{"gene":"NOL7","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2006,"finding":"NOL7 localizes to the nucleolus and functions as a tumor suppressor in cervical cancer; reintroduction into cervical carcinoma cells suppressed in vivo tumor growth and induced an angiogenic switch characterized by decreased VEGF production and increased thrombospondin-1 (TSP-1) production.","method":"Transfection/xenograft assay, fluorescence in situ hybridization (LOH analysis), protein localization","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo xenograft loss-of-function with defined angiogenic phenotype readout (VEGF decrease, TSP-1 increase), single lab but multiple readouts","pmids":["16205646"],"is_preprint":false},{"year":2010,"finding":"NOL7 requires cytosolic machinery for active nuclear import; three functional nuclear localization signals (NLSs) were identified, with NLS2 and NLS3 critical for rate and efficiency of nuclear targeting; four basic clusters within NLS2 and NLS3 independently mediate nucleolar targeting; nucleolar occupancy involves rapid nucleoplasmic shuttling but low nucleolar mobility; depletion of RNA (total or rRNA) causes a nucleoplasmic shift of NOL7, indicating RNA-dependent nucleolar targeting.","method":"In vitro nuclear import assay, deletion constructs, cytoplasmic pyruvate kinase fusion proteins, site-directed mutagenesis, FRAP, RNA depletion experiments","journal":"BMC cell biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (in vitro import assay, deletion constructs, mutagenesis, FRAP, RNA depletion) in a single rigorous study","pmids":["20875127"],"is_preprint":false},{"year":2010,"finding":"The NOL7 promoter is a TATA-less promoter regulated by transcription factors SP1, c-Myc, and RXRalpha, which bind to its promoter region; c-Myc and RXRalpha positively regulate NOL7 expression.","method":"5' RACE (transcriptional start site mapping), promoter deletion analysis, chromatin immunoprecipitation (ChIP)","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP confirms TF binding, deletion analysis defines essential promoter elements, single lab with two orthogonal methods","pmids":["20206243"],"is_preprint":false},{"year":2011,"finding":"Three alternatively spliced NOL7 isoforms exist with distinct localizations: SP1 (29 kD, long form) localizes to the nucleolar granular component and dissociates from the nucleolus during cell division; SP2 is nucleoplasmic; SP3 is cytoplasmic. Knockdown of NOL7-SP1 abrogates nucleolar architecture (particularly internal regions) and reduces cell proliferation. Nucleolar targeting is mediated by a C-terminal nucleolar localization sequence (NoLS), but high nucleolar binding affinity requires additional protein regions beyond the NoLS.","method":"Alternative splice isoform cloning, fluorescence localization, siRNA knockdown, domain dissection","journal":"Nucleus","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — isoform characterization with localization, knockdown phenotype, and domain dissection in single lab","pmids":["21818416"],"is_preprint":false},{"year":2012,"finding":"RB tumor suppressor positively regulates NOL7 at the transcriptional level by recruiting transcription factors and transcription machinery proteins to the NOL7 promoter; loss of RB represses NOL7 transcription by inhibiting assembly of these proteins at the promoter.","method":"Chromatin immunoprecipitation (ChIP), transcriptional reporter assays, RB loss-of-function analysis","journal":"Neoplasia","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP confirms RB and transcription factor recruitment to NOL7 promoter, single lab with multiple readouts","pmids":["23308053"],"is_preprint":false},{"year":2012,"finding":"NOL7 is an mRNA-binding protein that must localize to the nucleoplasm to exert its antiangiogenic effects; it associates with RNA-processing machinery and directly binds the 3'UTR of TSP-1 mRNA, increasing TSP-1 mRNA stability (increased mRNA half-life) and protein levels; NOL7-mediated post-transcriptional stabilization also affects a broader subset of angiogenesis-related mRNAs.","method":"RNA immunoprecipitation, 3'UTR luciferase reporter assay, mRNA half-life assay, RNA-binding protein characterization, localization mutant analysis","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (RIP, luciferase reporter with 3'UTR, mRNA half-life assay, localization mutants) in single rigorous study establishing direct RNA binding and mechanistic consequence","pmids":["23085760"],"is_preprint":false},{"year":2023,"finding":"NOL7 is the likely human ortholog of yeast Bud21 and functions as