{"gene":"TRNAU1AP","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":1999,"finding":"SECp43 (TRNAU1AP) was identified as a novel RNA-binding protein that associates specifically with mammalian selenocysteine tRNA (tRNA(Sec)), demonstrated by affinity purification of tRNA(Sec) from HeLa cell extracts using an anti-SECp43 antibody column. Recombinant SECp43 also pulled down a 48-kDa interacting protein, suggesting it participates in a multi-component selenocysteine insertion complex.","method":"Antibody affinity purification, recombinant protein pulldown, Northern blot, direct RNA sequencing","journal":"RNA","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal pulldown with antibody and recombinant protein, two orthogonal methods, single lab","pmids":["10606267"],"is_preprint":false},{"year":2005,"finding":"Knockdown of SECp43 in NIH3T3 and TCMK-1 cells by RNAi reduced methylation at the 2'-hydroxylribosyl moiety at the wobble position (Um34) of Sec tRNA([Ser]Sec), consequently reducing glutathione peroxidase 1 expression. SECp43 forms a complex with Sec tRNA([Ser]Sec) and SLA (soluble liver antigen), and loss of one protein affects the other's binding to the tRNA. SECp43 is located primarily in the nucleus; co-transfection with SLA caused nuclear translocation of SLA, suggesting SECp43 promotes shuttling of SLA and Sec tRNA between compartments.","method":"RNAi knockdown, methylation analysis of tRNA, co-immunoprecipitation, subcellular fractionation/localization, Western blot","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (RNAi, tRNA methylation assay, Co-IP, subcellular fractionation), consistent findings across cell lines, single lab","pmids":["16230358"],"is_preprint":false},{"year":2006,"finding":"SECp43 interacts with the selenocysteyl-tRNA([Ser]Sec)-EFsec complex in vitro. SECp43 co-expression promotes interaction between EFsec and SBP2 in vivo. SECp43 cotransfection with SLA/LP and SPS1 increases SLA/LP–SPS1 interaction and redistributes all three proteins to a predominantly nuclear localization. SECp43 overexpression increases selenocysteine incorporation and selenoprotein mRNA levels (the latter presumably via circumvention of nonsense-mediated decay).","method":"In vitro binding assay, co-immunoprecipitation, subcellular localization (transfection + imaging), selenocysteine incorporation assay, mRNA level measurement","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vitro binding plus multiple in vivo Co-IPs plus functional incorporation assay, multiple orthogonal methods, independent replication of key interactions with prior study","pmids":["16508009"],"is_preprint":false},{"year":2017,"finding":"SECp43 forms oligomers in eukaryotic cells, as demonstrated by BRET assay. Small-angle X-ray scattering of recombinant SECp43 revealed it is a globular protein comprising two RNA-binding domains. Phage display identified two residues (K166 and P167) required for SECp43 dimerization. SECp43 also interacts with selenocysteine synthase (SEPSECS) in mammalian cells (confirmed by BRET and co-immunoprecipitation).","method":"Bioluminescence resonance energy transfer (BRET), co-immunoprecipitation, small-angle X-ray scattering (SAXS), phage display mutagenesis","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — SAXS structural analysis combined with BRET and Co-IP functional validation and mutagenesis identifying dimerization residues, single lab but multiple orthogonal methods","pmids":["28414460"],"is_preprint":false},{"year":2015,"finding":"Constitutive deletion of SECp43 exons 7+8 in mice was embryonic lethal. Hepatocyte-specific deletion of exons 7+8 showed no significant changes in selenoprotein levels, tRNA([Ser]Sec) Um34 methylation, or selenoprotein mRNA abundance in liver, indicating the deleted domains are not essential for selenoprotein biosynthesis in hepatocytes. However, neuron-specific deletion of exons 7+8 impaired motor performance without affecting cerebral selenoprotein expression or cerebellar development, revealing a non-selenoprotein function in neurons. Truncated Secp43 mRNA increased in mutant livers, suggesting auto-regulation of Secp43 mRNA abundance.","method":"Conditional knockout mouse models, 75Se labeling, Western blot, enzymatic activity assays, tRNA methylation analysis, behavioral motor tests","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo conditional KO with multiple biochemical readouts and behavioral phenotyping, comprehensive negative result in liver with positive result (motor deficit) in neurons, single lab with multiple orthogonal methods","pmids":["26043259"],"is_preprint":false},{"year":2016,"finding":"Knockdown of Trnau1ap in H9c2 cardiomyocyte-like cells reduced expression of glutathione peroxidase, thioredoxin reductase, and selenoprotein K; inhibited cell proliferation; and induced apoptosis with