{"gene":"RAE1","run_date":"2026-04-28T19:45:45","timeline":{"discoveries":[{"year":1995,"finding":"S. pombe Rae1 is required for nuclear export of poly(A)+ RNA; rae1-1 temperature-sensitive mutant accumulates poly(A)+ RNA in the nucleus, and loss of rae1 also causes actin/tubulin disorganization and irreversible G2/M cell cycle arrest. Rae1 encodes a WD40-repeat protein.","method":"Temperature-sensitive mutant, fluorescence in situ hybridization (FISH) for poly(A)+ RNA, cell cycle analysis, gene complementation cloning","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — foundational loss-of-function with multiple orthogonal readouts (RNA export, cytoskeleton, cell cycle), replicated by subsequent work","pmids":["7706287"],"is_preprint":false},{"year":1996,"finding":"S. cerevisiae Gle2 (Rae1 homolog) localizes to nuclear pore complexes, is required for poly(A)+ RNA export (not protein import), and interacts genetically and physically with nucleoporins Nup100p; gle2 mutants show gross NPC and nuclear envelope structural perturbation.","method":"Genetic screen (colony-sectoring), indirect immunofluorescence, NPC fractionation, poly(A)+ RNA export assay, two-hybrid interaction","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods, foundational yeast study replicated in mammalian systems","pmids":["8970155"],"is_preprint":false},{"year":1997,"finding":"Human RAE1 cDNA partially suppresses the temperature-sensitive mRNA export defect of S. pombe rae1-1 mutant; epitope-tagged human Rae1 localizes to both nucleus and cytoplasm in HeLa cells, consistent with a role in nucleocytoplasmic trafficking.","method":"Heterologous complementation in fission yeast, poly(A)+ RNA export assay, immunofluorescence in HeLa cells","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 — functional complementation across species plus localization, but single study","pmids":["9370289"],"is_preprint":false},{"year":1997,"finding":"In S. pombe, Rae1 function is required for a process essential for mitotic advancement beyond mRNA export; rae1-deficient cells arrest at G2/M with elevated Cdc2p kinase, lack spindle formation, and lack spindle pole body separation. Rae1p localizes to the nuclear periphery.","method":"Temperature-sensitive mutant analysis, immunofluorescence, kinase activity assay, cell cycle arrest characterization","journal":"Yeast","confidence":"Medium","confidence_rationale":"Tier 2 — mechanistic dissection separating mRNA export from mitotic roles, single study","pmids":["9301023"],"is_preprint":false},{"year":1999,"finding":"Mammalian RAE1 binds directly to a GLEBS-like motif in NUP98 at the nuclear pore complex through multiple domains including WD-repeats and C-terminal extension; RAE1 shuttles between nucleus and cytoplasm in a temperature-dependent, RanGTP-independent manner; overexpression of the GLEBS-like motif inhibits NUP98 binding of RAE1 and causes nuclear accumulation of poly(A)+ RNA, establishing direct RAE1-NUP98 interaction as required for mRNA export.","method":"In vitro binding assay, chemical cross-linking, Xenopus oocyte microinjection, overexpression/competition experiments, poly(A)+ RNA localization","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro binding + functional microinjection + poly(A)+ RNA export assay with rescue/competition, multiple methods in single study","pmids":["10209021"],"is_preprint":false},{"year":2000,"finding":"Ct-RAE1 (Chironomus tentans RAE1 ortholog) does not associate with mRNP cotranscriptionally or in the nucleoplasm but instead binds the exported Balbiani ring RNP particle at the NPC (nuclear pore complex), and this interaction is correlated with presence of an exported RNP in the NPC channel.","method":"Immunoelectron microscopy on polytene chromosomes and nuclear pore complexes","journal":"RNA","confidence":"Medium","confidence_rationale":"Tier 2 — direct ultrastructural localization linked to functional transport event, single study","pmids":["11105759"],"is_preprint":false},{"year":2001,"finding":"Mouse RAE1 (Rae1beta) is a cell-surface GPI-anchored NKG2D ligand; ectopic expression of Rae1beta on tumor cells causes their rejection by NK cells and/or CD8+ T cells in syngeneic mice, demonstrating RAE1 as a functional NKG2D ligand that triggers anti-tumor immunity.","method":"Tumor transfection, in vivo syngeneic rejection assay, NK cell/T cell depletion experiments, immune priming assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — in vivo functional assay with cell-type depletion, highly cited, replicated by independent lab (PMID:11562472)","pmids":["11557981","11562472"],"is_preprint":false},{"year":2001,"finding":"Mouse RAE1 (Rae1gamma, Rae1delta) binds NKG2D with nanomolar affinity; soluble NKG2D-RAE1 interaction requires no additional co-factors. RAE1 and H60 compete directly for NKG2D occupancy, with H60 binding ~25-fold more tightly; the two interactions have distinct thermodynamic profiles (RAE1 interaction less temperature-dependent and makes less use of electrostatics).","method":"Surface plasmon resonance, isothermal titration calorimetry, competitive binding assay with soluble recombinant proteins","journal":"Immunity","confidence":"High","confidence_rationale":"Tier 1 — rigorous biophysical characterization with multiple methods, quantitative affinity measurements","pmids":["11520456"],"is_preprint":false},{"year":2001,"finding":"Human NKG2D forms stable complexes with monomeric MICA and MICB in solution without additional components; it also stably interacts with ULBP/N2DL proteins (human homologs of mouse RAE-1 family); glycosylation of MICA enhances but is not essential for NKG2D binding; a single amino acid at position 129 (alpha2 domain) of MICA alleles controls large differences in NKG2D affinity.","method":"Soluble receptor-ligand binding in solution, cell-surface binding assay, allelic variant comparison, mutagenesis","journal":"Immunogenetics","confidence":"High","confidence_rationale":"Tier 1 — reconstituted binary interaction in solution with mutagenesis, identifies ULBP/N2DL as human RAE-1 homologs","pmids":["11491531"],"is_preprint":false},{"year":2003,"finding":"Haploinsufficiency of Rae1 or Bub3 in mice causes mitotic checkpoint defects and chromosome missegregation; Rae1-null mice are embryonic lethal but without detectable mRNA nuclear export defects. Rae1 overexpression corrects both Rae1 and Bub3 haploinsufficiency. Combined Rae1/Bub3 haploinsufficiency greatly increases premature sister chromatid separation and tumorigenesis susceptibility.","method":"Conditional knockout mouse generation, chromosome segregation assay, mitotic checkpoint assay, mRNA export assay, overexpression rescue","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — mammalian KO genetics with multiple readouts (embryonic lethality, aneuploidy, checkpoint, tumor susceptibility), replicated findings","pmids":["12551952"],"is_preprint":false},{"year":2003,"finding":"Nup98, Rae1/Gle2, and TAP form specific binary and ternary complexes: Gle2 requires two TAP sites for stable interaction; TAP has highest affinity for a specific GLFG region of Nup98; the ternary Nup98-Gle2-TAP complex can form simultaneously; when Gle2 is Nup98-bound, it no longer binds TAP directly, suggesting Gle2 may deliver TAP to Nup98 during mRNA export.","method":"Co-immunoprecipitation, in vitro pulldown binding assays, mapping of interaction domains","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — multiple binary and ternary interaction mapping experiments, single lab","pmids":["12637516"],"is_preprint":false},{"year":2005,"finding":"VSV matrix (M) protein binds Rae1/mrnp41 directly and blocks mRNA nuclear export; an M protein mutant defective in Rae1 binding cannot inhibit mRNA export; overexpression of Rae1 fully reverts M protein-induced export inhibition; IFN-gamma induces Rae1 expression, providing a host counter-measure.","method":"Co-immunoprecipitation, mRNA export assay, M protein mutant analysis, Rae1 overexpression rescue, IFN-gamma induction assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — binding + loss-of-function mutant + rescue experiment, multiple orthogonal approaches","pmids":["15629720"],"is_preprint":false},{"year":2005,"finding":"Rae1 is a microtubule-associated protein and spindle assembly factor regulated by the RanGTP/importin-beta pathway in Xenopus egg extracts; Rae1 binds importin beta directly; Rae1 depletion severely inhibits mitotic spindle assembly; a purified Rae1 ribonucleoprotein complex stabilizes microtubules in a RanGTP/importin-beta-regulated manner requiring RNA; RNA itself plays a direct, translation-independent role in spindle assembly.","method":"Activity-based purification from Xenopus egg extracts, in vitro spindle assembly assay, immunodepletion, microtubule dynamics assay, RNA requirement test","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 — reconstitution in cell-free system, depletion, direct binding, multiple orthogonal methods in highly cited study","pmids":["15851029"],"is_preprint":false},{"year":2005,"finding":"Rae1 and Nup98 form a complex with Cdh1-activated APC (APC-Cdh1) in early mitosis and specifically inhibit APC-Cdh1-mediated ubiquitination of securin (but not cyclin B); combined Rae1/Nup98 haploinsufficiency causes premature securin destruction, premature sister chromatid separation, and severe aneuploidy. Dissociation of Rae1-Nup98 from APC-Cdh1 coincides with BubR1 release from APC-Cdc20 at the metaphase-to-anaphase transition.","method":"Mouse haploinsufficiency genetics, co-immunoprecipitation, ubiquitination assay, time-lapse microscopy, securin degradation assay","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1–2 — in vivo genetics + biochemical APC ubiquitination assay + co-IP, multiple methods, highly cited","pmids":["16355229"],"is_preprint":false},{"year":2006,"finding":"Rae1 and Nup98 form a ternary complex with APC-Cdh1 and securin in prometaphase; the Rae1-Nup98 complex does not prevent APC-Cdh1 from binding securin but instead prevents ubiquitination of already-bound securin, priming rapid securin degradation upon Rae1-Nup98 complex release at metaphase-to-anaphase transition.","method":"Co-immunoprecipitation showing ternary complex formation, ubiquitination assay in mouse cells, genetic mouse model","journal":"Cell cycle","confidence":"High","confidence_rationale":"Tier 2 — mechanistic refinement with co-IP of ternary complex + ubiquitination assay, builds directly on PMID:16355229","pmids":["16479161"],"is_preprint":false},{"year":2006,"finding":"Rae1 interacts with NuMA in a mitosis-specific manner; Rae1 binds a specific site on NuMA converting a NuMA dimer into a tetravalent MT crosslinker; reducing Rae1 or increasing NuMA causes multipolar spindle abnormalities; coupling NuMA overexpression to Rae1 overexpression, or NuMA depletion to Rae1 depletion, prevents aberrant spindles; overexpression of the Rae1-binding domain of NuMA alone causes spindle defects.","method":"Co-immunoprecipitation (mitosis-specific), domain mapping, RNAi knockdown, overexpression in HeLa cells, spindle phenotype analysis","journal":"Proceedings of the National Academy of Sciences","confidence":"High","confidence_rationale":"Tier 2 — reciprocal genetic and biochemical experiments with multiple gain/loss-of-function combinations","pmids":["17172455"],"is_preprint":false},{"year":2010,"finding":"Crystal structure of human Rae1 in complex with the GLEBS motif of Nup98 at 1.65 Å resolution: Rae1 forms a seven-bladed beta-propeller; Nup98 GLEBS forms an ~50-Å hairpin binding with its C-terminal arm to an invariant hydrophobic surface spanning the top face of the Rae1 beta-propeller; the C-terminal arm of GLEBS is necessary and sufficient for Rae1 binding; a tandem glutamate element is critical for complex formation; the Rae1-Nup98 complex binds single-stranded RNA.","method":"X-ray crystallography (1.65 Å), mutagenesis, in vitro binding assay, RNA-binding assay","journal":"Proceedings of the National Academy of Sciences","confidence":"High","confidence_rationale":"Tier 1 — high-resolution crystal structure validated by mutagenesis and binding assays","pmids":["20498086"],"is_preprint":false},{"year":2011,"finding":"Drosophila Rae1 is a component of the Highwire (Hiw)/Fsn E3 ubiquitin ligase complex in neurons; Rae1 physically and genetically interacts with Hiw; Rae1 loss causes NMJ morphological defects similar to hiw mutants and deregulates the MAP kinase kinase kinase Wallenda; Rae1 is necessary and sufficient to promote Hiw protein abundance by binding Hiw and protecting it from autophagy-mediated degradation.","method":"Tandem affinity purification/mass spectrometry, co-immunoprecipitation, genetic interaction (double mutants), neuromuscular junction morphology assay, Hiw protein stability assay","journal":"Nature neuroscience","confidence":"High","confidence_rationale":"Tier 2 — TAP-MS identification + reciprocal co-IP + epistasis + protein stability assay, multiple orthogonal methods","pmids":["21874015"],"is_preprint":false},{"year":2011,"finding":"RAE1 depletion disrupts NUP98 expression and localization, causing severe chromosome segregation defects; RAE1-NUP98 complex orchestrates proper chromosome segregation; in NUP98-HOXA9-transfected cells and AML patient samples, RAE1 protein is reduced and mislocalized, suggesting RAE1 dysfunction contributes to NUP98 fusion-mediated