{"gene":"PUS7","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2021,"finding":"Human PUS7 X-ray crystal structure resolved at 2.26 Å reveals two additional subdomains compared to its bacterial homolog; structural modeling and biochemical assays show that all structural elements of tRNA (not just the consensus sequence) are required for productive pseudouridylation, PUS7 binds non-modifiable RNAs with medium affinity to screen substrates, and product tRNA has significantly lower affinity for PUS7 facilitating dissociation.","method":"X-ray crystallography (2.26 Å), structural modeling, in vitro pseudouridylation assay, binding affinity measurements","journal":"Nucleic Acids Research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure combined with multiple orthogonal biochemical assays (binding, activity) in a single rigorous study","pmids":["34718722"],"is_preprint":false},{"year":2021,"finding":"PUS7 pseudouridylates tRNAs in glioblastoma stem cells (GSCs); this tRNA pseudouridylation controls codon-specific translation of key GSC regulators (including suppression of TYK2 translation, downregulating the interferon-STAT1 pathway), and is required for GSC tumorigenesis. Chemical inhibitors of PUS7 prevent pseudouridine modification and suppress tumorigenesis.","method":"Small RNA pseudouridine sequencing, loss-of-function (shRNA/inhibitors), in vivo mouse xenograft, translational profiling","journal":"Nature Cancer","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Ψ-seq, translational assays, in vivo), catalytic activity-dependence established","pmids":["35121864"],"is_preprint":false},{"year":2018,"finding":"Disease-causing truncating variants in PUS7 abolish PUS7 pseudouridylation activity on both tRNA and mRNA substrates; pus7 knockout in Drosophila produces behavioral defects (increased activity, disorientation, aggressiveness), establishing that RNA pseudouridylation by PUS7 is essential for neuronal function.","method":"In vitro pseudouridylation activity assay on tRNA and mRNA substrates, Drosophila knockout behavioral analysis","journal":"American Journal of Human Genetics","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct enzymatic activity assay with disease variants plus ortholog knockout in model organism with defined phenotypic readout","pmids":["30526862"],"is_preprint":false},{"year":2019,"finding":"Two PUS7 missense and frameshift variants identified in patients with intellectual disability result in decreased levels of Ψ13 in tRNAs; the corresponding S. cerevisiae ortholog missense variant fails to complement the growth defect of S. cerevisiae pus7Δ trm8Δ double mutants, placing PUS7 in the same pathway as TRM8.","method":"Functional tRNA pseudouridylation assay (Ψ13 quantification), yeast genetic complementation (pus7Δ trm8Δ epistasis)","journal":"Human Genetics","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — direct enzymatic assay plus genetic epistasis in yeast model, two orthogonal methods","pmids":["30778726"],"is_preprint":false},{"year":2022,"finding":"PUS7 deficiency in patient fibroblasts causes upregulation of total protein synthesis (including elevated MYC protein), demonstrating that PUS7 is a regulator of global protein translation rates.","method":"Patient fibroblast analysis, protein synthesis assay, western blotting for MYC and HPRT1","journal":"Molecular Genetics and Metabolism","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — defined cellular phenotype in patient-derived cells, single lab, limited mechanistic depth","pmids":["35144859"],"is_preprint":false},{"year":2019,"finding":"PUS7 directly interacts with SIRT1; the N-terminal region of PUS7 is essential for forming a stable complex with SIRT1, as established by pull-down and surface plasmon resonance assays.","method":"Pull-down assay, surface plasmon resonance (SPR), truncation analysis, molecular docking","journal":"Biochemical and Biophysical Research Communications","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — SPR and pulldown are direct binding methods but single lab, no functional consequence of the interaction established in this paper","pmids":["31451225"],"is_preprint":false},{"year":2022,"finding":"PUS7 promotes colorectal cancer cell proliferation by physically interacting with SIRT1 and activating the Wnt/β-catenin signaling pathway.","method":"Co-immunoprecipitation (Co-IP), RNA sequencing, knockdown/overexpression, in vitro and in vivo proliferation assays","journal":"Molecular Carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — Co-IP plus functional rescue, single lab, pathway placement via transcriptomic readout","pmids":["36222184"],"is_preprint":false},{"year":2021,"finding":"HSP90 interacts with PUS7 as a client protein, stabilizing PUS7 protein abundance; PUS7 in turn regulates LASP1 levels independently of its catalytic activity to promote colorectal cancer cell metastasis.","method":"Co-immunoprecipitation, mass spectrometry, RNA-seq, proteomics, knockdown/overexpression, in vivo metastasis assays","journal":"Journal of Experimental & Clinical Cancer Research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with MS identification, multiple functional assays, catalytic-independence demonstrated, single lab","pmids":["33990203"],"is_preprint":false},{"year":2024,"finding":"PUS7 pseudouridylates ALKBH3 mRNA at the U696 site, enhancing ALKBH3 mRNA translation efficiency, thereby suppressing gastric cancer progression; this activity requires PUS7 catalytic function.","method":"Locus-specific pseudouridine detection assay, polysome profiling, RT-qPCR, western blotting, xenograft models, catalytic mutant analysis","journal":"Clinical and Translational Medicine","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — site-specific Ψ detection combined with polysome profiling and catalytic mutant, multiple orthogonal methods in single study","pmids":["39175405"],"is_preprint":false},{"year":2025,"finding":"PUS7 pseudouridylates 7SK snRNA; loss of PUS7 leads to hypo-pseudouridylation of 7SK, promoting dissociation of P-TEFb from the 7SK complex, increasing Ser2 phosphorylation of RNA Pol II CTD, and enhancing transcription elongation. In colorectal cancer cells, hypo-pseudouridylation of 7SK upon PUS7 depletion promotes KLF6/DDIT3-mediated apoptosis and sensitizes cells to 5-FU.","method":"Pseudouridine sequencing of 7SK, Co-IP for P-TEFb/7SK complex, ChIP-seq for Ser2P Pol II, dCas13b-guided site-specific pseudouridylation, functional apoptosis/drug sensitivity assays","journal":"Nature Communications","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — multiple orthogonal methods (Ψ-seq, Co-IP, ChIP, engineered targeting system), mechanistic pathway fully established in single rigorous study","pmids":["41168165"],"is_preprint":false},{"year":2025,"finding":"PUS7 exhibits stress-induced cytoplasmic relocalization in both yeast and human epithelial cells; cytoplasmic PUS7 promotes pseudouridylation of hundreds of mRNA targets (enriched for divalent metal metabolism and ROS stress pathway transcripts) without affecting tRNA Ψ13/Ψ35 sites, and engineered cytoplasmic localization of PUS7 increases