{"gene":"PYM1","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2004,"finding":"PYM is a cytoplasmic RNA-binding protein excluded from the nucleus by CRM1-mediated nuclear export. Its N-terminal domain directly interacts with both Mago and Y14 simultaneously, capping their heterodimerization interface at conserved surface residues, as revealed by a crystal structure of the Drosophila ternary complex at 1.9 Å resolution.","method":"Crystal structure determination (1.9 Å), in vitro pulldown with recombinant proteins, nuclear export inhibition assays, tethering assays","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional validation, mutagenesis of interface residues, orthogonal biochemical assays, results confirmed with human proteins","pmids":["14968132"],"is_preprint":false},{"year":2007,"finding":"PYM binds the Y14-MAGOH (Mago) complex via one domain and independently binds the small (40S) ribosomal subunit and the 48S preinitiation complex via a separate domain, functioning as a bridge between EJC-bearing spliced mRNAs and the translation machinery to enhance translation of spliced mRNAs. PYM knockdown reduces translation efficiency of reporter mRNAs produced from intron-containing but not intronless pre-mRNAs.","method":"Co-immunoprecipitation, domain mapping, siRNA knockdown with translation reporter assays, ribosome sedimentation","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, domain-separation experiments, functional knockdown with specific reporter readout, single lab with multiple orthogonal methods","pmids":["18026120"],"is_preprint":false},{"year":2009,"finding":"PYM is an EJC disassembly factor: it binds the MAGOH-Y14 heterodimer component of fully assembled EJCs and dissociates them from spliced mRNAs both in vitro and in cells. EJC assembly intermediates are resistant to PYM. PYM overexpression disrupts EJC association with spliced mRNA and inhibits nonsense-mediated mRNA decay (NMD). Depletion of PYM causes accumulation of EJCs on spliced mRNAs and impairs EJC protein recycling.","method":"In vitro EJC disassembly assay, Co-immunoprecipitation, PYM overexpression and siRNA knockdown in cells, NMD reporter assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro reconstitution of disassembly activity, complementary gain- and loss-of-function cellular experiments, multiple orthogonal methods, replicated across conditions","pmids":["19410547"],"is_preprint":false},{"year":2010,"finding":"KSHV ORF57 protein directly interacts with PYM and recruits it to intronless viral mRNAs, enabling PYM to facilitate association of the 48S preinitiation complex with these EJC-lacking transcripts and thereby enhance their translation.","method":"Co-immunoprecipitation, ribosome sedimentation, biochemical interaction mapping","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct interaction shown by Co-IP, ribosome cosedimentation, single lab with multiple biochemical approaches","pmids":["20436455"],"is_preprint":false},{"year":2014,"finding":"In Drosophila, PYM (DmPYM) EJC-binding and disassembly activity is regulated by its own C-terminus, which modulates formation of the PYM-Y14-Mago ternary complex. Unlike human PYM, DmPYM does not interact with the small ribosomal subunit and can dismantle EJCs in a translation-independent manner upon overexpression. Elevated DmPYM N-terminus during oogenesis causes EJC dissociation from oskar mRNA, resulting in oskar mislocalization and female sterility. Loss of DmPYM is lethal in flies with reduced y14 or mago gene dosage, establishing PYM as a regulator of EJC homeostasis.","method":"In vivo transgenic overexpression and loss-of-function in Drosophila, biochemical ternary complex analysis, RNA immunoprecipitation (RIP), genetic epistasis","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo genetic and biochemical approaches, transgenic overexpression with defined mRNA localization phenotype, genetic epistasis with y14/mago, multiple orthogonal methods","pmids":["24967911"],"is_preprint":false},{"year":2023,"finding":"The first 160 amino acids of PYM (PYM1-160) are intrinsically disordered. PYM1-160 binds RNA independently of nucleotide sequence, forming a fuzzy protein-RNA complex. This RNA binding is incompatible with PYM's EJC interaction surface, suggesting that RNA binding down-regulates PYM's EJC recycling