leukemogenesis.","method":"RNAi knockdown, rescue experiments, immunofluorescence, NUP98-HOXA9 transgenic mice, AML patient samples","journal":"Cell cycle","confidence":"Medium","confidence_rationale":"Tier 2 — RNAi + rescue + transgenic mouse, but leukemogenesis link is correlative","pmids":["21467841"],"is_preprint":false},{"year":2012,"finding":"C. elegans RAE-1 is an evolutionarily conserved binding partner of RPM-1 (ortholog of human Pam/Highwire); RAE-1 binding region in RPM-1 is conserved and the Rae1-Pam interaction also occurs in humans; RAE-1 loss-of-function causes similar axon termination and synapse formation defects as rpm-1; RAE-1 colocalizes with RPM-1 in neurons and functions downstream of rpm-1.","method":"Mass spectrometry, co-immunoprecipitation, genetic epistasis (double mutants), immunofluorescence colocalization","journal":"The Journal of neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 — MS identification + co-IP + genetic epistasis, single study","pmids":["22357847"],"is_preprint":false},{"year":2012,"finding":"VSV M protein forms multiple distinct complexes with Rae1 and Nup98; intermediate molecular weight Rae1-Nup98 complexes interact most efficiently with M protein; silencing Rae1 reduces VSV's ability to inhibit host transcription (but not mRNA nuclear accumulation or translation inhibition); M protein-Rae1-Nup98 complexes associate with the chromatin fraction, suggesting a role in transcription inhibition beyond nuclear transport.","method":"Size exclusion chromatography, sedimentation velocity analysis, co-immunoprecipitation, Rae1 siRNA, chromatin fractionation","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 — multiple biochemical methods + siRNA with specific readout, single lab","pmids":["23028327"],"is_preprint":false},{"year":2014,"finding":"Crystal structure of the VSV M protein-Rae1-Nup98 ternary complex at 3.15 Å: M protein contacts the Rae1 beta-propeller via two protrusions ('finger' and 'thumb'); conserved Met51 (finger) inserts into a deep hydrophobic pocket on Rae1 with flanking acidic residues bonding to basic groove; M protein competes with oligonucleotide binding to Rae1-Nup98, and the finger peptide alone recapitulates this competition, suggesting Rae1 serves as a phosphate backbone-binding protein for mRNA during export.","method":"X-ray crystallography (3.15 Å), competitive nucleic acid binding assay, synthetic peptide competition assay","journal":"Proceedings of the National Academy of Sciences","confidence":"High","confidence_rationale":"Tier 1 — crystal structure + mutagenesis + competition binding assay, mechanistic model proposed and experimentally tested","pmids":["24927547"],"is_preprint":false},{"year":2016,"finding":"RAE-1 family NKG2D ligands are transcriptionally repressed by HDAC3 in healthy cells; mouse CMV protein m18 relieves this repression by interacting with Casein Kinase II and preventing it from activating HDAC3, thereby inducing RAE-1 expression; analogously, human herpesvirus HDAC-inhibiting proteins induce the human NKG2D ligand ULBP-1.","method":"Genetic knockout/complementation, co-immunoprecipitation (m18-CK2 interaction), HDAC inhibitor treatment, reporter assays, chromatin immunoprecipitation","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — mechanistic pathway (m18→CK2→HDAC3→RAE1) defined with co-IP, ChIP, genetic evidence, conserved to human","pmids":["27874833"],"is_preprint":false},{"year":2016,"finding":"The Hippo pathway targets Rae1 for degradation downstream of Warts/Lats kinase; Rae1 regulates cyclin B levels and organ size; Rae1 loss restricts cyclin B and organ size while Rae1 overexpression increases them; reducing Rae1 suppresses overgrowth caused by Hippo pathway loss; Rae1 acts post-transcriptionally to increase protein levels of Merlin, Hippo, and Warts, creating a feedback circuit.","method":"Genetic epistasis (Drosophila), biochemical co-IP, cyclin B quantification, organ size measurement, mammalian cell validation","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis + biochemistry in Drosophila and mammalian cells, but Warts-mediated Rae1 degradation mechanism not fully biochemically defined","pmids":["27494403"],"is_preprint":false},{"year":2018,"finding":"RAE1 is ubiquitinated and the deubiquitinating enzyme USP11 removes ubiquitin from RAE1; USP11 is associated with the mitotic spindle; USP11 knockdown reduces cell proliferation and increases multipolar spindle formation; USP11 functionally modulates RAE1's interaction with NuMA at the mitotic spindle through controlling RAE1 ubiquitination status.","method":"Co-immunoprecipitation, ubiquitination assay, lentiviral knockdown, multipolar spindle analysis, spindle immunofluorescence","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 — DUB-substrate relationship identified with biochemical ubiquitination assay + functional spindle phenotype, single lab","pmids":["29293652"],"is_preprint":false},{"year":2020,"finding":"Rae1 acetylation at lysine residues K80 and K87 by acetyltransferases GCN5 and PCAF protects Rae1 (mouse NKG2D ligand) from matrix metalloproteinase-mediated shedding; K80/K87 mutations abolish acetylation and desensitize tumor cells to NKG2D-dependent immune surveillance in vitro and in vivo.","method":"In vitro acetylation assay, mutagenesis (K80/K87A), shedding assay, NKG2D-dependent killing assay, in vivo tumor model","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 1–2 — biochemical acetylation + mutagenesis + functional killing assay in vitro and in vivo, single lab","pmids":["33279621"],"is_preprint":false},{"year":2021,"finding":"SARS-CoV-2 ORF6 copurifies with Rae1 and Nup98; this interaction is mapped to the C-terminus of ORF6 (Met58 critical); ORF6 causes nuclear entrapment of host mRNA and blocks expression of newly transcribed reporters; Rae1 overexpression restores reporter expression; SARS-CoV-2 ORF6 more strongly copurifies with Rae1/Nup98 than SARS-CoV ORF6; both block nuclear import of a broad range of host proteins through Rae1-Nup98 interactions.","method":"Co-purification (affinity), reporter assay, poly(A)+ RNA localization, single amino acid mutagenesis (Met58), Rae1 overexpression rescue, nuclear import assay","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 — co-purification + mutagenesis + rescue + functional import/export assay, multiple orthogonal methods","pmids":["33849972"],"is_preprint":false},{"year":2022,"finding":"Crystal structures of SARS-CoV-2 and SARS-CoV-1 ORF6 C-termini in complex with the Rae1-Nup98 heterodimer reveal that ORF6 occupies the same potential mRNA-binding groove of Rae1-Nup98 as VSV M protein; direct tight binding of ORF6 to the Rae1-Nup98 complex competitively inhibits RNA binding; the highly conserved M58 of ORF6 is critical for this interaction.","method":"X-ray crystallography, in vitro competitive RNA-binding assay, mutagenesis (M58)","journal":"Frontiers in molecular biosciences","confidence":"High","confidence_rationale":"Tier 1 — crystal structure + competitive binding assay + mutagenesis","pmids":["35096974"],"is_preprint":false},{"year":2023,"finding":"NUP98 and RAE1 are highly expressed in epidermal progenitors forming a nucleoplasmic complex; reduction of NUP98 or RAE1 abolishes regenerative capacity, inhibits proliferation, and induces premature differentiation; NUP98 binds chromatin near transcription start sites of key epigenetic regulators (DNMT1, UHRF1, EZH2) and sustains their expression; HDAC inhibition diminishes NUP98 chromatin binding and causes NUP98 and RAE1 to mislocalize interdependently to the nucleolus.","method":"ChIP-seq, knockdown, chromatin fractionation, immunofluorescence, epigenetic regulator expression analysis, HDAC inhibitor treatment","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP-seq + knockdown + localization, single lab, mechanistic detail of NUP98-RAE1 chromatin regulatory function","pmids":["37353594"],"is_preprint":false},{"year":2024,"finding":"Rae1 is required for SARS-CoV-2 ORF6-mediated inhibition of nucleocytoplasmic transport; Rae1 alone is not necessary to support p-STAT1 import or poly(A) RNA export under basal conditions; loss of Rae1 suppresses the transport inhibitory activity of ORF6; Rae1-Nup98 complex strategically positions ORF6 within the NPC where it alters FG-Nup interactions; Rae1 is required for normal viral protein production during SARS-CoV-2 infection.","method":"Rae1 knockdown/knockout, p-STAT1 nuclear import assay, poly(A)+ RNA export assay, viral infection, co-immunoprecipitation","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function with specific mechanistic readouts, single lab","pmids":["38507240"],"is_preprint":false},{"year":2008,"finding":"Retinoic acid downregulates Rae1 protein and mRNA expression in neuroblastoma cells; Rae1 overexpression prevents retinoic acid-induced APC-Cdh1 activation, Skp2 degradation, p27 accumulation, cell cycle arrest and differentiation; Cdh1 inhibition has similar effects; thus, Rae1 limits APC-Cdh1 activity to promote cell proliferation and its downregulation by retinoic acid facilitates differentiation.","method":"Immunoblot, RT-PCR, Rae1 overexpression and knockdown in SH-SY5Y cells, cell cycle analysis, differentiation assay","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — gain/loss-of-function + multiple downstream readouts in human cell line, single lab","pmids":["18212744"],"is_preprint":false},{"year":2012,"finding":"RAE-1 family NKG2D ligand expression in cancer cell lines and proliferating normal cells is directly coupled to cell cycle entry; E2F transcription factors directly transcriptionally activate Raet1 genes; RAE-1 induction occurs in primary cultures, embryonic brain, and healing wounds; wound healing is delayed in NKG2D-deficient mice.","method":"Transcriptional reporter assay, E2F ChIP/binding analysis, E2F overexpression/knockdown, NKG2D-deficient mouse wound healing model","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 — direct E2F-Raet1 promoter binding + E2F manipulation + in vivo NKG2D KO phenotype, multiple methods","pmids":["23166357"],"is_preprint":false},{"year":2014,"finding":"Induction of RAE1 NKG2D ligands by the DNA damage response requires a STING-dependent DNA sensor pathway involving TBK1 and IRF3; cytosolic DNA detected in RAE1-expressing lymphoma cells required DDR activation; DNA transfection into ligand-negative cells is sufficient to induce RAE1 expression; Irf3-haploinsufficient Eμ-Myc mice show reduced tumor RAE1 levels and reduced survival.","method":"STING/TBK1/IRF3 pharmacological inhibition and genetic KO, cytosolic DNA detection, DNA transfection assay, in vivo mouse lymphoma model","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — pathway dissection with genetic and pharmacological tools + in vivo validation, single lab","pmids":["24590060"],"is_preprint":false},{"year":2011,"finding":"RAE-1 expression requires activation of the PI3K pathway (specifically the p110α catalytic subunit) during MCMV infection and transformation; inhibition of p110α blocks RAE-1 induction by MCMV infection and reduces RAE-1 cell surface expression on transformed cells.","method":"PI3K isoform-selective pharmacological inhibition, siRNA knockdown of PI3K subunits, cell surface RAE-1 flow cytometry, viral infection assays","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 — pharmacological + genetic dissection with specific isoform identification, single lab","pmids":["21966273"],"is_preprint":false},{"year":2010,"finding":"MCMV m152/gp40 directly binds RAE-1 isoforms with 1:1 stoichiometry and Kd < 5 μM; binding affinity differs quantitatively among RAE-1 isoforms, corresponding to differential susceptibility to downregulation; RAE-1delta is resistant to downregulation because its mature surface-resident form has an intrinsic property (absence of PLWY motif in beta/gamma does not fully explain delta resistance), suggesting a novel escape mechanism from viral immunoevasion.","method":"Protein purification, size exclusion chromatography, analytical ultracentrifugation, isothermal titration calorimetry, cotransfection assay in HEK293T cells","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 — multiple rigorous biophysical methods quantifying direct m152-RAE1 interaction with isoform specificity","pmids":["20166740"],"is_preprint":false}],"current_model":"Human/mammalian RAE1 is a multifunctional WD40 beta-propeller protein that: (1) acts as an mRNA export factor by binding directly to the GLEBS motif of NUP98 at the nuclear pore complex (NPC), where it transiently associates with mRNP cargo and uses its RNA-binding surface to facilitate mRNA translocation; (2) functions as a mitotic regulator by forming a complex with NUP98 that inhibits APC-Cdh1-mediated ubiquitination of securin until the metaphase-to-anaphase transition, interacts with NuMA as a tetravalent MT crosslinker for bipolar spindle formation, and associates with microtubules as part of a RanGTP/importin-beta-regulated ribonucleoprotein complex required for spindle assembly; (3) serves as a cell-surface GPI-anchored NKG2D ligand (murine RAE-1 isoforms) whose expression is regulated by E2F transcription factors, PI3K/HDAC3 signaling, and DNA damage-activated STING-IRF3 pathways; and (4) is targeted by multiple viral proteins (VSV M protein, SARS-CoV-2 ORF6) that occupy the nucleic acid-binding groove of the Rae1-Nup98 complex to block nucleocytoplasmic transport and suppress host antiviral responses."