cellular fitness under ROS and divalent metal ion stress. Quantitative proteomics confirmed proteome reshaping consistent with mRNA-level regulation.","method":"Live-cell imaging/fractionation for localization, nanopore direct RNA sequencing for Ψ sites, engineered cytoplasmic PUS7 construct, ROS/metal stress fitness assays, quantitative proteomics (TMT)","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (localization, Ψ-seq, proteomics, engineered mutant), preprint not yet peer-reviewed","pmids":["41040199"],"is_preprint":true},{"year":2023,"finding":"PUS7 binds to both the 5' and 3' terminal regions of SARS-CoV-2 RNA (identified by RNA-protein interaction detection coupled with mass spectrometry); nanopore direct RNA sequencing revealed that modified PUS7 consensus sequences are present at both terminal regions of the viral RNA including within the transcription regulatory sequence leader.","method":"RNA-protein interaction detection (RaPID) coupled with mass spectrometry, nanopore direct RNA sequencing","journal":"Molecular Therapy: Nucleic Acids","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — MS-validated binding plus sequencing-based modification detection, single lab, functional consequence not fully established","pmids":["38028201"],"is_preprint":false},{"year":2024,"finding":"PUS7 knockdown in human cells increases global mRNA N6-methyladenosine (m6A) and 5-methylcytosine (m5C) levels, revealing an antagonistic relationship between pseudouridylation and these other RNA modifications. PUS7-dependent Ψ sites were identified in 8,624 positions in 1,246 mRNAs encoding proteins associated with ribosome biogenesis, translation, and energy metabolism.","method":"NanoPsiPy computational pipeline on nanopore direct RNA sequencing data, PUS7 knockdown, transcriptome-wide Ψ, m6A, and m5C profiling","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3–4 / Weak — primarily computational pipeline with knockdown validation, preprint, single lab, antagonistic relationship inferred from correlation","pmids":["38352483"],"is_preprint":true},{"year":2025,"finding":"PUS7 interacts with anillin (ANLN) as shown by co-immunoprecipitation; this interaction promotes pancreatic cancer cell proliferation, mobility, and glycolysis via activation of the MYC pathway.","method":"Co-immunoprecipitation, colony formation/EdU/transwell assays, ECAR/OCR measurement, xenograft models","journal":"Molecular and Cellular Biochemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP with functional assays, single lab, MYC pathway activation inferred without detailed mechanism","pmids":["40169466"],"is_preprint":false},{"year":2025,"finding":"PUS7 mutation in human patient cells and Drosophila model causes specific decrease in tRNA-Asp levels, leading to slow decoding at Aspartate codons, activation of the integrated stress response (ISR), and metabolic shift toward increased glycolysis and reduced mitochondrial respiration. Elevating tRNA-Asp expression, inhibiting the ISR, or dampening glycolysis rescues the aggressiveness phenotype, establishing the tRNA-Asp–ISR–glycolysis axis downstream of PUS7.","method":"tRNA quantification in patient cells and Drosophila, ribosome profiling (codon decoding), ISR activation assays, metabolic flux assays, genetic/pharmacological rescue experiments in Drosophila behavioral models","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (tRNA levels, codon decoding, metabolic assays, genetic epistasis rescue), preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.05.12.653498"],"is_preprint":true},{"year":2025,"finding":"PUS7 knockdown in the infralimbic prefrontal cortex (ILPFC) of mice selectively impairs fear extinction memory formation without altering baseline fear expression; fear extinction learning drives PUS7-mediated exonic pseudouridylation and upregulation of synaptogenic transcripts in the ILPFC.","method":"Stereotaxic PUS7 knockdown, behavioral fear conditioning/extinction assays, transcriptome-wide pseudouridylation profiling in mouse ILPFC","journal":"Molecular Brain","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — in vivo loss-of-function with defined behavioral phenotype plus Ψ profiling, single lab","pmids":["41094471"],"is_preprint":false},{"year":2025,"finding":"HSP90 interacts with PUS7 and regulates THUMPD1 expression in gastric cancer; this HSP90/PUS7/THUMPD1 axis promotes cell proliferation, migration, EMT, angiogenesis, and cisplatin resistance.","method":"Co-immunoprecipitation, western blotting, functional cell assays, inhibitor experiments","journal":"Scientific Reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP with functional assays, mechanistic link between PUS7 and THUMPD1 not fully detailed, single lab","pmids":["41107340"],"is_preprint":false},{"year":2026,"finding":"PUS7 enzymatic activity is required for its effects on TNBC cell stemness, migration, and colony formation, as demonstrated by a catalytic dead PUS7 mutant (PUS7-Mut) reversing the stimulating effects of wild-type PUS7 overexpression.","method":"Catalytic mutant overexpression, knockdown, stemness/migration/colony formation assays in MDA-MB-231 and MDA-MB-468 cells","journal":"Scientific Reports","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — catalytic mutant used to attribute phenotype to enzymatic activity, single lab, functional readout without downstream target identification","pmids":["41554761"],"is_preprint":false}],"current_model":"PUS7 is an RNA pseudouridine synthase that uses an extended multi-domain surface (including two metazoan-specific subdomains) for structure- and sequence-specific tRNA/mRNA recognition, depositing pseudouridine (Ψ) at tRNAs (notably Ψ13/Ψ35), 7SK snRNA, and hundreds of mRNAs; tRNA pseudouridylation controls codon-specific translation and tRNA-Asp levels to modulate the integrated stress response, 7SK pseudouridylation retains P-TEFb to suppress transcription elongation, mRNA pseudouridylation enhances translation efficiency of specific targets (e.g., ALKBH3), and stress-induced cytoplasmic relocalization of PUS7 reshapes the mRNA pseudouridylome to enhance fitness under oxidative and metal stress, while PUS7 also engages in catalysis-independent protein–protein interactions (with HSP90, SIRT1, ANLN) that contribute to cancer-relevant signaling."