a U3 Associated Protein (UTP) subunit of the small subunit processome; it is required for early pre-rRNA accumulation and pre-18S rRNA processing in human cells; NOL7 depletion leads to decreased protein synthesis and induction of the nucleolar stress response.","method":"siRNA knockdown, pre-rRNA processing assays (Northern blot/primer extension), protein synthesis assays, nucleolar stress response assays","journal":"RNA biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with multiple defined molecular phenotypes (pre-rRNA processing, protein synthesis, nucleolar stress), establishes pathway position as UTP component","pmids":["37246770"],"is_preprint":false},{"year":2024,"finding":"PQBP3/NOL7 directly binds PSME3 (proteasome activator complex subunit 3), decreasing PSME3 interaction with Lamin B1 and thereby preventing proteasomal Lamin B1 degradation; depletion of PQBP3/NOL7 causes nuclear membrane instability and release of genomic DNA to the cytosol, triggering senescence. Mutant ataxin-1 (ATXN1) sequesters PQBP3 into inclusion bodies, reducing nucleolar PQBP3 levels and causing a senescence phenotype in Purkinje cells in knock-in mice.","method":"Co-immunoprecipitation (direct binding assay), knockdown/depletion experiments, knock-in mouse model, nuclear membrane integrity assays, cytosolic DNA detection","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding assays, in vivo knock-in mouse model, multiple orthogonal readouts (Lamin B1 levels, DNA leakage, senescence markers) across cell and animal models","pmids":["39103492"],"is_preprint":false},{"year":2024,"finding":"PQBP3/NOL7 is an intrinsically disordered protein (IDP); bioinformatics and high-speed atomic force microscopy (HS-AFM) demonstrate that its N-terminal region is dynamically unstructured.","method":"Bioinformatics disorder prediction, high-speed atomic force microscopy (HS-AFM)","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1–3 / Moderate — HS-AFM provides direct structural visualization confirming bioinformatics prediction, but limited functional validation in single study","pmids":["39126896"],"is_preprint":false},{"year":2026,"finding":"NOL7 binds the 3'UTR of GADD45A mRNA, stabilizing GADD45A mRNA and upregulating GADD45A expression; the NOL7/GADD45A axis suppresses STAT3 phosphorylation at Ser727, thereby inhibiting ovarian cancer cell proliferation and angiogenesis.","method":"RNA immunoprecipitation, 3'UTR reporter assay, mRNA stability assay, western blot for pSTAT3-Ser727, in vivo xenograft","journal":"Cancer science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP confirms direct mRNA binding, stability assay confirms mechanism, STAT3 phosphorylation links to pathway, single lab","pmids":["41812272"],"is_preprint":false}],"current_model":"NOL7/PQBP3 is a multifunctional nucleolar protein that acts as a UTP-family ribosome biogenesis factor required for early pre-rRNA accumulation and pre-18S processing, an mRNA-binding protein that post-transcriptionally stabilizes TSP-1 and GADD45A mRNAs via their 3'UTRs to suppress angiogenesis and STAT3 signaling, a suppressor of cellular senescence through direct binding to PSME3 that prevents proteasomal Lamin B1 degradation, and an intrinsically disordered protein whose nuclear/nucleolar targeting is governed by defined NLS sequences and RNA-dependent mechanisms; its transcription is positively regulated by RB, c-Myc, and RXRalpha."},"narrative":{"mechanistic_narrative":"NOL7 (also termed PQBP3) is a multifunctional nucleolar protein that integrates ribosome biogenesis with tumor-suppressive control of angiogenesis and cellular senescence [PMID:16205646, PMID:37246770]. As a UTP-family component of the small subunit processome and the likely human ortholog of yeast Bud21, NOL7 is required for early pre-rRNA accumulation and pre-18S rRNA processing; its depletion lowers protein synthesis and triggers the nucleolar stress response [PMID:37246770]. Distinct from this nucleolar role, NOL7 acts in the nucleoplasm as an mRNA-binding protein that directly binds the 3'UTRs of TSP-1 and GADD45A mRNAs to stabilize them and raise their protein levels; TSP-1 stabilization drives an antiangiogenic switch with decreased VEGF, while the GADD45A axis suppresses STAT3 Ser727 phosphorylation to restrain proliferation and angiogenesis [PMID:16205646, PMID:23085760, PMID:41812272]. NOL7 additionally suppresses senescence by directly binding the proteasome activator subunit PSME3, blocking PSME3-mediated proteasomal degradation of Lamin B1 and thereby preserving nuclear membrane integrity; loss of nucleolar NOL7 causes Lamin