{"gene":"NXF1","run_date":"2026-04-29T11:37:57","timeline":{"discoveries":[{"year":2000,"finding":"NXF1 (TAP) has a conserved modular architecture comprising an RNP-type RNA-binding domain, leucine-rich repeats (LRR), an NTF2-like domain that heterodimerizes with p15/NXT1, and a UBA-like domain that mediates interaction with nucleoporins. NXF2, a human paralog, binds RNA, localizes to the nuclear envelope, and has RNA export activity, while NXF3 lacks these activities.","method":"Domain deletion analysis, RNA-binding assays, nuclear envelope localization by microscopy, RNA export reporter assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal functional assays (RNA binding, export, localization) in one study with defined domain mutants","pmids":["11073998"],"is_preprint":false},{"year":2001,"finding":"Overexpression of TAP/p15 (NXF1/NXT1) heterodimers bypasses nuclear retention and stimulates nuclear mRNA export. The LRR domain is essential for this activity, and the UBA-like domain strongly contributes. Heterodimer formation between NXF1 and p15 is required for efficient mRNA export.","method":"mRNA export reporter assays, domain deletion mutants, tethering assays in transfected cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — systematic domain mutagenesis with quantitative export readouts, replicated in multiple constructs","pmids":["11259411"],"is_preprint":false},{"year":2002,"finding":"NXF1-mediated mRNA export requires at minimum two nucleoporin-binding sites; these can be provided by the NTF2-like scaffold plus UBA-like domain, or by two copies of either domain in tandem. The function of the NTF2-like scaffold (and therefore p15) is confined to nucleoporin binding, not to imparting directionality or regulating cargo interactions per se.","method":"Domain swap/tandem duplication mutants expressed in cells; mRNA export reporter assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — systematic domain-swap mutagenesis with clear functional readouts","pmids":["12101235"],"is_preprint":false},{"year":2002,"finding":"NXT1/p15 functions as a critical cofactor for NXF1 (Tap)-mediated mRNA export by enhancing NXF1 binding to nucleoporins. Without NXT1, NXF1 cannot effectively interact with nuclear pore complex components, and both NXF1 nucleocytoplasmic shuttling and mRNA export are severely attenuated. Tap/NXT1 heterodimer forms a ternary complex with nucleoporins in vitro and in vivo.","method":"Co-IP, in vitro nucleoporin binding assays, mRNA export reporter assays in human and Drosophila cells; RNAi knockdown of Drosophila NXT1 causing poly(A)+ RNA nuclear accumulation","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal binding assays, RNAi phenotype in two cell systems, in vitro reconstitution","pmids":["11739738"],"is_preprint":false},{"year":2002,"finding":"The C-terminal FG-nucleoporin binding domain of NXF1 (Tap) adopts a distinctive four-helix structure joined to adjacent modules by a flexible Pro-rich linker. The F617A mutation suppresses FG-nucleoporin binding by this domain, establishing the structural basis for nuclear shuttling.","method":"NMR solution structure; site-directed mutagenesis (F617A)","journal":"Nature structural biology","confidence":"High","confidence_rationale":"Tier 1 — NMR structure with mutagenesis validation","pmids":["11875519"],"is_preprint":false},{"year":2001,"finding":"NXT1/p15 stimulates binding of a Tap–RNA complex to nucleoporins in vitro, and this interaction is necessary for nuclear export of an intron-containing viral mRNA in vivo. NXF1 contains separate domains for nucleoporin binding and NXT1 binding, both critical for export. NXT1 regulates the affinity of the Tap–RNA complex for nucleoporins, including p62.","method":"In vitro nucleoporin binding assays with recombinant proteins; site-directed mutagenesis; nuclear export reporter assays in vivo","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro reconstitution with recombinant proteins, mutagenesis, and in vivo export assays","pmids":["11579093"],"is_preprint":false},{"year":2003,"finding":"NXF1 (TAP) forms a stable binary and ternary complex with the nucleoporins Rae1/Gle2 and Nup98. Gle2 requires two sites on TAP for stable interaction. TAP has highest affinity for a specific region within the GLFG domain of Nup98, not all FG repeats equally. Gle2 and Nup98 may compete for TAP binding, suggesting Gle2 delivers TAP to Nup98.","method":"Co-IP, pulldown with defined protein domains; binary and ternary complex formation assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 — pulldown/co-IP with systematic domain mapping; single study","pmids":["12637516"],"is_preprint":false},{"year":2004,"finding":"RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the cytoplasmic filaments of the nuclear pore complex. Depletion of RanBP2 from Drosophila cells inhibits mRNA export and strongly reduces NXF1 localization at the NPC, releasing NXF1 into the cytoplasm; CRM1-dependent export and other nuclear/cytoplasmic proteins are unaffected.","method":"RNAi depletion of RanBP2 in Drosophila cells; fluorescence microscopy of NXF1 localization; poly(A)+ RNA FISH","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — specific knockdown with defined NXF1 localization and mRNA export phenotypes; parallel controls","pmids":["14729961"],"is_preprint":false},{"year":2006,"finding":"NXF1 (Tap) contains an alternatively spliced intron 10 that harbors a functional constitutive transport element (CTE). The resulting intron-retaining Tap mRNA is exported to the cytoplasm and translated into a small Tap protein detectable in human and monkey cells, demonstrating autoregulation through CTE-mediated export of its own intron-containing mRNA.","method":"RT-PCR, polyribosome fractionation, immunoblotting for small Tap protein, reporter export assays in Xenopus oocytes","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods including polysome fractionation, protein detection, and export assays","pmids":["16971948"],"is_preprint":false},{"year":2006,"finding":"Y14 (splicing factor) and NXF1 form mRNA export complexes that preferentially localize within and around nuclear speckles (SC35 domains) in living cells. BiFC and FRAP/FLIP reveal that roughly half the Y14–NXF1 complexes are immobile in vivo and depleted by ATP in permeabilized cells, suggesting ATP-dependent retention of a subset of mRNPs at speckles despite association with export proteins.","method":"Bimolecular fluorescence complementation (BiFC) in live MCF7 cells; FRAP; FLIP; co-immunoprecipitation","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 — live-cell BiFC and FRAP; single lab","pmids":["16431928"],"is_preprint":false},{"year":2001,"finding":"U2AF35 (small subunit of splicing factor U2AF) directly binds a distinct region of NXF1 (TAP) that also targets TAP to spliced mRNP. U2AF65 overexpression recruits U2AF35 and TAP to spliced mRNP and stimulates nuclear export, suggesting U2AF participates in mRNA export by facilitating TAP recruitment.","method":"Yeast two-hybrid, in vitro binding assays, immunoprecipitation of mRNP, export reporter assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — yeast two-hybrid confirmed by in vitro binding; export assays; single lab","pmids":["11724776"],"is_preprint":false},{"year":2009,"finding":"THOC5 (a TREX complex subunit) binds a distinct surface on the NTF2-like domain of NXF1 (Tap-p15), at a site non-overlapping with the Aly/REF binding site, allowing simultaneous binding. THOC5 is required for nuclear export of HSP70 mRNA but not bulk mRNA, identifying it as a specific export co-adaptor.","method":"GST pulldown mapping of binding surfaces; co-immunoprecipitation; siRNA knockdown with mRNA export assays (FISH for HSP70 mRNA)","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — reciprocal pulldowns defining non-overlapping binding sites; specific export phenotype with RNAi","pmids":["19165146"],"is_preprint":false},{"year":2010,"finding":"Arginine methylation of REF/ALY reduces its RNA-binding activity in vitro and in vivo. This reduced affinity is essential for efficient displacement of RNA from REF by NXF1 (TAP), promoting handover of mRNA cargo to NXF1. Arginine methylation does not affect the REF–TAP protein–protein interaction.","method":"Mass spectrometry mapping of methylation sites; in vitro RNA-binding assays with methylated/unmethylated REF; in vivo RNA immunoprecipitation; mRNA export assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 — MS-based methylation mapping, biochemical assays, and in vivo functional readout in one study","pmids":["20129943"],"is_preprint":false},{"year":2011,"finding":"NXF1 uses an intramolecular interaction to inhibit its own RNA-binding activity. When TREX subunits Aly and THOC5 contact NXF1, NXF1 adopts an open conformation that exposes its RNA-binding domain, enabling RNA binding. Combined knockdown of Aly and THOC5 reduces NXF1 bound to mRNA in vivo and causes severe mRNA export