},"narrative":{"mechanistic_narrative":"PUS7 is an RNA pseudouridine synthase that deposits pseudouridine (Ψ) across multiple RNA classes to control translation, transcription, and stress adaptation [PMID:35121864, PMID:41168165, PMID:41040199]. Its crystal structure reveals two subdomains beyond the bacterial homolog and a substrate-screening mechanism in which all structural elements of tRNA—not merely the consensus sequence—are required for productive modification, with low product affinity favoring dissociation [PMID:34718722]. Through tRNA pseudouridylation PUS7 controls codon-specific translation: in glioblastoma stem cells it tunes translation of regulators including suppression of TYK2 and the interferon-STAT1 pathway to drive tumorigenesis [PMID:35121864], and loss of PUS7-dependent ΨtRNA decreases tRNA-Asp levels, slowing Aspartate decoding and activating the integrated stress response with a metabolic shift toward glycolysis [PMID:bio_10.1101_2025.05.12.653498]. On mRNA, PUS7 pseudouridylates specific targets such as ALKBH3 at U696 to enhance translation efficiency [PMID:39175405], and stress drives its cytoplasmic relocalization to reshape the mRNA pseudouridylome enriched for metal-metabolism and ROS-response transcripts, increasing fitness under oxidative and metal stress [PMID:41040199]. PUS7 also pseudouridylates 7SK snRNA, retaining P-TEFb in the inactive 7SK complex to limit RNA Pol II CTD Ser2 phosphorylation and suppress transcription elongation [PMID:41168165]. Beyond catalysis, PUS7 engages catalysis-independent protein interactions—stabilized as an HSP90 client and binding SIRT1 and ANLN—to influence cancer-relevant signaling [PMID:31451225, PMID:33990203, PMID:36222184]. Biallelic loss-of-function variants in PUS7 cause an intellectual-disability disorder, with truncating and missense variants abolishing pseudouridylation of tRNA and mRNA, reducing Ψ13 in tRNA, and producing neuronal and behavioral defects in model organisms [PMID:30526862, PMID:30778726].","teleology":[{"year":2018,"claim":"Established PUS7 as a disease-relevant pseudouridine synthase by showing that human truncating variants abolish its enzymatic activity and that its loss disrupts neuronal function, linking RNA pseudouridylation to a heritable neurodevelopmental phenotype.","evidence":"In vitro pseudouridylation assays on tRNA and mRNA with disease variants plus Drosophila knockout behavioral analysis","pmids":["30526862"],"confidence":"High","gaps":["Did not identify the specific tRNA/mRNA targets whose loss drives neuronal dysfunction","Mechanistic link between Ψ loss and behavioral defect not resolved"]},{"year":2019,"claim":"Refined the disease mechanism by tying patient variants to reduced tRNA Ψ13 and placing PUS7 genetically in a tRNA-modification pathway shared with TRM8.","evidence":"Ψ13 quantification in patient material and yeast pus7Δ trm8Δ complementation/epistasis","pmids":["30778726"],"confidence":"High","gaps":["Functional consequence of Ψ13 loss on translation not directly shown","TRM8 epistasis mechanism in humans not established"]},{"year":2019,"claim":"First identified a catalysis-independent protein partner, showing PUS7 forms a stable complex with SIRT1 via its N-terminal region.","evidence":"Pull-down, surface plasmon resonance, and truncation analysis","pmids":["31451225"],"confidence":"Medium","gaps":["No functional consequence of the interaction established in this study","Whether binding affects catalysis untested"]},{"year":2021,"claim":"Defined the structural basis of substrate selection, revealing metazoan-specific subdomains and a screening mechanism requiring intact tRNA architecture with product release driven by low affinity.","evidence":"2.26 Å X-ray crystallography with in vitro activity and binding affinity assays","pmids":["34718722"],"confidence":"High","gaps":["Structure of PUS7 bound to mRNA or 7SK not resolved","Basis of mRNA versus tRNA target discrimination unclear"]},{"year":2021,"claim":"Connected PUS7 tRNA pseudouridylation to codon-specific translational control of oncogenic programs, demonstrating it sustains glioblastoma stem cell tumorigenesis and is druggable.","evidence":"Ψ-seq, shRNA/inhibitor loss-of-function, translational profiling, and mouse xenografts","pmids":["35121864"],"confidence":"High","gaps":["Full set of codon-affected transcripts beyond TYK2 not enumerated","Selectivity of chemical inhibitors not characterized in detail"]},{"year":2021,"claim":"Revealed a catalysis-independent oncogenic axis in which HSP90 stabilizes PUS7 protein and PUS7 regulates LASP1 to promote metastasis.","evidence":"Reciprocal Co-IP with MS, RNA-seq/proteomics, and in vivo metastasis assays with catalytic-independence shown","pmids":["33990203"],"confidence":"Medium","gaps":["Mechanism by which PUS7 regulates LASP1 levels not defined","Single lab; reciprocal validation of LASP1 regulation limited"]},{"year":2022,"claim":"Demonstrated PUS7 as a regulator of global translation rates, with deficiency elevating total protein synthesis and MYC.","evidence":"Patient fibroblast protein synthesis assays and western blotting","pmids":["35144859"],"confidence":"Medium","gaps":["Molecular link between Ψ loss and increased translation not established","Single patient-derived system"]},{"year":2022,"claim":"Extended the SIRT1 interaction to a functional cancer context, showing PUS7-SIRT1 binding activates Wnt/β-catenin signaling to drive colorectal cancer proliferation.","evidence":"Co-IP, RNA-seq, knockdown/overexpression, and in vitro/in vivo proliferation assays","pmids":["36222184"],"confidence":"Medium","gaps":["Whether the effect depends on PUS7 catalytic activity not resolved","Direct mechanistic link to Wnt pathway components inferred from transcriptomics"]},{"year":2024,"claim":"Provided site-resolved evidence for mRNA pseudouridylation as a translational enhancer, with PUS7 modifying ALKBH3 mRNA at U696 to boost its translation and suppress gastric cancer.","evidence":"Locus-specific Ψ detection, polysome profiling, and catalytic mutant analysis with xenografts","pmids":["39175405"],"confidence":"High","gaps":["How U696 Ψ mechanistically enhances ribosome loading not defined","Generality across other mRNA targets not addressed"]},{"year":2025,"claim":"Established a transcriptional role distinct from translation, showing PUS7 pseudouridylates 7SK snRNA to retain P-TEFb and suppress Pol II elongation, with loss promoting apoptosis and 5-FU sensitivity.","evidence":"7SK Ψ-seq, P-TEFb/7SK Co-IP, Ser2P Pol II ChIP-seq, and dCas13b-guided site-specific pseudouridylation","pmids":["41168165"],"confidence":"High","gaps":["How 7SK Ψ structurally affects P-TEFb retention not resolved","Breadth of elongation-controlled genes not fully mapped"]},{"year":2025,"claim":"Connected PUS7-dependent tRNA-Asp depletion to the integrated stress response and a glycolytic metabolic shift, defining a tRNA-Asp–ISR–glycolysis axis that explains the neuronal phenotype.","evidence":"tRNA quantification, ribosome profiling for codon decoding, metabolic flux, and genetic/pharmacological rescue in Drosophila (preprint)","pmids":["bio_10.1101_2025.05.12.653498"],"confidence":"Medium","gaps":["Preprint not yet peer-reviewed","Why tRNA-Asp is selectively sensitive to PUS7 loss unclear"]},{"year":2025,"claim":"Showed stress-induced cytoplasmic relocalization reprograms the mRNA pseudouridylome toward metal/ROS-response transcripts, conferring fitness under oxidative and metal stress independently of tRNA sites.","evidence":"Live-cell imaging/fractionation, nanopore direct RNA Ψ-seq, engineered cytoplasmic PUS7, stress fitness assays, and TMT proteomics (preprint)","pmids":["41040199"],"confidence":"Medium","gaps":["Preprint not yet peer-reviewed","Signal triggering relocalization not identified"]},{"year":2025,"claim":"Implicated PUS7 in learning-dependent neuronal gene regulation, showing fear extinction drives PUS7-mediated exonic pseudouridylation of synaptogenic transcripts required for extinction memory.","evidence":"Stereotaxic knockdown, fear conditioning/extinction behavior, and transcriptome-wide Ψ profiling in mouse ILPFC","pmids":["41094471"],"confidence":"Medium","gaps":["Specific Ψ targets driving memory not pinpointed","Whether effect requires catalytic activity not tested"]},{"year":2025,"claim":"Identified PUS7 as a SARS-CoV-2 RNA-binding protein recognizing consensus motifs at viral terminal regions, raising a host-modification interface with viral RNA.","evidence":"RaPID coupled with mass spectrometry and nanopore direct RNA sequencing","pmids":["38028201"],"confidence":"Medium","gaps":["Functional consequence of binding for viral replication not established","Whether PUS7 actually pseudouridylates viral RNA not demonstrated"]},{"year":null,"claim":"It remains unresolved how PUS7's catalytic (Ψ deposition on tRNA, mRNA, 7SK) and catalysis-independent (HSP90/SIRT1/ANLN scaffolding) activities are partitioned and coordinated across cell types and stress states.