B1 loss, cytosolic genomic DNA release, and senescence [PMID:39103492]. NOL7 is an intrinsically disordered protein with a dynamically unstructured N-terminus, and its nuclear/nucleolar targeting is governed by defined NLS/NoLS sequences and RNA-dependent retention, with alternatively spliced isoforms partitioning between nucleolus, nucleoplasm, and cytoplasm [PMID:20875127, PMID:21818416, PMID:39126896]. Its transcription is positively controlled by RB, c-Myc, and RXRalpha [PMID:20206243, PMID:23308053].","teleology":[{"year":2006,"claim":"Established NOL7 as a nucleolar tumor suppressor with a defined functional output, answering whether loss of this locus contributes to cancer through a specific phenotype.","evidence":"Xenograft reintroduction assays with LOH analysis and protein localization in cervical carcinoma cells","pmids":["16205646"],"confidence":"Medium","gaps":["Molecular mechanism of the angiogenic switch (VEGF/TSP-1) not defined","Direct molecular targets unidentified at this stage"]},{"year":2010,"claim":"Defined the sequence determinants and dynamics of NOL7 subcellular targeting, explaining how the protein reaches the nucleolus and is retained there.","evidence":"In vitro nuclear import assays, pyruvate kinase fusion constructs, site-directed mutagenesis, FRAP, and RNA depletion","pmids":["20875127"],"confidence":"High","gaps":["Identity of the RNA species mediating nucleolar retention not pinpointed","Import receptors/karyopherins not identified"]},{"year":2010,"claim":"Identified upstream transcriptional regulators of NOL7, addressing how its expression is controlled.","evidence":"5' RACE start-site mapping, promoter deletion analysis, and ChIP for SP1, c-Myc, and RXRalpha","pmids":["20206243"],"confidence":"Medium","gaps":["Functional consequence of TF binding on phenotype not tested","Conditions driving regulation in vivo unknown"]},{"year":2011,"claim":"Resolved that NOL7 exists as isoforms with distinct localizations and that the nucleolar isoform maintains nucleolar architecture and proliferation, linking localization to function.","evidence":"Splice isoform cloning, fluorescence localization, siRNA knockdown, and domain dissection","pmids":["21818416"],"confidence":"Medium","gaps":["Molecular basis of nucleolar architecture maintenance unresolved","Functions of nucleoplasmic and cytoplasmic isoforms not defined"]},{"year":2012,"claim":"Showed RB positively regulates NOL7 transcription by enabling assembly of factors at its promoter, connecting a master tumor suppressor to NOL7 expression.","evidence":"ChIP, transcriptional reporter assays, and RB loss-of-function analysis","pmids":["23308053"],"confidence":"Medium","gaps":["Identity of the recruited machinery only partially defined","Whether RB-NOL7 axis drives the tumor-suppressive phenotype not directly tested"]},{"year":2012,"claim":"Defined the molecular mechanism of NOL7's antiangiogenic activity by establishing it as a nucleoplasmic mRNA-binding protein that stabilizes TSP-1 mRNA via its 3'UTR.","evidence":"RNA immunoprecipitation, 3'UTR luciferase reporter, mRNA half-life assays, and localization-mutant analysis","pmids":["23085760"],"confidence":"High","gaps":["Sequence/structural motif recognized in the 3'UTR not mapped","Full set of stabilized angiogenesis mRNAs not enumerated"]},{"year":2023,"claim":"Placed NOL7 in the ribosome biogenesis pathway as a UTP/SSU-processome subunit required for pre-18S processing, distinguishing its nucleolar housekeeping role from its mRNA-stabilizing role.","evidence":"siRNA knockdown with pre-rRNA processing, protein synthesis, and nucleolar stress assays","pmids":["37246770"],"confidence":"High","gaps":["Structural position within the SSU processome not resolved","Relationship between processome role and tumor-suppressor functions not integrated"]},{"year":2024,"claim":"Established a mechanism for NOL7-dependent senescence suppression: direct binding to PSME3 protects Lamin B1 from proteasomal degradation and maintains nuclear envelope integrity.","evidence":"Reciprocal Co-IP, depletion experiments, ATXN1 knock-in mouse model, nuclear membrane integrity and cytosolic DNA detection assays","pmids":["39103492"],"confidence":"High","gaps":["How PQBP3/NOL7 sequestration by mutant ATXN1 mechanistically scales to neurodegeneration not fully defined","Stoichiometry of NOL7-PSME3-Lamin B1 interplay unresolved"]},{"year":2024,"claim":"Provided structural insight that NOL7 is an intrinsically disordered protein, relevant to its multivalent binding and dynamic nucleolar behavior.","evidence":"Bioinformatics disorder prediction and high-speed