Affinage

WDR35

WD repeat-containing protein 35 · UniProt Q9P2L0

Length
1181 aa
Mass
133.5 kDa
Annotated
2026-06-11
24 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

WDR35 (IFT121) is a component of the retrograde intraflagellar transport (IFT-A) complex that governs the assembly and protein composition of the primary cilium (PMID:17021254, PMID:21473986). Across C. elegans, mouse, and human cells, WDR35 localizes to the ciliary base and centrosomes and is essential for ciliogenesis: its loss produces shortened or absent cilia and accumulation of core IFT machinery, the signature of disrupted retrograde transport (PMID:17021254, PMID:21473986). Structural modeling and in situ cryo-EM established that WDR35, like other IFT-A subunits, shares deep homology with α and β' COPI coatomer subunits and functions as a membrane coat protein—binding lipids directly and delivering vesicle-borne membrane cargo required for cilium elongation (PMID:21473986, PMID:34734804). Beyond bulk membrane delivery, WDR35 is specifically required for ciliary entry of the Hedgehog signaling proteins EVC, EVC2, and Smoothened; in its absence these cargoes fail to enter the cilium even though general retrograde transport is intact in retrograde-motor mutants, demonstrating a cargo-selective import role that supports Hedgehog pathway output during embryogenesis (PMID:25908617). Through this control of ciliary Hedgehog signaling WDR35 acts upstream of Gli2 to promote osteogenic differentiation (PMID:30790652), and human WDR35 mutations cause skeletal ciliopathies of the short-rib polydactyly/Sensenbrenner spectrum (PMID:21473986, PMID:25908617).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2006 High

    Established that the WDR35 ortholog is a ciliary IFT protein associated with the retrograde IFT-A subcomplex, answering whether it acts in transport machinery rather than as a static structural protein.

    Evidence C. elegans genetics, fluorescence localization, and epistasis with bbs and che-11 IFT mutants

    PMID:17021254

    Open questions at the time
    • Did not define molecular cargo or binding partners
    • Mechanism of retrograde specificity not resolved
  2. 2011 High

    Demonstrated WDR35 is required for ciliogenesis in mammals and linked it to Hedgehog-dependent development and human skeletal ciliopathy, while structural modeling first hinted at a coatomer-like trafficking role.

    Evidence Immunofluorescence in mouse embryos, ciliogenesis assays in patient and Wdr35-mutant fibroblasts, structural homology modeling, and mouse mutant phenotyping

    PMID:21473986

    Open questions at the time
    • Coatomer homology was inferred from modeling, not direct structure
    • Specific cargoes not identified
  3. 2015 High

    Distinguished WDR35's role in selective cargo entry from general retrograde transport by showing EVC, EVC2, and SMO fail to enter cilia in Wdr35 mutants but not in retrograde-motor (Dync2h1) mutants.

    Evidence Immunofluorescence in Wdr35-/- versus Dync2h1-/- fibroblasts, disease-cDNA rescue, and Hedgehog signaling assays

    PMID:25908617

    Open questions at the time
    • Direct cargo-WDR35 binding not biochemically demonstrated
    • Mechanism distinguishing cargo entry from retrograde transport unresolved
  4. 2017 Medium

    Placed WDR35 with IFT43 as functionally cooperating satellite members of IFT-A based on shared mutant ciliopathy phenotypes.

    Evidence Human genetics, patient-cell cilia assays, and phenotypic comparison of IFT43 and WDR35 mutants

    PMID:28400947

    Open questions at the time
    • Direct interaction inferred, not shown by Co-IP or reconstitution in this study
    • Stoichiometry within IFT-A undefined
  5. 2018 Medium

    Revealed a dual anterograde and retrograde IFT requirement for the WDR35 ortholog specifically in distal ciliary segments, refining the view that IFT-A acts only in retrograde transport.

    Evidence Time-lapse live imaging of IFT88-GFP movement in Drosophila Oseg4 mutants

    PMID:29983040

    Open questions at the time
    • Single model organism
    • Molecular basis of segment-specific dual role unknown
  6. 2019 Medium

    Connected WDR35 to Hedgehog/Gli2-dependent osteogenic differentiation, linking its ciliary function to a tissue-level developmental output.