},"narrative":{"teleology":[{"year":1995,"claim":"Establishing that RAE1 is an essential mRNA export factor and WD40-repeat protein resolved what gene product mediates poly(A)+ RNA nuclear export in fission yeast, and revealed a dual connection to cell cycle progression.","evidence":"Temperature-sensitive rae1-1 mutant in S. pombe with FISH for poly(A)+ RNA accumulation, cell cycle analysis showing G2/M arrest","pmids":["7706287"],"confidence":"High","gaps":["Mechanism of mRNA engagement unknown","Whether cell cycle arrest is direct or secondary to export block unclear","No metazoan data"]},{"year":1996,"claim":"Demonstration that the budding yeast homolog Gle2 localizes to NPCs and interacts with nucleoporin Nup100p established that RAE1 functions at the nuclear pore rather than in the nucleoplasm.","evidence":"Indirect immunofluorescence, NPC fractionation, and two-hybrid interaction with Nup100p in S. cerevisiae","pmids":["8970155"],"confidence":"High","gaps":["Direct binding partner in metazoans not yet identified","RNA-binding activity not tested"]},{"year":1999,"claim":"Identification of NUP98 as the direct binding partner of mammalian RAE1 via a GLEBS motif, and demonstration that this interaction is required for mRNA export, established the core RAE1–NUP98 axis at the NPC.","evidence":"In vitro binding, chemical cross-linking, Xenopus oocyte microinjection with GLEBS competition blocking poly(A)+ RNA export","pmids":["10209021"],"confidence":"High","gaps":["Structural basis of GLEBS recognition unknown","Whether RAE1 contacts mRNA directly unresolved"]},{"year":2000,"claim":"Ultrastructural evidence that RAE1 binds mRNP cargo specifically at the NPC channel — not cotranscriptionally — established it as a transient NPC-associated export factor rather than an mRNP packaging component.","evidence":"Immunoelectron microscopy on Chironomus tentans Balbiani ring mRNP at nuclear pores","pmids":["11105759"],"confidence":"Medium","gaps":["Single organism (dipteran), generality to mammals not directly shown","Molecular contacts between RAE1 and mRNP undefined"]},{"year":2001,"claim":"Discovery that murine RAE-1 isoforms are GPI-anchored cell-surface NKG2D ligands that trigger NK cell and CD8+ T cell anti-tumor rejection established a distinct immune function for the RAE-1 gene family, separate from the nucleoporin-associated mRNA export protein.","evidence":"Tumor transfection with Rae1beta, in vivo syngeneic rejection with NK/T cell depletion; SPR and ITC measuring nanomolar NKG2D binding","pmids":["11557981","11520456"],"confidence":"High","gaps":["Regulation of RAE-1 surface expression unknown","Structural basis of NKG2D–RAE-1 recognition not yet solved","Human ortholog functional equivalence assumed but not tested"]},{"year":2003,"claim":"Rae1 haploinsufficiency in mice revealed an essential mitotic checkpoint role separable from mRNA export: Rae1+/− mice showed chromosome missegregation and tumor susceptibility without detectable export defects, and genetic interaction with Bub3 indicated a shared spindle checkpoint pathway.","evidence":"Conditional knockout mice with chromosome segregation assay, mitotic checkpoint assay, and mRNA export measurement; Rae1/Bub3 compound haploinsufficiency","pmids":["12551952"],"confidence":"High","gaps":["Molecular mechanism of checkpoint function unknown","Whether RAE1 directly participates in spindle checkpoint signaling or acts indirectly unresolved"]},{"year":2005,"claim":"Two breakthrough studies defined RAE1's mitotic mechanisms: (1) Rae1–Nup98 complex inhibits APC/C-Cdh1 ubiquitination of securin to prevent premature sister chromatid separation, and (2) Rae1 is a RanGTP/importin-beta-regulated microtubule-associated spindle assembly factor whose function requires associated RNA.","evidence":"APC ubiquitination assay and mouse haploinsufficiency genetics (securin); activity-based purification from Xenopus egg extracts with immunodepletion and microtubule dynamics assay (spindle assembly)","pmids":["16355229","15851029"],"confidence":"High","gaps":["How securin inhibition is relieved at metaphase-anaphase transition not fully defined","Identity of the RNA species required for spindle assembly unknown","How the mRNA export and mitotic functions are temporally coordinated unclear"]},{"year":2005,"claim":"VSV M protein was shown to directly bind RAE1 and block mRNA export, with a loss-of-binding M mutant unable to inhibit export and RAE1 overexpression fully rescuing the block — establishing RAE1–NUP98 as a viral target for host gene expression shutoff.","evidence":"Co-immunoprecipitation, M protein mutant analysis, RAE1 overexpression rescue, mRNA export assay","pmids":["15629720"],"confidence":"High","gaps":["Structural basis of M protein–RAE1 interaction unknown at this time","Whether other viruses exploit the same mechanism unresolved"]},{"year":2006,"claim":"RAE1 was found to interact with NuMA in a mitosis-specific manner, converting the NuMA dimer into a tetravalent microtubule crosslinker essential for bipolar spindle formation — establishing a third distinct mitotic role for RAE1.","evidence":"Mitosis-specific co-immunoprecipitation, domain mapping, reciprocal RNAi/overexpression titration of RAE1 and NuMA with spindle phenotype scoring in HeLa cells","pmids":["17172455"],"confidence":"High","gaps":["Structural details of the RAE1–NuMA interface unknown","How RAE1 allocation between NuMA and NUP98 is regulated during mitosis unclear"]},{"year":2010,"claim":"The 1.65 Å crystal structure of human RAE1–NUP98(GLEBS) revealed a seven-bladed beta-propeller architecture with a conserved basic groove for ssRNA binding, providing the structural framework for understanding both mRNA export and viral mimicry mechanisms.","evidence":"X-ray crystallography at 1.65 Å with mutagenesis validation and RNA-binding assay","pmids":["20498086"],"confidence":"High","gaps":["No structure of RAE1 bound to mRNA substrate","How RNA binding contributes to export selectivity unresolved"]},{"year":2011,"claim":"A neuronal function was uncovered: Drosophila and C. elegans RAE1 stabilizes the Highwire/RPM-1 E3 ubiquitin ligase by protecting it from autophagy-mediated degradation, with loss of RAE1 causing axon termination and synapse formation defects — extending RAE1 function beyond nucleocytoplasmic transport and mitosis.","evidence":"TAP-MS, co-immunoprecipitation, genetic epistasis, NMJ morphology analysis in Drosophila; MS, co-IP, and epistasis in C. elegans with conservation to human Pam","pmids":["21874015","22357847"],"confidence":"High","gaps":["Mechanism by which RAE1 shields Highwire from autophagy not defined","Whether this function operates in mammalian neurons in vivo unknown"]},{"year":2012,"claim":"Transcriptional regulation of murine RAE-1 NKG2D ligands was linked to E2F transcription factors driving expression during cell cycle entry, coupling innate immune surveillance to proliferative status.","evidence":"E2F ChIP at Raet1 promoters, E2F overexpression/knockdown, NKG2D-deficient mouse wound healing model","pmids":["23166357"],"confidence":"High","gaps":["Whether E2F regulation applies to human ULBP orthologs not directly shown","Epigenetic layers beyond E2F incompletely mapped"]},{"year":2014,"claim":"Crystal structures of VSV M protein bound to RAE1–NUP98 revealed that M protein inserts a methionine finger into the RNA-binding groove of RAE1, directly competing with mRNA — establishing the structural basis for viral hijacking of the export machinery.","evidence":"X-ray crystallography at 3.15 Å, competitive nucleic acid binding assay, synthetic peptide competition","pmids":["24927547"],"confidence":"High","gaps":["Whether all paramyxo/rhabdovirus M proteins use the same mechanism unknown","In vivo relevance of groove occupancy vs. other M protein functions not fully separated"]},{"year":2016,"claim":"HDAC3 was identified as a transcriptional repressor of RAE-1 NKG2D ligands, with MCMV protein m18 relieving this repression via Casein Kinase II inhibition — defining a viral strategy that paradoxically activates innate immunity.","evidence":"HDAC3 knockout/complementation, m18–CK2 co-immunoprecipitation, ChIP, HDAC inhibitor treatment","pmids":["27874833"],"confidence":"High","gaps":["How HDAC3-mediated repression is maintained in uninfected cells mechanistically incomplete","Whether m18-induced RAE-1 has net pro- or anti-viral outcome in vivo unclear"]},{"year":2021,"claim":"SARS-CoV-2 ORF6 was shown to bind RAE1–NUP98 via a critical Met58 residue, blocking both mRNA export and protein nuclear import — establishing coronavirus exploitation of the same RAE1 groove targeted by VSV M protein.","evidence":"Co-purification, Met58 mutagenesis, poly(A)+ RNA localization, reporter rescue by RAE1 overexpression, nuclear import assay","pmids":["33849972"],"confidence":"High","gaps":["Structural details not yet available at this point","Contribution of RAE1 targeting to COVID-19 pathogenesis unknown"]},{"year":2022,"claim":"Crystal structures of SARS-CoV-1 and SARS-CoV-2 ORF6 C-termini bound to RAE1–NUP98 confirmed competitive occupancy of the mRNA-binding groove, unifying the structural mechanism of viral immune evasion across RNA virus families.","evidence":"X-ray crystallography, competitive RNA-binding assay, Met58 mutagenesis","pmids":["35096974"],"confidence":"High","gaps":["Whether therapeutic targeting of the RAE1 groove could block viral evasion untested","No structure of RAE1 with a physiological mRNA substrate for comparison"]},{"year":null,"claim":"Key open questions include: the identity and structural basis of physiological mRNA substrates bound in the RAE1 groove during export; how RAE1 is partitioned among its NPC-export, APC/C-inhibitory, NuMA-crosslinking, and chromatin-regulatory functions during the cell cycle; and whether the neuronal Highwire-stabilizing function operates in mammalian neurons in vivo.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of RAE1 bound to a physiological mRNA","Temporal regulation of RAE1 allocation among distinct complexes undefined","Mammalian in vivo validation of neuronal Highwire/Pam stabilization missing"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,4,5,16,21,27]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[12,15]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[13,14,30]},{"term_id":"GO:0048018","term_label":"receptor ligand activity","supporting_discovery_ids":[6,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,2,4,28]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[2,12]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[20,28]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[12,15,24]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[6,7]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,4,5,11,16,21]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[9,13,14,15,24]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[6,7,22,31,32]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[4,26,29]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[26,27,29]}],"complexes":["RAE1-NUP98","APC/C-Cdh1-RAE1-NUP98","RAE1-NuMA","Highwire/RPM-1 E3 ligase complex"],"partners":["NUP98","NUMA1","BUB3","CDH1","KLRK1","USP11","RANBP2","NXF1"],"other_free_text":[]},"mechanistic_narrative":"RAE1 is a WD40-repeat beta-propeller protein that functions at the nexus of mRNA nuclear export and mitotic regulation. As a seven-bladed beta-propeller, RAE1 binds the GLEBS motif of NUP98 at the nuclear pore complex, where it engages single-stranded RNA through a conserved basic groove to facilitate mRNA translocation; this same groove is competitively targeted by viral proteins including VSV M protein and SARS-CoV-2 ORF6 to block nucleocytoplasmic transport and suppress host antiviral responses [PMID:20498086, PMID:24927547, PMID:35096974]. During mitosis, the RAE1–NUP98 complex inhibits APC/C-Cdh1-mediated ubiquitination of securin until the metaphase-to-anaphase transition, and RAE1 independently interacts with NuMA to convert it into a tetravalent microtubule crosslinker required for bipolar spindle assembly; haploinsufficiency of RAE1 causes chromosome missegregation and tumor susceptibility in mice [PMID:16355229, PMID:17172455, PMID:12551952]. Separately, the murine RAE-1 family encodes GPI-anchored cell-surface NKG2D ligands whose expression is transcriptionally controlled by E2F, PI3K/HDAC3, and STING-IRF3 pathways and whose engagement of NKG2D activates NK cell and CD8+ T cell anti-tumor immunity [PMID:11557981, PMID:23166357, PMID:27874833]."