block.","method":"Biochemical conformation assay; RNA-binding assays with recombinant proteins; siRNA double knockdown with RNA immunoprecipitation and FISH","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 — reconstituted conformational switch with recombinant proteins; validated in vivo by RNAi and RIP","pmids":["22893130"],"is_preprint":false},{"year":2011,"finding":"The mammalian nuclear pore protein Tpr restricts nuclear export of mRNAs with retained introns that traffic through the NXF1/NXT1 pathway. Knockdown of Tpr significantly increases export and translation of CTE-containing mRNA (NXF1 pathway), but has no effect on Rev/RRE-dependent (CRM1 pathway) or completely spliced mRNA export.","method":"RNAi knockdown of Tpr; mRNA export reporter assays comparing CTE vs. RRE pathways","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 — specific pathway comparison by knockdown; single lab","pmids":["21613532"],"is_preprint":false},{"year":2011,"finding":"Multiple karyopherins (importin β, karyopherin β2/transportin, importin 4, importin 11, importin α) can import NXF1 into the nucleus by recognizing two NLS epitopes in the N-terminal tail: an N-terminal basic segment and a C-terminal PY-NLS (R-X2-5-P-Y motif). Mutation of both epitopes mislocalizes NXF1 to the cytoplasm and significantly impairs mRNA export.","method":"Biochemical binding assays with recombinant karyopherins; mutagenesis of NLS epitopes; fluorescence microscopy of NXF1 localization; mRNA export assays","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — systematic mutagenesis with binding assays, localization, and functional export readout; multiple karyopherins tested","pmids":["21965294"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of human NXF1 (first three domains: RRM, LRR, NTF2-like) together with NXT1 at 3.4 Å resolution reveals a domain-swapped dimer forming a 2-fold symmetric RNA-binding platform. The linker between LRR and NTF2-like domains interacts with NXT1. This symmetric platform facilitates recognition and export of CTE-RNA (a 2-fold symmetric stem-loop), as confirmed by biochemical and cellular assays.","method":"X-ray crystallography; biochemical RNA-binding assays; mRNA export reporter assays in cells","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 — crystal structure at 3.4 Å supplemented by biochemical and cellular validation","pmids":["25628361"],"is_preprint":false},{"year":2016,"finding":"SR proteins (SRSF1–7) function as NXF1 export adaptors, coupling pre-mRNA processing to mRNA export. iCLIP analysis shows NXF1 and SR proteins bind mRNA at adjacent sites. SRSF3 is the most potent NXF1 adaptor, conferring sequence specificity to NXF1 RNA binding in last exons. SRSF3 and SRSF7 bind different sites in last exons, regulate 3' UTR length in opposing ways, and both promote NXF1 recruitment to mRNA, coupling alternative splicing/polyadenylation to NXF1-mediated export.","method":"iCLIP transcriptome-wide mapping; siRNA knockdown with mRNA export assays; co-IP; reporter assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — transcriptome-wide iCLIP combined with systematic knockdown and multiple functional assays","pmids":["26944680"],"is_preprint":false},{"year":2019,"finding":"NXF1 coordinates transcriptional dynamics, alternative polyadenylation (APA), and mRNA export. NXF1 knockdown results in RNA polymerase II accumulation at the 3' end of genes and promotes usage of proximal PASs (shorter 3' UTRs). NXF1 cooperates with CFI-68 to facilitate nuclear export of long 3' UTR isoforms bearing UGUA motifs.","method":"siRNA knockdown; RNA-seq; 3'-seq for APA analysis; ChIP-seq for Pol II; RNA immunoprecipitation; co-IP","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — genome-wide multi-omics with mechanistic co-IP validation; multiple orthogonal methods","pmids":["30819645"],"is_preprint":false},{"year":2019,"finding":"In living yeast, Mex67 (NXF1 ortholog) localizes to the NPC independently of mRNA, occupying FG-repeat binding sites. Its essential function is spatially restricted to the NPC: a fusion of Mex67 to nucleoporin Nup116 rescues MEX67 deletion. Mex67 functions as a mobile NPC component that receives mRNA export substrates at the central channel.","method":"Quantitative live-cell fluorescence microscopy (FRAP, single-molecule); genetic complementation with Mex67-Nup116 fusion","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1–2 — live-cell quantitative imaging with genetic rescue; demonstrates spatial restriction of essential function","pmids":["31753862"],"is_preprint":false},{"year":2019,"finding":"NXF1 localizes consistently to the cytoplasmic side of nuclear pore complexes as shown by super-resolution microscopy. Initial mRNP binding to the NPC does not require NXF1, but release into the cytoplasm does. FLIM-FRET inside single NPCs shows that Dbp5 helicase-mediated mRNA release is conserved from yeast to humans.","method":"Super-resolution microscopy; FLIM-FRET in single NPCs; dominant-negative NXF1 and mRNA export block experiments","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — super-resolution localization combined with FLIM-FRET and functional export block experiments","pmids":["31375530"],"is_preprint":false},{"year":2003,"finding":"The Nxf1 natural allele Mvb1 from Mus musculus castaneus suppresses the effects of retrovirus insertional mutations by controlling levels of correctly processed mRNA, revealing an unexpected link between the mRNA export receptor NXF1 and pre-mRNA processing.","method":"Positional complementation cloning; congenic mouse strains; mRNA processing assays","journal":"Nature genetics","confidence":"Medium","confidence_rationale":"Tier 2 — positional cloning with functional validation in vivo; single natural allele study","pmids":["14517553"],"is_preprint":false},{"year":2009,"finding":"RBM15B/OTT3 directly interacts with NXF1 via its C-terminal region (mapped by mutagenesis) and also binds Aly/REF, functioning as a cofactor of NXF1 to regulate mRNA export. OTT3 (and the paralog RBM15) associates with the nuclear envelope and splicing factor compartment.","method":"Co-immunoprecipitation; mutational analysis; subcellular localization by microscopy","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 — co-IP with mutagenesis; single lab, no direct export assay for the interaction domain","pmids":["19586903"],"is_preprint":false},{"year":2009,"finding":"EBV protein EB2 contains an N-terminal nuclear export signal (NES, aa 61–146) with arginine-rich domains that directly interact with NXF1/TAP, and this interaction mediates CRM1-independent nuclear export of viral and reporter mRNAs.","method":"Co-IP; domain deletion mapping; RNA export reporter assays; tethering assays with MS2-coat protein","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 3 — co-IP and reporter assays; direct interaction mapping; single lab","pmids":["19793817"],"is_preprint":false},{"year":2011,"finding":"U2AF65 interacts directly and specifically with expanded CAG repeat RNA via its RRM3 domain. U2AF65, expanded CAG RNA, and NXF1 form an RNA/protein complex in which U2AF65 acts as an adaptor to link the expanded CAG RNA to NXF1 for nuclear export. Reduction of U2AF50/65 function exacerbates nuclear accumulation of expanded CAG RNA and toxicity in Drosophila and mouse models.","method":"RNA immunoprecipitation; co-immunoprecipitation; RNAi and mutant analysis in Drosophila; polyQ transgenic mice","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 — RIP and co-IP showing ternary complex; RNAi phenotype in multiple model organisms; single lab","pmids":["21725067"],"is_preprint":false},{"year":2002,"finding":"An element in the 3' UTR of human LINE-1 retrotransposons (L1-NBE) binds NXF1 (TAP) in vitro as strongly as the viral CTE, but uses a different and only partially overlapping binding domain on NXF1. L1-NBE can mediate nuclear export of unspliced RNAs in Xenopus oocytes and human cells, suggesting NXF1 mediates export of endogenous intronless retrotransposon mRNAs.","method":"In vitro RNA selection (SELEX-like); gel mobility shift competition assays; domain deletion of NXF1; export reporter assays in Xenopus oocytes and human cells","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro binding with domain mapping and in vivo export assays; single lab","pmids":["12003494"],"is_preprint":false},{"year":2024,"finding":"ISGylation of hnRNPA2B1 (mediated by PCAT6 lncRNA scaffolding ISG15) protects hnRNPA2B1 from ubiquitin-mediated degradation. As an m6A reader, hnRNPA2B1 selectively mediates nuclear export of m6A-tagged mRNAs via the ALYREF/NXF1 complex, promoting stemness gene expression in breast cancer.","method":"Co-immunoprecipitation; RNA immunoprecipitation; siRNA knockdown; m6A-seq; nuclear/cytoplasmic fractionation","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 — co-IP and RIP demonstrating ternary m6A-RNA/hnRNPA2B1/ALYREF/NXF1 complex; multiple assays; single