    Evidence Overexpression and siRNA knockdown in AF-MSCs and C3H10T1/2 cells with osteogenic marker assays and Gli2 epistasis

    PMID:30790652

    Open questions at the time
    • Single lab
    • Direct link between ciliary cargo transport and Gli2 activation not dissected
  7. 2019 Low

    Proposed a non-ciliary role for WDR35 as a negative regulator of mTORC1 via interaction with Rag GTPases.

    Evidence Co-immunoprecipitation, overexpression, and S6 phosphorylation assays, with ER localization by immunostaining

    PMID:30570184

    Open questions at the time
    • Single Co-IP and overexpression only, no endogenous loss-of-function confirmation
    • Physiological relevance to ciliary function unclear
  8. 2021 High

    Provided direct structural and biochemical evidence that WDR35 is a COPI-like membrane coat protein delivering ciliary membrane cargo, resolving the long-standing coatomer hypothesis.

    Evidence Mouse Wdr35 mutant analysis, in situ cryo-EM, recombinant protein-lipid binding, and ciliary membrane protein imaging

    PMID:34734804

    Open questions at the time
    • Cargo-selectivity determinants at molecular level not fully defined
    • Coupling of coat function to retrograde transport unresolved
  9. 2021 Low

    Suggested WDR35 influences subcellular localization of acetylated tubulin through CCT chaperone and Rag GTPase interactions.

    Evidence Mass spectrometry interactomics and immunostaining in WDR35 partial-knockout and RagA-knockout 293T cells

    PMID:33610917

    Open questions at the time
    • MS-based interactions without reconstitution or mutagenesis validation
    • Partial knockout system; endogenous mechanism uncertain

Open questions

Synthesis pass · forward-looking unresolved questions
  • How WDR35 selects specific signaling cargoes (EVC/EVC2/SMO) for ciliary entry and how its coat function is mechanistically coupled to retrograde IFT remain unresolved.
  • No molecular map of cargo-recognition determinants
  • Coordination between coat-mediated delivery and IFT-A retrograde transport undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 2 GO:0008289 lipid binding 1
Localization
GO:0005929 cilium 3 GO:0005815 microtubule organizing center 1 GO:0031410 cytoplasmic vesicle 1
Pathway
R-HSA-1266738 Developmental Biology 2 R-HSA-162582 Signal Transduction 2 R-HSA-9609507 Protein localization 2
Partners
EVCEVC2IFT43RAGASMOTCP1
Complex memberships
IFT-A complex