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model distinguishing when PUS7 acts as enzyme versus scaffold","Regulation of nuclear-cytoplasmic partitioning incompletely defined","Direct mRNA target rules for productive pseudouridylation in vivo not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,1,2,8,9]},{"term_id":"GO:0016853","term_label":"isomerase activity","supporting_discovery_ids":[0,8]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,11]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[1,4,8]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[9,10]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[10]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,8,9]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,4,14]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[9]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[10,14]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[2,3,6,7]}],"complexes":["7SK snRNP"],"partners":["SIRT1","HSP90","ANLN","P-TEFB"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96PZ0","full_name":"Pseudouridylate synthase 7 homolog","aliases":[],"length_aa":661,"mass_kda":75.0,"function":"Pseudouridylate synthase that catalyzes pseudouridylation of RNAs (PubMed:28073919, PubMed:29628141, PubMed:30778726, PubMed:31477916, PubMed:34718722, PubMed:35051350). Acts as a regulator of protein synthesis in embryonic stem cells by mediating pseudouridylation of RNA fragments derived from tRNAs (tRFs): pseudouridylated tRFs inhibit translation by targeting the translation initiation complex (PubMed:29628141). Also catalyzes pseudouridylation of mRNAs: mediates pseudouridylation of mRNAs with the consensus sequence 5'-UGUAG-3' (PubMed:28073919, PubMed:31477916, PubMed:35051350). Acts as a regulator of pre-mRNA splicing by mediating pseudouridylation of pre-mRNAs at locations associated with alternatively spliced regions (PubMed:35051350). Pseudouridylation of pre-mRNAs near splice sites directly regulates mRNA splicing and mRNA 3'-end processing (PubMed:35051350). In addition to mRNAs and tRNAs, binds other types of RNAs, such as snRNAs, Y RNAs and vault RNAs, suggesting that it can catalyze pseudouridylation of many RNA types (PubMed:29628141)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q96PZ0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PUS7","classification":"Not Classified","n_dependent_lines":13,"n_total_lines":1208,"dependency_fraction":0.01076158940397351},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"SSB","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/PUS7","total_profiled":1310},"omim":[{"mim_id":"618342","title":"INTELLECTUAL DEVELOPMENTAL DISORDER WITH ABNORMAL BEHAVIOR, MICROCEPHALY, AND SHORT STATURE; IDDABS","url":"https://www.omim.org/entry/618342"},{"mim_id":"616261","title":"PSEUDOURIDYLATE SYNTHASE 7; PUS7","url":"https://www.omim.org/entry/616261"},{"mim_id":"610726","title":"TRUB PSEUDOURIDINE SYNTHASE FAMILY MEMBER 1; TRUB1","url":"https://www.omim.org/entry/610726"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PUS7"},"hgnc":{"alias_symbol":["FLJ20485"],"prev_symbol":[]},"alphafold":{"accession":"Q96PZ0","domains":[{"cath_id":"-","chopping":"120-137_348-371_584-643","consensus_level":"high","plddt":93.7424,"start":120,"end":643},{"cath_id":"3.30.70.3160","chopping":"144-156_251-340","consensus_level":"high","plddt":92.4883,"start":144,"end":340},{"cath_id":"3.30.1370","chopping":"164-242","consensus_level":"high","plddt":79.3256,"start":164,"end":242},{"cath_id":"3.30.2350.20","chopping":"471-577","consensus_level":"medium","plddt":95.3636,"start":471,"end":577},{"cath_id":"1.10.1510","chopping":"388-470","consensus_level":"medium","plddt":93.4124,"start":388,"end":470}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96PZ0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96PZ0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96PZ0-F1-predicted_aligned_error_v6.png","plddt_mean":80.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PUS7","jax_strain_url":"https://www.jax.org/strain/search?query=PUS7"},"sequence":{"accession":"Q96PZ0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96PZ0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96PZ0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96PZ0"}},"corpus_meta":[{"pmid":"35121864","id":"PMC_35121864","title":"Targeting PUS7 suppresses tRNA pseudouridylation and glioblastoma tumorigenesis.","date":"2021","source":"Nature cancer","url":"https://pubmed.ncbi.nlm.nih.gov/35121864","citation_count":136,"is_preprint":false},{"pmid":"30526862","id":"PMC_30526862","title":"Variants in PUS7 Cause Intellectual Disability with Speech Delay, Microcephaly, Short Stature, and Aggressive Behavior.","date":"2018","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30526862","citation_count":99,"is_preprint":false},{"pmid":"30778726","id":"PMC_30778726","title":"PUS7 mutations impair pseudouridylation in humans and cause intellectual disability and microcephaly.","date":"2019","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30778726","citation_count":72,"is_preprint":false},{"pmid":"33990203","id":"PMC_33990203","title":"HSP90-dependent PUS7 overexpression facilitates the metastasis of colorectal cancer cells by regulating LASP1 abundance.","date":"2021","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/33990203","citation_count":52,"is_preprint":false},{"pmid":"34718722","id":"PMC_34718722","title":"The human pseudouridine synthase PUS7 recognizes RNA with an extended multi-domain binding surface.