degradation, metabolic signaling, and innate antiviral defense. As the obligate auxiliary subunit of the FTSJ1 tRNA 2'-O-methyltransferase, WDR6 enables Gm34 modification of specific tRNAs (including tRNAPhe), with the FTSJ1–WDR6 complex exhibiting distinct substrate specificity from the FTSJ1–THADA complex that catalyzes Nm32 [PMID:32558197, PMID:40483304]. WDR6 also serves as a substrate receptor within the CUL4A–DDB1–ROC1 E3 ubiquitin ligase complex, recruiting targets such as UVRAG for proteasomal degradation—thereby suppressing autophagy-mediated p65/NF-κB clearance and promoting TNFα-driven immunosuppression in hepatocellular carcinoma—and engaging OSR1 kinase in a phosphorylation-dependent manner to regulate ion homeostasis [PMID:36947051, PMID:31614064]. Additionally, WDR6 promotes hepatic de novo lipogenesis during insulin resistance by facilitating PPP1CB dephosphorylation at Thr316, linking it to fatty acid synthase transcriptional control through DNA-PKcs and USF1 [PMID:37735236].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Establishing that WDR6 has a growth-suppressive role: coexpression with LKB1 synergistically enhanced G1 arrest and p27(Kip1) expression, positioning WDR6 as a modulator of cell cycle control through the LKB1 tumor-suppressor pathway.\",\n      \"evidence\": \"Yeast two-hybrid, colony formation assay, cell cycle analysis, and p27(Kip1) promoter reporter in HeLa cells\",\n      \"pmids\": [\"17216128\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No reciprocal Co-IP or in vitro reconstitution of the WDR6–LKB1 interaction\", \"Mechanism by which WDR6 augments LKB1-dependent p27(Kip1) promoter activity is undefined\", \"Not tested outside HeLa cells\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"A genome-wide siRNA screen revealed WDR6 as an innate immune restriction factor against vaccinia virus, acting independently of SAMD9 in the same defense pathway.\",\n      \"evidence\": \"Genome-wide siRNA screen, CRISPR/Cas9 knockout, and immunoprecipitation in HeLa cells with vaccinia virus K1L-C7L deletion mutant\",\n      \"pmids\": [\"26242627\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism of antiviral restriction by WDR6 remains unknown\", \"Whether WDR6 restricts other poxviruses or unrelated viruses untested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Independent CRISPR knockout confirmed WDR6 as a vaccinia restriction factor and demonstrated that SAMD9 protein levels are unaffected in WDR6 KO cells, definitively establishing independent mechanisms.\",\n      \"evidence\": \"CRISPR/Cas9 knockout, viral replication assay, and western blot in HeLa cells\",\n      \"pmids\": [\"30209174\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream effector pathway of WDR6 antiviral activity still uncharacterized\", \"Partial (not complete) rescue of viral replication in KO cells suggests redundant restriction factors\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"WDR6 was identified as a DDB1-CUL4 E3 ligase substrate receptor that targets OSR1 kinase for ubiquitylation in a phosphorylation-dependent manner, revealing WDR6's role in regulated protein degradation and ion homeostasis.\",\n      \"evidence\": \"Affinity pulldown, mass spectrometry, proteasomal and neddylation inhibitor assays, and ubiquitylation assay\",\n      \"pmids\": [\"31614064\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological consequence of OSR1 degradation not demonstrated in animal models\", \"WDxR motif usage by WDR6 not structurally characterized at this time\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"In vitro reconstitution demonstrated that WDR6 is the essential auxiliary subunit of FTSJ1 for 2'-O-methylation at position 34 (Gm34) of tRNAs, requiring prior m1G37 modification—establishing a tRNA modification cascade and a non-degradative molecular function for WDR6.\",\n      \"evidence\": \"Co-immunoprecipitation, in vitro reconstitution of methyltransferase activity, and tRNA modification analysis\",\n      \"pmids\": [\"32558197\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural information on the FTSJ1–WDR6 complex\", \"Full repertoire of tRNA substrates beyond tRNAPhe not comprehensively mapped\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Two studies expanded WDR6's role in metabolic and immune regulation: WDR6 promotes hepatic de novo lipogenesis by facilitating PPP1CB Thr316 dephosphorylation during insulin resistance, and WDR6 drives hepatocellular carcinoma progression by targeting UVRAG for CUL4A–DDB1-mediated ubiquitin degradation, which blocks autophagic clearance of p65/NF-κB and establishes a pro-tumorigenic TNFα–WDR6 positive feedback loop.