activity.","method":"NMR spectroscopy, RNA binding assays, structural characterization of intrinsically disordered region","journal":"Frontiers in molecular biosciences","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — NMR structural characterization and RNA binding assays, single lab, functional interpretation partially inferential","pmids":["37065448"],"is_preprint":false},{"year":2025,"finding":"PYM1 interaction with the EJC (via RBM8A/MAGOH heterodimer) is required for translation-independent EJC destabilization but is dispensable for translation-dependent EJC disassembly. PYM1 interaction-deficient EJCs accumulate at non-canonical (away from canonical upstream exon-exon junction) positions, particularly on transcripts with no or few introns. Such non-canonical EJCs can induce NMD when positioned downstream of stop codons. PYM1 depletion stabilizes mRNAs with fewer and longer exons that localize to ER-associated TIS-granules. Flavivirus capsid protein interaction with PYM1 mimics PYM1 depletion to reshape host mRNA regulation.","method":"PYM1 interaction-deficient EJC mutants in HEK293 cells, eCLIP/iCLIP for EJC occupancy mapping, siRNA knockdown, RNA-seq, NMD reporter assays, flavivirus infection","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — separation-of-function mutants, genome-wide EJC occupancy mapping, multiple orthogonal approaches including viral infection validation, published in peer-reviewed journal","pmids":["40885765"],"is_preprint":false},{"year":2025,"finding":"Flavivirus capsid protein directly interacts with PYM1, and cells expressing flavivirus capsid protein or infected with flaviviruses show similar changes in EJC occupancy and gene expression as PYM1 depletion, indicating that viruses hijack PYM1's EJC specificity function to alter host mRNA regulation.","method":"Co-immunoprecipitation of PYM1-flavivirus capsid interaction, viral infection experiments, RNA-seq comparison","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and transcriptomic validation, preprint version of peer-reviewed work; interaction confirmed in published paper (PMID 40885765)","pmids":["40161626"],"is_preprint":true}],"current_model":"PYM1 (also known as PYM/WIBG) is a cytoplasmic, intrinsically disordered EJC disassembly and specificity factor that directly binds the MAGOH-Y14 (RBM8A) heterodimer of the exon junction complex via its N-terminal domain (whose structure with Mago-Y14 is resolved crystallographically) and, via a separate domain, binds the 40S ribosomal subunit/48S preinitiation complex; PYM1 disassembles fully assembled EJCs from spliced mRNAs (both in vitro and in vivo), mediating EJC recycling and limiting accumulation of non-canonical EJCs on intron-poor transcripts, thereby suppressing aberrant NMD—a function regulated by RNA binding to its disordered region and by its own C-terminus in Drosophila, and hijacked by flavivirus capsid proteins and KSHV ORF57 to reshape host mRNA translation and stability."},"narrative":{"mechanistic_narrative":"PYM1 (PYM/WIBG) is a cytoplasmic factor that controls the lifecycle and positional specificity of the exon junction complex (EJC) on spliced mRNAs [PMID:14968132, PMID:19410547]. Its N-terminal domain directly and simultaneously contacts the MAGOH–Y14 (RBM8A) heterodimer, capping their dimerization interface, while a separate domain engages the 40S ribosomal subunit and the 48S preinitiation complex, allowing PYM1 to bridge EJC-bearing mRNAs to the translation machinery and enhance translation of intron-derived transcripts [PMID:14968132, PMID:18026120]. Acting on fully assembled EJCs (but not assembly intermediates), PYM1 dissociates the complex from mRNA to drive EJC recycling; overexpression strips EJCs and suppresses nonsense-mediated decay (NMD), whereas depletion causes EJCs to accumulate on spliced mRNAs [PMID:19410547]. This recycling function enforces EJC deposition specificity: loss of the PYM1–EJC interaction permits non-canonical EJCs to accumulate away from canonical exon-exon junctions, especially on intron-poor transcripts, where they trigger aberrant NMD, and PYM1 depletion stabilizes mRNAs with few, long exons that localize to ER-associated TIS-granules [PMID:40885765]. PYM1 activity is autoregulated: its first 160 residues are intrinsically disordered and bind RNA in a sequence-independent, fuzzy