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/34718722","citation_count":39,"is_preprint":false},{"pmid":"34827123","id":"PMC_34827123","title":"The Identification of RNA Modification Gene PUS7 as a Potential Biomarker of Ovarian Cancer.","date":"2021","source":"Biology","url":"https://pubmed.ncbi.nlm.nih.gov/34827123","citation_count":32,"is_preprint":false},{"pmid":"36222184","id":"PMC_36222184","title":"PUS7 promotes the proliferation of colorectal cancer cells by directly stabilizing SIRT1 to activate the Wnt/β-catenin pathway.","date":"2022","source":"Molecular carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/36222184","citation_count":27,"is_preprint":false},{"pmid":"39175405","id":"PMC_39175405","title":"PUS7-dependent pseudouridylation of ALKBH3 mRNA inhibits gastric cancer progression.","date":"2024","source":"Clinical and translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39175405","citation_count":24,"is_preprint":false},{"pmid":"34657723","id":"PMC_34657723","title":"PUS7: a targetable epitranscriptomic regulator of glioblastoma growth.","date":"2021","source":"Trends in pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34657723","citation_count":16,"is_preprint":false},{"pmid":"35144859","id":"PMC_35144859","title":"PUS7 deficiency in human patients causes profound neurodevelopmental phenotype by dysregulating protein translation.","date":"2022","source":"Molecular genetics and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/35144859","citation_count":13,"is_preprint":false},{"pmid":"38028201","id":"PMC_38028201","title":"Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome.","date":"2023","source":"Molecular therapy. Nucleic acids","url":"https://pubmed.ncbi.nlm.nih.gov/38028201","citation_count":12,"is_preprint":false},{"pmid":"33100873","id":"PMC_33100873","title":"Next generation sequencing reveals novel homozygous frameshift in PUS7 and splice acceptor variants in AASS gene leading to intellectual disability, developmental delay, dysmorphic feature and microcephaly.","date":"2020","source":"Saudi journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33100873","citation_count":10,"is_preprint":false},{"pmid":"38352483","id":"PMC_38352483","title":"Integrative analysis of nanopore direct RNA sequencing data reveals a role of PUS7-dependent pseudouridylation in regulation of m 6 A and m 5 C modifications.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38352483","citation_count":5,"is_preprint":false},{"pmid":"40169466","id":"PMC_40169466","title":"PUS7 promotes the progression of pancreatic cancer by interacting ANLN to activate MYC pathway.","date":"2025","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40169466","citation_count":4,"is_preprint":false},{"pmid":"37067188","id":"PMC_37067188","title":"A PUS7 gene pathogenic variant causing self-injurious behavior, sleep disturbances, and developmental delay: A case report.","date":"2023","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/37067188","citation_count":3,"is_preprint":false},{"pmid":"41168165","id":"PMC_41168165","title":"Pseudouridylation of 7SK by PUS7 regulates Pol II transcription elongation.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41168165","citation_count":2,"is_preprint":false},{"pmid":"41040199","id":"PMC_41040199","title":"Cytoplasmic localization of PUS7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41040199","citation_count":2,"is_preprint":false},{"pmid":"31451225","id":"PMC_31451225","title":"Biochemical insight into pseudouridine synthase 7 (PUS7) as a novel interactor of sirtuin, SIRT1.","date":"2019","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/31451225","citation_count":2,"is_preprint":false},{"pmid":"40699665","id":"PMC_40699665","title":"Identification and Characterization of the RNA Modifying Factors PUS7 and WTAP as Key Components for the Control of Tumor Biological Processes in Renal Cell Carcinomas.","date":"2025","source":"Current issues in molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/40699665","citation_count":2,"is_preprint":false},{"pmid":"41496500","id":"PMC_41496500","title":"Multi-omics analysis identifies PUS7 as an immune modulator driving NETs-mediated macrophage polarization in pancreatic cancer.","date":"2026","source":"Clinical and translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41496500","citation_count":1,"is_preprint":false},{"pmid":"41094471","id":"PMC_41094471","title":"PUS7-dependent Ψ reshapes specific synaptic gene exons to facilitate fear extinction memory formation.","date":"2025","source":"Molecular brain","url":"https://pubmed.ncbi.nlm.nih.gov/41094471","citation_count":1,"is_preprint":false},{"pmid":"41107340","id":"PMC_41107340","title":"HSP90/PUS7/THUMPD1 promotes metastasis and cisplatin resistance in gastric cancer cells.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/41107340","citation_count":0,"is_preprint":false},{"pmid":"41279304","id":"PMC_41279304","title":"Nano-Mod-Amp reveals RNA sequence, structural and cell type specific features of pseudouridylation by PUS7.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41279304","citation_count":0,"is_preprint":false},{"pmid":"41554761","id":"PMC_41554761","title":"The pseudouridine synthase PUS7 is associated with stemness and represents a potential therapeutic target in triple-negative breast cancer cells.","date":"2026","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/41554761","citation_count":0,"is_preprint":false},{"pmid":"42249560","id":"PMC_42249560","title":"Novel Variants in PUS7 Associated With Intellectual Disability and Growth Retardation: Expanding the Clinical Spectrum in 13 Patients.","date":"2026","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/42249560","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.05.12.653498","title":"<i>Pus7</i>  mutation links tRNA dysregulation to aggressive behavior through activation of the integrated stress response and glycolytic reprogramming","date":"2025-05-12","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.12.653498","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13174,"output_tokens":4407,"usd":0.052813,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12610,"output_tokens":4621,"usd":0.089288,"stage2_stop_reason":"end_turn"},"total_usd":0.142101,"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\": 2021,\n      \"finding\": \"Human PUS7 X-ray crystal structure resolved at 2.26 Å reveals two additional subdomains compared to its bacterial homolog; structural modeling and biochemical assays show that all structural elements of tRNA (not just the consensus sequence) are required for productive pseudouridylation, PUS7 binds non-modifiable RNAs with medium affinity to screen substrates, and product tRNA has significantly lower affinity for PUS7 facilitating dissociation.\",\n      \"method\": \"X-ray crystallography (2.26 Å), structural modeling, in vitro pseudouridylation assay, binding affinity measurements\",\n      \"journal\": \"Nucleic Acids Research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure combined with multiple orthogonal biochemical assays (binding, activity) in a single rigorous study\",\n      \"pmids\": [\"34718722\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PUS7 pseudouridylates tRNAs in glioblastoma stem cells (GSCs); this tRNA pseudouridylation controls codon-specific translation of key GSC regulators (including suppression of TYK2 translation, downregulating the interferon-STAT1 pathway), and is required for GSC tumorigenesis. Chemical inhibitors of PUS7 prevent pseudouridine modification and suppress tumorigenesis.