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2006 C. elegans IFTA-1 (ortholog of WDR35/IFT121) localizes to the base of cilia and undergoes intraflagellar transport (IFT). Loss of IFTA-1 causes shortened cilia with accumulation of core IFT machinery components, indicative of retrograde transport defects. Localization studies in bbs mutant cilia (where anterograde IFT assemblies are destabilized) and in che-11 IFT mutants demonstrated that IFTA-1 is closely associated with the IFT-A subcomplex, which is implicated in retrograde IFT. C. elegans genetics, fluorescence localization, chemosensory behavioral assays, epistasis with bbs and che-11 mutants Molecular biology of the cell High 17021254
2011 WDR35 localizes to cilia and centrosomes throughout the developing mouse embryo. Human and mouse fibroblasts lacking WDR35 fail to produce cilia. Loss of Wdr35 in mice causes midgestation lethality with Hedgehog signaling pathway defects. Structural modeling revealed strong homology of WDR35 to COPI coatamer subunits involved in vesicular trafficking, and human SRP mutations affect key structural elements in WDR35. Immunofluorescence localization in embryos, fibroblast cilia formation assay in patient-derived and Wdr35 mouse mutant cells, structural homology modeling, mouse mutant phenotypic analysis American journal of human genetics High 21473986
2015 WDR35/IFT121 is specifically required for entry of EVC, EVC2, and Smoothened (SMO) into the ciliary compartment. In Wdr35−/− cells, these three proteins failed to localize to cilia, but did localize in cilia of the retrograde motor mutant Dync2h1−/−, indicating a specific role for WDR35 in cargo entry rather than general retrograde transport. Expression of disease-associated Wdr35 cDNAs in Wdr35−/− fibroblasts produced Hedgehog signaling defects resembling those of Evc−/− and Evc2−/− mutants. Immunofluorescence in Wdr35−/− and Dync2h1−/− fibroblasts, rescue experiments with disease cDNAs, Hedgehog signaling assays Human molecular genetics High 25908617
2021 WDR35 (IFT121) has a coat protein function: in Wdr35 mouse mutants, small cilia form but fail to enrich in diverse classes of ciliary membrane proteins, non-core IFT-A components are degraded, and core IFT-A components accumulate at the ciliary base. 'Coat-less' vesicles accumulate and fail to fuse with Wdr35 mutant cilia. Recombinant non-core IFT-A proteins can bind directly to lipids. In situ cryo-EM provided first structural evidence of a coat function for WDR35 in delivering ciliary membrane cargo necessary for cilia elongation. Deep sequence homology of WDR35 and other IFT-A subunits to α and β' COPI coatomer subunits was demonstrated. Mouse Wdr35 mutant analysis, cryo-EM (in situ), recombinant protein–lipid binding assay, immunofluorescence of ciliary membrane proteins, electron microscopy of vesicles eLife High 34734804
2017 WDR35/IFT121 directly interacts with IFT43, a satellite member of the retrograde IFT-A complex. IFT43 mutations produce an SRPS phenotype similar to that caused by WDR35 mutations, and IFT43 is required for ciliogenesis. The phenotypic similarity supports that IFT43 and WDR35 function together as satellite interactors within the IFT-A complex. Human genetics, cilia formation assay in patient cells, phenotypic comparison between IFT43 and WDR35 mutant patients Cilia Medium 28400947
2018 Drosophila Oseg4 (WDR35 ortholog) is required for both retrograde IFT and anterograde IFT movement in distal cilia segments, as revealed by time-lapse live-cell imaging of IFT88-GFP (NOMPB-GFP) movement in Oseg4 mutant flies. This dual function was not previously established and distinguishes distal from proximal ciliary segments in IFT dynamics. Time-lapse live-cell fluorescence imaging of IFT in Drosophila cilia, Oseg4 mutant analysis Molecules and cells Medium 29983040
2019 WDR35 interacts with RagA (and RagB/RagC), small Ras-like GTPases that activate mTORC1. Overexpression of WDR35 results in decreased phosphorylation of ribosomal S6 protein in a RagA-, RagB-, and RagC-dependent manner, indicating WDR35 may negatively regulate mTORC1 activity. WDR35 was found to be present in the endoplasmic reticulum but not in lysosomes. Co-immunoprecipitation, overexpression, S6 phosphorylation assay, subcellular localization by immunostaining Genes to cells Low 30570184
2021 WDR35 associates with CCT complex proteins including TCP1/CCT1 (molecular chaperones for α-tubulin folding), identified by mass spectrometry. In WDR35 partial-knockout 293T cells, acetylated α-tubulin is dispersed rather than concentrated near primary cilia. RagA (GDP form) shows strong binding to WDR35 and negatively regulates primary cilium formation. These data suggest WDR35 is involved in subcellular localization of acetylated tubulin via interactions with TCP1 and/or RagA family proteins. Mass spectrometry interactomics, immunostaining in WDR35 partial-knockout and RagA-knockout cells, Co-immunoprecipitation Biochemical and biophysical research communications Low 33610917
2019 In amniotic fluid-derived mesenchymal stem cells with reduced WDR35 expression, cilia formation is impaired. WDR35 overexpression repairs cilia formation and, together with Gli2, enhances ALP activity and expression of osteogenic differentiation markers (RUNX2, OCN, BSP, ALP). WDR35 silencing in C3H10T1/2 cells inhibits cilia formation and osteogenic differentiation, and this effect can be attenuated by Gli2 overexpression, placing WDR35 upstream of Gli signaling in osteogenic differentiation. WDR35 overexpression and siRNA knockdown in AF-MSCs and C3H10T1/2 cells, ALP activity assay, qRT-PCR for osteogenic markers, cilia formation assay, epistasis with Gli2 overexpression Gene Medium 30790652