lab","pmids":["38626369"],"is_preprint":false},{"year":2021,"finding":"SRSF1 and SRSF7 bind clustered motifs within the cytoplasmic accumulation region (CAR-N) of intronless lncRNA NKILA, facilitating TREX complex recruitment and subsequent NXF1-dependent (TREX-TAP pathway) nuclear export of NKILA. NKILA lacking CAR-N is retained in the nucleus and cannot inhibit breast cancer cell migration.","method":"RNP pulldown with mass spectrometry; siRNA screening; RNA FISH; co-IP; nuclear/cytoplasmic fractionation; knock-in cell models","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 — MS-identified interactors validated by RIP and siRNA with functional localization and migration readout; single lab","pmids":["34096602"],"is_preprint":false},{"year":2010,"finding":"NXF1/TAP is required for nuclear export of specific influenza A virus mRNAs. siRNA depletion of NXF1 inhibits nuclear export of intronless HA mRNA and spliced M2/unspliced M1 transcripts (late genes), while early gene mRNAs show less dependency. This indicates influenza co-opts the NXF1 mRNA export pathway for a subset of its mRNAs.","method":"siRNA knockdown of NXF1, Aly, and UAP56; RNA FISH/fractionation for viral mRNA localization; comparison to DRB treatment","journal":"The Journal of general virology","confidence":"Medium","confidence_rationale":"Tier 2 — siRNA with viral mRNA export phenotype; systematic comparison of pathway components","pmids":["20071484"],"is_preprint":false},{"year":2014,"finding":"NXF1 is required for nuclear export of both spliced and unspliced murine leukemia virus (MLV) RNA transcripts. A cis-acting element in the MLV pol gene (CAE) interacts with NXF1, and NXF1 disruption abolishes CAE function and causes nuclear retention or degradation of viral RNAs.","method":"siRNA knockdown of NXF1; RNA FISH and nuclear/cytoplasmic fractionation; CAE-NXF1 interaction by pulldown","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 — RNAi with specific viral RNA export phenotype; direct NXF1-CAE interaction demonstrated","pmids":["24478440"],"is_preprint":false}],"current_model":"NXF1 (TAP) is the principal mRNA nuclear export receptor that operates as a modular protein (RRM, LRR, NTF2-like, UBA domains) forming an obligate heterodimer with NXT1/p15; this heterodimer is loaded onto processed mRNAs via multiple adaptor proteins (including SR proteins SRSF3/7, TREX subunits Aly/REF and THOC5, and U2AF), driven into an RNA-binding-competent open conformation by TREX, and translocates mRNP through the nuclear pore complex by sequential interactions with FG-nucleoporins (including RanBP2/Nup358 on cytoplasmic filaments), where it functions as a mobile NPC component; release of cargo into the cytoplasm on the cytoplasmic face requires Dbp5 helicase activity, while NXF1 nuclear re-import depends on redundant karyopherins recognizing dual NLS epitopes in its N-terminal tail."},"narrative":{"teleology":[{"year":2000,"claim":"Establishing NXF1's modular domain architecture (RRM, LRR, NTF2-like, UBA) and that each domain contributes distinct functions — RNA binding, heterodimerization with p15/NXT1, and nucleoporin interaction — provided the first structural framework for understanding how a single protein can bind cargo and traverse the NPC.","evidence":"Domain deletion analysis with RNA-binding, localization, and export reporter assays for NXF1–3 paralogs","pmids":["11073998"],"confidence":"High","gaps":["No atomic-resolution structure at this stage","Relative contributions of domains to bulk vs. specific mRNA export unknown"]},{"year":2001,"claim":"Demonstrating that NXT1/p15 is an obligate cofactor that enhances NXF1 binding to nucleoporins — and that the LRR and UBA domains are both essential for mRNA export — defined the heterodimer as the functional export unit and identified nucleoporin binding as the rate-limiting step.","evidence":"In vitro nucleoporin binding assays with recombinant proteins; RNAi in Drosophila; domain mutagenesis with export reporters","pmids":["11259411","11739738","11579093"],"confidence":"High","gaps":["Mechanism of NXT1-induced enhancement of nucleoporin affinity not structurally resolved","Identity of all relevant FG-nucleoporin partners incomplete"]},{"year":2001,"claim":"Identification of U2AF35 as a direct NXF1-binding partner that recruits NXF1 to spliced mRNP linked mRNA export to the splicing machinery, establishing the principle that adaptor proteins couple processing to export.","evidence":"Yeast two-hybrid, in vitro binding, mRNP immunoprecipitation, and export reporters","pmids":["11724776"],"confidence":"Medium","gaps":["Relative contribution of U2AF vs. other adaptors to bulk mRNA export not quantified","No structural detail of the U2AF–NXF1 interface"]},{"year":2002,"claim":"Domain-swap experiments showing that two nucleoporin-binding modules (any combination of NTF2-like and UBA) are both necessary and sufficient for NPC translocation established a 'bivalent grip' model for FG-repeat-mediated transport, while revealing that NXT1's role is confined to nucleoporin binding rather than directionality.","evidence":"Tandem domain duplication and swap mutants with mRNA export reporters","pmids":["12101235"],"confidence":"High","gaps":["How directionality is imposed if not by NXT1 remained open","Energetics of translocation through FG meshwork unresolved"]},{"year":2002,"claim":"Discovery that NXF1 directly binds a LINE-1 3′ UTR element (L1-NBE) using a partially distinct binding surface revealed that NXF1 exports endogenous intronless retrotransposon mRNAs, broadening its cargo repertoire beyond spliced mRNA.","evidence":"In vitro RNA selection, gel-shift competition, domain deletion, and export assays in Xenopus oocytes and human cells","pmids":["12003494"],"confidence":"Medium","gaps":["Physiological significance for L1 retrotransposition not directly tested","Structural basis of differential binding mode unresolved"]},{"year":2003,"claim":"Mapping NXF1 interactions with Rae1/Gle2 and Nup98 GLFG repeats, and showing competitive binding, suggested an ordered hand-off mechanism through sequential nucleoporin stations during NPC transit.","evidence":"Co-IP and pulldown with defined protein domains; binary and ternary complex formation","pmids":["12637516"],"confidence":"Medium","gaps":["Order of nucleoporin encounters during transit not established in vivo","Affinity measurements for different FG-repeat types lacking"]},{"year":2004,"claim":"RanBP2/Nup358 was identified as the major cytoplasmic-face docking site for NXF1–NXT1, and its depletion caused specific mRNA export block without affecting CRM1 export, establishing the terminal NPC station for the NXF1 pathway.","evidence":"RNAi of RanBP2 in Drosophila cells; NXF1 localization by fluorescence microscopy; poly(A)+ RNA FISH","pmids":["14729961"],"confidence":"High","gaps":["Mechanism of NXF1 release from RanBP2 into the cytoplasm unknown","Contribution of other cytoplasmic nucleoporins not excluded"]},{"year":2006,"claim":"Discovery that NXF1's own intron 10 contains a functional CTE whose retention produces an exported, translated short isoform revealed an autoregulatory feedback loop — the export receptor controls its own mRNA processing and export.","evidence":"RT-PCR, polyribosome fractionation, immunoblotting, and CTE export assays in Xenopus oocytes","pmids":["16971948"],"confidence":"High","gaps":["Physiological conditions that modulate the ratio of full-length to short isoform unknown","Function of the small NXF1 protein product uncharacterized"]},{"year":2009,"claim":"THOC5 was shown to bind a surface on the NXF1 NTF2-like domain non-overlapping with Aly/REF, allowing simultaneous engagement, and was required specifically for HSP70 mRNA export — establishing that TREX subunits act as transcript-selective co-adaptors rather than generic loading factors.","evidence":"GST pulldown mapping; co-IP; siRNA with FISH for HSP70 mRNA","pmids":["19165146"],"confidence":"High","gaps":["Full repertoire of THOC5-dependent transcripts unknown at this stage","Structural basis of simultaneous Aly/THOC5 binding not resolved"]},{"year":2010,"claim":"Arginine methylation of Aly/REF was shown to weaken its RNA affinity without disrupting the Aly–NXF1 protein interaction, thereby facilitating cargo handover from Aly to NXF1 — the first post-translational mechanism regulating adaptor-to-receptor RNA transfer.","evidence":"Mass spectrometry of methylation sites; in vitro RNA-binding with methylated/unmethylated REF; in vivo RIP; export assays","pmids":["20129943"],"confidence":"High","gaps":["Whether other TREX adaptors are similarly regulated by PTMs unknown","Enzymes responsible for REF methylation not identified in this study"]},{"year":2011,"claim":"The intramolecular autoinhibition model was established: NXF1's N-terminal domains fold back to mask the RNA-binding surface, and TREX components (Aly + THOC5) relieve this inhibition to generate an open, RNA-competent conformation — explaining why NXF1 alone does not bind bulk