atomic force microscopy","pmids":["39126896"],"confidence":"Medium","gaps":["Functional link between disorder and specific binding partners not tested","Limited functional validation in this study"]},{"year":2026,"claim":"Extended the mRNA-stabilization paradigm to a second target by showing NOL7 stabilizes GADD45A mRNA to suppress STAT3 Ser727 signaling and ovarian cancer growth.","evidence":"RNA immunoprecipitation, 3'UTR reporter, mRNA stability assays, pSTAT3-Ser727 western blot, and xenografts","pmids":["41812272"],"confidence":"Medium","gaps":["Direct mechanism linking GADD45A to STAT3 phosphorylation not defined","Whether TSP-1 and GADD45A stabilization use a shared recognition mechanism unknown"]},{"year":null,"claim":"How NOL7's nucleolar ribosome-biogenesis role mechanistically connects to its nucleoplasmic mRNA-stabilizing and PSME3/Lamin B1 senescence-suppressing functions remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model linking processome function to mRNA stabilization","Determinants partitioning NOL7 between nucleolar and nucleoplasmic functional pools not defined","RNA-binding specificity motif uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[5,9]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[6]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[3,5]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[6]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[7]}],"complexes":["small subunit (SSU) processome"],"partners":["PSME3","LMNB1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UMY1","full_name":"U3 small nucleolar RNA-associated protein NOL7","aliases":["Nucleolar protein 7","Nucleolar protein of 27 kDa"],"length_aa":257,"mass_kda":29.4,"function":"Functions as part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit that coordinates the first two steps of ribosome biogenesis in transcription of the primary transcript pre-RNA and pre-18S processing (PubMed:34516797, PubMed:37246770). During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome (PubMed:34516797). This subunit is required for processing of the 5'-external transcribed spacer sequence (5'ETS) of the primary transcript pre-rRNA to yield the 18S rRNA (PubMed:37246770). Also plays a role in maintaining early pre-rRNA levels, either by assisting in its transcription or stability (PubMed:37246770)","subcellular_location":"Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/Q9UMY1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/NOL7","classification":"Common Essential","n_dependent_lines":994,"n_total_lines":1208,"dependency_fraction":0.8228476821192053},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"FBL","stoichiometry":0.2},{"gene":"IPO5","stoichiometry":0.2},{"gene":"RAB11A","stoichiometry":0.2},{"gene":"RACK1","stoichiometry":0.2},{"gene":"SRP9","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/NOL7","total_profiled":1310},"omim":[{"mim_id":"611533","title":"NUCLEOLAR PROTEIN 7; NOL7","url":"https://www.omim.org/entry/611533"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoli","reliability":"Supported"},{"location":"Mitotic chromosome","reliability":"Supported"},{"location":"Mitochondria","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NOL7"},"hgnc":{"alias_symbol":["NOP27","RARG-1","dJ223E5.2"],"prev_symbol":["C6orf90","PQBP3"]},"alphafold":{"accession":"Q9UMY1","domains":[{"cath_id":"1.20.5","chopping":"70-113","consensus_level":"medium","plddt":86.9511,"start":70,"end":113}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UMY1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UMY1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UMY1-F1-predicted_aligned_error_v6.png","plddt_mean":71.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NOL7","jax_strain_url":"https://www.jax.org/strain/search?query=NOL7"},"sequence":{"accession":"Q9UMY1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UMY1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UMY1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UMY1"}},"corpus_meta":[{"pmid":"16205646","id":"PMC_16205646","title":"NOL7 is a nucleolar candidate tumor suppressor gene in cervical cancer that modulates the angiogenic phenotype.","date":"2006","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/16205646","citation_count":33,"is_preprint":false},{"pmid":"23308053","id":"PMC_23308053","title":"The RB tumor suppressor positively regulates transcription of the anti-angiogenic protein NOL7.","date":"2012","source":"Neoplasia (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/23308053","citation_count":14,"is_preprint":false},{"pmid":"20875127","id":"PMC_20875127","title":"Identification