\",\n      \"method\": \"Small RNA pseudouridine sequencing, loss-of-function (shRNA/inhibitors), in vivo mouse xenograft, translational profiling\",\n      \"journal\": \"Nature Cancer\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Ψ-seq, translational assays, in vivo), catalytic activity-dependence established\",\n      \"pmids\": [\"35121864\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Disease-causing truncating variants in PUS7 abolish PUS7 pseudouridylation activity on both tRNA and mRNA substrates; pus7 knockout in Drosophila produces behavioral defects (increased activity, disorientation, aggressiveness), establishing that RNA pseudouridylation by PUS7 is essential for neuronal function.\",\n      \"method\": \"In vitro pseudouridylation activity assay on tRNA and mRNA substrates, Drosophila knockout behavioral analysis\",\n      \"journal\": \"American Journal of Human Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct enzymatic activity assay with disease variants plus ortholog knockout in model organism with defined phenotypic readout\",\n      \"pmids\": [\"30526862\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Two PUS7 missense and frameshift variants identified in patients with intellectual disability result in decreased levels of Ψ13 in tRNAs; the corresponding S. cerevisiae ortholog missense variant fails to complement the growth defect of S. cerevisiae pus7Δ trm8Δ double mutants, placing PUS7 in the same pathway as TRM8.\",\n      \"method\": \"Functional tRNA pseudouridylation assay (Ψ13 quantification), yeast genetic complementation (pus7Δ trm8Δ epistasis)\",\n      \"journal\": \"Human Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — direct enzymatic assay plus genetic epistasis in yeast model, two orthogonal methods\",\n      \"pmids\": [\"30778726\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PUS7 deficiency in patient fibroblasts causes upregulation of total protein synthesis (including elevated MYC protein), demonstrating that PUS7 is a regulator of global protein translation rates.\",\n      \"method\": \"Patient fibroblast analysis, protein synthesis assay, western blotting for MYC and HPRT1\",\n      \"journal\": \"Molecular Genetics and Metabolism\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — defined cellular phenotype in patient-derived cells, single lab, limited mechanistic depth\",\n      \"pmids\": [\"35144859\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PUS7 directly interacts with SIRT1; the N-terminal region of PUS7 is essential for forming a stable complex with SIRT1, as established by pull-down and surface plasmon resonance assays.\",\n      \"method\": \"Pull-down assay, surface plasmon resonance (SPR), truncation analysis, molecular docking\",\n      \"journal\": \"Biochemical and Biophysical Research Communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — SPR and pulldown are direct binding methods but single lab, no functional consequence of the interaction established in this paper\",\n      \"pmids\": [\"31451225\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PUS7 promotes colorectal cancer cell proliferation by physically interacting with SIRT1 and activating the Wnt/β-catenin signaling pathway.\",\n      \"method\": \"Co-immunoprecipitation (Co-IP), RNA sequencing, knockdown/overexpression, in vitro and in vivo proliferation assays\",\n      \"journal\": \"Molecular Carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — Co-IP plus functional rescue, single lab, pathway placement via transcriptomic readout\",\n      \"pmids\": [\"36222184\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HSP90 interacts with PUS7 as a client protein, stabilizing PUS7 protein abundance; PUS7 in turn regulates LASP1 levels independently of its catalytic activity to promote colorectal cancer cell metastasis.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, RNA-seq, proteomics, knockdown/overexpression, in vivo metastasis assays\",\n      \"journal\": \"Journal of Experimental & Clinical Cancer Research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with MS identification, multiple functional assays, catalytic-independence demonstrated, single lab\",\n      \"pmids\": [\"33990203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PUS7 pseudouridylates ALKBH3 mRNA at the U696 site, enhancing ALKBH3 mRNA translation efficiency, thereby suppressing gastric cancer progression; this activity requires PUS7 catalytic function.\",\n      \"method\": \"Locus-specific pseudouridine detection assay, polysome profiling, RT-qPCR, western blotting, xenograft models, catalytic mutant analysis\",\n      \"journal\": \"Clinical and Translational Medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — site-specific Ψ detection combined with polysome profiling and catalytic mutant, multiple orthogonal methods in single study\",\n      \"pmids\": [\"39175405\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PUS7 pseudouridylates 7SK snRNA; loss of PUS7 leads to hypo-pseudouridylation of 7SK, promoting dissociation of P-TEFb from the 7SK complex, increasing Ser2 phosphorylation of RNA Pol II CTD, and enhancing transcription elongation. In colorectal cancer cells, hypo-pseudouridylation of 7SK upon PUS7 depletion promotes KLF6/DDIT3-mediated apoptosis and sensitizes cells to 5-FU.\",\n      \"method\": \"Pseudouridine sequencing of 7SK, Co-IP for P-TEFb/7SK complex, ChIP-seq for Ser2P Pol II, dCas13b-guided site-specific pseudouridylation, functional apoptosis/drug sensitivity assays\",\n      \"journal\": \"Nature Communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — multiple orthogonal methods (Ψ-seq, Co-IP, ChIP, engineered targeting system), mechanistic pathway fully established in single rigorous study\",\n      \"pmids\": [\"41168165\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PUS7 exhibits stress-induced cytoplasmic relocalization in both yeast and human epithelial cells; cytoplasmic PUS7 promotes pseudouridylation of hundreds of mRNA targets (enriched for divalent metal metabolism and ROS stress pathway transcripts) without affecting tRNA Ψ13/Ψ35 sites, and engineered cytoplasmic localization of PUS7 increases cellular fitness under ROS and divalent metal ion stress. Quantitative proteomics confirmed proteome reshaping consistent with mRNA-level regulation.\",\n      \"method\": \"Live-cell imaging/fractionation for localization, nanopore direct RNA sequencing for Ψ sites, engineered cytoplasmic PUS7 construct, ROS/metal stress fitness assays, quantitative proteomics (TMT)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (localization, Ψ-seq, proteomics, engineered mutant), preprint not yet peer-reviewed\",\n      \"pmids\": [\"41040199\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PUS7 binds to both the 5' and 3' terminal regions of SARS-CoV-2 RNA (identified by RNA-protein interaction detection coupled with mass spectrometry); nanopore direct RNA sequencing revealed that modified PUS7 consensus sequences are present at both terminal regions of the viral RNA including within the transcription regulatory sequence leader.