increased Bax and decreased Bcl-2 expression. Overexpression promoted cell growth. PI3K/Akt signaling pathway was activated in Trnau1ap-underexpressing cells.","method":"siRNA knockdown, overexpression plasmid transfection, MTT/PCNA/Annexin V/caspase-3 assays, Western blot","journal":"Molecular medicine reports","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — loss- and gain-of-function in cell line with multiple functional readouts, but pathway placement (PI3K/Akt) based on phosphorylation Western blot only, single lab","pmids":["28101579"],"is_preprint":false},{"year":2018,"finding":"Lentiviral shRNA knockdown of Trnau1ap in NIH3T3, JEG-3, and Bewo cells reduced selenoprotein expression, decreased cell proliferation and migration, and attenuated Akt phosphorylation in the PI3K/Akt pathway.","method":"Lentiviral shRNA knockdown, CCK-8 proliferation assay, wound scratch migration assay, Western blot for p-Akt","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — knockdown in multiple cell lines with functional and signaling readouts, pathway placement by single method (phospho-Western), single lab","pmids":["29758194"],"is_preprint":false},{"year":2024,"finding":"Tethered function splicing reporter assays and enhanced cross-linking immunoprecipitation (eCLIP) combined with RNA sequencing and affinity purification-mass spectrometry revealed that TRNAU1AP modulates hundreds of endogenous splicing events, indicating a direct role in alternative splicing in addition to its known function in selenocysteine incorporation.","method":"Tethered function luciferase splicing reporters (718 RBPs screened), eCLIP, RNA sequencing, affinity purification-mass spectrometry","journal":"Nature biotechnology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — integrative multi-assay approach (eCLIP + RNA-seq + AP-MS) in a large systematic screen; TRNAU1AP-specific mechanistic depth is limited to the integrative analysis, single study","pmids":["38168984"],"is_preprint":false},{"year":2026,"finding":"TRNAU1AP interacts with EEFSEC (the selenocysteine-specific elongation factor) and forms a phase-separated complex that enhances EEFSEC binding to sec-tRNA(sec), thereby promoting translation of multiple selenoproteins in glioblastoma stem cells. IGF2BP3 upregulates TRNAU1AP expression through m6A-dependent transcript stabilization. Loss of TRNAU1AP impairs glioblastoma stem cell proliferation, self-renewal, and tumorigenesis.","method":"RNA immunoprecipitation, phase-separation assays, polysome profiling, proteomics, spatial transcriptomics, gain- and loss-of-function assays, RNA stability analysis","journal":"Neuro-oncology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (RIP, phase-separation assay, polysome profiling, proteomics) establishing a mechanistic interaction and functional consequence, single lab but comprehensive methodology","pmids":["42080969"],"is_preprint":false}],"current_model":"TRNAU1AP (SECp43) is an RNA-binding protein that forms a nuclear-enriched supramolecular complex with Sec tRNA([Ser]Sec), SLA/LP, EFsec, SBP2, and SEPSECS to orchestrate selenocysteine biosynthesis and incorporation, including regulating Um34 methylation of Sec tRNA; it also interacts with EEFSEC in a phase-separated complex to enhance selenoprotein translation, and independently modulates hundreds of alternative splicing events and cell proliferation/migration via PI3K/Akt signaling."},"narrative":{"mechanistic_narrative":"TRNAU1AP (SECp43) is an RNA-binding protein that orchestrates selenocysteine biosynthesis and incorporation by nucleating a supramolecular complex around selenocysteine tRNA (tRNA([Ser]Sec)) [PMID:10606267, PMID:16230358]. It binds tRNA([Ser]Sec) directly and assembles with SLA/LP, EFsec/EEFSEC, SBP2, SPS1, and the selenocysteine synthase SEPSECS, promoting pairwise interactions among these factors and redistributing them to a predominantly nuclear localization [PMID:16230358, PMID:16508009, PMID:28414460]. Functionally, SECp43 is required for 2'-O-methylation (Um34) of the wobble position of Sec tRNA, and its loss reduces this modification and downstream selenoprotein expression including glutathione peroxidase 1 [PMID:16230358]; conversely, overexpression increases selenocysteine incorporation and selenoprotein mRNA levels [PMID:16508009]. Structurally it is a globular two-RNA-binding-domain protein that homo-oligomerizes via residues K166 and P167 [PMID:28414460]. In glioblastoma stem cells TRNAU1AP forms a phase-separated complex with EEFSEC that enhances EEFSEC binding to sec-tRNA(sec) and boosts selenoprotein translation, supporting proliferation, self-renewal, and tumorigenesis downstream of m6A-dependent stabilization by IGF2BP3 [PMID:42080969]. Beyond selenoprotein metabolism, TRNAU1AP directly modulates hundreds of alternative splicing events [PMID:38168984], and its