manner that is sterically incompatible with EJC engagement, providing a negative regulatory input on recycling [PMID:37065448]. PYM1 is a host target hijacked by viruses—KSHV ORF57 recruits PYM1 to intronless viral mRNAs to promote their translation [PMID:20436455], and the flavivirus capsid protein binds PYM1 to mimic its depletion and reshape host EJC occupancy and gene expression [PMID:40885765, PMID:40161626].","teleology":[{"year":2004,"claim":"Established the structural basis of how PYM recognizes the EJC core: a single N-terminal domain that simultaneously contacts Mago and Y14 by capping their heterodimer interface.","evidence":"1.9 Å crystal structure of the Drosophila PYM–Mago–Y14 ternary complex with in vitro pulldowns and nuclear export assays","pmids":["14968132"],"confidence":"High","gaps":["Did not establish the cellular consequence of EJC binding (recycling vs. disassembly)","Functional role of regions outside the N-terminal Mago-Y14-binding domain unresolved"]},{"year":2007,"claim":"Showed PYM is a bifunctional bridge, using one domain for the EJC and a separate domain for the 40S/48S ribosomal complex to couple EJC-marked spliced mRNAs to enhanced translation.","evidence":"Reciprocal Co-IP, domain mapping, ribosome sedimentation, and siRNA knockdown with intron-containing vs. intronless translation reporters","pmids":["18026120"],"confidence":"High","gaps":["Did not determine whether ribosome engagement is required for EJC removal","Mechanism linking translation initiation to EJC fate not defined"]},{"year":2009,"claim":"Defined PYM as an EJC disassembly and recycling factor, linking its activity directly to suppression of NMD.","evidence":"In vitro EJC disassembly reconstitution plus gain- and loss-of-function in cells with NMD reporter assays","pmids":["19410547"],"confidence":"High","gaps":["Did not separate translation-dependent from translation-independent disassembly","Genome-wide consequences for EJC positioning not addressed"]},{"year":2014,"claim":"Demonstrated in vivo that PYM regulates EJC homeostasis and is autoregulated by its own C-terminus, with disruption causing mRNA mislocalization and developmental defects.","evidence":"Drosophila transgenic overexpression/loss-of-function, ternary complex biochemistry, RIP, and genetic epistasis with y14/mago","pmids":["24967911"],"confidence":"High","gaps":["DmPYM lacks ribosome binding, so translation-coupling conclusions do not transfer directly to humans","C-terminal autoregulatory mechanism not structurally resolved"]},{"year":2023,"claim":"Revealed an intrinsic autoinhibitory mechanism: the disordered N-terminal region binds RNA sequence-independently in a manner mutually exclusive with EJC binding.","evidence":"NMR spectroscopy and RNA-binding assays on the PYM1-160 disordered region","pmids":["37065448"],"confidence":"Medium","gaps":["Functional downregulation of EJC recycling by RNA binding is inferential, not directly demonstrated in cells","Physiological RNA targets and stoichiometry unknown"]},{"year":2025,"claim":"Separated PYM1's two activities and established its role as an EJC positional-specificity factor that prevents non-canonical EJC deposition and aberrant NMD, a function viruses exploit.","evidence":"PYM1 interaction-deficient EJC mutants in HEK293 cells, eCLIP/iCLIP occupancy mapping, RNA-seq, NMD reporters, and flavivirus infection","pmids":["40885765"],"confidence":"High","gaps":["Mechanism by which PYM1 selectively targets non-canonical EJCs not defined","Link between stabilized long-exon mRNAs and TIS-granule localization mechanistically unresolved"]},{"year":2025,"claim":"Identified the flavivirus capsid protein as a direct PYM1 interactor that phenocopies PYM1 depletion to reshape host mRNA regulation.","evidence":"Co-IP of PYM1–capsid interaction with viral infection and RNA-seq comparison (preprint)","pmids":["40161626"],"confidence":"Medium","gaps":["Preprint version; binding interface on PYM1 not mapped","Functional consequence for viral replication not established"]},{"year":null,"claim":"How PYM1 distinguishes canonical from non-canonical EJC positions and how its RNA-binding autoinhibition is regulated in vivo remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of PYM1 acting on a non-canonically positioned EJC","Trigger that switches PYM1 between