Affinage

WDR6

tRNA (34-2'-O)-methyltransferase regulator WDR6 · UniProt Q9NNW5

Round 2 corrected
Length
1121 aa
Mass
121.7 kDa
Annotated
2026-04-28
56 papers in source corpus 12 papers cited in narrative 12 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

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).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 2000 Medium

    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

    PMID:10903905

    Open questions at the time
    • No functional activity or binding partner identified
    • Predicted transmembrane domain never validated experimentally
  2. 2007 Medium

    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)

    PMID:17216128 PMID:17720279

    Open questions at the time
    • 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
  3. 2015 High

    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

    PMID:26242627

    Open questions at the time
    • Molecular mechanism of viral restriction unknown—no viral or host target identified
    • Restriction phenotype weaker than SAMD9 KO; biological significance unclear
  4. 2018 Medium

    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

    PMID:30209174

    Open questions at the time
    • Mechanism by which WDR6 restricts virus still unknown
    • Not tested in primary immune cells or in vivo infection models
  5. 2019 High

    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

    PMID:31586407

    Open questions at the time
    • Structure determined for yeast ortholog; human FTSJ1–WDR6 structure not yet available
    • Only tRNAPhe substrate modeled; positioning of other tRNA substrates untested
  6. 2019 Medium

    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

    PMID:31614064

    Open questions at the time
    • 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
  7. 2020 High

    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

    PMID:32558197

    Open questions at the time
    • WDR6-specific knockout phenotype on tRNA modification and codon decoding not tested
    • Contribution to neurodevelopment inferred from FTSJ1 mutations, not WDR6 patient data
  8. 2023 High

    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

    PMID:36947051

    Open questions at the time
    • Applicability beyond HCC not tested
    • Structural basis of WDR6–UVRAG interface not resolved
  9. 2023 High

    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

    PMID:37735236

    Open questions at the time
    • Whether WDR6 acts as a PP1 regulatory subunit or an indirect scaffold not resolved
    • No genetic loss-of-function in human hepatocytes
  10. 2024 Medium

    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

    PMID:38882062

    Open questions at the time
    • Mutagenesis performed in yeast; equivalent mutations not tested in human WDR6
    • Only tRNAPhe substrate examined
  11. 2025 Medium

    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

    PMID:40483304

    Open questions at the time
    • 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

Open questions

Synthesis pass · forward-looking unresolved questions
  • 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.
  • 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

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 6 GO:0003723 RNA binding 3
Localization
GO:0005829 cytosol 2 GO:0005634 nucleus 1
Pathway
GO:0098772 molecular function regulator activity 6 R-HSA-8953854 Metabolism of RNA 4 R-HSA-168256 Immune System 2 R-HSA-392499 Metabolism of proteins 2 R-HSA-1430728 Metabolism 1 R-HSA-9612973 Autophagy 1
Partners
CUL4ADDB1FTSJ1IRS4LKB1OSR1PPP1CBUVRAG
Complex memberships
CUL4A–DDB1–ROC1–WDR6 E3 ubiquitin ligase complexFTSJ1–WDR6 tRNA 2′-O-methyltransferase complex

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 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. cDNA cloning, Northern blot analysis, fluorescence in situ hybridization (FISH) Biochemical and biophysical research communications Medium 10903905
2007 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. Yeast two-hybrid screening, immunofluorescence co-localization, colony formation assay, cell cycle analysis, p27(Kip1) promoter-reporter assay Molecular and cellular biochemistry Medium 17216128
2007 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. Suppression subtractive hybridization, co-immunoprecipitation, quantitative RT-PCR, in vitro hormone treatment Neurobiology of aging Medium 17720279
2015 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. Genome-wide siRNA screen, CRISPR/Cas9 knockout, viral replication assays, immunoprecipitation mBio High 26242627
2018 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. CRISPR/Cas9 knockout, viral replication assay, western blot Journal of virology Medium 30209174
2019 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. Affinity pull-down, mass spectrometry, proteasomal and neddylation inhibitor experiments, ubiquitylation assays Chembiochem Medium 31614064
2019 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. X-ray crystallography, small-angle X-ray scattering (SAXS), in vitro methyltransferase assay, site-directed mutagenesis Nucleic acids research High 31586407
2020 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. Co-immunoprecipitation, in vitro reconstitution of methyltransferase activity, mass spectrometry-based tRNA modification analysis, ribosome profiling/codon usage analysis, FTSJ1 knockout cells EMBO reports High 32558197
2023 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. 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 EMBO molecular medicine High 36947051
2023 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. Co-immunoprecipitation, phosphorylation assays, transcriptional reporter assays, molecular dynamics simulation, mouse in vivo hepatic steatosis model, pharmacological inhibition Nature metabolism High 37735236
2024 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. Site-directed mutagenesis, in vivo yeast complementation, immunoprecipitation, tRNA modification assay ACS omega Medium 38882062
2025 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. Cryo-electron microscopy, biochemical binding assays, site-directed mutagenesis Communications biology Medium 40483304