and functional analysis of NOL7 nuclear and nucleolar localization signals.","date":"2010","source":"BMC cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/20875127","citation_count":13,"is_preprint":false},{"pmid":"23085760","id":"PMC_23085760","title":"The novel tumor suppressor NOL7 post-transcriptionally regulates thrombospondin-1 expression.","date":"2012","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/23085760","citation_count":10,"is_preprint":false},{"pmid":"21818416","id":"PMC_21818416","title":"The dynamics of the alternatively spliced NOL7 gene products and role in nucleolar architecture.","date":"2011","source":"Nucleus (Austin, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/21818416","citation_count":8,"is_preprint":false},{"pmid":"37246770","id":"PMC_37246770","title":"Human nucleolar protein 7 (NOL7) is required for early pre-rRNA accumulation and pre-18S rRNA processing.","date":"2023","source":"RNA biology","url":"https://pubmed.ncbi.nlm.nih.gov/37246770","citation_count":7,"is_preprint":false},{"pmid":"20206243","id":"PMC_20206243","title":"Identification and characterization of the human NOL7 gene promoter.","date":"2010","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/20206243","citation_count":6,"is_preprint":false},{"pmid":"39103492","id":"PMC_39103492","title":"PQBP3 prevents senescence by suppressing PSME3-mediated proteasomal Lamin B1 degradation.","date":"2024","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/39103492","citation_count":4,"is_preprint":false},{"pmid":"39126896","id":"PMC_39126896","title":"PQBP3/NOL7 is an intrinsically disordered protein.","date":"2024","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/39126896","citation_count":0,"is_preprint":false},{"pmid":"41812272","id":"PMC_41812272","title":"NOL7 Inhibits Ovarian Cancer Progression and Suppresses Angiogenesis by Stabilizing GADD45A to Deactivate STAT3.","date":"2026","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/41812272","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6665,"output_tokens":2653,"usd":0.029895,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9964,"output_tokens":3372,"usd":0.06706,"stage2_stop_reason":"end_turn"},"total_usd":0.096955,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"NOL7 localizes to the nucleolus and functions as a tumor suppressor in cervical cancer; reintroduction into cervical carcinoma cells suppressed in vivo tumor growth and induced an angiogenic switch characterized by decreased VEGF production and increased thrombospondin-1 (TSP-1) production.\",\n      \"method\": \"Transfection/xenograft assay, fluorescence in situ hybridization (LOH analysis), protein localization\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo xenograft loss-of-function with defined angiogenic phenotype readout (VEGF decrease, TSP-1 increase), single lab but multiple readouts\",\n      \"pmids\": [\"16205646\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"NOL7 requires cytosolic machinery for active nuclear import; three functional nuclear localization signals (NLSs) were identified, with NLS2 and NLS3 critical for rate and efficiency of nuclear targeting; four basic clusters within NLS2 and NLS3 independently mediate nucleolar targeting; nucleolar occupancy involves rapid nucleoplasmic shuttling but low nucleolar mobility; depletion of RNA (total or rRNA) causes a nucleoplasmic shift of NOL7, indicating RNA-dependent nucleolar targeting.\",\n      \"method\": \"In vitro nuclear import assay, deletion constructs, cytoplasmic pyruvate kinase fusion proteins, site-directed mutagenesis, FRAP, RNA depletion experiments\",\n      \"journal\": \"BMC cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (in vitro import assay, deletion constructs, mutagenesis, FRAP, RNA depletion) in a single rigorous study\",\n      \"pmids\": [\"20875127\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The NOL7 promoter is a TATA-less promoter regulated by transcription factors SP1, c-Myc, and RXRalpha, which bind to its promoter region; c-Myc and RXRalpha positively regulate NOL7 expression.