RNA-bound (autoinhibited) and EJC-bound states unknown","Physiological regulators of PYM1 recycling activity uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,6]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]},{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[2,6]}],"complexes":["exon junction complex (EJC)"],"partners":["MAGOH","RBM8A","ORF57"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BRP8","full_name":"Partner of Y14 and mago","aliases":["PYM homolog 1 exon junction complex-associated factor","Protein wibg homolog"],"length_aa":204,"mass_kda":22.7,"function":"Key regulator of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmark for the intron exon structure of genes and directs post-transcriptional processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA decay (NMD) or translation. Acts as an EJC disassembly factor, allowing translation-dependent EJC removal and recycling by disrupting mature EJC from spliced mRNAs. Its association with the 40S ribosomal subunit probably prevents a translation-independent disassembly of the EJC from spliced mRNAs, by restricting its activity to mRNAs that have been translated. Interferes with NMD and enhances translation of spliced mRNAs, probably by antagonizing EJC functions. May bind RNA; the relevance of RNA-binding remains unclear in vivo, RNA-binding was detected by PubMed:14968132, while PubMed:19410547 did not detect RNA-binding activity independently of the EJC","subcellular_location":"Cytoplasm; Nucleus, nucleolus; Nucleus, nucleoplasm","url":"https://www.uniprot.org/uniprotkb/Q9BRP8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PYM1","classification":"Common Essential","n_dependent_lines":456,"n_total_lines":1208,"dependency_fraction":0.37748344370860926},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"RBM8A","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PYM1","total_profiled":1310},"omim":[{"mim_id":"619753","title":"PYM HOMOLOG 1, EXON JUNCTION COMPLEX-ASSOCIATED FACTOR; PYM1","url":"https://www.omim.org/entry/619753"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nucleoli","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"},{"location":"Cell Junctions","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PYM1"},"hgnc":{"alias_symbol":["PYM"],"prev_symbol":["WIBG"]},"alphafold":{"accession":"Q9BRP8","domains":[{"cath_id":"1.20.58","chopping":"145-201","consensus_level":"high","plddt":91.3423,"start":145,"end":201}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BRP8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BRP8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BRP8-F1-predicted_aligned_error_v6.png","plddt_mean":74.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PYM1","jax_strain_url":"https://www.jax.org/strain/search?query=PYM1"},"sequence":{"accession":"Q9BRP8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BRP8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BRP8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BRP8"}},"corpus_meta":[{"pmid":"19410547","id":"PMC_19410547","title":"Disassembly of exon junction complexes by PYM.","date":"2009","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/19410547","citation_count":163,"is_preprint":false},{"pmid":"18026120","id":"PMC_18026120","title":"PYM binds the cytoplasmic exon-junction complex and ribosomes to enhance translation of spliced mRNAs.","date":"2007","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/18026120","citation_count":97,"is_preprint":false},{"pmid":"14968132","id":"PMC_14968132","title":"Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex.","date":"2004","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/14968132","citation_count":82,"is_preprint":false},{"pmid":"20436455","id":"PMC_20436455","title":"Kaposi's sarcoma-associated herpesvirus ORF57 protein interacts with PYM to enhance translation of viral intronless mRNAs.","date":"2010","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/20436455","citation_count":61,"is_preprint":false},{"pmid":"16953428","id":"PMC_16953428","title":"Biochemical and cellular characterization of the plant ortholog of PYM, a protein that interacts with the exon junction complex core proteins Mago and Y14.","date":"2006","source":"Planta","url":"https://pubmed.ncbi.nlm.nih.gov/16953428","citation_count":26,"is_preprint":false},{"pmid":"24967911","id":"PMC_24967911","title":"The