Source papers

Stage 0 corpus · 56 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2005 Towards a proteome-scale map of the human protein-protein interaction network. Nature 2090 16189514
2012 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 1718 22658674
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2006 A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 1362 16751776
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2014 A proteome-scale map of the human interactome network. Cell 977 25416956
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2018 High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Molecular cell 580 29395067
1994 Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 492 8125298
2014 Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Nature 445 25231870
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2015 A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. Cell 433 26638075
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2001 WD-repeat proteins: structure characteristics, biological function, and their involvement in human diseases. Cellular and molecular life sciences : CMLS 404 11814058
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2014 A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. Cell 325 25036637
2010 Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell 318 21145461
2018 An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nature communications 201 29568061
2020 Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. Nature cell biology 194 32203420
2013 The protein interaction landscape of the human CMGC kinase group. Cell reports 174 23602568
2012 NOTCH1 nuclear interactome reveals key regulators of its transcriptional activity and oncogenic function. Molecular cell 174 23022380
2011 Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor. Nature biotechnology 172 21706016
2013 Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. Nature methods 170 23455922
2020 UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Nature cell biology 168 32807901
2021 Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets. JAMA neurology 153 33523105
2015 Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1. Human mutation 117 26310293
2014 Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification. RNA biology 92 25625329
2014 Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes. RNA (New York, N.Y.) 65 25404562
2015 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. mBio 63 26242627
2020 Intellectual disability-associated gene ftsj1 is responsible for 2'-O-methylation of specific tRNAs. EMBO reports 48 32558197
2009 Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns. Nucleic acids research 45 19906709
2007 Association of LKB1 with a WD-repeat protein WDR6 is implicated in cell growth arrest and p27(Kip1) induction. Molecular and cellular biochemistry 32 17216128
2025 Genome-wide analyses identify 30 loci associated with obsessive-compulsive disorder. Nature genetics 29 40360802
2023 Upregulation of WDR6 drives hepatic de novo lipogenesis in insulin resistance in mice. Nature metabolism 29 37735236
2018 Human Host Range Restriction of the Vaccinia Virus C7/K1 Double Deletion Mutant Is Mediated by an Atypical Mode of Translation Inhibition. Journal of virology 23 30209174
2019 Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition. Nucleic acids research 21 31586407
2013 Global DNA methylation screening of liver in piperonyl butoxide-treated mice in a two-stage hepatocarcinogenesis model. Toxicology letters 20 23968726
2007 Identification and characterization of an insulin receptor substrate 4-interacting protein in rat brain: implications for longevity. Neurobiology of aging 20 17720279
2023 Multiomic prioritisation of risk genes for anorexia nervosa. Psychological medicine 16 36803885
2023 Targeting WDxR motif reprograms immune microenvironment and inhibits hepatocellular carcinoma progression. EMBO molecular medicine 16 36947051
2025 Genome-wide analyses identify 30 loci associated with obsessive-compulsive disorder. medRxiv : the preprint server for health sciences 15 38712091
2016 Whole-exome sequencing analysis in twin sibling males with an anterior cruciate ligament rupture. Injury 14 27692106
2000 Molecular cloning, expression analysis, and chromosome mapping of WDR6, a novel human WD-repeat gene. Biochemical and biophysical research communications 13 10903905
2017 Suppression subtractive hybridization identified differentially expressed genes in colorectal cancer: microRNA-451a as a novel colorectal cancer-related gene. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 12 28468585
2019 The Cul4-DDB1-WDR3/WDR6 Complex Binds SPAK and OSR1 Kinases in a Phosphorylation-Dependent Manner. Chembiochem : a European journal of chemical biology 10 31614064
2022 Identification of a Trm732 Motif Required for 2'-O-methylation of the tRNA Anticodon Loop by Trm7. ACS omega 7 35559166
2023 PABPN1 functions as a predictive biomarker in colorectal carcinoma. Molecular biology reports 2 38158471
2025 Structural insights into tRNA recognition of the human FTSJ1-THADA complex. Communications biology 1 40483304
2025 Machine Learning Reveals Common Regulatory Mechanisms Mediated by Autophagy-Related Genes in the Development of Inflammatory Bowel Disease and Major Depressive Disorder. Genes 0 41595424
2024 Identification of Amino Acids in Trm734 Required for 2'-O-Methylation of the tRNAPhe Wobble Residue. ACS omega 0 38882062