},"prefetch_data":{"uniprot":{"accession":"P78406","full_name":"mRNA export factor RAE1","aliases":["Rae1 protein homolog","mRNA-associated protein mrnp 41"],"length_aa":368,"mass_kda":41.0,"function":"Acts as a mRNA export factor involved in nucleocytoplasmic transport (PubMed:20498086, PubMed:33849972). Plays a role in mitotic bipolar spindle formation (PubMed:17172455). May function in attaching cytoplasmic mRNPs to the cytoskeleton both directly or indirectly (PubMed:17172455)","subcellular_location":"Cytoplasm; Nucleus; Cytoplasm, cytoskeleton, spindle pole; Nucleus envelope","url":"https://www.uniprot.org/uniprotkb/P78406/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RAE1","classification":"Common Essential","n_dependent_lines":1203,"n_total_lines":1208,"dependency_fraction":0.9958609271523179},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"NUP214","stoichiometry":4.0},{"gene":"ELOVL1","stoichiometry":0.2},{"gene":"HSP90B1","stoichiometry":0.2},{"gene":"MAP4","stoichiometry":0.2},{"gene":"NUMA1","stoichiometry":0.2},{"gene":"RAN","stoichiometry":0.2},{"gene":"RANBP1","stoichiometry":0.2},{"gene":"VCP","stoichiometry":0.2},{"gene":"XPO1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RAE1","total_profiled":1310},"omim":[{"mim_id":"619247","title":"SPINDLE- AND KINETOCHORE-ASSOCIATED COMPLEX, SUBUNIT 3; SKA3","url":"https://www.omim.org/entry/619247"},{"mim_id":"611817","title":"KILLER CELL LECTIN-LIKE RECEPTOR, SUBFAMILY K, MEMBER 1; KLRK1","url":"https://www.omim.org/entry/611817"},{"mim_id":"604147","title":"PTTG1 REGULATOR OF SISTER CHROMATID SEPARATION, SECURIN; PTTG1","url":"https://www.omim.org/entry/604147"},{"mim_id":"603343","title":"RIBONUCLEIC ACID EXPORT PROTEIN 1; RAE1","url":"https://www.omim.org/entry/603343"},{"mim_id":"603182","title":"INTERLEUKIN ENHANCER-BINDING FACTOR 3; ILF3","url":"https://www.omim.org/entry/603182"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nucleoli fibrillar center","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"testis","ntpm":96.1}],"url":"https://www.proteinatlas.org/search/RAE1"},"hgnc":{"alias_symbol":["Mnrp41","Gle2"],"prev_symbol":[]},"alphafold":{"accession":"P78406","domains":[{"cath_id":"2.130.10.10","chopping":"42-191","consensus_level":"medium","plddt":97.8419,"start":42,"end":191},{"cath_id":"2.130.10.10","chopping":"209-318","consensus_level":"medium","plddt":95.6831,"start":209,"end":318}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P78406","model_url":"https://alphafold.ebi.ac.uk/files/AF-P78406-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P78406-F1-predicted_aligned_error_v6.png","plddt_mean":92.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RAE1","jax_strain_url":"https://www.jax.org/strain/search?query=RAE1"},"sequence":{"accession":"P78406","fasta_url":"https://rest.uniprot.org/uniprotkb/P78406.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P78406/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P78406"}},"corpus_meta":[{"pmid":"11557981","id":"PMC_11557981","title":"Rae1 and H60 ligands of the NKG2D receptor stimulate tumour immunity.","date":"2001","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/11557981","citation_count":753,"is_preprint":false},{"pmid":"11562472","id":"PMC_11562472","title":"Ectopic expression of retinoic acid early inducible-1 gene (RAE-1) permits natural killer cell-mediated rejection of a MHC class I-bearing tumor in vivo.","date":"2001","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/11562472","citation_count":454,"is_preprint":false},{"pmid":"11491531","id":"PMC_11491531","title":"Interactions of human NKG2D with its ligands MICA, MICB, and homologs of the mouse RAE-1 protein family.","date":"2001","source":"Immunogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/11491531","citation_count":377,"is_preprint":false},{"pmid":"12551952","id":"PMC_12551952","title":"Rae1 is an essential mitotic checkpoint regulator that cooperates with Bub3 to prevent chromosome missegregation.","date":"2003","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/12551952","citation_count":302,"is_preprint":false},{"pmid":"15851029","id":"PMC_15851029","title":"A Rae1-containing ribonucleoprotein complex is required for mitotic spindle assembly.","date":"2005","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/15851029","citation_count":231,"is_preprint":false},{"pmid":"10209021","id":"PMC_10209021","title":"RAE1 is a shuttling mRNA export factor that binds to a GLEBS-like NUP98 motif at the nuclear pore complex through multiple domains.","date":"1999","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/10209021","citation_count":206,"is_preprint":false},{"pmid":"15629720","id":"PMC_15629720","title":"VSV disrupts the Rae1/mrnp41 mRNA nuclear export pathway.","date":"2005","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/15629720","citation_count":197,"is_preprint":false},{"pmid":"16355229","id":"PMC_16355229","title":"The Rae1-Nup98 complex prevents aneuploidy by inhibiting securin degradation.","date":"2005","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/16355229","citation_count":157,"is_preprint":false},{"pmid":"8970155","id":"PMC_8970155","title":"GLE2, a Saccharomyces cerevisiae homologue of the Schizosaccharomyces pombe export factor RAE1, is required for nuclear pore complex structure and function.","date":"1996","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/8970155","citation_count":149,"is_preprint":false},{"pmid":"16476774","id":"PMC_16476774","title":"Early aging-associated phenotypes in Bub3/Rae1 haploinsufficient mice.","date":"2006","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/16476774","citation_count":148,"is_preprint":false},{"pmid":"24590060","id":"PMC_24590060","title":"RAE1 ligands for the NKG2D receptor are regulated by STING-dependent DNA sensor pathways in lymphoma.","date":"2014","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/24590060","citation_count":145,"is_preprint":false},{"pmid":"7706287","id":"PMC_7706287","title":"A mutation in the Schizosaccharomyces pombe rae1 gene causes defects in poly(A)+ RNA export and in the cytoskeleton.","date":"1995","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7706287","citation_count":142,"is_preprint":false},{"pmid":"18753637","id":"PMC_18753637","title":"Mononuclear myeloid-derived \"suppressor\" cells express RAE-1 and activate natural killer cells.","date":"2008","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/18753637","citation_count":128,"is_preprint":false},{"pmid":"33849972","id":"PMC_33849972","title":"SARS-CoV-2 ORF6 Disrupts Bidirectional Nucleocytoplasmic Transport through Interactions with Rae1 and Nup98.","date":"2021","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/33849972","citation_count":125,"is_preprint":false},{"pmid":"30559192","id":"PMC_30559192","title":"F-box protein RAE1 regulates the stability of the aluminum-resistance transcription factor STOP1 in Arabidopsis.","date":"2018","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/30559192","citation_count":119,"is_preprint":false},{"pmid":"12637516","id":"PMC_12637516","title":"Complex formation among the RNA export proteins Nup98, Rae1/Gle2, and TAP.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12637516","citation_count":113,"is_preprint":false},{"pmid":"17673545","id":"PMC_17673545","title":"Retinoic acid signaling sensitizes hepatic stellate cells to NK cell killing via upregulation of NK cell activating ligand RAE1.","date":"2007","source":"American journal of physiology. Gastrointestinal and liver physiology","url":"https://pubmed.ncbi.nlm.nih.gov/17673545","citation_count":101,"is_preprint":false},{"pmid":"23166357","id":"PMC_23166357","title":"RAE-1 ligands for the NKG2D receptor are regulated by E2F transcription factors, which control cell cycle entry.","date":"2012","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/23166357","citation_count":100,"is_preprint":false},{"pmid":"20498086","id":"PMC_20498086","title":"Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1.","date":"2010","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/20498086","citation_count":99,"is_preprint":false},{"pmid":"17172455","id":"PMC_17172455","title":"Rae1 interaction with NuMA is required for bipolar spindle formation.","date":"2006","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/17172455","citation_count":96,"is_preprint":false},{"pmid":"25351459","id":"PMC_25351459","title":"IL-30 (IL27p28) attenuates liver fibrosis through inducing NKG2D-rae1 interaction between NKT and activated hepatic stellate cells in mice.","date":"2014","source":"Hepatology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/25351459","citation_count":89,"is_preprint":false},{"pmid":"8982867","id":"PMC_8982867","title":"Genomic structures and characterization of Rae1 family members encoding GPI-anchored cell surface proteins and expressed predominantly in embryonic mouse brain.","date":"1996","source":"Journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8982867","citation_count":85,"is_preprint":false},{"pmid":"11520456","id":"PMC_11520456","title":"Molecular competition for NKG2D: H60 and RAE1 compete unequally for NKG2D with dominance of H60.","date":"2001","source":"Immunity","url":"https://pubmed.ncbi.nlm.nih.gov/11520456","citation_count":83,"is_preprint":false},{"pmid":"23028327","id":"PMC_23028327","title":"Complexes of vesicular stomatitis virus matrix protein with host Rae1 and Nup98 involved in inhibition of host transcription.","date":"2012","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/23028327","citation_count":65,"is_preprint":false},{"pmid":"33360543","id":"PMC_33360543","title":"Overexpression of SARS-CoV-2 protein ORF6 dislocates RAE1 and NUP98 from the nuclear pore complex.","date":"2020","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/33360543","citation_count":63,"is_preprint":false},{"pmid":"24927547","id":"PMC_24927547","title":"Vesiculoviral matrix (M) protein occupies nucleic acid binding site at nucleoporin pair (Rae1 • Nup98).","date":"2014","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/24927547","citation_count":61,"is_preprint":false},{"pmid":"18212744","id":"PMC_18212744","title":"Retinoic acid downregulates Rae1 leading to APC(Cdh1) activation and neuroblastoma SH-SY5Y differentiation.","date":"2008","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/18212744","citation_count":55,"is_preprint":false},{"pmid":"9370289","id":"PMC_9370289","title":"The human RAE1 gene is a functional homologue of Schizosaccharomyces pombe rae1 gene involved in nuclear export of Poly(A)+ RNA.","date":"1997","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/9370289","citation_count":53,"is_preprint":false},{"pmid":"16479161","id":"PMC_16479161","title":"Securin associates with APCCdh1 in prometaphase but its destruction is delayed by Rae1 and Nup98 until the metaphase/anaphase transition.","date":"2006","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/16479161","citation_count":51,"is_preprint":false},{"pmid":"33528836","id":"PMC_33528836","title":"Degradation of STOP1 mediated by the F-box proteins RAH1 and RAE1 balances aluminum resistance and plant growth in Arabidopsis thaliana.","date":"2021","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/33528836","citation_count":48,"is_preprint":false},{"pmid":"12594837","id":"PMC_12594837","title":"Natural killer cell-mediated lysis of dorsal root ganglia neurons via RAE1/NKG2D interactions.","date":"2003","source":"European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/12594837","citation_count":46,"is_preprint":false},{"pmid":"21966273","id":"PMC_21966273","title":"Expression of the RAE-1 family of stimulatory NK-cell ligands requires activation of the PI3K pathway during viral infection and transformation.","date":"2011","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/21966273","citation_count":46,"is_preprint":false},{"pmid":"19392703","id":"PMC_19392703","title":"Dual functions of Nicotiana benthamiana Rae1 in interphase and mitosis.","date":"2009","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/19392703","citation_count":45,"is_preprint":false},{"pmid":"21467841","id":"PMC_21467841","title":"RNA export factor RAE1 contributes to NUP98-HOXA9-mediated leukemogenesis.","date":"2011","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/21467841","citation_count":42,"is_preprint":false},{"pmid":"21874015","id":"PMC_21874015","title":"Drosophila Rae1 controls the abundance of the ubiquitin ligase Highwire in post-mitotic neurons.","date":"2011","source":"Nature neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/21874015","citation_count":42,"is_preprint":false},{"pmid":"35096974","id":"PMC_35096974","title":"Molecular Mechanism of SARS-CoVs Orf6 Targeting the Rae1-Nup98 Complex to Compete With mRNA Nuclear Export.","date":"2022","source":"Frontiers in molecular biosciences","url":"https://pubmed.ncbi.nlm.nih.gov/35096974","citation_count":41,"is_preprint":false},{"pmid":"22357847","id":"PMC_22357847","title":"RAE-1, a novel PHR binding protein, is required for axon termination and synapse formation in Caenorhabditis elegans.","date":"2012","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/22357847","citation_count":40,"is_preprint":false},{"pmid":"9301023","id":"PMC_9301023","title":"Advancement through mitosis requires rae1 gene function in fission yeast.","date":"1997","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/9301023","citation_count":36,"is_preprint":false},{"pmid":"19494006","id":"PMC_19494006","title":"Differential susceptibility of RAE-1 isoforms to mouse cytomegalovirus.","date":"2009","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/19494006","citation_count":36,"is_preprint":false},{"pmid":"20530257","id":"PMC_20530257","title":"Intact NKG2D-independent function of NK cells chronically stimulated with the NKG2D ligand Rae-1.","date":"2010","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/20530257","citation_count":35,"is_preprint":false},{"pmid":"16980040","id":"PMC_16980040","title":"The effect of renal ischemia-reperfusion injury on expression of RAE-1 and H60 in mice kidney.","date":"2006","source":"Transplantation proceedings","url":"https://pubmed.ncbi.nlm.nih.gov/16980040","citation_count":29,"is_preprint":false},{"pmid":"23788425","id":"PMC_23788425","title":"Drosophila rae1 is required for male meiosis and spermatogenesis.","date":"2013","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/23788425","citation_count":26,"is_preprint":false},{"pmid":"20166740","id":"PMC_20166740","title":"Direct interaction of the mouse cytomegalovirus m152/gp40 immunoevasin with RAE-1 isoforms.","date":"2010","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20166740","citation_count":26,"is_preprint":false},{"pmid":"28363943","id":"PMC_28363943","title":"Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis.","date":"2017","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/28363943","citation_count":25,"is_preprint":false},{"pmid":"34008277","id":"PMC_34008277","title":"Mitotic checkpoint regulator RAE1 promotes tumor growth in colorectal cancer.","date":"2021","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/34008277","citation_count":24,"is_preprint":false},{"pmid":"21046555","id":"PMC_21046555","title":"RAE-1 is expressed in the adult subventricular zone and controls cell proliferation of neurospheres.","date":"2011","source":"Glia","url":"https://pubmed.ncbi.nlm.nih.gov/21046555","citation_count":23,"is_preprint":false},{"pmid":"14729268","id":"PMC_14729268","title":"Characterization of the Drosophila Rae1 protein as a G1 phase regulator of the cell cycle.","date":"2004","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/14729268","citation_count":22,"is_preprint":false},{"pmid":"27874833","id":"PMC_27874833","title":"A Herpesviral induction of RAE-1 NKG2D ligand expression occurs through release of HDAC mediated repression.","date":"2016","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/27874833","citation_count":21,"is_preprint":false},{"pmid":"29293652","id":"PMC_29293652","title":"USP11 deubiquitinates RAE1 and plays a key role in bipolar spindle formation.