\",\n      \"evidence\": \"Co-IP, phosphorylation assays, mouse liver metabolic models, orthotopic tumor implantation, ubiquitination assays, chromatin accessibility assays, flow cytometry of immune infiltrates\",\n      \"pmids\": [\"37735236\", \"36947051\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the CRL4-WDR6 E3 ligase has additional substrates beyond UVRAG and OSR1 is unknown\", \"Relative contribution of WDR6-PPP1CB interaction versus WDR6 E3 ligase activity to metabolic phenotypes is unclear\", \"XLIX compound specificity and pharmacokinetics not fully characterized\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Cryo-EM structures of FTSJ1–THADA (with and without tRNA) established the structural basis for how partner choice (WDR6 vs. THADA) dictates FTSJ1 substrate specificity—FTSJ1–WDR6 for Nm34 and FTSJ1–THADA for Nm32—resolving how a single methyltransferase achieves position-specific tRNA modification through distinct auxiliary subunits.\",\n      \"evidence\": \"Cryo-EM, site-directed mutagenesis, and biochemical modification assays\",\n      \"pmids\": [\"40483304\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No cryo-EM structure of the FTSJ1–WDR6 complex itself has been solved\", \"Structural determinants within WDR6 that position the tRNA anticodon loop for Nm34 modification remain unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include the molecular mechanism of WDR6's antiviral restriction activity, the structure of the FTSJ1–WDR6 complex, the full spectrum of CRL4-WDR6 E3 ligase substrates, and how WDR6's distinct functions (tRNA modification, ubiquitin ligase, lipogenesis regulation) are coordinated or compartmentalized in cells.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of FTSJ1–WDR6\", \"Antiviral mechanism remains molecularly undefined\", \"Integration of diverse WDR6 functions into a unified cell-biological model is lacking\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 4, 5, 6, 7]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [5, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [5, 8]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4, 7]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [2, 3, 7]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\n      \"FTSJ1-WDR6 tRNA methyltransferase complex\",\n      \"CUL4A-DDB1-ROC1-WDR6 E3 ubiquitin ligase complex\"\n    ],\n    \"partners\": [\n      \"FTSJ1\",\n      \"DDB1\",\n      \"CUL4A\",\n      \"PPP1CB\",\n      \"UVRAG\",\n      \"LKB1\",\n      \"OSR1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"WDR6 is a large WD40-repeat scaffold protein that functions in tRNA modification, ubiquitin-dependent protein degradation, and metabolic signaling. As the obligate partner of the 2′-O-methyltransferase FTSJ1, WDR6 uses its three β-propeller domains to position tRNA substrates for 2′-O-methylation at the anticodon wobble position (Nm34), with residues near the active site critical for tRNA engagement rather than complex integrity [PMID:31586407, PMID:32558197, PMID:38882062]. WDR6 also serves as a substrate receptor in CUL4A–DDB1–ROC1 E3 ubiquitin ligase complexes, targeting UVRAG for degradation to suppress autophagy and amplify TNFα/NF-κB signaling in hepatocellular carcinoma, and binding SPAK/OSR1 kinases in a phosphorylation-dependent manner linked to ion homeostasis [PMID:36947051, PMID:31614064]. Additionally, WDR6 promotes hepatic de novo lipogenesis during insulin resistance by facilitating PPP1CB dephosphorylation and downstream fatty acid synthase transcription, and acts as a host restriction factor limiting vaccinia virus replication independently of SAMD9 [PMID:37735236, PMID:26242627].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Molecular cloning of WDR6 established it as a ubiquitously expressed, large WD-repeat protein with 11 WD-repeat units arranged in two clusters, providing the foundational gene structure for all subsequent functional studies.