\",\n      \"method\": \"RNA-protein interaction detection (RaPID) coupled with mass spectrometry, nanopore direct RNA sequencing\",\n      \"journal\": \"Molecular Therapy: Nucleic Acids\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — MS-validated binding plus sequencing-based modification detection, single lab, functional consequence not fully established\",\n      \"pmids\": [\"38028201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PUS7 knockdown in human cells increases global mRNA N6-methyladenosine (m6A) and 5-methylcytosine (m5C) levels, revealing an antagonistic relationship between pseudouridylation and these other RNA modifications. PUS7-dependent Ψ sites were identified in 8,624 positions in 1,246 mRNAs encoding proteins associated with ribosome biogenesis, translation, and energy metabolism.\",\n      \"method\": \"NanoPsiPy computational pipeline on nanopore direct RNA sequencing data, PUS7 knockdown, transcriptome-wide Ψ, m6A, and m5C profiling\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3–4 / Weak — primarily computational pipeline with knockdown validation, preprint, single lab, antagonistic relationship inferred from correlation\",\n      \"pmids\": [\"38352483\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PUS7 interacts with anillin (ANLN) as shown by co-immunoprecipitation; this interaction promotes pancreatic cancer cell proliferation, mobility, and glycolysis via activation of the MYC pathway.\",\n      \"method\": \"Co-immunoprecipitation, colony formation/EdU/transwell assays, ECAR/OCR measurement, xenograft models\",\n      \"journal\": \"Molecular and Cellular Biochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP with functional assays, single lab, MYC pathway activation inferred without detailed mechanism\",\n      \"pmids\": [\"40169466\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PUS7 mutation in human patient cells and Drosophila model causes specific decrease in tRNA-Asp levels, leading to slow decoding at Aspartate codons, activation of the integrated stress response (ISR), and metabolic shift toward increased glycolysis and reduced mitochondrial respiration. Elevating tRNA-Asp expression, inhibiting the ISR, or dampening glycolysis rescues the aggressiveness phenotype, establishing the tRNA-Asp–ISR–glycolysis axis downstream of PUS7.\",\n      \"method\": \"tRNA quantification in patient cells and Drosophila, ribosome profiling (codon decoding), ISR activation assays, metabolic flux assays, genetic/pharmacological rescue experiments in Drosophila behavioral models\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (tRNA levels, codon decoding, metabolic assays, genetic epistasis rescue), preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.05.12.653498\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PUS7 knockdown in the infralimbic prefrontal cortex (ILPFC) of mice selectively impairs fear extinction memory formation without altering baseline fear expression; fear extinction learning drives PUS7-mediated exonic pseudouridylation and upregulation of synaptogenic transcripts in the ILPFC.\",\n      \"method\": \"Stereotaxic PUS7 knockdown, behavioral fear conditioning/extinction assays, transcriptome-wide pseudouridylation profiling in mouse ILPFC\",\n      \"journal\": \"Molecular Brain\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — in vivo loss-of-function with defined behavioral phenotype plus Ψ profiling, single lab\",\n      \"pmids\": [\"41094471\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"HSP90 interacts with PUS7 and regulates THUMPD1 expression in gastric cancer; this HSP90/PUS7/THUMPD1 axis promotes cell proliferation, migration, EMT, angiogenesis, and cisplatin resistance.\",\n      \"method\": \"Co-immunoprecipitation, western blotting, functional cell assays, inhibitor experiments\",\n      \"journal\": \"Scientific Reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP with functional assays, mechanistic link between PUS7 and THUMPD1 not fully detailed, single lab\",\n      \"pmids\": [\"41107340\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PUS7 enzymatic activity is required for its effects on TNBC cell stemness, migration, and colony formation, as demonstrated by a catalytic dead PUS7 mutant (PUS7-Mut) reversing the stimulating effects of wild-type PUS7 overexpression.\",\n      \"method\": \"Catalytic mutant overexpression, knockdown, stemness/migration/colony formation assays in MDA-MB-231 and MDA-MB-468 cells\",\n      \"journal\": \"Scientific Reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — catalytic mutant used to attribute phenotype to enzymatic activity, single lab, functional readout without downstream target identification\",\n      \"pmids\": [\"41554761\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PUS7 is an RNA pseudouridine synthase that uses an extended multi-domain surface (including two metazoan-specific subdomains) for structure- and sequence-specific tRNA/mRNA recognition, depositing pseudouridine (Ψ) at tRNAs (notably Ψ13/Ψ35), 7SK snRNA, and hundreds of mRNAs; tRNA pseudouridylation controls codon-specific translation and tRNA-Asp levels to modulate the integrated stress response, 7SK pseudouridylation retains P-TEFb to suppress transcription elongation, mRNA pseudouridylation enhances translation efficiency of specific targets (e.g., ALKBH3), and stress-induced cytoplasmic relocalization of PUS7 reshapes the mRNA pseudouridylome to enhance fitness under oxidative and metal stress, while PUS7 also engages in catalysis-independent protein–protein interactions (with HSP90, SIRT1, ANLN) that contribute to cancer-relevant signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PUS7 is an RNA pseudouridine synthase that deposits pseudouridine (Ψ) across multiple RNA classes to control translation, transcription, and stress adaptation [#1, #9, #10]. Its crystal structure reveals two subdomains beyond the bacterial homolog and a substrate-screening mechanism in which all structural elements of tRNA—not merely the consensus sequence—are required for productive modification, with low product affinity favoring dissociation [#0]. Through tRNA pseudouridylation PUS7 controls codon-specific translation: in glioblastoma stem cells it tunes translation of regulators including suppression of TYK2 and the interferon-STAT1 pathway to drive tumorigenesis [#1], and loss of PUS7-dependent ΨtRNA decreases tRNA-Asp levels, slowing Aspartate decoding and activating the integrated stress response with a metabolic shift toward glycolysis [#14]. On mRNA, PUS7 pseudouridylates specific targets such as ALKBH3 at U696 to enhance translation efficiency [#8], and stress drives its cytoplasmic relocalization to reshape the mRNA pseudouridylome enriched for metal-metabolism and ROS-response transcripts, increasing fitness under oxidative and metal stress [#10]. PUS7 also pseudouridylates 7SK snRNA, retaining P-TEFb in the inactive 7SK complex to limit RNA Pol II CTD Ser2 phosphorylation and suppress transcription elongation [#9]. Beyond catalysis, PUS7 engages catalysis-independent protein interactions—stabilized as an HSP90 client and binding SIRT1 and ANLN—to influence cancer-relevant signaling [#5, #7, #6]. Biallelic loss-of-function variants in PUS7 cause an intellectual-disability disorder, with truncating and missense variants abolishing pseudouridylation of tRNA and mRNA, reducing Ψ13 in tRNA, and producing neuronal and behavioral defects in model organisms [#2, #3].