mRNA.","evidence":"Biochemical conformation assay with recombinant proteins; siRNA double knockdown with RIP and FISH","pmids":["22893130"],"confidence":"High","gaps":["Atomic-resolution structure of the closed autoinhibited conformation not available","Whether additional factors can also open NXF1 independently of TREX unknown"]},{"year":2011,"claim":"Identification of dual NLS epitopes (N-terminal basic and PY-NLS) recognized by multiple redundant karyopherins explained the robustness of NXF1 nuclear re-import and showed that mislocalization of NXF1 to the cytoplasm impairs mRNA export.","evidence":"Binding assays with recombinant karyopherins; NLS mutagenesis; localization microscopy; export assays","pmids":["21965294"],"confidence":"High","gaps":["Relative contribution of each karyopherin under physiological conditions unknown","Whether NLS accessibility is regulated during the export cycle unresolved"]},{"year":2015,"claim":"The 3.4 Å crystal structure of NXF1 (RRM–LRR–NTF2-like)–NXT1 revealed a domain-swapped dimer forming a symmetric RNA-binding platform that explains recognition of the 2-fold symmetric CTE stem-loop, providing the first near-complete structural view of the export receptor.","evidence":"X-ray crystallography; biochemical RNA-binding assays; cellular export reporters","pmids":["25628361"],"confidence":"High","gaps":["Structure of NXF1 bound to cellular mRNA (non-CTE) lacking","UBA domain not resolved in this crystal form"]},{"year":2016,"claim":"Transcriptome-wide iCLIP demonstrated that SR proteins SRSF3 and SRSF7 are major NXF1 adaptors that bind adjacent to NXF1 on mRNA last exons, conferring sequence specificity and coupling alternative polyadenylation to export — expanding the adaptor concept beyond TREX.","evidence":"iCLIP; siRNA knockdown with mRNA export assays; co-IP; reporter assays","pmids":["26944680"],"confidence":"High","gaps":["Whether SR-mediated and TREX-mediated NXF1 recruitment are sequential or parallel on the same transcript unclear","Contribution of each SR protein to individual transcript export not fully resolved"]},{"year":2019,"claim":"NXF1 was found to coordinate transcription termination and alternative polyadenylation: its depletion causes Pol II accumulation at 3′ ends and proximal PAS usage, and it cooperates with CFI-68 to export long 3′ UTR isoforms, linking NXF1 to co-transcriptional RNA processing beyond splicing.","evidence":"siRNA; RNA-seq; 3′-seq; Pol II ChIP-seq; RIP; co-IP","pmids":["30819645"],"confidence":"High","gaps":["Whether NXF1 directly modulates Pol II processivity or acts indirectly through RNA topology unknown","Mechanism of CFI-68–NXF1 cooperation at UGUA motifs not structurally defined"]},{"year":2019,"claim":"Super-resolution and live-cell imaging placed NXF1 predominantly at the cytoplasmic face of the NPC and showed it functions as a mobile NPC component: mRNP docking does not require NXF1, but cytoplasmic release does, with Dbp5 helicase providing the terminal remodeling step conserved from yeast to humans.","evidence":"Super-resolution microscopy; FLIM-FRET in single NPCs; Mex67–Nup116 fusion rescue in yeast; dominant-negative NXF1 experiments","pmids":["31375530","31753862"],"confidence":"High","gaps":["How Dbp5 specifically strips NXF1 from mRNP at the cytoplasmic face not structurally resolved","Whether NXF1 residence time at the NPC is regulated under stress conditions unknown"]},{"year":null,"claim":"Key open questions include: the atomic structure of autoinhibited NXF1, how multiple adaptor pathways (TREX, SR proteins, U2AF) are coordinated on a single transcript, and how NXF1-dependent export is regulated during stress, viral infection, and differentiation.","evidence":"","pmids":[],"confidence":"High","gaps":["No structure of full-length NXF1 in the autoinhibited closed conformation","Hierarchical rules for adaptor engagement on individual transcripts undefined","Regulatory mechanisms modulating NXF1 activity under physiological stress not characterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,13,16,17,25]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[2,4,19,20]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,3,5,7]}],"localization":[{"term_id":"GO:0005635","term_label":"nuclear envelope","supporting_discovery_ids":[0,7,20]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[9,15]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[15,20]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,3,8,13,17,18]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[2,7,15,19,20]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[18,21]}],"complexes":["NXF1-NXT1 heterodimer","TREX complex"],"partners":["NXT1","ALYREF","THOC5","SRSF3","SRSF7","U2AF1","RANBP2","RBM15B"],"other_free_text":[]},"mechanistic_narrative":"NXF1 (TAP) is the principal mRNA nuclear export receptor in metazoans, coupling pre-mRNA processing to nuclear pore complex (NPC) translocation through coordinated interactions with adaptor proteins, nucleoporins, and its obligate heterodimeric partner NXT1/p15. NXF1 adopts an autoinhibited conformation in which its RNA-binding domain is masked by intramolecular contacts; TREX subunits Aly/REF and THOC5 bind non-overlapping surfaces on NXF1 to induce an open, RNA-binding-competent state, while SR proteins SRSF3 and SRSF7 function as sequence-specific adaptors that recruit NXF1 to mRNA 3′ ends and couple alternative polyadenylation to export [PMID:22893130, PMID:26944680, PMID:19165146]. The NXF1–NXT1 heterodimer translocates mRNP through the NPC via at least two FG-nucleoporin-binding sites provided by its NTF2-like and UBA domains, docks preferentially at cytoplasmic filament nucleoporin RanBP2/Nup358, and releases cargo on the cytoplasmic face through Dbp5 helicase activity [PMID:12101235, PMID:14729961, PMID:31375530]. NXF1 also autoregulates its own expression through a constitutive transport element within a retained intron, and its nuclear re-import requires redundant karyopherins recognizing dual NLS epitopes in the N-terminal tail [PMID:16971948, PMID:21965294]."},"prefetch_data":{"uniprot":{"accession":"Q9UBU9","full_name":"Nuclear RNA export factor 1","aliases":["Tip-associated protein","Tip-associating protein","mRNA export factor TAP"],"length_aa":619,"mass_kda":70.2,"function":"Involved in the nuclear export of mRNA species bearing retroviral constitutive transport elements (CTE) and in the export of mRNA from the nucleus to the cytoplasm (TAP/NFX1 pathway) (PubMed:10924507). The NXF1-NXT1 heterodimer is involved in the export of HSP70 mRNA in conjunction with ALYREF/THOC4 and THOC5 components of the TREX complex (PubMed:18364396, PubMed:19165146, PubMed:9660949). ALYREF/THOC4-bound mRNA is thought to be transferred to the NXF1-NXT1 heterodimer for export (PubMed:18364396, PubMed:19165146, PubMed:9660949). Also involved in nuclear export of m6A-containing mRNAs: interaction between SRSF3 and YTHDC1 facilitates m6A-containing mRNA-binding to both SRSF3 and NXF1, promoting mRNA nuclear export (PubMed:28984244)","subcellular_location":"Nucleus; Nucleus, nucleoplasm; Nucleus speckle; Nucleus, nuclear pore complex; Nucleus envelope; Cytoplasm; Cytoplasm, Stress granule","url":"https://www.uniprot.org/uniprotkb/Q9UBU9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/NXF1","classification":"Common Essential","n_dependent_lines":1194,"n_total_lines":1208,"dependency_fraction":0.9884105960264901},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000162231","cell_line_id":"CID001566","localizations":[{"compartment":"nuclear_membrane","grade":3},{"compartment":"nuclear_punctae","grade":3},{"compartment":"nucleoplasm","grade":2}],"interactors":[{"gene":"NFYA","stoichiometry":10.0},{"gene":"PES1","stoichiometry":10.0},{"gene":"MAPRE1","stoichiometry":0.2},{"gene":"EEF1A1;EEF1A1P5","stoichiometry":0.2},{"gene":"NXT2","stoichiometry":0.2},{"gene":"RAN","stoichiometry":0.2},{"gene":"XPO1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001566","total_profiled":1310},"omim":[{"mim_id":"621181","title":"NF-KAPPA-B-INTERACTING LONG NONCODING RNA; NKILA","url":"https://www.omim.org/entry/621181"},{"mim_id":"620833","title":"RNA-BINDING MOTIF PROTEIN 33; RBM33","url":"https://www.omim.org/entry/620833"},{"mim_id":"619906","title":"DExD-BOX HELICASE 39A; DDX39A","url":"https://www.omim.org/entry/619906"},{"mim_id":"618640","title":"ZINC FINGER CCCH DOMAIN-CONTAINING PROTEIN 3; ZC3H3","url":"https://www.omim.org/entry/618640"},{"mim_id":"617037","title":"NONCODING RNA ACTIVATED BY DNA DAMAGE; NORAD","url":"https://www.omim.org/entry/617037"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NXF1"},"hgnc":{"alias_symbol":["TAP","Mex67","DKFZp667O0311"],"prev_symbol":[]},"alphafold":{"accession":"Q9UBU9","domains":[{"cath_id":"3.30.70.330","chopping":"119-192","consensus_level":"high","plddt":90.443,"start":119,"end":192},{"cath_id":"3.80.10.10","chopping":"205-354","consensus_level":"high","plddt":94.3693,"start":205,"end":354},{"cath_id":"3.10.450.50","chopping":"380-545","consensus_level":"high","plddt":95.1878,"start":380,"end":545},{"cath_id":"1.10.8.10","chopping":"564-616","consensus_level":"high","plddt":74.5919,"start":564,"end":616}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UBU9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UBU9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UBU9-F1-predicted_aligned_error_v6.png","plddt_mean":79.