\",\n      \"method\": \"5' RACE (transcriptional start site mapping), promoter deletion analysis, chromatin immunoprecipitation (ChIP)\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP confirms TF binding, deletion analysis defines essential promoter elements, single lab with two orthogonal methods\",\n      \"pmids\": [\"20206243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Three alternatively spliced NOL7 isoforms exist with distinct localizations: SP1 (29 kD, long form) localizes to the nucleolar granular component and dissociates from the nucleolus during cell division; SP2 is nucleoplasmic; SP3 is cytoplasmic. Knockdown of NOL7-SP1 abrogates nucleolar architecture (particularly internal regions) and reduces cell proliferation. Nucleolar targeting is mediated by a C-terminal nucleolar localization sequence (NoLS), but high nucleolar binding affinity requires additional protein regions beyond the NoLS.\",\n      \"method\": \"Alternative splice isoform cloning, fluorescence localization, siRNA knockdown, domain dissection\",\n      \"journal\": \"Nucleus\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — isoform characterization with localization, knockdown phenotype, and domain dissection in single lab\",\n      \"pmids\": [\"21818416\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"RB tumor suppressor positively regulates NOL7 at the transcriptional level by recruiting transcription factors and transcription machinery proteins to the NOL7 promoter; loss of RB represses NOL7 transcription by inhibiting assembly of these proteins at the promoter.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), transcriptional reporter assays, RB loss-of-function analysis\",\n      \"journal\": \"Neoplasia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP confirms RB and transcription factor recruitment to NOL7 promoter, single lab with multiple readouts\",\n      \"pmids\": [\"23308053\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"NOL7 is an mRNA-binding protein that must localize to the nucleoplasm to exert its antiangiogenic effects; it associates with RNA-processing machinery and directly binds the 3'UTR of TSP-1 mRNA, increasing TSP-1 mRNA stability (increased mRNA half-life) and protein levels; NOL7-mediated post-transcriptional stabilization also affects a broader subset of angiogenesis-related mRNAs.\",\n      \"method\": \"RNA immunoprecipitation, 3'UTR luciferase reporter assay, mRNA half-life assay, RNA-binding protein characterization, localization mutant analysis\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (RIP, luciferase reporter with 3'UTR, mRNA half-life assay, localization mutants) in single rigorous study establishing direct RNA binding and mechanistic consequence\",\n      \"pmids\": [\"23085760\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NOL7 is the likely human ortholog of yeast Bud21 and functions as a U3 Associated Protein (UTP) subunit of the small subunit processome; it is required for early pre-rRNA accumulation and pre-18S rRNA processing in human cells; NOL7 depletion leads to decreased protein synthesis and induction of the nucleolar stress response.\",\n      \"method\": \"siRNA knockdown, pre-rRNA processing assays (Northern blot/primer extension), protein synthesis assays, nucleolar stress response assays\",\n      \"journal\": \"RNA biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with multiple defined molecular phenotypes (pre-rRNA processing, protein synthesis, nucleolar stress), establishes pathway position as UTP component\",\n      \"pmids\": [\"37246770\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PQBP3/NOL7 directly binds PSME3 (proteasome activator complex subunit 3), decreasing PSME3 interaction with Lamin B1 and thereby preventing proteasomal Lamin B1 degradation; depletion of PQBP3/NOL7 causes nuclear membrane instability and release of genomic DNA to the cytosol, triggering senescence. Mutant ataxin-1 (ATXN1) sequesters PQBP3 into inclusion bodies, reducing nucleolar PQBP3 levels and causing a senescence phenotype in Purkinje cells in knock-in mice.\",\n      \"method\": \"Co-immunoprecipitation (direct binding assay), knockdown/depletion experiments, knock-in mouse model, nuclear membrane integrity assays, cytosolic DNA detection\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding assays, in vivo knock-in mouse model, multiple orthogonal readouts (Lamin B1 levels, DNA leakage, senescence markers) across cell and animal models\",\n      \"pmids\": [\"39103492\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PQBP3/NOL7 is an intrinsically disordered protein (IDP); bioinformatics and high-speed atomic force microscopy (HS-AFM) demonstrate that its N-terminal region is dynamically unstructured.