Source papers

Stage 0 corpus · 24 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2010 Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. American journal of human genetics 232 20817137
2011 Human and mouse mutations in WDR35 cause short-rib polydactyly syndromes due to abnormal ciliogenesis. American journal of human genetics 111 21473986
2006 The WD repeat-containing protein IFTA-1 is required for retrograde intraflagellar transport. Molecular biology of the cell 91 17021254
2015 Specific variants in WDR35 cause a distinctive form of Ellis-van Creveld syndrome by disrupting the recruitment of the EvC complex and SMO into the cilium. Human molecular genetics 49 25908617
2012 WDR35 mutation in siblings with Sensenbrenner syndrome: a ciliopathy with variable phenotype. American journal of medical genetics. Part A 41 22987818
2021 A WDR35-dependent coat protein complex transports ciliary membrane cargo vesicles to cilia. eLife 35 34734804
2017 Mutations in IFT-A satellite core component genes IFT43 and IFT121 produce short rib polydactyly syndrome with distinctive campomelia. Cilia 29 28400947
2012 Bupivacaine-induced apoptosis independently of WDR35 expression in mouse neuroblastoma Neuro2a cells. BMC neuroscience 14 23227925
2017 Uncommon runs of homozygosity disclose homozygous missense mutations in two ciliopathy-related genes (SPAG17 and WDR35) in a patient with multiple brain and skeletal anomalies. European journal of medical genetics 13 29174089
2017 Exome sequencing for the differential diagnosis of ciliary chondrodysplasias: Example of a WDR35 mutation case and review of the literature. European journal of medical genetics 12 28870638
2015 A relatively mild skeletal ciliopathy phenotype consistent with cranioectodermal dysplasia is associated with a homozygous nonsynonymous mutation in WDR35. American journal of medical genetics. Part A 12 26691894
2020 Prenatal genetic diagnosis of cranioectodermal dysplasia in a Polish family with compound heterozygous variants in WDR35. American journal of medical genetics. Part A 9 32804427
2013 Enhanced expression of WD repeat-containing protein 35 (WDR35) stimulated by domoic acid in rat hippocampus: involvement of reactive oxygen species generation and p38 mitogen-activated protein kinase activation. BMC neuroscience 9 23289926
2021 Interfamilial clinical variability in four Polish families with cranioectodermal dysplasia and identical compound heterozygous variants in WDR35. American journal of medical genetics. Part A 8 33421337
2017 Clinical and molecular genetic characterization of a male patient with Sensenbrenner syndrome (cranioectodermal dysplasia) and biallelic WDR35 mutations. Birth defects research 7 29134781
2019 RagA, an mTORC1 activator, interacts with a hedgehog signaling protein, WDR35/IFT121. Genes to cells : devoted to molecular & cellular mechanisms 6 30570184
2018 Time-Lapse Live-Cell Imaging Reveals Dual Function of Oseg4, Drosophila WDR35, in Ciliary Protein Trafficking. Molecules and cells 5 29983040
2022 WDR35 variants in a cranioectodermal dysplasia patient with early onset end-stage renal disease and retinal dystrophy. American journal of medical genetics. Part A 3 35875935
2023 Ciliary phenotyping in renal epithelial cells in a cranioectodermal dysplasia patient with WDR35 variants. Frontiers in molecular biosciences 2 38161384
2021 WDR35 is involved in subcellular localization of acetylated tubulin in 293T cells. Biochemical and biophysical research communications 2 33610917
2020 Association study of genetic variants at TTC32-WDR35 gene cluster with coronary artery disease in Chinese Han population. Journal of clinical laboratory analysis 2 33009702
2025 Case Report: Prenatal diagnosis of novel compound heterozygous variants in WDR35 gene causing short-rib thoracic dysplasia 7 with or without polydactyly. Frontiers in pediatrics 0 39877340
2025 Aberrant Splicing Caused by Compound Heterozygous Variants in WDR35 Identified in a Fetus With Cranioectodermal Dysplasia 2. Prenatal diagnosis 0 40445021
2019 Down-regulated WDR35 contributes to fetal anomaly via regulation of osteogenic differentiation. Gene 0 30790652

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