depletion impairs proliferation and migration with attenuated PI3K/Akt signaling across multiple cell types [PMID:28101579, PMID:29758194]. In vivo, constitutive deletion of exons 7+8 is embryonic lethal, yet hepatocyte-specific deletion leaves selenoprotein biosynthesis intact while neuron-specific deletion impairs motor performance, revealing a selenoprotein-independent function in neurons [PMID:26043259].","teleology":[{"year":1999,"claim":"Established that SECp43 is a tRNA(Sec)-specific RNA-binding protein and a candidate component of the selenocysteine insertion machinery, answering what molecule this previously uncharacterized protein engages.","evidence":"Antibody affinity purification of tRNA(Sec) and recombinant protein pulldown from HeLa extracts","pmids":["10606267"],"confidence":"Medium","gaps":["Identity of the 48-kDa interacting protein not defined","No functional consequence of the tRNA association established","Single lab, in vitro association only"]},{"year":2005,"claim":"Showed SECp43 is functionally required for Um34 methylation of Sec tRNA and for selenoprotein output, and links to SLA, defining its role in tRNA maturation and intracellular trafficking.","evidence":"RNAi knockdown in NIH3T3/TCMK-1 with tRNA methylation assay, Co-IP, and subcellular fractionation","pmids":["16230358"],"confidence":"High","gaps":["Direct catalytic role in methylation versus scaffolding not separated","Mechanism of SLA nuclear shuttling unresolved"]},{"year":2006,"claim":"Placed SECp43 as an organizer that promotes assembly among EFsec, SBP2, SLA/LP and SPS1 and enhances selenocysteine incorporation, building the multi-component complex model.","evidence":"In vitro binding, in vivo Co-IPs, subcellular localization, and selenocysteine incorporation/mRNA assays","pmids":["16508009"],"confidence":"High","gaps":["Stoichiometry and architecture of the assembled complex unknown","NMD-circumvention mechanism inferred, not directly demonstrated"]},{"year":2017,"claim":"Defined the protein's oligomeric and domain architecture and added SEPSECS as a partner, providing a structural basis for its scaffolding function.","evidence":"BRET, Co-IP, SAXS, and phage-display mutagenesis identifying dimerization residues K166/P167","pmids":["28414460"],"confidence":"High","gaps":["No high-resolution crystal/cryo-EM structure","Functional consequence of dimerization for selenoprotein synthesis not tested"]},{"year":2015,"claim":"Revealed tissue-specific and selenoprotein-independent functions in vivo, dissociating SECp43 requirement in hepatocytes from an essential role in neurons and embryonic development.","evidence":"Conditional exon 7+8 knockout mice with 75Se labeling, tRNA methylation, enzyme assays, and motor behavioral tests","pmids":["26043259"],"confidence":"High","gaps":["Molecular basis of the neuronal motor phenotype unidentified","Domains beyond exons 7+8 may carry the essential function","Mechanism of Secp43 mRNA auto-regulation unknown"]},{"year":2016,"claim":"Connected TRNAU1AP to cell survival and proliferation, implicating PI3K/Akt signaling in cardiomyocyte-like cells.","evidence":"siRNA knockdown and overexpression in H9c2 with proliferation, apoptosis, and phospho-Western readouts","pmids":["28101579"],"confidence":"Medium","gaps":["PI3K/Akt placement based on phospho-Western only","Whether proliferation effect is downstream of selenoprotein loss not resolved"]},{"year":2018,"claim":"Generalized the proliferation/migration and PI3K/Akt link across additional cell lines, reinforcing a role in cell growth tied to selenoprotein expression.","evidence":"Lentiviral shRNA knockdown in NIH3T3/JEG-3/Bewo with proliferation, migration, and p-Akt assays","pmids":["29758194"],"confidence":"Medium","gaps":["Direct mechanism linking TRNAU1AP to Akt phosphorylation undefined","Pathway placement by single method"]},{"year":2024,"claim":"Uncovered a function beyond selenoprotein incorporation by showing TRNAU1AP directly regulates alternative splicing genome-wide.","evidence":"Tethered-function splicing reporters, eCLIP, RNA-seq, and AP-MS in a 718-RBP systematic screen","pmids":["38168984"],"confidence":"Medium","gaps":["Specific RNA targets and splicing regulatory mechanism not detailed","Relationship to selenocysteine function unexplored"]},{"year":2026,"claim":"Demonstrated that TRNAU1AP drives selenoprotein translation via phase separation with EEFSEC and is exploited by glioblastoma stem cells, linking the selenoprotein function to tumor biology and m6A regulation.","evidence":"RIP, phase-separation assays, polysome profiling, proteomics, spatial transcriptomics, and gain/loss-of-function in glioblastoma stem cells","pmids":["42080969"],"confidence":"High","gaps":["Determinants and reversibility of phase separation not mapped","Generality beyond glioblastoma stem cells untested"]},{"year":null,"claim":"How