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/29293652","citation_count":20,"is_preprint":false},{"pmid":"11779145","id":"PMC_11779145","title":"High levels of RAE-1 isoforms on mouse tumor cell lines assessed by anti-\"pan\" RAE-1 antibody confer tumor susceptibility to NK cells.","date":"2002","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/11779145","citation_count":19,"is_preprint":false},{"pmid":"30814639","id":"PMC_30814639","title":"RAE1 mediated ZEB1 expression promotes epithelial-mesenchymal transition in breast cancer.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/30814639","citation_count":16,"is_preprint":false},{"pmid":"11105759","id":"PMC_11105759","title":"The Ct-RAE1 protein interacts with Balbiani ring RNP particles at the nuclear pore.","date":"2000","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/11105759","citation_count":16,"is_preprint":false},{"pmid":"27444966","id":"PMC_27444966","title":"RAE-1 expression is induced during experimental autoimmune encephalomyelitis and is correlated with microglia cell proliferation.","date":"2016","source":"Brain, behavior, and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/27444966","citation_count":15,"is_preprint":false},{"pmid":"39060273","id":"PMC_39060273","title":"The RAE1-STOP1-GL2-RHD6 module regulates the ALMT1-dependent aluminum resistance in Arabidopsis.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39060273","citation_count":15,"is_preprint":false},{"pmid":"28181567","id":"PMC_28181567","title":"The mitotic checkpoint regulator RAE1 induces aggressive breast cancer cell phenotypes by mediating epithelial-mesenchymal transition.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28181567","citation_count":14,"is_preprint":false},{"pmid":"27494403","id":"PMC_27494403","title":"The Hippo Pathway Targets Rae1 to Regulate Mitosis and Organ Size and to Feed Back to Regulate Upstream Components Merlin, Hippo, and Warts.","date":"2016","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/27494403","citation_count":12,"is_preprint":false},{"pmid":"32599603","id":"PMC_32599603","title":"Kupffer Cells Regulate Natural Killer Cells Via the NK group 2, Member D (NKG2D)/Retinoic Acid Early Inducible-1 (RAE-1) Interaction and Cytokines in a Primary Biliary Cholangitis Mouse Model.","date":"2020","source":"Medical science monitor : international medical journal of experimental and clinical research","url":"https://pubmed.ncbi.nlm.nih.gov/32599603","citation_count":11,"is_preprint":false},{"pmid":"37353594","id":"PMC_37353594","title":"NUP98 and RAE1 sustain progenitor function through HDAC-dependent chromatin targeting to escape from nucleolar localization.","date":"2023","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/37353594","citation_count":9,"is_preprint":false},{"pmid":"38507240","id":"PMC_38507240","title":"SARS-CoV-2 Orf6 is positioned in the nuclear pore complex by Rae1 to inhibit nucleocytoplasmic transport.","date":"2024","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/38507240","citation_count":9,"is_preprint":false},{"pmid":"28799069","id":"PMC_28799069","title":"Rae1-mediated nuclear export of Rnc1 is an important determinant in controlling MAPK signaling.","date":"2017","source":"Current genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28799069","citation_count":9,"is_preprint":false},{"pmid":"28867566","id":"PMC_28867566","title":"Activity analysis of LTR12C as an effective regulatory element of the RAE1 gene.","date":"2017","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/28867566","citation_count":9,"is_preprint":false},{"pmid":"33279621","id":"PMC_33279621","title":"Lysine acetylation of NKG2D ligand Rae-1 stabilizes the protein and sensitizes tumor cells to NKG2D immune surveillance.","date":"2020","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/33279621","citation_count":9,"is_preprint":false},{"pmid":"24350772","id":"PMC_24350772","title":"Activation of cellular immunity and marked inhibition of liver cancer in a mouse model following gene therapy and tumor expression of GM-SCF, IL-21, and Rae-1.","date":"2013","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/24350772","citation_count":9,"is_preprint":false},{"pmid":"22910142","id":"PMC_22910142","title":"Polymeric delivery of therapeutic RAE-1 plasmid to the pancreatic islets for the prevention of type 1 diabetes.","date":"2012","source":"Journal of controlled release : official journal of the Controlled Release Society","url":"https://pubmed.ncbi.nlm.nih.gov/22910142","citation_count":9,"is_preprint":false},{"pmid":"24495546","id":"PMC_24495546","title":"Generation of a monoclonal antibody against the glycosylphosphatidylinositol-linked protein Rae-1 using genetically engineered tumor cells.","date":"2014","source":"Biological procedures online","url":"https://pubmed.ncbi.nlm.nih.gov/24495546","citation_count":8,"is_preprint":false},{"pmid":"32333709","id":"PMC_32333709","title":"Rae1 drives NKG2D binding-dependent tumor development in mice by activating mTOR and STAT3 pathways in tumor cells.","date":"2020","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/32333709","citation_count":7,"is_preprint":false},{"pmid":"37142436","id":"PMC_37142436","title":"Shutdown of multidrug transporter bmrCD mRNA expression mediated by the ribosome-associated endoribonuclease (Rae1) cleavage in a new cryptic ORF.","date":"2023","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/37142436","citation_count":5,"is_preprint":false},{"pmid":"37774541","id":"PMC_37774541","title":"RAE1 promotes nitrosamine-induced malignant transformation of human esophageal epithelial cells through PPARα-mediated lipid metabolism.","date":"2023","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/37774541","citation_count":5,"is_preprint":false},{"pmid":"38712050","id":"PMC_38712050","title":"The Chlamydia trachomatis secreted effector CebN targets nucleoporins and Rae1 to antagonize STAT1 nuclear import.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38712050","citation_count":4,"is_preprint":false},{"pmid":"16980045","id":"PMC_16980045","title":"Yisheng injection decreases the expression of H60 and RAE-1 genes in ischemic mice liver.","date":"2006","source":"Transplantation proceedings","url":"https://pubmed.ncbi.nlm.nih.gov/16980045","citation_count":4,"is_preprint":false},{"pmid":"38417691","id":"PMC_38417691","title":"RAE1 promotes gastric carcinogenesis and epithelial-mesenchymal transition.","date":"2024","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/38417691","citation_count":3,"is_preprint":false},{"pmid":"28776765","id":"PMC_28776765","title":"Saccharomyces cerevisiae Gle2/Rae1 is involved in septin organization, essential for cell cycle progression.","date":"2017","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/28776765","citation_count":3,"is_preprint":false},{"pmid":"39526400","id":"PMC_39526400","title":"Targeting CLK2 and serine/arginine-rich splicing factors inhibits multiple myeloma through downregulating RAE1 by nonsense-mediated mRNA decay mechanism.","date":"2024","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/39526400","citation_count":2,"is_preprint":false},{"pmid":"40683483","id":"PMC_40683483","title":"RAE1-armoured DC vaccine boosts NKG2D-CAR-T cells elicited anti-solid tumour treatment.","date":"2025","source":"Pharmacological research","url":"https://pubmed.ncbi.nlm.nih.gov/40683483","citation_count":2,"is_preprint":false},{"pmid":"40483744","id":"PMC_40483744","title":"Nuclearporin subcomplex Nup98/Rae1 is vital for maternal-to-zygotic transition during early embryonic development.","date":"2025","source":"Theriogenology","url":"https://pubmed.ncbi.nlm.nih.gov/40483744","citation_count":0,"is_preprint":false},{"pmid":"17490545","id":"PMC_17490545","title":"[Effects of NKG2D and its ligands RAE-1 and H60 on graft-versus-tumor response].","date":"2007","source":"Zhongguo shi yan xue ye xue za zhi","url":"https://pubmed.ncbi.nlm.nih.gov/17490545","citation_count":0,"is_preprint":false},{"pmid":"40360986","id":"PMC_40360986","title":"The RAE1-STOP1 module regulates ABA sensitivity in early seedlings of Arabidopsis.","date":"2025","source":"BMC plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/40360986","citation_count":0,"is_preprint":false},{"pmid":"12545745","id":"PMC_12545745","title":"[Establishment of rat alveolar type II epithelial cell line RAE-1 and its biological characteristics].","date":"2002","source":"Wei sheng yan jiu = Journal of hygiene research","url":"https://pubmed.ncbi.nlm.nih.gov/12545745","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.06.04.657793","title":"The endoribonuclease Rae1 from <i>Bacillus subtilis</i> cleaves mRNA upstream of stalled ribosomes","date":"2025-06-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.04.657793","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.04.09.647954","title":"The leader proteins of Theiler’s virus and Boone cardiovirus use a combination of Short Linear Motifs (SLiMs) to target RSK kinases to the nuclear pore complex","date":"2025-04-10","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.09.647954","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.09.19.677134","title":"Methionine matters: a common mechanism of viral inhibition of host defense identified via AI-assisted molecular dynamics","date":"2025-09-19","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.19.677134","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.11.26.625382","title":"Unconventional mRNA processing and degradation pathways for the polycistronic yrzI mRNA in B. subtilis","date":"2024-11-26","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.26.625382","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.06.09.598107","title":"The RAE1-STOP1 Module Reduces Sensitivity to Exogenous ABA Treatment by Regulating ABI5 in Arabidopsis","date":"2024-06-09","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.09.598107","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":39550,"output_tokens":9225,"usd":0.128513},"stage2":{"model":"claude-opus-4-6","input_tokens":13029,"output_tokens":4311,"usd":0.25938},"total_usd":0.387893,"stage1_batch_id":"msgbatch_01SUR8NDzVrNmyszWyJeCct7","stage2_batch_id":"msgbatch_01G7Yfutko3cDWzejrwH5AMx","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1995,\n      \"finding\": \"S. pombe Rae1 is required for nuclear export of poly(A)+ RNA; rae1-1 temperature-sensitive mutant accumulates poly(A)+ RNA in the nucleus, and loss of rae1 also causes actin/tubulin disorganization and irreversible G2/M cell cycle arrest. Rae1 encodes a WD40-repeat protein.\",\n      \"method\": \"Temperature-sensitive mutant, fluorescence in situ hybridization (FISH) for poly(A)+ RNA, cell cycle analysis, gene complementation cloning\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — foundational loss-of-function with multiple orthogonal readouts (RNA export, cytoskeleton, cell cycle), replicated by subsequent work\",\n      \"pmids\": [\"7706287\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"S. cerevisiae Gle2 (Rae1 homolog) localizes to nuclear pore complexes, is required for poly(A)+ RNA export (not protein import), and interacts genetically and physically with nucleoporins Nup100p; gle2 mutants show gross NPC and nuclear envelope structural perturbation.