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NXF1","jax_strain_url":"https://www.jax.org/strain/search?query=NXF1"},"sequence":{"accession":"Q9UBU9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UBU9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UBU9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UBU9"}},"corpus_meta":[{"pmid":"11403571","id":"PMC_11403571","title":"The 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pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"NXF1 (TAP) has a conserved modular architecture comprising an RNP-type RNA-binding domain, leucine-rich repeats (LRR), an NTF2-like domain that heterodimerizes with p15/NXT1, and a UBA-like domain that mediates interaction with nucleoporins. NXF2, a human paralog, binds RNA, localizes to the nuclear envelope, and has RNA export activity, while NXF3 lacks these activities.\",\n      \"method\": \"Domain deletion analysis, RNA-binding assays, nuclear envelope localization by microscopy, RNA export reporter assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal functional assays (RNA binding, export, localization) in one study with defined domain mutants\",\n      \"pmids\": [\"11073998\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Overexpression of TAP/p15 (NXF1/NXT1) heterodimers bypasses nuclear retention and stimulates nuclear mRNA export. The LRR domain is essential for this activity, and the UBA-like domain strongly contributes. Heterodimer formation between NXF1 and p15 is required for efficient mRNA export.\",\n      \"method\": \"mRNA export reporter assays, domain deletion mutants, tethering assays in transfected cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — systematic domain mutagenesis with quantitative export readouts, replicated in multiple constructs\",\n      \"pmids\": [\"11259411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"NXF1-mediated mRNA export requires at minimum two nucleoporin-binding sites; these can be provided by the NTF2-like scaffold plus UBA-like domain, or by two copies of either domain in tandem. The function of the NTF2-like scaffold (and therefore p15) is confined to nucleoporin binding, not to imparting directionality or regulating cargo interactions per se.\",\n      \"method\": \"Domain swap/tandem duplication mutants expressed in cells; mRNA export reporter assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — systematic domain-swap mutagenesis with clear functional readouts\",\n      \"pmids\": [\"12101235\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"NXT1/p15 functions as a critical cofactor for NXF1 (Tap)-mediated mRNA export by enhancing NXF1 binding to nucleoporins. Without NXT1, NXF1 cannot effectively interact with nuclear pore complex components, and both NXF1 nucleocytoplasmic shuttling and mRNA export are severely attenuated. Tap/NXT1 heterodimer forms a ternary complex with nucleoporins in vitro and in vivo.\",\n      \"method\": \"Co-IP, in vitro nucleoporin binding assays, mRNA export reporter assays in human and Drosophila cells; RNAi knockdown of Drosophila NXT1 causing poly(A)+ RNA nuclear accumulation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal binding assays, RNAi phenotype in two cell systems, in vitro reconstitution\",\n      \"pmids\": [\"11739738\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"The C-terminal FG-nucleoporin binding domain of NXF1 (Tap) adopts a distinctive four-helix structure joined to adjacent modules by a flexible Pro-rich linker. The F617A mutation suppresses FG-nucleoporin binding by this domain, establishing the structural basis for nuclear shuttling.\",\n      \"method\": \"NMR solution structure; site-directed mutagenesis (F617A)\",\n      \"journal\": \"Nature structural biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — NMR structure with mutagenesis validation\",\n      \"pmids\": [\"11875519\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"NXT1/p15 stimulates binding of a Tap–RNA complex to nucleoporins in vitro, and this interaction is necessary for nuclear export of an intron-containing viral mRNA in vivo. NXF1 contains separate domains for nucleoporin binding and NXT1 binding, both critical for export. NXT1 regulates the affinity of the Tap–RNA complex for nucleoporins, including p62.\",\n      \"method\": \"In vitro nucleoporin binding assays with recombinant proteins; site-directed mutagenesis; nuclear export reporter assays in vivo\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro reconstitution with recombinant proteins, mutagenesis, and in vivo export assays\",\n      \"pmids\": [\"11579093\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"NXF1 (TAP) forms a stable binary and ternary complex with the nucleoporins Rae1/Gle2 and Nup98. Gle2 requires two sites on TAP for stable interaction. TAP has highest affinity for a specific region within the GLFG domain of Nup98, not all FG repeats equally. Gle2 and Nup98 may compete for TAP binding, suggesting Gle2 delivers TAP to Nup98.\",\n      \"method\": \"Co-IP, pulldown with defined protein domains; binary and ternary complex formation assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — pulldown/co-IP with systematic domain mapping; single study\",\n      \"pmids\": [\"12637516\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the cytoplasmic filaments of the nuclear pore complex. Depletion of RanBP2 from Drosophila cells inhibits mRNA export and strongly reduces NXF1 localization at the NPC, releasing NXF1 into the cytoplasm; CRM1-dependent export and other nuclear/cytoplasmic proteins are unaffected.\",\n      \"method\": \"RNAi depletion of RanBP2 in Drosophila cells; fluorescence microscopy of NXF1 localization; poly(A)+ RNA FISH\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — specific knockdown with defined NXF1 localization and mRNA export phenotypes; parallel controls\",\n      \"pmids\": [\"14729961\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"NXF1 (Tap) contains an alternatively spliced intron 10 that harbors a functional constitutive transport element (CTE). The resulting intron-retaining Tap mRNA is exported to the cytoplasm and translated into a small Tap protein detectable in human and monkey cells, demonstrating autoregulation through CTE-mediated export of its own intron-containing mRNA.\",\n      \"method\": \"RT-PCR, polyribosome fractionation, immunoblotting for small Tap protein, reporter export assays in Xenopus oocytes\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods including polysome fractionation, protein detection, and export assays\",\n      \"pmids\": [\"16971948\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Y14 (splicing factor) and NXF1 form mRNA export complexes that preferentially localize within and around nuclear speckles (SC35 domains) in living cells. BiFC and FRAP/FLIP reveal that roughly half the Y14–NXF1 complexes are immobile in vivo and depleted by ATP in permeabilized cells, suggesting ATP-dependent retention of a subset of mRNPs at speckles despite association with export proteins.\",\n      \"method\": \"Bimolecular fluorescence complementation (BiFC) in live MCF7 cells; FRAP; FLIP; co-immunoprecipitation\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — live-cell BiFC and FRAP; single lab\",\n      \"pmids\": [\"16431928\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"U2AF35 (small subunit of splicing factor U2AF) directly binds a distinct region of NXF1 (TAP) that also targets TAP to spliced mRNP. U2AF65 overexpression recruits U2AF35 and TAP to spliced mRNP and stimulates nuclear export, suggesting U2AF participates in mRNA export by facilitating TAP recruitment.\",\n      \"method\": \"Yeast two-hybrid, in vitro binding assays, immunoprecipitation of mRNP, export reporter assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — yeast two-hybrid confirmed by in vitro binding; export assays; single lab\",\n      \"pmids\": [\"11724776\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"THOC5 (a TREX complex subunit) binds a distinct surface on the NTF2-like domain of NXF1 (Tap-p15), at a site non-overlapping with the Aly/REF binding site, allowing simultaneous binding. THOC5 is required for nuclear export of HSP70 mRNA but not bulk mRNA, identifying it as a specific export co-adaptor.