the dual roles in selenocysteine incorporation and alternative splicing are integrated, and the molecular identity of its selenoprotein-independent neuronal function, remain open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model connecting tRNA-complex scaffolding to splicing regulation","Neuronal essential substrate/pathway unidentified","No high-resolution structure of assembled complexes"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,3,8]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[2,8]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,2]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,2,8]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[7]}],"complexes":["selenocysteine insertion/Sec tRNA biosynthesis complex"],"partners":["SLA","EEFSEC","SBP2","SEPSECS","SPS1","IGF2BP3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NX07","full_name":"tRNA selenocysteine 1-associated protein 1","aliases":["SECp43","tRNA selenocysteine-associated protein 1"],"length_aa":287,"mass_kda":32.5,"function":"Involved in the early steps of selenocysteine biosynthesis and tRNA(Sec) charging to the later steps resulting in the cotranslational incorporation of selenocysteine into selenoproteins (PubMed:16508009). Stabilizes the SECISBP2, EEFSEC and tRNA(Sec) complex (PubMed:16508009). May be involved in the methylation of tRNA(Sec) (PubMed:16508009). Enhances efficiency of selenoproteins synthesis (PubMed:16508009)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9NX07/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TRNAU1AP","classification":"Not Classified","n_dependent_lines":352,"n_total_lines":1208,"dependency_fraction":0.2913907284768212},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TRNAU1AP","total_profiled":1310},"omim":[{"mim_id":"619597","title":"tRNA SELENOCYSTEINE 1-ASSOCIATED PROTEIN 1; TRNAU1AP","url":"https://www.omim.org/entry/619597"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TRNAU1AP"},"hgnc":{"alias_symbol":["SECP43","FLJ20503"],"prev_symbol":["TRSPAP1"]},"alphafold":{"accession":"Q9NX07","domains":[{"cath_id":"3.30.70.330","chopping":"2-82","consensus_level":"high","plddt":94.0532,"start":2,"end":82},{"cath_id":"3.30.70.330","chopping":"95-173","consensus_level":"high","plddt":93.8489,"start":95,"end":173}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NX07","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NX07-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NX07-F1-predicted_aligned_error_v6.png","plddt_mean":75.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRNAU1AP","jax_strain_url":"https://www.jax.org/strain/search?query=TRNAU1AP"},"sequence":{"accession":"Q9NX07","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NX07.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NX07/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NX07"}},"corpus_meta":[{"pmid":"17553827","id":"PMC_17553827","title":"The selenoproteome exhibits widely varying, tissue-specific dependence on selenoprotein P for selenium supply.","date":"2007","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/17553827","citation_count":146,"is_preprint":false},{"pmid":"16508009","id":"PMC_16508009","title":"Supramolecular complexes mediate selenocysteine incorporation in vivo.","date":"2006","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16508009","citation_count":120,"is_preprint":false},{"pmid":"28977470","id":"PMC_28977470","title":"The PRMT5/WDR77 complex regulates alternative splicing through ZNF326 in breast cancer.","date":"2017","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/28977470","citation_count":72,"is_preprint":false},{"pmid":"16230358","id":"PMC_16230358","title":"Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16230358","citation_count":66,"is_preprint":false},{"pmid":"10606267","id":"PMC_10606267","title":"Identification of a protein component of a mammalian tRNA(Sec) complex implicated in the decoding of UGA as selenocysteine.","date":"1999","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/10606267","citation_count":34,"is_preprint":false},{"pmid":"16766053","id":"PMC_16766053","title":"Identification of Leishmania selenoproteins and SECIS element.","date":"2006","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/16766053","citation_count":32,"is_preprint":false},{"pmid":"20659579","id":"PMC_20659579","title":"Zebrafish (Danio rerio) vary by strain and sex in their behavioral and transcriptional responses to selenium supplementation.","date":"2010","source":"Comparative biochemistry and physiology. Part A, Molecular & integrative physiology","url":"https://pubmed.ncbi.nlm.nih.gov/20659579","citation_count":30,"is_preprint":false},{"pmid":"32172502","id":"PMC_32172502","title":"Selenium Deficiency-Induced Damage and Altered Expression of Mitochondrial Biogenesis