\",\n      \"method\": \"Genetic screen (colony-sectoring), indirect immunofluorescence, NPC fractionation, poly(A)+ RNA export assay, two-hybrid interaction\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods, foundational yeast study replicated in mammalian systems\",\n      \"pmids\": [\"8970155\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"Human RAE1 cDNA partially suppresses the temperature-sensitive mRNA export defect of S. pombe rae1-1 mutant; epitope-tagged human Rae1 localizes to both nucleus and cytoplasm in HeLa cells, consistent with a role in nucleocytoplasmic trafficking.\",\n      \"method\": \"Heterologous complementation in fission yeast, poly(A)+ RNA export assay, immunofluorescence in HeLa cells\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional complementation across species plus localization, but single study\",\n      \"pmids\": [\"9370289\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"In S. pombe, Rae1 function is required for a process essential for mitotic advancement beyond mRNA export; rae1-deficient cells arrest at G2/M with elevated Cdc2p kinase, lack spindle formation, and lack spindle pole body separation. Rae1p localizes to the nuclear periphery.\",\n      \"method\": \"Temperature-sensitive mutant analysis, immunofluorescence, kinase activity assay, cell cycle arrest characterization\",\n      \"journal\": \"Yeast\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mechanistic dissection separating mRNA export from mitotic roles, single study\",\n      \"pmids\": [\"9301023\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Mammalian RAE1 binds directly to a GLEBS-like motif in NUP98 at the nuclear pore complex through multiple domains including WD-repeats and C-terminal extension; RAE1 shuttles between nucleus and cytoplasm in a temperature-dependent, RanGTP-independent manner; overexpression of the GLEBS-like motif inhibits NUP98 binding of RAE1 and causes nuclear accumulation of poly(A)+ RNA, establishing direct RAE1-NUP98 interaction as required for mRNA export.\",\n      \"method\": \"In vitro binding assay, chemical cross-linking, Xenopus oocyte microinjection, overexpression/competition experiments, poly(A)+ RNA localization\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro binding + functional microinjection + poly(A)+ RNA export assay with rescue/competition, multiple methods in single study\",\n      \"pmids\": [\"10209021\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Ct-RAE1 (Chironomus tentans RAE1 ortholog) does not associate with mRNP cotranscriptionally or in the nucleoplasm but instead binds the exported Balbiani ring RNP particle at the NPC (nuclear pore complex), and this interaction is correlated with presence of an exported RNP in the NPC channel.\",\n      \"method\": \"Immunoelectron microscopy on polytene chromosomes and nuclear pore complexes\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct ultrastructural localization linked to functional transport event, single study\",\n      \"pmids\": [\"11105759\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Mouse RAE1 (Rae1beta) is a cell-surface GPI-anchored NKG2D ligand; ectopic expression of Rae1beta on tumor cells causes their rejection by NK cells and/or CD8+ T cells in syngeneic mice, demonstrating RAE1 as a functional NKG2D ligand that triggers anti-tumor immunity.\",\n      \"method\": \"Tumor transfection, in vivo syngeneic rejection assay, NK cell/T cell depletion experiments, immune priming assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo functional assay with cell-type depletion, highly cited, replicated by independent lab (PMID:11562472)\",\n      \"pmids\": [\"11557981\", \"11562472\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Mouse RAE1 (Rae1gamma, Rae1delta) binds NKG2D with nanomolar affinity; soluble NKG2D-RAE1 interaction requires no additional co-factors. RAE1 and H60 compete directly for NKG2D occupancy, with H60 binding ~25-fold more tightly; the two interactions have distinct thermodynamic profiles (RAE1 interaction less temperature-dependent and makes less use of electrostatics).\",\n      \"method\": \"Surface plasmon resonance, isothermal titration calorimetry, competitive binding assay with soluble recombinant proteins\",\n      \"journal\": \"Immunity\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — rigorous biophysical characterization with multiple methods, quantitative affinity measurements\",\n      \"pmids\": [\"11520456\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Human NKG2D forms stable complexes with monomeric MICA and MICB in solution without additional components; it also stably interacts with ULBP/N2DL proteins (human homologs of mouse RAE-1 family); glycosylation of MICA enhances but is not essential for NKG2D binding; a single amino acid at position 129 (alpha2 domain) of MICA alleles controls large differences in NKG2D affinity.\",\n      \"method\": \"Soluble receptor-ligand binding in solution, cell-surface binding assay, allelic variant comparison, mutagenesis\",\n      \"journal\": \"Immunogenetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted binary interaction in solution with mutagenesis, identifies ULBP/N2DL as human RAE-1 homologs\",\n      \"pmids\": [\"11491531\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Haploinsufficiency of Rae1 or Bub3 in mice causes mitotic checkpoint defects and chromosome missegregation; Rae1-null mice are embryonic lethal but without detectable mRNA nuclear export defects. Rae1 overexpression corrects both Rae1 and Bub3 haploinsufficiency. Combined Rae1/Bub3 haploinsufficiency greatly increases premature sister chromatid separation and tumorigenesis susceptibility.\",\n      \"method\": \"Conditional knockout mouse generation, chromosome segregation assay, mitotic checkpoint assay, mRNA export assay, overexpression rescue\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — mammalian KO genetics with multiple readouts (embryonic lethality, aneuploidy, checkpoint, tumor susceptibility), replicated findings\",\n      \"pmids\": [\"12551952\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Nup98, Rae1/Gle2, and TAP form specific binary and ternary complexes: Gle2 requires two TAP sites for stable interaction; TAP has highest affinity for a specific GLFG region of Nup98; the ternary Nup98-Gle2-TAP complex can form simultaneously; when Gle2 is Nup98-bound, it no longer binds TAP directly, suggesting Gle2 may deliver TAP to Nup98 during mRNA export.\",\n      \"method\": \"Co-immunoprecipitation, in vitro pulldown binding assays, mapping of interaction domains\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple binary and ternary interaction mapping experiments, single lab\",\n      \"pmids\": [\"12637516\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"VSV matrix (M) protein binds Rae1/mrnp41 directly and blocks mRNA nuclear export; an M protein mutant defective in Rae1 binding cannot inhibit mRNA export; overexpression of Rae1 fully reverts M protein-induced export inhibition; IFN-gamma induces Rae1 expression, providing a host counter-measure.\",\n      \"method\": \"Co-immunoprecipitation, mRNA export assay, M protein mutant analysis, Rae1 overexpression rescue, IFN-gamma induction assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — binding + loss-of-function mutant + rescue experiment, multiple orthogonal approaches\",\n      \"pmids\": [\"15629720\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Rae1 is a microtubule-associated protein and spindle assembly factor regulated by the RanGTP/importin-beta pathway in Xenopus egg extracts; Rae1 binds importin beta directly; Rae1 depletion severely inhibits mitotic spindle assembly; a purified Rae1 ribonucleoprotein complex stabilizes microtubules in a RanGTP/importin-beta-regulated manner requiring RNA; RNA itself plays a direct, translation-independent role in spindle assembly.\",\n      \"method\": \"Activity-based purification from Xenopus egg extracts, in vitro spindle assembly assay, immunodepletion, microtubule dynamics assay, RNA requirement test\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstitution in cell-free system, depletion, direct binding, multiple orthogonal methods in highly cited study\",\n      \"pmids\": [\"15851029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Rae1 and Nup98 form a complex with Cdh1-activated APC (APC-Cdh1) in early mitosis and specifically inhibit APC-Cdh1-mediated ubiquitination of securin (but not cyclin B); combined Rae1/Nup98 haploinsufficiency causes premature securin destruction, premature sister chromatid separation, and severe aneuploidy. Dissociation of Rae1-Nup98 from APC-Cdh1 coincides with BubR1 release from APC-Cdc20 at the metaphase-to-anaphase transition.\",\n      \"method\": \"Mouse haploinsufficiency genetics, co-immunoprecipitation, ubiquitination assay, time-lapse microscopy, securin degradation assay\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vivo genetics + biochemical APC ubiquitination assay + co-IP, multiple methods, highly cited\",\n      \"pmids\": [\"16355229\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Rae1 and Nup98 form a ternary complex with APC-Cdh1 and securin in prometaphase; the Rae1-Nup98 complex does not prevent APC-Cdh1 from binding securin but instead prevents ubiquitination of already-bound securin, priming rapid securin degradation upon Rae1-Nup98 complex release at metaphase-to-anaphase transition.\",\n      \"method\": \"Co-immunoprecipitation showing ternary complex formation, ubiquitination assay in mouse cells, genetic mouse model\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — mechanistic refinement with co-IP of ternary complex + ubiquitination assay, builds directly on PMID:16355229\",\n      \"pmids\": [\"16479161\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Rae1 interacts with NuMA in a mitosis-specific manner; Rae1 binds a specific site on NuMA converting a NuMA dimer into a tetravalent MT crosslinker; reducing Rae1 or increasing NuMA causes multipolar spindle abnormalities; coupling NuMA overexpression to Rae1 overexpression, or NuMA depletion to Rae1 depletion, prevents aberrant spindles; overexpression of the Rae1-binding domain of NuMA alone causes spindle defects.\",\n      \"method\": \"Co-immunoprecipitation (mitosis-specific), domain mapping, RNAi knockdown, overexpression in HeLa cells, spindle phenotype analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal genetic and biochemical experiments with multiple gain/loss-of-function combinations\",\n      \"pmids\": [\"17172455\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Crystal structure of human Rae1 in complex with the GLEBS motif of Nup98 at 1.65 Å resolution: Rae1 forms a seven-bladed beta-propeller; Nup98 GLEBS forms an ~50-Å hairpin binding with its C-terminal arm to an invariant hydrophobic surface spanning the top face of the Rae1 beta-propeller; the C-terminal arm of GLEBS is necessary and sufficient for Rae1 binding; a tandem glutamate element is critical for complex formation; the Rae1-Nup98 complex binds single-stranded RNA.\",\n      \"method\": \"X-ray crystallography (1.65 Å), mutagenesis, in vitro binding assay, RNA-binding assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution crystal structure validated by mutagenesis and binding assays\",\n      \"pmids\": [\"20498086\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Drosophila Rae1 is a component of the Highwire (Hiw)/Fsn E3 ubiquitin ligase complex in neurons; Rae1 physically and genetically interacts with Hiw; Rae1 loss causes NMJ morphological defects similar to hiw mutants and deregulates the MAP kinase kinase kinase Wallenda; Rae1 is necessary and sufficient to promote Hiw protein abundance by binding Hiw and protecting it from autophagy-mediated degradation.\",\n      \"method\": \"Tandem affinity purification/mass spectrometry, co-immunoprecipitation, genetic interaction (double mutants), neuromuscular junction morphology assay, Hiw protein stability assay\",\n      \"journal\": \"Nature neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — TAP-MS identification + reciprocal co-IP + epistasis + protein stability assay, multiple orthogonal methods\",\n      \"pmids\": [\"21874015\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"RAE1 depletion disrupts NUP98 expression and localization, causing severe chromosome segregation defects; RAE1-NUP98 complex orchestrates proper chromosome segregation; in NUP98-HOXA9-transfected cells and AML patient samples, RAE1 protein is reduced and mislocalized, suggesting RAE1 dysfunction contributes to NUP98 fusion-mediated leukemogenesis.\",\n      \"method\": \"RNAi knockdown, rescue experiments, immunofluorescence, NUP98-HOXA9 transgenic mice, AML patient samples\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — RNAi + rescue + transgenic mouse, but leukemogenesis link is correlative\",\n      \"pmids\": [\"21467841\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"C. elegans RAE-1 is an evolutionarily conserved binding partner of RPM-1 (ortholog of human Pam/Highwire); RAE-1 binding region in RPM-1 is conserved and the Rae1-Pam interaction also occurs in humans; RAE-1 loss-of-function causes similar axon termination and synapse formation defects as rpm-1; RAE-1 colocalizes with RPM-1 in neurons and functions downstream of rpm-1.