EJC binding and dissociating activity of PYM is regulated in Drosophila.","date":"2014","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24967911","citation_count":23,"is_preprint":false},{"pmid":"17268597","id":"PMC_17268597","title":"Mn(dca)2(pym)2 and Mn(dca)2(pym)(H2O) {dca = dicyanamide; pym = pyrimidine}: New coordination polymers exhibiting 1- and 2-D topologies.","date":"2007","source":"Dalton transactions (Cambridge, England : 2003)","url":"https://pubmed.ncbi.nlm.nih.gov/17268597","citation_count":7,"is_preprint":false},{"pmid":"39800267","id":"PMC_39800267","title":"Pym-18a, a novel pyrimidine derivative ameliorates glucocorticoid induced osteoblast apoptosis and promotes osteogenesis via autophagy and PINK 1/Parkin mediated mitophagy induction.","date":"2025","source":"Biochemical pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/39800267","citation_count":4,"is_preprint":false},{"pmid":"37065448","id":"PMC_37065448","title":"The EJC disassembly factor PYM is an intrinsically disordered protein and forms a fuzzy complex with RNA.","date":"2023","source":"Frontiers in molecular biosciences","url":"https://pubmed.ncbi.nlm.nih.gov/37065448","citation_count":3,"is_preprint":false},{"pmid":"35641396","id":"PMC_35641396","title":"Novel GSK-3 kinase inhibitor Pym-5 induces GSK-3β rather than GSK-3α-dependent melanogenesis in murine melanoma cells.","date":"2022","source":"Journal of dermatological science","url":"https://pubmed.ncbi.nlm.nih.gov/35641396","citation_count":3,"is_preprint":false},{"pmid":"12475417","id":"PMC_12475417","title":"[The role of mitogen-activated protein kinase (MAPK) pathway in the action mechanism of PYM-induced KB cells apoptosis].","date":"2002","source":"Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology","url":"https://pubmed.ncbi.nlm.nih.gov/12475417","citation_count":3,"is_preprint":false},{"pmid":"40885765","id":"PMC_40885765","title":"PYM1 limits non-canonical Exon Junction Complex occupancy in a gene architecture dependent manner to tune mRNA expression.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/40885765","citation_count":2,"is_preprint":false},{"pmid":"40161626","id":"PMC_40161626","title":"PYM1 limits non-canonical Exon Junction Complex occupancy in a gene architecture dependent manner to tune mRNA expression.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40161626","citation_count":0,"is_preprint":false},{"pmid":"16288335","id":"PMC_16288335","title":"[Experimental study of interstitial chemotherapy with PYM delivered from a solid implantable biodegradable polymer against human tongue SCC in tumor-bearing nude mice].","date":"2005","source":"Shanghai kou qiang yi xue = Shanghai journal of stomatology","url":"https://pubmed.ncbi.nlm.nih.gov/16288335","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.09.19.613823","title":"Insecticide resistance in  <i>Myzus persicae</i>  collected from sweet pepper","date":"2024-09-22","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.19.613823","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9227,"output_tokens":2400,"usd":0.031841,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9483,"output_tokens":2832,"usd":0.059108,"stage2_stop_reason":"end_turn"},"total_usd":0.090949,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"PYM is a cytoplasmic RNA-binding protein excluded from the nucleus by CRM1-mediated nuclear export. Its N-terminal domain directly interacts with both Mago and Y14 simultaneously, capping their heterodimerization interface at conserved surface residues, as revealed by a crystal structure of the Drosophila ternary complex at 1.9 Å resolution.\",\n      \"method\": \"Crystal structure determination (1.9 Å), in vitro pulldown with recombinant proteins, nuclear export inhibition assays, tethering assays\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional validation, mutagenesis of interface residues, orthogonal biochemical assays, results confirmed with human proteins\",\n      \"pmids\": [\"14968132\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"PYM binds the Y14-MAGOH (Mago) complex via one domain and independently binds the small (40S) ribosomal subunit and the 48S preinitiation complex via a separate domain, functioning as a bridge between EJC-bearing spliced mRNAs and the translation machinery to enhance translation of spliced mRNAs. PYM knockdown reduces translation efficiency of reporter mRNAs produced from intron-containing but not intronless pre-mRNAs.