Markers in the Kidneys of Mice.","date":"2020","source":"Biological trace element research","url":"https://pubmed.ncbi.nlm.nih.gov/32172502","citation_count":26,"is_preprint":false},{"pmid":"38168984","id":"PMC_38168984","title":"Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion.","date":"2024","source":"Nature biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/38168984","citation_count":20,"is_preprint":false},{"pmid":"28414460","id":"PMC_28414460","title":"Analysis of Novel Interactions between Components of the Selenocysteine Biosynthesis Pathway, SEPHS1, SEPHS2, SEPSECS, and SECp43.","date":"2017","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28414460","citation_count":18,"is_preprint":false},{"pmid":"32065787","id":"PMC_32065787","title":"Novel somatic alterations underlie Chinese papillary thyroid carcinoma.","date":"2020","source":"Cancer biomarkers : section A of Disease markers","url":"https://pubmed.ncbi.nlm.nih.gov/32065787","citation_count":18,"is_preprint":false},{"pmid":"24817701","id":"PMC_24817701","title":"Adjustments, extinction, and remains of selenocysteine incorporation machinery in the nematode lineage.","date":"2014","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/24817701","citation_count":18,"is_preprint":false},{"pmid":"33895963","id":"PMC_33895963","title":"Selenium Deficiency Leads to Changes in Renal Fibrosis Marker Proteins and Wnt/β-Catenin Signaling Pathway Components.","date":"2021","source":"Biological trace element research","url":"https://pubmed.ncbi.nlm.nih.gov/33895963","citation_count":14,"is_preprint":false},{"pmid":"26043259","id":"PMC_26043259","title":"Expression of Selenoproteins Is Maintained in Mice Carrying Mutations in SECp43, the tRNA Selenocysteine 1 Associated Protein (Trnau1ap).","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/26043259","citation_count":12,"is_preprint":false},{"pmid":"24854764","id":"PMC_24854764","title":"Effects of acclimation salinity on the expression of selenoproteins in the tilapia, Oreochromis mossambicus.","date":"2014","source":"Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)","url":"https://pubmed.ncbi.nlm.nih.gov/24854764","citation_count":11,"is_preprint":false},{"pmid":"28101579","id":"PMC_28101579","title":"Role of tRNA selenocysteine 1 associated protein 1 in the proliferation and apoptosis of cardiomyocyte‑like H9c2 cells.","date":"2016","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/28101579","citation_count":9,"is_preprint":false},{"pmid":"29758194","id":"PMC_29758194","title":"Knockdown of Trnau1ap inhibits the proliferation and migration of NIH3T3, JEG-3 and Bewo cells via the PI3K/Akt signaling pathway.","date":"2018","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/29758194","citation_count":8,"is_preprint":false},{"pmid":"42080969","id":"PMC_42080969","title":"Phase separation of TRNAU1AP protein sustains selenoprotein translation and promotes glioblastoma tumorigenesis.","date":"2026","source":"Neuro-oncology","url":"https://pubmed.ncbi.nlm.nih.gov/42080969","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11132,"output_tokens":2714,"usd":0.037053,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9986,"output_tokens":3261,"usd":0.065727,"stage2_stop_reason":"end_turn"},"total_usd":0.10278,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"SECp43 (TRNAU1AP) was identified as a novel RNA-binding protein that associates specifically with mammalian selenocysteine tRNA (tRNA(Sec)), demonstrated by affinity purification of tRNA(Sec) from HeLa cell extracts using an anti-SECp43 antibody column. Recombinant SECp43 also pulled down a 48-kDa interacting protein, suggesting it participates in a multi-component selenocysteine insertion complex.\",\n      \"method\": \"Antibody affinity purification, recombinant protein pulldown, Northern blot, direct RNA sequencing\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal pulldown with antibody and recombinant protein, two orthogonal methods, single lab\",\n      \"pmids\": [\"10606267\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Knockdown of SECp43 in NIH3T3 and TCMK-1 cells by RNAi reduced methylation at the 2'-hydroxylribosyl moiety at the wobble position (Um34) of Sec tRNA([Ser]Sec), consequently reducing glutathione peroxidase 1 expression. SECp43 forms a complex with Sec tRNA([Ser]Sec) and SLA (soluble liver antigen), and loss of one protein affects the other's binding to the tRNA. SECp43 is located primarily in the nucleus; co-transfection with SLA caused nuclear translocation of SLA, suggesting SECp43 promotes shuttling of SLA and Sec tRNA between compartments.