\",\n      \"method\": \"Mass spectrometry, co-immunoprecipitation, genetic epistasis (double mutants), immunofluorescence colocalization\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — MS identification + co-IP + genetic epistasis, single study\",\n      \"pmids\": [\"22357847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"VSV M protein forms multiple distinct complexes with Rae1 and Nup98; intermediate molecular weight Rae1-Nup98 complexes interact most efficiently with M protein; silencing Rae1 reduces VSV's ability to inhibit host transcription (but not mRNA nuclear accumulation or translation inhibition); M protein-Rae1-Nup98 complexes associate with the chromatin fraction, suggesting a role in transcription inhibition beyond nuclear transport.\",\n      \"method\": \"Size exclusion chromatography, sedimentation velocity analysis, co-immunoprecipitation, Rae1 siRNA, chromatin fractionation\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple biochemical methods + siRNA with specific readout, single lab\",\n      \"pmids\": [\"23028327\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Crystal structure of the VSV M protein-Rae1-Nup98 ternary complex at 3.15 Å: M protein contacts the Rae1 beta-propeller via two protrusions ('finger' and 'thumb'); conserved Met51 (finger) inserts into a deep hydrophobic pocket on Rae1 with flanking acidic residues bonding to basic groove; M protein competes with oligonucleotide binding to Rae1-Nup98, and the finger peptide alone recapitulates this competition, suggesting Rae1 serves as a phosphate backbone-binding protein for mRNA during export.\",\n      \"method\": \"X-ray crystallography (3.15 Å), competitive nucleic acid binding assay, synthetic peptide competition assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure + mutagenesis + competition binding assay, mechanistic model proposed and experimentally tested\",\n      \"pmids\": [\"24927547\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RAE-1 family NKG2D ligands are transcriptionally repressed by HDAC3 in healthy cells; mouse CMV protein m18 relieves this repression by interacting with Casein Kinase II and preventing it from activating HDAC3, thereby inducing RAE-1 expression; analogously, human herpesvirus HDAC-inhibiting proteins induce the human NKG2D ligand ULBP-1.\",\n      \"method\": \"Genetic knockout/complementation, co-immunoprecipitation (m18-CK2 interaction), HDAC inhibitor treatment, reporter assays, chromatin immunoprecipitation\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — mechanistic pathway (m18→CK2→HDAC3→RAE1) defined with co-IP, ChIP, genetic evidence, conserved to human\",\n      \"pmids\": [\"27874833\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The Hippo pathway targets Rae1 for degradation downstream of Warts/Lats kinase; Rae1 regulates cyclin B levels and organ size; Rae1 loss restricts cyclin B and organ size while Rae1 overexpression increases them; reducing Rae1 suppresses overgrowth caused by Hippo pathway loss; Rae1 acts post-transcriptionally to increase protein levels of Merlin, Hippo, and Warts, creating a feedback circuit.\",\n      \"method\": \"Genetic epistasis (Drosophila), biochemical co-IP, cyclin B quantification, organ size measurement, mammalian cell validation\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis + biochemistry in Drosophila and mammalian cells, but Warts-mediated Rae1 degradation mechanism not fully biochemically defined\",\n      \"pmids\": [\"27494403\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RAE1 is ubiquitinated and the deubiquitinating enzyme USP11 removes ubiquitin from RAE1; USP11 is associated with the mitotic spindle; USP11 knockdown reduces cell proliferation and increases multipolar spindle formation; USP11 functionally modulates RAE1's interaction with NuMA at the mitotic spindle through controlling RAE1 ubiquitination status.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, lentiviral knockdown, multipolar spindle analysis, spindle immunofluorescence\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — DUB-substrate relationship identified with biochemical ubiquitination assay + functional spindle phenotype, single lab\",\n      \"pmids\": [\"29293652\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Rae1 acetylation at lysine residues K80 and K87 by acetyltransferases GCN5 and PCAF protects Rae1 (mouse NKG2D ligand) from matrix metalloproteinase-mediated shedding; K80/K87 mutations abolish acetylation and desensitize tumor cells to NKG2D-dependent immune surveillance in vitro and in vivo.\",\n      \"method\": \"In vitro acetylation assay, mutagenesis (K80/K87A), shedding assay, NKG2D-dependent killing assay, in vivo tumor model\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 — biochemical acetylation + mutagenesis + functional killing assay in vitro and in vivo, single lab\",\n      \"pmids\": [\"33279621\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SARS-CoV-2 ORF6 copurifies with Rae1 and Nup98; this interaction is mapped to the C-terminus of ORF6 (Met58 critical); ORF6 causes nuclear entrapment of host mRNA and blocks expression of newly transcribed reporters; Rae1 overexpression restores reporter expression; SARS-CoV-2 ORF6 more strongly copurifies with Rae1/Nup98 than SARS-CoV ORF6; both block nuclear import of a broad range of host proteins through Rae1-Nup98 interactions.\",\n      \"method\": \"Co-purification (affinity), reporter assay, poly(A)+ RNA localization, single amino acid mutagenesis (Met58), Rae1 overexpression rescue, nuclear import assay\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — co-purification + mutagenesis + rescue + functional import/export assay, multiple orthogonal methods\",\n      \"pmids\": [\"33849972\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Crystal structures of SARS-CoV-2 and SARS-CoV-1 ORF6 C-termini in complex with the Rae1-Nup98 heterodimer reveal that ORF6 occupies the same potential mRNA-binding groove of Rae1-Nup98 as VSV M protein; direct tight binding of ORF6 to the Rae1-Nup98 complex competitively inhibits RNA binding; the highly conserved M58 of ORF6 is critical for this interaction.\",\n      \"method\": \"X-ray crystallography, in vitro competitive RNA-binding assay, mutagenesis (M58)\",\n      \"journal\": \"Frontiers in molecular biosciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure + competitive binding assay + mutagenesis\",\n      \"pmids\": [\"35096974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NUP98 and RAE1 are highly expressed in epidermal progenitors forming a nucleoplasmic complex; reduction of NUP98 or RAE1 abolishes regenerative capacity, inhibits proliferation, and induces premature differentiation; NUP98 binds chromatin near transcription start sites of key epigenetic regulators (DNMT1, UHRF1, EZH2) and sustains their expression; HDAC inhibition diminishes NUP98 chromatin binding and causes NUP98 and RAE1 to mislocalize interdependently to the nucleolus.\",\n      \"method\": \"ChIP-seq, knockdown, chromatin fractionation, immunofluorescence, epigenetic regulator expression analysis, HDAC inhibitor treatment\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP-seq + knockdown + localization, single lab, mechanistic detail of NUP98-RAE1 chromatin regulatory function\",\n      \"pmids\": [\"37353594\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Rae1 is required for SARS-CoV-2 ORF6-mediated inhibition of nucleocytoplasmic transport; Rae1 alone is not necessary to support p-STAT1 import or poly(A) RNA export under basal conditions; loss of Rae1 suppresses the transport inhibitory activity of ORF6; Rae1-Nup98 complex strategically positions ORF6 within the NPC where it alters FG-Nup interactions; Rae1 is required for normal viral protein production during SARS-CoV-2 infection.\",\n      \"method\": \"Rae1 knockdown/knockout, p-STAT1 nuclear import assay, poly(A)+ RNA export assay, viral infection, co-immunoprecipitation\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with specific mechanistic readouts, single lab\",\n      \"pmids\": [\"38507240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Retinoic acid downregulates Rae1 protein and mRNA expression in neuroblastoma cells; Rae1 overexpression prevents retinoic acid-induced APC-Cdh1 activation, Skp2 degradation, p27 accumulation, cell cycle arrest and differentiation; Cdh1 inhibition has similar effects; thus, Rae1 limits APC-Cdh1 activity to promote cell proliferation and its downregulation by retinoic acid facilitates differentiation.\",\n      \"method\": \"Immunoblot, RT-PCR, Rae1 overexpression and knockdown in SH-SY5Y cells, cell cycle analysis, differentiation assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — gain/loss-of-function + multiple downstream readouts in human cell line, single lab\",\n      \"pmids\": [\"18212744\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"RAE-1 family NKG2D ligand expression in cancer cell lines and proliferating normal cells is directly coupled to cell cycle entry; E2F transcription factors directly transcriptionally activate Raet1 genes; RAE-1 induction occurs in primary cultures, embryonic brain, and healing wounds; wound healing is delayed in NKG2D-deficient mice.\",\n      \"method\": \"Transcriptional reporter assay, E2F ChIP/binding analysis, E2F overexpression/knockdown, NKG2D-deficient mouse wound healing model\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct E2F-Raet1 promoter binding + E2F manipulation + in vivo NKG2D KO phenotype, multiple methods\",\n      \"pmids\": [\"23166357\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Induction of RAE1 NKG2D ligands by the DNA damage response requires a STING-dependent DNA sensor pathway involving TBK1 and IRF3; cytosolic DNA detected in RAE1-expressing lymphoma cells required DDR activation; DNA transfection into ligand-negative cells is sufficient to induce RAE1 expression; Irf3-haploinsufficient Eμ-Myc mice show reduced tumor RAE1 levels and reduced survival.\",\n      \"method\": \"STING/TBK1/IRF3 pharmacological inhibition and genetic KO, cytosolic DNA detection, DNA transfection assay, in vivo mouse lymphoma model\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — pathway dissection with genetic and pharmacological tools + in vivo validation, single lab\",\n      \"pmids\": [\"24590060\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"RAE-1 expression requires activation of the PI3K pathway (specifically the p110α catalytic subunit) during MCMV infection and transformation; inhibition of p110α blocks RAE-1 induction by MCMV infection and reduces RAE-1 cell surface expression on transformed cells.\",\n      \"method\": \"PI3K isoform-selective pharmacological inhibition, siRNA knockdown of PI3K subunits, cell surface RAE-1 flow cytometry, viral infection assays\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — pharmacological + genetic dissection with specific isoform identification, single lab\",\n      \"pmids\": [\"21966273\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"MCMV m152/gp40 directly binds RAE-1 isoforms with 1:1 stoichiometry and Kd < 5 μM; binding affinity differs quantitatively among RAE-1 isoforms, corresponding to differential susceptibility to downregulation; RAE-1delta is resistant to downregulation because its mature surface-resident form has an intrinsic property (absence of PLWY motif in beta/gamma does not fully explain delta resistance), suggesting a novel escape mechanism from viral immunoevasion.\",\n      \"method\": \"Protein purification, size exclusion chromatography, analytical ultracentrifugation, isothermal titration calorimetry, cotransfection assay in HEK293T cells\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple rigorous biophysical methods quantifying direct m152-RAE1 interaction with isoform specificity\",\n      \"pmids\": [\"20166740\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"Human/mammalian RAE1 is a multifunctional WD40 beta-propeller protein that: (1) acts as an mRNA export factor by binding directly to the GLEBS motif of NUP98 at the nuclear pore complex (NPC), where it transiently associates with mRNP cargo and uses its RNA-binding surface to facilitate mRNA translocation; (2) functions as a mitotic regulator by forming a complex with NUP98 that inhibits APC-Cdh1-mediated ubiquitination of securin until the metaphase-to-anaphase transition, interacts with NuMA as a tetravalent MT crosslinker for bipolar spindle formation, and associates with microtubules as part of a RanGTP/importin-beta-regulated ribonucleoprotein complex required for spindle assembly; (3) serves as a cell-surface GPI-anchored NKG2D ligand (murine RAE-1 isoforms) whose expression is regulated by E2F transcription factors, PI3K/HDAC3 signaling, and DNA damage-activated STING-IRF3 pathways; and (4) is targeted by multiple viral proteins (VSV M protein, SARS-CoV-2 ORF6) that occupy the nucleic acid-binding groove of the Rae1-Nup98 complex to block nucleocytoplasmic transport and suppress host antiviral responses.