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping, siRNA knockdown with translation reporter assays, ribosome sedimentation\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, domain-separation experiments, functional knockdown with specific reporter readout, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"18026120\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"PYM is an EJC disassembly factor: it binds the MAGOH-Y14 heterodimer component of fully assembled EJCs and dissociates them from spliced mRNAs both in vitro and in cells. EJC assembly intermediates are resistant to PYM. PYM overexpression disrupts EJC association with spliced mRNA and inhibits nonsense-mediated mRNA decay (NMD). Depletion of PYM causes accumulation of EJCs on spliced mRNAs and impairs EJC protein recycling.\",\n      \"method\": \"In vitro EJC disassembly assay, Co-immunoprecipitation, PYM overexpression and siRNA knockdown in cells, NMD reporter assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro reconstitution of disassembly activity, complementary gain- and loss-of-function cellular experiments, multiple orthogonal methods, replicated across conditions\",\n      \"pmids\": [\"19410547\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"KSHV ORF57 protein directly interacts with PYM and recruits it to intronless viral mRNAs, enabling PYM to facilitate association of the 48S preinitiation complex with these EJC-lacking transcripts and thereby enhance their translation.\",\n      \"method\": \"Co-immunoprecipitation, ribosome sedimentation, biochemical interaction mapping\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct interaction shown by Co-IP, ribosome cosedimentation, single lab with multiple biochemical approaches\",\n      \"pmids\": [\"20436455\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In Drosophila, PYM (DmPYM) EJC-binding and disassembly activity is regulated by its own C-terminus, which modulates formation of the PYM-Y14-Mago ternary complex. Unlike human PYM, DmPYM does not interact with the small ribosomal subunit and can dismantle EJCs in a translation-independent manner upon overexpression. Elevated DmPYM N-terminus during oogenesis causes EJC dissociation from oskar mRNA, resulting in oskar mislocalization and female sterility. Loss of DmPYM is lethal in flies with reduced y14 or mago gene dosage, establishing PYM as a regulator of EJC homeostasis.\",\n      \"method\": \"In vivo transgenic overexpression and loss-of-function in Drosophila, biochemical ternary complex analysis, RNA immunoprecipitation (RIP), genetic epistasis\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo genetic and biochemical approaches, transgenic overexpression with defined mRNA localization phenotype, genetic epistasis with y14/mago, multiple orthogonal methods\",\n      \"pmids\": [\"24967911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The first 160 amino acids of PYM (PYM1-160) are intrinsically disordered. PYM1-160 binds RNA independently of nucleotide sequence, forming a fuzzy protein-RNA complex. This RNA binding is incompatible with PYM's EJC interaction surface, suggesting that RNA binding down-regulates PYM's EJC recycling activity.\",\n      \"method\": \"NMR spectroscopy, RNA binding assays, structural characterization of intrinsically disordered region\",\n      \"journal\": \"Frontiers in molecular biosciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — NMR structural characterization and RNA binding assays, single lab, functional interpretation partially inferential\",\n      \"pmids\": [\"37065448\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PYM1 interaction with the EJC (via RBM8A/MAGOH heterodimer) is required for translation-independent EJC destabilization but is dispensable for translation-dependent EJC disassembly. PYM1 interaction-deficient EJCs accumulate at non-canonical (away from canonical upstream exon-exon junction) positions, particularly on transcripts with no or few introns. Such non-canonical EJCs can induce NMD when positioned downstream of stop codons. PYM1 depletion stabilizes mRNAs with fewer and longer exons that localize to ER-associated TIS-granules. Flavivirus capsid protein interaction with PYM1 mimics PYM1 depletion to reshape host mRNA regulation.