\",\n      \"evidence\": \"cDNA cloning, Northern blot, and FISH mapping in human tissues\",\n      \"pmids\": [\"10903905\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional activity or binding partner identified\",\n        \"Predicted transmembrane domain never validated experimentally\"\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identification of WDR6 as an interactor of both LKB1 (enhancing p27Kip1-dependent cell cycle arrest) and IRS-4 in hypothalamic neurons (regulated by insulin/IGF-I) placed WDR6 at the intersection of growth-suppressive and metabolic signaling pathways, though the direct biochemical mechanisms remained undefined.\",\n      \"evidence\": \"Yeast two-hybrid, co-IP, cell cycle analysis and promoter-reporter assays (LKB1); suppression subtractive hybridization and co-IP in rat brain (IRS-4)\",\n      \"pmids\": [\"17216128\", \"17720279\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"LKB1–WDR6 interaction based on yeast two-hybrid without biochemical reconstitution of direct binding\",\n        \"Downstream effectors linking WDR6–IRS-4 to metabolic outputs not identified\",\n        \"No in vivo loss-of-function data for either interaction\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"A genome-wide siRNA screen identified WDR6 as a host restriction factor for vaccinia virus, acting independently of the known restriction factor SAMD9, thereby revealing an unexpected innate immune function for a WD-repeat scaffold protein.\",\n      \"evidence\": \"Genome-wide siRNA screen and CRISPR/Cas9 knockout with viral replication assays in HeLa cells\",\n      \"pmids\": [\"26242627\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular mechanism of viral restriction unknown—no viral or host target identified\",\n        \"Restriction phenotype weaker than SAMD9 KO; biological significance unclear\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Independent CRISPR knockout confirmed WDR6 as a vaccinia restriction factor that is less dominant than SAMD9 and does not regulate SAMD9 levels, solidifying the existence of a parallel antiviral pathway.\",\n      \"evidence\": \"CRISPR/Cas9 knockout, viral replication assay, western blot in HeLa cells\",\n      \"pmids\": [\"30209174\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which WDR6 restricts virus still unknown\",\n        \"Not tested in primary immune cells or in vivo infection models\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Crystal structures of the yeast Trm7–Trm734 complex revealed that WDR6's ortholog forms a three-β-propeller V-shaped cleft that docks the catalytic methyltransferase and positions the tRNA D-arm for 2′-O-methylation at position 34, providing the first atomic-resolution mechanism for WDR6's role in tRNA modification.\",\n      \"evidence\": \"X-ray crystallography, SAXS, in vitro methyltransferase assay, and site-directed mutagenesis of yeast Trm7–Trm734\",\n      \"pmids\": [\"31586407\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structure determined for yeast ortholog; human FTSJ1–WDR6 structure not yet available\",\n        \"Only tRNAPhe substrate modeled; positioning of other tRNA substrates untested\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Discovery that WDR6 integrates into CUL4–DDB1 E3 ligase complexes and binds OSR1 kinase in a phosphorylation-dependent manner established WDR6 as a bona fide substrate receptor for cullin-RING ligases, linking it to ubiquitin-dependent regulation of ion homeostasis.\",\n      \"evidence\": \"Affinity pull-down, mass spectrometry, proteasomal/neddylation inhibitor experiments, and ubiquitylation assays\",\n      \"pmids\": [\"31614064\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"In vivo ubiquitylation of OSR1 by CRL4–WDR6 not demonstrated\",\n        \"Functional impact on ion transport not directly measured\",\n        \"Overlap between WDR6 and WDR3 substrate-receptor roles not delineated\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"In vitro reconstitution of the human FTSJ1–WDR6 complex demonstrated Nm34 methyltransferase activity dependent on prior m1G37 modification, and ribosome profiling showed that loss of this modification selectively impairs UUU codon decoding, connecting WDR6 to translational fidelity and nervous system development.