\",\n      \"method\": \"Bioinformatics disorder prediction, high-speed atomic force microscopy (HS-AFM)\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–3 / Moderate — HS-AFM provides direct structural visualization confirming bioinformatics prediction, but limited functional validation in single study\",\n      \"pmids\": [\"39126896\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"NOL7 binds the 3'UTR of GADD45A mRNA, stabilizing GADD45A mRNA and upregulating GADD45A expression; the NOL7/GADD45A axis suppresses STAT3 phosphorylation at Ser727, thereby inhibiting ovarian cancer cell proliferation and angiogenesis.\",\n      \"method\": \"RNA immunoprecipitation, 3'UTR reporter assay, mRNA stability assay, western blot for pSTAT3-Ser727, in vivo xenograft\",\n      \"journal\": \"Cancer science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP confirms direct mRNA binding, stability assay confirms mechanism, STAT3 phosphorylation links to pathway, single lab\",\n      \"pmids\": [\"41812272\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NOL7/PQBP3 is a multifunctional nucleolar protein that acts as a UTP-family ribosome biogenesis factor required for early pre-rRNA accumulation and pre-18S processing, an mRNA-binding protein that post-transcriptionally stabilizes TSP-1 and GADD45A mRNAs via their 3'UTRs to suppress angiogenesis and STAT3 signaling, a suppressor of cellular senescence through direct binding to PSME3 that prevents proteasomal Lamin B1 degradation, and an intrinsically disordered protein whose nuclear/nucleolar targeting is governed by defined NLS sequences and RNA-dependent mechanisms; its transcription is positively regulated by RB, c-Myc, and RXRalpha.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NOL7 (also termed PQBP3) is a multifunctional nucleolar protein that integrates ribosome biogenesis with tumor-suppressive control of angiogenesis and cellular senescence [#0, #6]. As a UTP-family component of the small subunit processome and the likely human ortholog of yeast Bud21, NOL7 is required for early pre-rRNA accumulation and pre-18S rRNA processing; its depletion lowers protein synthesis and triggers the nucleolar stress response [#6]. Distinct from this nucleolar role, NOL7 acts in the nucleoplasm as an mRNA-binding protein that directly binds the 3'UTRs of TSP-1 and GADD45A mRNAs to stabilize them and raise their protein levels; TSP-1 stabilization drives an antiangiogenic switch with decreased VEGF, while the GADD45A axis suppresses STAT3 Ser727 phosphorylation to restrain proliferation and angiogenesis [#0, #5, #9]. NOL7 additionally suppresses senescence by directly binding the proteasome activator subunit PSME3, blocking PSME3-mediated proteasomal degradation of Lamin B1 and thereby preserving nuclear membrane integrity; loss of nucleolar NOL7 causes Lamin B1 loss, cytosolic genomic DNA release, and senescence [#7]. NOL7 is an intrinsically disordered protein with a dynamically unstructured N-terminus, and its nuclear/nucleolar targeting is governed by defined NLS/NoLS sequences and RNA-dependent retention, with alternatively spliced isoforms partitioning between nucleolus, nucleoplasm, and cytoplasm [#1, #3, #8]. Its transcription is positively controlled by RB, c-Myc, and RXRalpha [#2, #4].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Established NOL7 as a nucleolar tumor suppressor with a defined functional output, answering whether loss of this locus contributes to cancer through a specific phenotype.\",\n      \"evidence\": \"Xenograft reintroduction assays with LOH analysis and protein localization in cervical carcinoma cells\",\n      \"pmids\": [\"16205646\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism of the angiogenic switch (VEGF/TSP-1) not defined\", \"Direct molecular targets unidentified at this stage\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined the sequence determinants and dynamics of NOL7 subcellular targeting, explaining how the protein reaches the nucleolus and is retained there.\",\n      \"evidence\": \"In vitro nuclear import assays, pyruvate kinase fusion constructs, site-directed mutagenesis, FRAP, and RNA depletion\",\n      \"pmids\": [\"20875127\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the RNA species mediating nucleolar retention not pinpointed\", \"Import receptors/karyopherins not identified\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identified upstream transcriptional regulators of NOL7, addressing how its expression is controlled.\",\n      \"evidence\": \"5' RACE start-site mapping, promoter deletion analysis, and ChIP for SP1, c-Myc, and RXRalpha\",\n      \"pmids\": [\"20206243\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of TF binding on phenotype not tested\", \"Conditions driving regulation in vivo unknown\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Resolved that NOL7 exists as isoforms with distinct localizations and that the nucleolar isoform maintains nucleolar architecture and proliferation, linking localization to function.