\",\n      \"method\": \"PYM1 interaction-deficient EJC mutants in HEK293 cells, eCLIP/iCLIP for EJC occupancy mapping, siRNA knockdown, RNA-seq, NMD reporter assays, flavivirus infection\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — separation-of-function mutants, genome-wide EJC occupancy mapping, multiple orthogonal approaches including viral infection validation, published in peer-reviewed journal\",\n      \"pmids\": [\"40885765\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Flavivirus capsid protein directly interacts with PYM1, and cells expressing flavivirus capsid protein or infected with flaviviruses show similar changes in EJC occupancy and gene expression as PYM1 depletion, indicating that viruses hijack PYM1's EJC specificity function to alter host mRNA regulation.\",\n      \"method\": \"Co-immunoprecipitation of PYM1-flavivirus capsid interaction, viral infection experiments, RNA-seq comparison\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and transcriptomic validation, preprint version of peer-reviewed work; interaction confirmed in published paper (PMID 40885765)\",\n      \"pmids\": [\"40161626\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"PYM1 (also known as PYM/WIBG) is a cytoplasmic, intrinsically disordered EJC disassembly and specificity factor that directly binds the MAGOH-Y14 (RBM8A) heterodimer of the exon junction complex via its N-terminal domain (whose structure with Mago-Y14 is resolved crystallographically) and, via a separate domain, binds the 40S ribosomal subunit/48S preinitiation complex; PYM1 disassembles fully assembled EJCs from spliced mRNAs (both in vitro and in vivo), mediating EJC recycling and limiting accumulation of non-canonical EJCs on intron-poor transcripts, thereby suppressing aberrant NMD—a function regulated by RNA binding to its disordered region and by its own C-terminus in Drosophila, and hijacked by flavivirus capsid proteins and KSHV ORF57 to reshape host mRNA translation and stability.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PYM1 (PYM/WIBG) is a cytoplasmic factor that controls the lifecycle and positional specificity of the exon junction complex (EJC) on spliced mRNAs [#0, #2]. Its N-terminal domain directly and simultaneously contacts the MAGOH–Y14 (RBM8A) heterodimer, capping their dimerization interface, while a separate domain engages the 40S ribosomal subunit and the 48S preinitiation complex, allowing PYM1 to bridge EJC-bearing mRNAs to the translation machinery and enhance translation of intron-derived transcripts [#0, #1]. Acting on fully assembled EJCs (but not assembly intermediates), PYM1 dissociates the complex from mRNA to drive EJC recycling; overexpression strips EJCs and suppresses nonsense-mediated decay (NMD), whereas depletion causes EJCs to accumulate on spliced mRNAs [#2]. This recycling function enforces EJC deposition specificity: loss of the PYM1–EJC interaction permits non-canonical EJCs to accumulate away from canonical exon-exon junctions, especially on intron-poor transcripts, where they trigger aberrant NMD, and PYM1 depletion stabilizes mRNAs with few, long exons that localize to ER-associated TIS-granules [#6]. PYM1 activity is autoregulated: its first 160 residues are intrinsically disordered and bind RNA in a sequence-independent, fuzzy manner that is sterically incompatible with EJC engagement, providing a negative regulatory input on recycling [#5]. PYM1 is a host target hijacked by viruses—KSHV ORF57 recruits PYM1 to intronless viral mRNAs to promote their translation [#3], and the flavivirus capsid protein binds PYM1 to mimic its depletion and reshape host EJC occupancy and gene expression [#6, #7].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established the structural basis of how PYM recognizes the EJC core: a single N-terminal domain that simultaneously contacts Mago and Y14 by capping their heterodimer interface.