\",\n      \"method\": \"RNAi knockdown, methylation analysis of tRNA, co-immunoprecipitation, subcellular fractionation/localization, Western blot\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (RNAi, tRNA methylation assay, Co-IP, subcellular fractionation), consistent findings across cell lines, single lab\",\n      \"pmids\": [\"16230358\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"SECp43 interacts with the selenocysteyl-tRNA([Ser]Sec)-EFsec complex in vitro. SECp43 co-expression promotes interaction between EFsec and SBP2 in vivo. SECp43 cotransfection with SLA/LP and SPS1 increases SLA/LP–SPS1 interaction and redistributes all three proteins to a predominantly nuclear localization. SECp43 overexpression increases selenocysteine incorporation and selenoprotein mRNA levels (the latter presumably via circumvention of nonsense-mediated decay).\",\n      \"method\": \"In vitro binding assay, co-immunoprecipitation, subcellular localization (transfection + imaging), selenocysteine incorporation assay, mRNA level measurement\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vitro binding plus multiple in vivo Co-IPs plus functional incorporation assay, multiple orthogonal methods, independent replication of key interactions with prior study\",\n      \"pmids\": [\"16508009\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SECp43 forms oligomers in eukaryotic cells, as demonstrated by BRET assay. Small-angle X-ray scattering of recombinant SECp43 revealed it is a globular protein comprising two RNA-binding domains. Phage display identified two residues (K166 and P167) required for SECp43 dimerization. SECp43 also interacts with selenocysteine synthase (SEPSECS) in mammalian cells (confirmed by BRET and co-immunoprecipitation).\",\n      \"method\": \"Bioluminescence resonance energy transfer (BRET), co-immunoprecipitation, small-angle X-ray scattering (SAXS), phage display mutagenesis\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — SAXS structural analysis combined with BRET and Co-IP functional validation and mutagenesis identifying dimerization residues, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"28414460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Constitutive deletion of SECp43 exons 7+8 in mice was embryonic lethal. Hepatocyte-specific deletion of exons 7+8 showed no significant changes in selenoprotein levels, tRNA([Ser]Sec) Um34 methylation, or selenoprotein mRNA abundance in liver, indicating the deleted domains are not essential for selenoprotein biosynthesis in hepatocytes. However, neuron-specific deletion of exons 7+8 impaired motor performance without affecting cerebral selenoprotein expression or cerebellar development, revealing a non-selenoprotein function in neurons. Truncated Secp43 mRNA increased in mutant livers, suggesting auto-regulation of Secp43 mRNA abundance.\",\n      \"method\": \"Conditional knockout mouse models, 75Se labeling, Western blot, enzymatic activity assays, tRNA methylation analysis, behavioral motor tests\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo conditional KO with multiple biochemical readouts and behavioral phenotyping, comprehensive negative result in liver with positive result (motor deficit) in neurons, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"26043259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Knockdown of Trnau1ap in H9c2 cardiomyocyte-like cells reduced expression of glutathione peroxidase, thioredoxin reductase, and selenoprotein K; inhibited cell proliferation; and induced apoptosis with increased Bax and decreased Bcl-2 expression. Overexpression promoted cell growth. PI3K/Akt signaling pathway was activated in Trnau1ap-underexpressing cells.\",\n      \"method\": \"siRNA knockdown, overexpression plasmid transfection, MTT/PCNA/Annexin V/caspase-3 assays, Western blot\",\n      \"journal\": \"Molecular medicine reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — loss- and gain-of-function in cell line with multiple functional readouts, but pathway placement (PI3K/Akt) based on phosphorylation Western blot only, single lab\",\n      \"pmids\": [\"28101579\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Lentiviral shRNA knockdown of Trnau1ap in NIH3T3, JEG-3, and Bewo cells reduced selenoprotein expression, decreased cell proliferation and migration, and attenuated Akt phosphorylation in the PI3K/Akt pathway.\",\n      \"method\": \"Lentiviral shRNA knockdown, CCK-8 proliferation assay, wound scratch migration assay, Western blot for p-Akt\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — knockdown in multiple cell lines with functional and signaling readouts, pathway placement by single method (phospho-Western), single lab\",\n      \"pmids\": [\"29758194\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Tethered function splicing reporter assays and enhanced cross-linking immunoprecipitation (eCLIP) combined with RNA sequencing and affinity purification-mass spectrometry revealed that TRNAU1AP modulates hundreds of endogenous splicing events, indicating a direct role in alternative splicing in addition to its known function in selenocysteine incorporation.