\",\n      \"method\": \"GST pulldown mapping of binding surfaces; co-immunoprecipitation; siRNA knockdown with mRNA export assays (FISH for HSP70 mRNA)\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal pulldowns defining non-overlapping binding sites; specific export phenotype with RNAi\",\n      \"pmids\": [\"19165146\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Arginine methylation of REF/ALY reduces its RNA-binding activity in vitro and in vivo. This reduced affinity is essential for efficient displacement of RNA from REF by NXF1 (TAP), promoting handover of mRNA cargo to NXF1. Arginine methylation does not affect the REF–TAP protein–protein interaction.\",\n      \"method\": \"Mass spectrometry mapping of methylation sites; in vitro RNA-binding assays with methylated/unmethylated REF; in vivo RNA immunoprecipitation; mRNA export assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — MS-based methylation mapping, biochemical assays, and in vivo functional readout in one study\",\n      \"pmids\": [\"20129943\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"NXF1 uses an intramolecular interaction to inhibit its own RNA-binding activity. When TREX subunits Aly and THOC5 contact NXF1, NXF1 adopts an open conformation that exposes its RNA-binding domain, enabling RNA binding. Combined knockdown of Aly and THOC5 reduces NXF1 bound to mRNA in vivo and causes severe mRNA export block.\",\n      \"method\": \"Biochemical conformation assay; RNA-binding assays with recombinant proteins; siRNA double knockdown with RNA immunoprecipitation and FISH\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — reconstituted conformational switch with recombinant proteins; validated in vivo by RNAi and RIP\",\n      \"pmids\": [\"22893130\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The mammalian nuclear pore protein Tpr restricts nuclear export of mRNAs with retained introns that traffic through the NXF1/NXT1 pathway. Knockdown of Tpr significantly increases export and translation of CTE-containing mRNA (NXF1 pathway), but has no effect on Rev/RRE-dependent (CRM1 pathway) or completely spliced mRNA export.\",\n      \"method\": \"RNAi knockdown of Tpr; mRNA export reporter assays comparing CTE vs. RRE pathways\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — specific pathway comparison by knockdown; single lab\",\n      \"pmids\": [\"21613532\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Multiple karyopherins (importin β, karyopherin β2/transportin, importin 4, importin 11, importin α) can import NXF1 into the nucleus by recognizing two NLS epitopes in the N-terminal tail: an N-terminal basic segment and a C-terminal PY-NLS (R-X2-5-P-Y motif). Mutation of both epitopes mislocalizes NXF1 to the cytoplasm and significantly impairs mRNA export.\",\n      \"method\": \"Biochemical binding assays with recombinant karyopherins; mutagenesis of NLS epitopes; fluorescence microscopy of NXF1 localization; mRNA export assays\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — systematic mutagenesis with binding assays, localization, and functional export readout; multiple karyopherins tested\",\n      \"pmids\": [\"21965294\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of human NXF1 (first three domains: RRM, LRR, NTF2-like) together with NXT1 at 3.4 Å resolution reveals a domain-swapped dimer forming a 2-fold symmetric RNA-binding platform. The linker between LRR and NTF2-like domains interacts with NXT1. This symmetric platform facilitates recognition and export of CTE-RNA (a 2-fold symmetric stem-loop), as confirmed by biochemical and cellular assays.\",\n      \"method\": \"X-ray crystallography; biochemical RNA-binding assays; mRNA export reporter assays in cells\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure at 3.4 Å supplemented by biochemical and cellular validation\",\n      \"pmids\": [\"25628361\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SR proteins (SRSF1–7) function as NXF1 export adaptors, coupling pre-mRNA processing to mRNA export. iCLIP analysis shows NXF1 and SR proteins bind mRNA at adjacent sites. SRSF3 is the most potent NXF1 adaptor, conferring sequence specificity to NXF1 RNA binding in last exons. SRSF3 and SRSF7 bind different sites in last exons, regulate 3' UTR length in opposing ways, and both promote NXF1 recruitment to mRNA, coupling alternative splicing/polyadenylation to NXF1-mediated export.\",\n      \"method\": \"iCLIP transcriptome-wide mapping; siRNA knockdown with mRNA export assays; co-IP; reporter assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — transcriptome-wide iCLIP combined with systematic knockdown and multiple functional assays\",\n      \"pmids\": [\"26944680\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NXF1 coordinates transcriptional dynamics, alternative polyadenylation (APA), and mRNA export. NXF1 knockdown results in RNA polymerase II accumulation at the 3' end of genes and promotes usage of proximal PASs (shorter 3' UTRs). NXF1 cooperates with CFI-68 to facilitate nuclear export of long 3' UTR isoforms bearing UGUA motifs.\",\n      \"method\": \"siRNA knockdown; RNA-seq; 3'-seq for APA analysis; ChIP-seq for Pol II; RNA immunoprecipitation; co-IP\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide multi-omics with mechanistic co-IP validation; multiple orthogonal methods\",\n      \"pmids\": [\"30819645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In living yeast, Mex67 (NXF1 ortholog) localizes to the NPC independently of mRNA, occupying FG-repeat binding sites. Its essential function is spatially restricted to the NPC: a fusion of Mex67 to nucleoporin Nup116 rescues MEX67 deletion. Mex67 functions as a mobile NPC component that receives mRNA export substrates at the central channel.\",\n      \"method\": \"Quantitative live-cell fluorescence microscopy (FRAP, single-molecule); genetic complementation with Mex67-Nup116 fusion\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — live-cell quantitative imaging with genetic rescue; demonstrates spatial restriction of essential function\",\n      \"pmids\": [\"31753862\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NXF1 localizes consistently to the cytoplasmic side of nuclear pore complexes as shown by super-resolution microscopy. Initial mRNP binding to the NPC does not require NXF1, but release into the cytoplasm does. FLIM-FRET inside single NPCs shows that Dbp5 helicase-mediated mRNA release is conserved from yeast to humans.\",\n      \"method\": \"Super-resolution microscopy; FLIM-FRET in single NPCs; dominant-negative NXF1 and mRNA export block experiments\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — super-resolution localization combined with FLIM-FRET and functional export block experiments\",\n      \"pmids\": [\"31375530\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"The Nxf1 natural allele Mvb1 from Mus musculus castaneus suppresses the effects of retrovirus insertional mutations by controlling levels of correctly processed mRNA, revealing an unexpected link between the mRNA export receptor NXF1 and pre-mRNA processing.\",\n      \"method\": \"Positional complementation cloning; congenic mouse strains; mRNA processing assays\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — positional cloning with functional validation in vivo; single natural allele study\",\n      \"pmids\": [\"14517553\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"RBM15B/OTT3 directly interacts with NXF1 via its C-terminal region (mapped by mutagenesis) and also binds Aly/REF, functioning as a cofactor of NXF1 to regulate mRNA export. OTT3 (and the paralog RBM15) associates with the nuclear envelope and splicing factor compartment.\",\n      \"method\": \"Co-immunoprecipitation; mutational analysis; subcellular localization by microscopy\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — co-IP with mutagenesis; single lab, no direct export assay for the interaction domain\",\n      \"pmids\": [\"19586903\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"EBV protein EB2 contains an N-terminal nuclear export signal (NES, aa 61–146) with arginine-rich domains that directly interact with NXF1/TAP, and this interaction mediates CRM1-independent nuclear export of viral and reporter mRNAs.\",\n      \"method\": \"Co-IP; domain deletion mapping; RNA export reporter assays; tethering assays with MS2-coat protein\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — co-IP and reporter assays; direct interaction mapping; single lab\",\n      \"pmids\": [\"19793817\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"U2AF65 interacts directly and specifically with expanded CAG repeat RNA via its RRM3 domain. U2AF65, expanded CAG RNA, and NXF1 form an RNA/protein complex in which U2AF65 acts as an adaptor to link the expanded CAG RNA to NXF1 for nuclear export. Reduction of U2AF50/65 function exacerbates nuclear accumulation of expanded CAG RNA and toxicity in Drosophila and mouse models.