\",\n      \"evidence\": \"1.9 Å crystal structure of the Drosophila PYM–Mago–Y14 ternary complex with in vitro pulldowns and nuclear export assays\",\n      \"pmids\": [\"14968132\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish the cellular consequence of EJC binding (recycling vs. disassembly)\", \"Functional role of regions outside the N-terminal Mago-Y14-binding domain unresolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Showed PYM is a bifunctional bridge, using one domain for the EJC and a separate domain for the 40S/48S ribosomal complex to couple EJC-marked spliced mRNAs to enhanced translation.\",\n      \"evidence\": \"Reciprocal Co-IP, domain mapping, ribosome sedimentation, and siRNA knockdown with intron-containing vs. intronless translation reporters\",\n      \"pmids\": [\"18026120\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not determine whether ribosome engagement is required for EJC removal\", \"Mechanism linking translation initiation to EJC fate not defined\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defined PYM as an EJC disassembly and recycling factor, linking its activity directly to suppression of NMD.\",\n      \"evidence\": \"In vitro EJC disassembly reconstitution plus gain- and loss-of-function in cells with NMD reporter assays\",\n      \"pmids\": [\"19410547\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not separate translation-dependent from translation-independent disassembly\", \"Genome-wide consequences for EJC positioning not addressed\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrated in vivo that PYM regulates EJC homeostasis and is autoregulated by its own C-terminus, with disruption causing mRNA mislocalization and developmental defects.\",\n      \"evidence\": \"Drosophila transgenic overexpression/loss-of-function, ternary complex biochemistry, RIP, and genetic epistasis with y14/mago\",\n      \"pmids\": [\"24967911\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"DmPYM lacks ribosome binding, so translation-coupling conclusions do not transfer directly to humans\", \"C-terminal autoregulatory mechanism not structurally resolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed an intrinsic autoinhibitory mechanism: the disordered N-terminal region binds RNA sequence-independently in a manner mutually exclusive with EJC binding.\",\n      \"evidence\": \"NMR spectroscopy and RNA-binding assays on the PYM1-160 disordered region\",\n      \"pmids\": [\"37065448\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional downregulation of EJC recycling by RNA binding is inferential, not directly demonstrated in cells\", \"Physiological RNA targets and stoichiometry unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Separated PYM1's two activities and established its role as an EJC positional-specificity factor that prevents non-canonical EJC deposition and aberrant NMD, a function viruses exploit.\",\n      \"evidence\": \"PYM1 interaction-deficient EJC mutants in HEK293 cells, eCLIP/iCLIP occupancy mapping, RNA-seq, NMD reporters, and flavivirus infection\",\n      \"pmids\": [\"40885765\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which PYM1 selectively targets non-canonical EJCs not defined\", \"Link between stabilized long-exon mRNAs and TIS-granule localization mechanistically unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified the flavivirus capsid protein as a direct PYM1 interactor that phenocopies PYM1 depletion to reshape host mRNA regulation.\",\n      \"evidence\": \"Co-IP of PYM1–capsid interaction with viral infection and RNA-seq comparison (preprint)\",\n      \"pmids\": [\"40161626\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint version; binding interface on PYM1 not mapped\", \"Functional consequence for viral replication not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PYM1 distinguishes canonical from non-canonical EJC positions and how its RNA-binding autoinhibition is regulated in vivo remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of PYM1 acting on a non-canonically positioned EJC\", \"Trigger that switches PYM1 between RNA-bound (autoinhibited) and EJC-bound states unknown\", \"Physiological regulators of PYM1 recycling activity uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 6]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [2, 6]},\n      {\"term_id\": \"R-HSA-72766\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [\"exon junction complex (EJC)\"],\n    \"partners\": [\"MAGOH\", \"RBM8A\", \"ORF57\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}