\",\n      \"method\": \"Tethered function luciferase splicing reporters (718 RBPs screened), eCLIP, RNA sequencing, affinity purification-mass spectrometry\",\n      \"journal\": \"Nature biotechnology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — integrative multi-assay approach (eCLIP + RNA-seq + AP-MS) in a large systematic screen; TRNAU1AP-specific mechanistic depth is limited to the integrative analysis, single study\",\n      \"pmids\": [\"38168984\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TRNAU1AP interacts with EEFSEC (the selenocysteine-specific elongation factor) and forms a phase-separated complex that enhances EEFSEC binding to sec-tRNA(sec), thereby promoting translation of multiple selenoproteins in glioblastoma stem cells. IGF2BP3 upregulates TRNAU1AP expression through m6A-dependent transcript stabilization. Loss of TRNAU1AP impairs glioblastoma stem cell proliferation, self-renewal, and tumorigenesis.\",\n      \"method\": \"RNA immunoprecipitation, phase-separation assays, polysome profiling, proteomics, spatial transcriptomics, gain- and loss-of-function assays, RNA stability analysis\",\n      \"journal\": \"Neuro-oncology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (RIP, phase-separation assay, polysome profiling, proteomics) establishing a mechanistic interaction and functional consequence, single lab but comprehensive methodology\",\n      \"pmids\": [\"42080969\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TRNAU1AP (SECp43) is an RNA-binding protein that forms a nuclear-enriched supramolecular complex with Sec tRNA([Ser]Sec), SLA/LP, EFsec, SBP2, and SEPSECS to orchestrate selenocysteine biosynthesis and incorporation, including regulating Um34 methylation of Sec tRNA; it also interacts with EEFSEC in a phase-separated complex to enhance selenoprotein translation, and independently modulates hundreds of alternative splicing events and cell proliferation/migration via PI3K/Akt signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TRNAU1AP (SECp43) is an RNA-binding protein that orchestrates selenocysteine biosynthesis and incorporation by nucleating a supramolecular complex around selenocysteine tRNA (tRNA([Ser]Sec)) [#0, #1]. It binds tRNA([Ser]Sec) directly and assembles with SLA/LP, EFsec/EEFSEC, SBP2, SPS1, and the selenocysteine synthase SEPSECS, promoting pairwise interactions among these factors and redistributing them to a predominantly nuclear localization [#1, #2, #3]. Functionally, SECp43 is required for 2'-O-methylation (Um34) of the wobble position of Sec tRNA, and its loss reduces this modification and downstream selenoprotein expression including glutathione peroxidase 1 [#1]; conversely, overexpression increases selenocysteine incorporation and selenoprotein mRNA levels [#2]. Structurally it is a globular two-RNA-binding-domain protein that homo-oligomerizes via residues K166 and P167 [#3]. In glioblastoma stem cells TRNAU1AP forms a phase-separated complex with EEFSEC that enhances EEFSEC binding to sec-tRNA(sec) and boosts selenoprotein translation, supporting proliferation, self-renewal, and tumorigenesis downstream of m6A-dependent stabilization by IGF2BP3 [#8]. Beyond selenoprotein metabolism, TRNAU1AP directly modulates hundreds of alternative splicing events [#7], and its depletion impairs proliferation and migration with attenuated PI3K/Akt signaling across multiple cell types [#5, #6]. In vivo, constitutive deletion of exons 7+8 is embryonic lethal, yet hepatocyte-specific deletion leaves selenoprotein biosynthesis intact while neuron-specific deletion impairs motor performance, revealing a selenoprotein-independent function in neurons [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established that SECp43 is a tRNA(Sec)-specific RNA-binding protein and a candidate component of the selenocysteine insertion machinery, answering what molecule this previously uncharacterized protein engages.\",\n      \"evidence\": \"Antibody affinity purification of tRNA(Sec) and recombinant protein pulldown from HeLa extracts\",\n      \"pmids\": [\"10606267\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of the 48-kDa interacting protein not defined\", \"No functional consequence of the tRNA association established\", \"Single lab, in vitro association only\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Showed SECp43 is functionally required for Um34 methylation of Sec tRNA and for selenoprotein output, and links to SLA, defining its role in tRNA maturation and intracellular trafficking.