\",\n      \"method\": \"RNA immunoprecipitation; co-immunoprecipitation; RNAi and mutant analysis in Drosophila; polyQ transgenic mice\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — RIP and co-IP showing ternary complex; RNAi phenotype in multiple model organisms; single lab\",\n      \"pmids\": [\"21725067\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"An element in the 3' UTR of human LINE-1 retrotransposons (L1-NBE) binds NXF1 (TAP) in vitro as strongly as the viral CTE, but uses a different and only partially overlapping binding domain on NXF1. L1-NBE can mediate nuclear export of unspliced RNAs in Xenopus oocytes and human cells, suggesting NXF1 mediates export of endogenous intronless retrotransposon mRNAs.\",\n      \"method\": \"In vitro RNA selection (SELEX-like); gel mobility shift competition assays; domain deletion of NXF1; export reporter assays in Xenopus oocytes and human cells\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro binding with domain mapping and in vivo export assays; single lab\",\n      \"pmids\": [\"12003494\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ISGylation of hnRNPA2B1 (mediated by PCAT6 lncRNA scaffolding ISG15) protects hnRNPA2B1 from ubiquitin-mediated degradation. As an m6A reader, hnRNPA2B1 selectively mediates nuclear export of m6A-tagged mRNAs via the ALYREF/NXF1 complex, promoting stemness gene expression in breast cancer.\",\n      \"method\": \"Co-immunoprecipitation; RNA immunoprecipitation; siRNA knockdown; m6A-seq; nuclear/cytoplasmic fractionation\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — co-IP and RIP demonstrating ternary m6A-RNA/hnRNPA2B1/ALYREF/NXF1 complex; multiple assays; single lab\",\n      \"pmids\": [\"38626369\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SRSF1 and SRSF7 bind clustered motifs within the cytoplasmic accumulation region (CAR-N) of intronless lncRNA NKILA, facilitating TREX complex recruitment and subsequent NXF1-dependent (TREX-TAP pathway) nuclear export of NKILA. NKILA lacking CAR-N is retained in the nucleus and cannot inhibit breast cancer cell migration.\",\n      \"method\": \"RNP pulldown with mass spectrometry; siRNA screening; RNA FISH; co-IP; nuclear/cytoplasmic fractionation; knock-in cell models\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — MS-identified interactors validated by RIP and siRNA with functional localization and migration readout; single lab\",\n      \"pmids\": [\"34096602\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"NXF1/TAP is required for nuclear export of specific influenza A virus mRNAs. siRNA depletion of NXF1 inhibits nuclear export of intronless HA mRNA and spliced M2/unspliced M1 transcripts (late genes), while early gene mRNAs show less dependency. This indicates influenza co-opts the NXF1 mRNA export pathway for a subset of its mRNAs.\",\n      \"method\": \"siRNA knockdown of NXF1, Aly, and UAP56; RNA FISH/fractionation for viral mRNA localization; comparison to DRB treatment\",\n      \"journal\": \"The Journal of general virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — siRNA with viral mRNA export phenotype; systematic comparison of pathway components\",\n      \"pmids\": [\"20071484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NXF1 is required for nuclear export of both spliced and unspliced murine leukemia virus (MLV) RNA transcripts. A cis-acting element in the MLV pol gene (CAE) interacts with NXF1, and NXF1 disruption abolishes CAE function and causes nuclear retention or degradation of viral RNAs.\",\n      \"method\": \"siRNA knockdown of NXF1; RNA FISH and nuclear/cytoplasmic fractionation; CAE-NXF1 interaction by pulldown\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — RNAi with specific viral RNA export phenotype; direct NXF1-CAE interaction demonstrated\",\n      \"pmids\": [\"24478440\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NXF1 (TAP) is the principal mRNA nuclear export receptor that operates as a modular protein (RRM, LRR, NTF2-like, UBA domains) forming an obligate heterodimer with NXT1/p15; this heterodimer is loaded onto processed mRNAs via multiple adaptor proteins (including SR proteins SRSF3/7, TREX subunits Aly/REF and THOC5, and U2AF), driven into an RNA-binding-competent open conformation by TREX, and translocates mRNP through the nuclear pore complex by sequential interactions with FG-nucleoporins (including RanBP2/Nup358 on cytoplasmic filaments), where it functions as a mobile NPC component; release of cargo into the cytoplasm on the cytoplasmic face requires Dbp5 helicase activity, while NXF1 nuclear re-import depends on redundant karyopherins recognizing dual NLS epitopes in its N-terminal tail.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"NXF1 (TAP) is the principal mRNA nuclear export receptor in metazoans, coupling pre-mRNA processing to nuclear pore complex (NPC) translocation through coordinated interactions with adaptor proteins, nucleoporins, and its obligate heterodimeric partner NXT1/p15. NXF1 adopts an autoinhibited conformation in which its RNA-binding domain is masked by intramolecular contacts; TREX subunits Aly/REF and THOC5 bind non-overlapping surfaces on NXF1 to induce an open, RNA-binding-competent state, while SR proteins SRSF3 and SRSF7 function as sequence-specific adaptors that recruit NXF1 to mRNA 3′ ends and couple alternative polyadenylation to export [PMID:22893130, PMID:26944680, PMID:19165146]. The NXF1–NXT1 heterodimer translocates mRNP through the NPC via at least two FG-nucleoporin-binding sites provided by its NTF2-like and UBA domains, docks preferentially at cytoplasmic filament nucleoporin RanBP2/Nup358, and releases cargo on the cytoplasmic face through Dbp5 helicase activity [PMID:12101235, PMID:14729961, PMID:31375530]. NXF1 also autoregulates its own expression through a constitutive transport element within a retained intron, and its nuclear re-import requires redundant karyopherins recognizing dual NLS epitopes in the N-terminal tail [PMID:16971948, PMID:21965294].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Establishing NXF1's modular domain architecture (RRM, LRR, NTF2-like, UBA) and that each domain contributes distinct functions — RNA binding, heterodimerization with p15/NXT1, and nucleoporin interaction — provided the first structural framework for understanding how a single protein can bind cargo and traverse the NPC.\",\n      \"evidence\": \"Domain deletion analysis with RNA-binding, localization, and export reporter assays for NXF1–3 paralogs\",\n      \"pmids\": [\"11073998\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No atomic-resolution structure at this stage\", \"Relative contributions of domains to bulk vs. specific mRNA export unknown\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Demonstrating that NXT1/p15 is an obligate cofactor that enhances NXF1 binding to nucleoporins — and that the LRR and UBA domains are both essential for mRNA export — defined the heterodimer as the functional export unit and identified nucleoporin binding as the rate-limiting step.\",\n      \"evidence\": \"In vitro nucleoporin binding assays with recombinant proteins; RNAi in Drosophila; domain mutagenesis with export reporters\",\n      \"pmids\": [\"11259411\", \"11739738\", \"11579093\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of NXT1-induced enhancement of nucleoporin affinity not structurally resolved\", \"Identity of all relevant FG-nucleoporin partners incomplete\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Identification of U2AF35 as a direct NXF1-binding partner that recruits NXF1 to spliced mRNP linked mRNA export to the splicing machinery, establishing the principle that adaptor proteins couple processing to export.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro binding, mRNP immunoprecipitation, and export reporters\",\n      \"pmids\": [\"11724776\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relative contribution of U2AF vs. other adaptors to bulk mRNA export not quantified\", \"No structural detail of the U2AF–NXF1 interface\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Domain-swap experiments showing that two nucleoporin-binding modules (any combination of NTF2-like and UBA) are both necessary and sufficient for NPC translocation established a 'bivalent grip' model for FG-repeat-mediated transport, while revealing that NXT1's role is confined to nucleoporin binding rather than directionality.\",\n      \"evidence\": \"Tandem domain duplication and swap mutants with mRNA export reporters\",\n      \"pmids\": [\"12101235\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How directionality is imposed if not by NXT1 remained open\", \"Energetics of translocation through FG meshwork unresolved\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Discovery that NXF1 directly binds a LINE-1 3′ UTR element (L1-NBE) using a partially distinct binding surface revealed that NXF1 exports endogenous intronless retrotransposon mRNAs, broadening its cargo repertoire beyond spliced mRNA.