\",\n      \"evidence\": \"Co-IP, reconstituted in vitro methyltransferase assay, mass spectrometry-based tRNA modification analysis, ribosome profiling in FTSJ1 KO cells\",\n      \"pmids\": [\"32558197\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"WDR6-specific knockout phenotype on tRNA modification and codon decoding not tested\",\n        \"Contribution to neurodevelopment inferred from FTSJ1 mutations, not WDR6 patient data\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"WDR6 was shown to recruit UVRAG to the CUL4A–DDB1–ROC1 complex via its WDxR motif for ubiquitin-dependent degradation, suppressing autophagy-mediated p65 turnover and establishing a WDR6–TNFα positive feedback loop that drives immunosuppression in hepatocellular carcinoma—directly linking WDR6's E3 ligase adaptor function to tumor immune evasion.\",\n      \"evidence\": \"Co-IP, ubiquitylation assay, CRISPR KO in immune-competent mouse tumor models, ATAC-seq, flow cytometry, peptide competition\",\n      \"pmids\": [\"36947051\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Applicability beyond HCC not tested\",\n        \"Structural basis of WDR6–UVRAG interface not resolved\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"WDR6 was found to promote hepatic de novo lipogenesis by scaffolding PPP1CB dephosphorylation at Thr316, activating a DNA-PK/USF1 cascade that drives fatty acid synthase transcription during insulin resistance, revealing a metabolic adaptor role distinct from its E3 ligase and tRNA functions.\",\n      \"evidence\": \"Co-IP, phosphorylation assays, transcriptional reporters, molecular dynamics simulation, mouse hepatic steatosis model, pharmacological inhibition\",\n      \"pmids\": [\"37735236\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether WDR6 acts as a PP1 regulatory subunit or an indirect scaffold not resolved\",\n        \"No genetic loss-of-function in human hepatocytes\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Systematic mutagenesis of Trm734 residues near the Trm7 active site separated the tRNA-positioning function from complex formation, demonstrating that WDR6's catalytic contribution is specifically in substrate engagement, not in stabilizing the heterodimer.\",\n      \"evidence\": \"Site-directed mutagenesis, yeast complementation, immunoprecipitation, tRNA modification assay\",\n      \"pmids\": [\"38882062\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mutagenesis performed in yeast; equivalent mutations not tested in human WDR6\",\n        \"Only tRNAPhe substrate examined\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Cryo-EM of the FTSJ1–THADA complex confirmed that FTSJ1 uses structurally distinct interfaces to engage THADA (for Nm32) versus WDR6 (for Nm34), establishing the specificity determinants that partition substrate selection between the two modification complexes.\",\n      \"evidence\": \"Cryo-EM, biochemical binding assays, site-directed mutagenesis\",\n      \"pmids\": [\"40483304\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"WDR6-specific structural conclusions are inferred by comparison; no cryo-EM structure of human FTSJ1–WDR6 complex itself\",\n        \"Whether WDR6 and THADA compete or are temporally regulated is unknown\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"A high-resolution structure of the human FTSJ1–WDR6–tRNA ternary complex, the molecular mechanism of WDR6-mediated vaccinia virus restriction, and the integration of WDR6's E3 ligase, tRNA modification, and lipogenic scaffolding functions within a unified cellular regulatory framework remain to be determined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No human FTSJ1–WDR6 atomic structure available\",\n        \"Mechanism of antiviral restriction entirely unknown at the molecular level\",\n        \"Whether the three major WDR6 functions (tRNA modification, CRL4 substrate adaptor, PPP1CB scaffold) involve the same or distinct WDR6 pools/domains is unresolved\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [5, 6, 7, 8, 9, 10]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [6, 7, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [7, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5, 6, 7, 8, 9, 10]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [6, 7, 10, 11]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [5, 8]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"complexes\": [\n      \"FTSJ1–WDR6 tRNA 2′-O-methyltransferase complex\",\n      \"CUL4A–DDB1–ROC1–WDR6 E3 ubiquitin ligase complex\"\n    ],\n    \"partners\": [\n      \"FTSJ1\",\n      \"DDB1\",\n      \"CUL4A\",\n      \"UVRAG\",\n      \"PPP1CB\",\n      \"OSR1\",\n      \"LKB1\",\n      \"IRS4\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}