\",\n      \"evidence\": \"Splice isoform cloning, fluorescence localization, siRNA knockdown, and domain dissection\",\n      \"pmids\": [\"21818416\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of nucleolar architecture maintenance unresolved\", \"Functions of nucleoplasmic and cytoplasmic isoforms not defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Showed RB positively regulates NOL7 transcription by enabling assembly of factors at its promoter, connecting a master tumor suppressor to NOL7 expression.\",\n      \"evidence\": \"ChIP, transcriptional reporter assays, and RB loss-of-function analysis\",\n      \"pmids\": [\"23308053\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of the recruited machinery only partially defined\", \"Whether RB-NOL7 axis drives the tumor-suppressive phenotype not directly tested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined the molecular mechanism of NOL7's antiangiogenic activity by establishing it as a nucleoplasmic mRNA-binding protein that stabilizes TSP-1 mRNA via its 3'UTR.\",\n      \"evidence\": \"RNA immunoprecipitation, 3'UTR luciferase reporter, mRNA half-life assays, and localization-mutant analysis\",\n      \"pmids\": [\"23085760\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Sequence/structural motif recognized in the 3'UTR not mapped\", \"Full set of stabilized angiogenesis mRNAs not enumerated\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Placed NOL7 in the ribosome biogenesis pathway as a UTP/SSU-processome subunit required for pre-18S processing, distinguishing its nucleolar housekeeping role from its mRNA-stabilizing role.\",\n      \"evidence\": \"siRNA knockdown with pre-rRNA processing, protein synthesis, and nucleolar stress assays\",\n      \"pmids\": [\"37246770\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural position within the SSU processome not resolved\", \"Relationship between processome role and tumor-suppressor functions not integrated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established a mechanism for NOL7-dependent senescence suppression: direct binding to PSME3 protects Lamin B1 from proteasomal degradation and maintains nuclear envelope integrity.\",\n      \"evidence\": \"Reciprocal Co-IP, depletion experiments, ATXN1 knock-in mouse model, nuclear membrane integrity and cytosolic DNA detection assays\",\n      \"pmids\": [\"39103492\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How PQBP3/NOL7 sequestration by mutant ATXN1 mechanistically scales to neurodegeneration not fully defined\", \"Stoichiometry of NOL7-PSME3-Lamin B1 interplay unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided structural insight that NOL7 is an intrinsically disordered protein, relevant to its multivalent binding and dynamic nucleolar behavior.\",\n      \"evidence\": \"Bioinformatics disorder prediction and high-speed atomic force microscopy\",\n      \"pmids\": [\"39126896\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional link between disorder and specific binding partners not tested\", \"Limited functional validation in this study\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Extended the mRNA-stabilization paradigm to a second target by showing NOL7 stabilizes GADD45A mRNA to suppress STAT3 Ser727 signaling and ovarian cancer growth.\",\n      \"evidence\": \"RNA immunoprecipitation, 3'UTR reporter, mRNA stability assays, pSTAT3-Ser727 western blot, and xenografts\",\n      \"pmids\": [\"41812272\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct mechanism linking GADD45A to STAT3 phosphorylation not defined\", \"Whether TSP-1 and GADD45A stabilization use a shared recognition mechanism unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NOL7's nucleolar ribosome-biogenesis role mechanistically connects to its nucleoplasmic mRNA-stabilizing and PSME3/Lamin B1 senescence-suppressing functions remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking processome function to mRNA stabilization\", \"Determinants partitioning NOL7 between nucleolar and nucleoplasmic functional pools not defined\", \"RNA-binding specificity motif uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [5, 9]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [3, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"complexes\": [\"small subunit (SSU) processome\"],\n    \"partners\": [\"PSME3\", \"LMNB1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}