\",\n      \"evidence\": \"In vitro RNA selection, gel-shift competition, domain deletion, and export assays in Xenopus oocytes and human cells\",\n      \"pmids\": [\"12003494\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological significance for L1 retrotransposition not directly tested\", \"Structural basis of differential binding mode unresolved\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Mapping NXF1 interactions with Rae1/Gle2 and Nup98 GLFG repeats, and showing competitive binding, suggested an ordered hand-off mechanism through sequential nucleoporin stations during NPC transit.\",\n      \"evidence\": \"Co-IP and pulldown with defined protein domains; binary and ternary complex formation\",\n      \"pmids\": [\"12637516\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Order of nucleoporin encounters during transit not established in vivo\", \"Affinity measurements for different FG-repeat types lacking\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"RanBP2/Nup358 was identified as the major cytoplasmic-face docking site for NXF1–NXT1, and its depletion caused specific mRNA export block without affecting CRM1 export, establishing the terminal NPC station for the NXF1 pathway.\",\n      \"evidence\": \"RNAi of RanBP2 in Drosophila cells; NXF1 localization by fluorescence microscopy; poly(A)+ RNA FISH\",\n      \"pmids\": [\"14729961\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of NXF1 release from RanBP2 into the cytoplasm unknown\", \"Contribution of other cytoplasmic nucleoporins not excluded\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Discovery that NXF1's own intron 10 contains a functional CTE whose retention produces an exported, translated short isoform revealed an autoregulatory feedback loop — the export receptor controls its own mRNA processing and export.\",\n      \"evidence\": \"RT-PCR, polyribosome fractionation, immunoblotting, and CTE export assays in Xenopus oocytes\",\n      \"pmids\": [\"16971948\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological conditions that modulate the ratio of full-length to short isoform unknown\", \"Function of the small NXF1 protein product uncharacterized\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"THOC5 was shown to bind a surface on the NXF1 NTF2-like domain non-overlapping with Aly/REF, allowing simultaneous engagement, and was required specifically for HSP70 mRNA export — establishing that TREX subunits act as transcript-selective co-adaptors rather than generic loading factors.\",\n      \"evidence\": \"GST pulldown mapping; co-IP; siRNA with FISH for HSP70 mRNA\",\n      \"pmids\": [\"19165146\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full repertoire of THOC5-dependent transcripts unknown at this stage\", \"Structural basis of simultaneous Aly/THOC5 binding not resolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Arginine methylation of Aly/REF was shown to weaken its RNA affinity without disrupting the Aly–NXF1 protein interaction, thereby facilitating cargo handover from Aly to NXF1 — the first post-translational mechanism regulating adaptor-to-receptor RNA transfer.\",\n      \"evidence\": \"Mass spectrometry of methylation sites; in vitro RNA-binding with methylated/unmethylated REF; in vivo RIP; export assays\",\n      \"pmids\": [\"20129943\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other TREX adaptors are similarly regulated by PTMs unknown\", \"Enzymes responsible for REF methylation not identified in this study\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"The intramolecular autoinhibition model was established: NXF1's N-terminal domains fold back to mask the RNA-binding surface, and TREX components (Aly + THOC5) relieve this inhibition to generate an open, RNA-competent conformation — explaining why NXF1 alone does not bind bulk mRNA.\",\n      \"evidence\": \"Biochemical conformation assay with recombinant proteins; siRNA double knockdown with RIP and FISH\",\n      \"pmids\": [\"22893130\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic-resolution structure of the closed autoinhibited conformation not available\", \"Whether additional factors can also open NXF1 independently of TREX unknown\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identification of dual NLS epitopes (N-terminal basic and PY-NLS) recognized by multiple redundant karyopherins explained the robustness of NXF1 nuclear re-import and showed that mislocalization of NXF1 to the cytoplasm impairs mRNA export.\",\n      \"evidence\": \"Binding assays with recombinant karyopherins; NLS mutagenesis; localization microscopy; export assays\",\n      \"pmids\": [\"21965294\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contribution of each karyopherin under physiological conditions unknown\", \"Whether NLS accessibility is regulated during the export cycle unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"The 3.4 Å crystal structure of NXF1 (RRM–LRR–NTF2-like)–NXT1 revealed a domain-swapped dimer forming a symmetric RNA-binding platform that explains recognition of the 2-fold symmetric CTE stem-loop, providing the first near-complete structural view of the export receptor.\",\n      \"evidence\": \"X-ray crystallography; biochemical RNA-binding assays; cellular export reporters\",\n      \"pmids\": [\"25628361\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of NXF1 bound to cellular mRNA (non-CTE) lacking\", \"UBA domain not resolved in this crystal form\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Transcriptome-wide iCLIP demonstrated that SR proteins SRSF3 and SRSF7 are major NXF1 adaptors that bind adjacent to NXF1 on mRNA last exons, conferring sequence specificity and coupling alternative polyadenylation to export — expanding the adaptor concept beyond TREX.\",\n      \"evidence\": \"iCLIP; siRNA knockdown with mRNA export assays; co-IP; reporter assays\",\n      \"pmids\": [\"26944680\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether SR-mediated and TREX-mediated NXF1 recruitment are sequential or parallel on the same transcript unclear\", \"Contribution of each SR protein to individual transcript export not fully resolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"NXF1 was found to coordinate transcription termination and alternative polyadenylation: its depletion causes Pol II accumulation at 3′ ends and proximal PAS usage, and it cooperates with CFI-68 to export long 3′ UTR isoforms, linking NXF1 to co-transcriptional RNA processing beyond splicing.\",\n      \"evidence\": \"siRNA; RNA-seq; 3′-seq; Pol II ChIP-seq; RIP; co-IP\",\n      \"pmids\": [\"30819645\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether NXF1 directly modulates Pol II processivity or acts indirectly through RNA topology unknown\", \"Mechanism of CFI-68–NXF1 cooperation at UGUA motifs not structurally defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Super-resolution and live-cell imaging placed NXF1 predominantly at the cytoplasmic face of the NPC and showed it functions as a mobile NPC component: mRNP docking does not require NXF1, but cytoplasmic release does, with Dbp5 helicase providing the terminal remodeling step conserved from yeast to humans.\",\n      \"evidence\": \"Super-resolution microscopy; FLIM-FRET in single NPCs; Mex67–Nup116 fusion rescue in yeast; dominant-negative NXF1 experiments\",\n      \"pmids\": [\"31375530\", \"31753862\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How Dbp5 specifically strips NXF1 from mRNP at the cytoplasmic face not structurally resolved\", \"Whether NXF1 residence time at the NPC is regulated under stress conditions unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include: the atomic structure of autoinhibited NXF1, how multiple adaptor pathways (TREX, SR proteins, U2AF) are coordinated on a single transcript, and how NXF1-dependent export is regulated during stress, viral infection, and differentiation.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structure of full-length NXF1 in the autoinhibited closed conformation\", \"Hierarchical rules for adaptor engagement on individual transcripts undefined\", \"Regulatory mechanisms modulating NXF1 activity under physiological stress not characterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 13, 16, 17, 25]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [2, 4, 19, 20]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 3, 5, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [0, 7, 20]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [9, 15]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [15, 20]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 3, 8, 13, 17, 18]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [2, 7, 15, 19, 20]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [18, 21]}\n    ],\n    \"complexes\": [\n      \"NXF1-NXT1 heterodimer\",\n      \"TREX complex\"\n    ],\n    \"partners\": [\n      \"NXT1\",\n      \"ALYREF\",\n      \"THOC5\",\n      \"SRSF3\",\n      \"SRSF7\",\n      \"U2AF1\",\n      \"RANBP2\",\n      \"RBM15B\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}