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"RAE1 is a WD40-repeat beta-propeller protein that functions at the nexus of mRNA nuclear export and mitotic regulation. As a seven-bladed beta-propeller, RAE1 binds the GLEBS motif of NUP98 at the nuclear pore complex, where it engages single-stranded RNA through a conserved basic groove to facilitate mRNA translocation; this same groove is competitively targeted by viral proteins including VSV M protein and SARS-CoV-2 ORF6 to block nucleocytoplasmic transport and suppress host antiviral responses [PMID:20498086, PMID:24927547, PMID:35096974]. During mitosis, the RAE1–NUP98 complex inhibits APC/C-Cdh1-mediated ubiquitination of securin until the metaphase-to-anaphase transition, and RAE1 independently interacts with NuMA to convert it into a tetravalent microtubule crosslinker required for bipolar spindle assembly; haploinsufficiency of RAE1 causes chromosome missegregation and tumor susceptibility in mice [PMID:16355229, PMID:17172455, PMID:12551952]. Separately, the murine RAE-1 family encodes GPI-anchored cell-surface NKG2D ligands whose expression is transcriptionally controlled by E2F, PI3K/HDAC3, and STING-IRF3 pathways and whose engagement of NKG2D activates NK cell and CD8+ T cell anti-tumor immunity [PMID:11557981, PMID:23166357, PMID:27874833].\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Establishing that RAE1 is an essential mRNA export factor and WD40-repeat protein resolved what gene product mediates poly(A)+ RNA nuclear export in fission yeast, and revealed a dual connection to cell cycle progression.\",\n      \"evidence\": \"Temperature-sensitive rae1-1 mutant in S. pombe with FISH for poly(A)+ RNA accumulation, cell cycle analysis showing G2/M arrest\",\n      \"pmids\": [\"7706287\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of mRNA engagement unknown\", \"Whether cell cycle arrest is direct or secondary to export block unclear\", \"No metazoan data\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Demonstration that the budding yeast homolog Gle2 localizes to NPCs and interacts with nucleoporin Nup100p established that RAE1 functions at the nuclear pore rather than in the nucleoplasm.\",\n      \"evidence\": \"Indirect immunofluorescence, NPC fractionation, and two-hybrid interaction with Nup100p in S. cerevisiae\",\n      \"pmids\": [\"8970155\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct binding partner in metazoans not yet identified\", \"RNA-binding activity not tested\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Identification of NUP98 as the direct binding partner of mammalian RAE1 via a GLEBS motif, and demonstration that this interaction is required for mRNA export, established the core RAE1–NUP98 axis at the NPC.\",\n      \"evidence\": \"In vitro binding, chemical cross-linking, Xenopus oocyte microinjection with GLEBS competition blocking poly(A)+ RNA export\",\n      \"pmids\": [\"10209021\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of GLEBS recognition unknown\", \"Whether RAE1 contacts mRNA directly unresolved\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Ultrastructural evidence that RAE1 binds mRNP cargo specifically at the NPC channel — not cotranscriptionally — established it as a transient NPC-associated export factor rather than an mRNP packaging component.\",\n      \"evidence\": \"Immunoelectron microscopy on Chironomus tentans Balbiani ring mRNP at nuclear pores\",\n      \"pmids\": [\"11105759\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single organism (dipteran), generality to mammals not directly shown\", \"Molecular contacts between RAE1 and mRNP undefined\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Discovery that murine RAE-1 isoforms are GPI-anchored cell-surface NKG2D ligands that trigger NK cell and CD8+ T cell anti-tumor rejection established a distinct immune function for the RAE-1 gene family, separate from the nucleoporin-associated mRNA export protein.\",\n      \"evidence\": \"Tumor transfection with Rae1beta, in vivo syngeneic rejection with NK/T cell depletion; SPR and ITC measuring nanomolar NKG2D binding\",\n      \"pmids\": [\"11557981\", \"11520456\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Regulation of RAE-1 surface expression unknown\", \"Structural basis of NKG2D–RAE-1 recognition not yet solved\", \"Human ortholog functional equivalence assumed but not tested\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Rae1 haploinsufficiency in mice revealed an essential mitotic checkpoint role separable from mRNA export: Rae1+/− mice showed chromosome missegregation and tumor susceptibility without detectable export defects, and genetic interaction with Bub3 indicated a shared spindle checkpoint pathway.\",\n      \"evidence\": \"Conditional knockout mice with chromosome segregation assay, mitotic checkpoint assay, and mRNA export measurement; Rae1/Bub3 compound haploinsufficiency\",\n      \"pmids\": [\"12551952\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism of checkpoint function unknown\", \"Whether RAE1 directly participates in spindle checkpoint signaling or acts indirectly unresolved\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Two breakthrough studies defined RAE1's mitotic mechanisms: (1) Rae1–Nup98 complex inhibits APC/C-Cdh1 ubiquitination of securin to prevent premature sister chromatid separation, and (2) Rae1 is a RanGTP/importin-beta-regulated microtubule-associated spindle assembly factor whose function requires associated RNA.\",\n      \"evidence\": \"APC ubiquitination assay and mouse haploinsufficiency genetics (securin); activity-based purification from Xenopus egg extracts with immunodepletion and microtubule dynamics assay (spindle assembly)\",\n      \"pmids\": [\"16355229\", \"15851029\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How securin inhibition is relieved at metaphase-anaphase transition not fully defined\", \"Identity of the RNA species required for spindle assembly unknown\", \"How the mRNA export and mitotic functions are temporally coordinated unclear\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"VSV M protein was shown to directly bind RAE1 and block mRNA export, with a loss-of-binding M mutant unable to inhibit export and RAE1 overexpression fully rescuing the block — establishing RAE1–NUP98 as a viral target for host gene expression shutoff.\",\n      \"evidence\": \"Co-immunoprecipitation, M protein mutant analysis, RAE1 overexpression rescue, mRNA export assay\",\n      \"pmids\": [\"15629720\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of M protein–RAE1 interaction unknown at this time\", \"Whether other viruses exploit the same mechanism unresolved\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"RAE1 was found to interact with NuMA in a mitosis-specific manner, converting the NuMA dimer into a tetravalent microtubule crosslinker essential for bipolar spindle formation — establishing a third distinct mitotic role for RAE1.\",\n      \"evidence\": \"Mitosis-specific co-immunoprecipitation, domain mapping, reciprocal RNAi/overexpression titration of RAE1 and NuMA with spindle phenotype scoring in HeLa cells\",\n      \"pmids\": [\"17172455\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural details of the RAE1–NuMA interface unknown\", \"How RAE1 allocation between NuMA and NUP98 is regulated during mitosis unclear\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"The 1.65 Å crystal structure of human RAE1–NUP98(GLEBS) revealed a seven-bladed beta-propeller architecture with a conserved basic groove for ssRNA binding, providing the structural framework for understanding both mRNA export and viral mimicry mechanisms.\",\n      \"evidence\": \"X-ray crystallography at 1.65 Å with mutagenesis validation and RNA-binding assay\",\n      \"pmids\": [\"20498086\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structure of RAE1 bound to mRNA substrate\", \"How RNA binding contributes to export selectivity unresolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"A neuronal function was uncovered: Drosophila and C. elegans RAE1 stabilizes the Highwire/RPM-1 E3 ubiquitin ligase by protecting it from autophagy-mediated degradation, with loss of RAE1 causing axon termination and synapse formation defects — extending RAE1 function beyond nucleocytoplasmic transport and mitosis.\",\n      \"evidence\": \"TAP-MS, co-immunoprecipitation, genetic epistasis, NMJ morphology analysis in Drosophila; MS, co-IP, and epistasis in C. elegans with conservation to human Pam\",\n      \"pmids\": [\"21874015\", \"22357847\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which RAE1 shields Highwire from autophagy not defined\", \"Whether this function operates in mammalian neurons in vivo unknown\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Transcriptional regulation of murine RAE-1 NKG2D ligands was linked to E2F transcription factors driving expression during cell cycle entry, coupling innate immune surveillance to proliferative status.\",\n      \"evidence\": \"E2F ChIP at Raet1 promoters, E2F overexpression/knockdown, NKG2D-deficient mouse wound healing model\",\n      \"pmids\": [\"23166357\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether E2F regulation applies to human ULBP orthologs not directly shown\", \"Epigenetic layers beyond E2F incompletely mapped\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Crystal structures of VSV M protein bound to RAE1–NUP98 revealed that M protein inserts a methionine finger into the RNA-binding groove of RAE1, directly competing with mRNA — establishing the structural basis for viral hijacking of the export machinery.\",\n      \"evidence\": \"X-ray crystallography at 3.15 Å, competitive nucleic acid binding assay, synthetic peptide competition\",\n      \"pmids\": [\"24927547\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether all paramyxo/rhabdovirus M proteins use the same mechanism unknown\", \"In vivo relevance of groove occupancy vs. other M protein functions not fully separated\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"HDAC3 was identified as a transcriptional repressor of RAE-1 NKG2D ligands, with MCMV protein m18 relieving this repression via Casein Kinase II inhibition — defining a viral strategy that paradoxically activates innate immunity.\",\n      \"evidence\": \"HDAC3 knockout/complementation, m18–CK2 co-immunoprecipitation, ChIP, HDAC inhibitor treatment\",\n      \"pmids\": [\"27874833\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How HDAC3-mediated repression is maintained in uninfected cells mechanistically incomplete\", \"Whether m18-induced RAE-1 has net pro- or anti-viral outcome in vivo unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"SARS-CoV-2 ORF6 was shown to bind RAE1–NUP98 via a critical Met58 residue, blocking both mRNA export and protein nuclear import — establishing coronavirus exploitation of the same RAE1 groove targeted by VSV M protein.\",\n      \"evidence\": \"Co-purification, Met58 mutagenesis, poly(A)+ RNA localization, reporter rescue by RAE1 overexpression, nuclear import assay\",\n      \"pmids\": [\"33849972\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural details not yet available at this point\", \"Contribution of RAE1 targeting to COVID-19 pathogenesis unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Crystal structures of SARS-CoV-1 and SARS-CoV-2 ORF6 C-termini bound to RAE1–NUP98 confirmed competitive occupancy of the mRNA-binding groove, unifying the structural mechanism of viral immune evasion across RNA virus families.\",\n      \"evidence\": \"X-ray crystallography, competitive RNA-binding assay, Met58 mutagenesis\",\n      \"pmids\": [\"35096974\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether therapeutic targeting of the RAE1 groove could block viral evasion untested\", \"No structure of RAE1 with a physiological mRNA substrate for comparison\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include: the identity and structural basis of physiological mRNA substrates bound in the RAE1 groove during export; how RAE1 is partitioned among its NPC-export, APC/C-inhibitory, NuMA-crosslinking, and chromatin-regulatory functions during the cell cycle; and whether the neuronal Highwire-stabilizing function operates in mammalian neurons in vivo.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of RAE1 bound to a physiological mRNA\", \"Temporal regulation of RAE1 allocation among distinct complexes undefined\", \"Mammalian in vivo validation of neuronal Highwire/Pam stabilization missing\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 4, 5, 16, 21, 27]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [12, 15]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [13, 14, 30]},\n      {\"term_id\": \"GO:0048018\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 2, 4, 28]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2, 12]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [20, 28]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [12, 15, 24]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 4, 5, 11, 16, 21]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [9, 13, 14, 15, 24]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [6, 7, 22, 31, 32]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [4, 26, 29]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [26, 27, 29]}\n    ],\n    \"complexes\": [\n      \"RAE1-NUP98\",\n      \"APC/C-Cdh1-RAE1-NUP98\",\n      \"RAE1-NuMA\",\n      \"Highwire/RPM-1 E3 ligase complex\"\n    ],\n    \"partners\": [\n      \"NUP98\",\n      \"NUMA1\",\n      \"BUB3\",\n      \"CDH1\",\n      \"KLRK1\",\n      \"USP11\",\n      \"RANBP2\",\n      \"NXF1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}