\",\n      \"evidence\": \"RNAi knockdown in NIH3T3/TCMK-1 with tRNA methylation assay, Co-IP, and subcellular fractionation\",\n      \"pmids\": [\"16230358\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct catalytic role in methylation versus scaffolding not separated\", \"Mechanism of SLA nuclear shuttling unresolved\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Placed SECp43 as an organizer that promotes assembly among EFsec, SBP2, SLA/LP and SPS1 and enhances selenocysteine incorporation, building the multi-component complex model.\",\n      \"evidence\": \"In vitro binding, in vivo Co-IPs, subcellular localization, and selenocysteine incorporation/mRNA assays\",\n      \"pmids\": [\"16508009\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and architecture of the assembled complex unknown\", \"NMD-circumvention mechanism inferred, not directly demonstrated\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined the protein's oligomeric and domain architecture and added SEPSECS as a partner, providing a structural basis for its scaffolding function.\",\n      \"evidence\": \"BRET, Co-IP, SAXS, and phage-display mutagenesis identifying dimerization residues K166/P167\",\n      \"pmids\": [\"28414460\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution crystal/cryo-EM structure\", \"Functional consequence of dimerization for selenoprotein synthesis not tested\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Revealed tissue-specific and selenoprotein-independent functions in vivo, dissociating SECp43 requirement in hepatocytes from an essential role in neurons and embryonic development.\",\n      \"evidence\": \"Conditional exon 7+8 knockout mice with 75Se labeling, tRNA methylation, enzyme assays, and motor behavioral tests\",\n      \"pmids\": [\"26043259\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of the neuronal motor phenotype unidentified\", \"Domains beyond exons 7+8 may carry the essential function\", \"Mechanism of Secp43 mRNA auto-regulation unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Connected TRNAU1AP to cell survival and proliferation, implicating PI3K/Akt signaling in cardiomyocyte-like cells.\",\n      \"evidence\": \"siRNA knockdown and overexpression in H9c2 with proliferation, apoptosis, and phospho-Western readouts\",\n      \"pmids\": [\"28101579\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"PI3K/Akt placement based on phospho-Western only\", \"Whether proliferation effect is downstream of selenoprotein loss not resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Generalized the proliferation/migration and PI3K/Akt link across additional cell lines, reinforcing a role in cell growth tied to selenoprotein expression.\",\n      \"evidence\": \"Lentiviral shRNA knockdown in NIH3T3/JEG-3/Bewo with proliferation, migration, and p-Akt assays\",\n      \"pmids\": [\"29758194\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct mechanism linking TRNAU1AP to Akt phosphorylation undefined\", \"Pathway placement by single method\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Uncovered a function beyond selenoprotein incorporation by showing TRNAU1AP directly regulates alternative splicing genome-wide.\",\n      \"evidence\": \"Tethered-function splicing reporters, eCLIP, RNA-seq, and AP-MS in a 718-RBP systematic screen\",\n      \"pmids\": [\"38168984\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific RNA targets and splicing regulatory mechanism not detailed\", \"Relationship to selenocysteine function unexplored\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstrated that TRNAU1AP drives selenoprotein translation via phase separation with EEFSEC and is exploited by glioblastoma stem cells, linking the selenoprotein function to tumor biology and m6A regulation.\",\n      \"evidence\": \"RIP, phase-separation assays, polysome profiling, proteomics, spatial transcriptomics, and gain/loss-of-function in glioblastoma stem cells\",\n      \"pmids\": [\"42080969\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Determinants and reversibility of phase separation not mapped\", \"Generality beyond glioblastoma stem cells untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the dual roles in selenocysteine incorporation and alternative splicing are integrated, and the molecular identity of its selenoprotein-independent neuronal function, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model connecting tRNA-complex scaffolding to splicing regulation\", \"Neuronal essential substrate/pathway unidentified\", \"No high-resolution structure of assembled complexes\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 3, 8]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [2, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 2, 8]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"complexes\": [\"selenocysteine insertion/Sec tRNA biosynthesis complex\"],\n    \"partners\": [\"SLA\", \"EEFSEC\", \"SBP2\", \"SEPSECS\", \"SPS1\", \"IGF2BP3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}