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Established PUS7 as a disease-relevant pseudouridine synthase by showing that human truncating variants abolish its enzymatic activity and that its loss disrupts neuronal function, linking RNA pseudouridylation to a heritable neurodevelopmental phenotype.\",\n      \"evidence\": \"In vitro pseudouridylation assays on tRNA and mRNA with disease variants plus Drosophila knockout behavioral analysis\",\n      \"pmids\": [\"30526862\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the specific tRNA/mRNA targets whose loss drives neuronal dysfunction\", \"Mechanistic link between Ψ loss and behavioral defect not resolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Refined the disease mechanism by tying patient variants to reduced tRNA Ψ13 and placing PUS7 genetically in a tRNA-modification pathway shared with TRM8.\",\n      \"evidence\": \"Ψ13 quantification in patient material and yeast pus7Δ trm8Δ complementation/epistasis\",\n      \"pmids\": [\"30778726\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of Ψ13 loss on translation not directly shown\", \"TRM8 epistasis mechanism in humans not established\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"First identified a catalysis-independent protein partner, showing PUS7 forms a stable complex with SIRT1 via its N-terminal region.\",\n      \"evidence\": \"Pull-down, surface plasmon resonance, and truncation analysis\",\n      \"pmids\": [\"31451225\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional consequence of the interaction established in this study\", \"Whether binding affects catalysis untested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined the structural basis of substrate selection, revealing metazoan-specific subdomains and a screening mechanism requiring intact tRNA architecture with product release driven by low affinity.\",\n      \"evidence\": \"2.26 Å X-ray crystallography with in vitro activity and binding affinity assays\",\n      \"pmids\": [\"34718722\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of PUS7 bound to mRNA or 7SK not resolved\", \"Basis of mRNA versus tRNA target discrimination unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Connected PUS7 tRNA pseudouridylation to codon-specific translational control of oncogenic programs, demonstrating it sustains glioblastoma stem cell tumorigenesis and is druggable.\",\n      \"evidence\": \"Ψ-seq, shRNA/inhibitor loss-of-function, translational profiling, and mouse xenografts\",\n      \"pmids\": [\"35121864\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full set of codon-affected transcripts beyond TYK2 not enumerated\", \"Selectivity of chemical inhibitors not characterized in detail\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Revealed a catalysis-independent oncogenic axis in which HSP90 stabilizes PUS7 protein and PUS7 regulates LASP1 to promote metastasis.\",\n      \"evidence\": \"Reciprocal Co-IP with MS, RNA-seq/proteomics, and in vivo metastasis assays with catalytic-independence shown\",\n      \"pmids\": [\"33990203\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which PUS7 regulates LASP1 levels not defined\", \"Single lab; reciprocal validation of LASP1 regulation limited\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated PUS7 as a regulator of global translation rates, with deficiency elevating total protein synthesis and MYC.\",\n      \"evidence\": \"Patient fibroblast protein synthesis assays and western blotting\",\n      \"pmids\": [\"35144859\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular link between Ψ loss and increased translation not established\", \"Single patient-derived system\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended the SIRT1 interaction to a functional cancer context, showing PUS7-SIRT1 binding activates Wnt/β-catenin signaling to drive colorectal cancer proliferation.\",\n      \"evidence\": \"Co-IP, RNA-seq, knockdown/overexpression, and in vitro/in vivo proliferation assays\",\n      \"pmids\": [\"36222184\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the effect depends on PUS7 catalytic activity not resolved\", \"Direct mechanistic link to Wnt pathway components inferred from transcriptomics\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided site-resolved evidence for mRNA pseudouridylation as a translational enhancer, with PUS7 modifying ALKBH3 mRNA at U696 to boost its translation and suppress gastric cancer.\",\n      \"evidence\": \"Locus-specific Ψ detection, polysome profiling, and catalytic mutant analysis with xenografts\",\n      \"pmids\": [\"39175405\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How U696 Ψ mechanistically enhances ribosome loading not defined\", \"Generality across other mRNA targets not addressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established a transcriptional role distinct from translation, showing PUS7 pseudouridylates 7SK snRNA to retain P-TEFb and suppress Pol II elongation, with loss promoting apoptosis and 5-FU sensitivity.\",\n      \"evidence\": \"7SK Ψ-seq, P-TEFb/7SK Co-IP, Ser2P Pol II ChIP-seq, and dCas13b-guided site-specific pseudouridylation\",\n      \"pmids\": [\"41168165\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How 7SK Ψ structurally affects P-TEFb retention not resolved\", \"Breadth of elongation-controlled genes not fully mapped\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected PUS7-dependent tRNA-Asp depletion to the integrated stress response and a glycolytic metabolic shift, defining a tRNA-Asp–ISR–glycolysis axis that explains the neuronal phenotype.\",\n      \"evidence\": \"tRNA quantification, ribosome profiling for codon decoding, metabolic flux, and genetic/pharmacological rescue in Drosophila (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.05.12.653498\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint not yet peer-reviewed\", \"Why tRNA-Asp is selectively sensitive to PUS7 loss unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed stress-induced cytoplasmic relocalization reprograms the mRNA pseudouridylome toward metal/ROS-response transcripts, conferring fitness under oxidative and metal stress independently of tRNA sites.\",\n      \"evidence\": \"Live-cell imaging/fractionation, nanopore direct RNA Ψ-seq, engineered cytoplasmic PUS7, stress fitness assays, and TMT proteomics (preprint)\",\n      \"pmids\": [\"41040199\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint not yet peer-reviewed\", \"Signal triggering relocalization not identified\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Implicated PUS7 in learning-dependent neuronal gene regulation, showing fear extinction drives PUS7-mediated exonic pseudouridylation of synaptogenic transcripts required for extinction memory.\",\n      \"evidence\": \"Stereotaxic knockdown, fear conditioning/extinction behavior, and transcriptome-wide Ψ profiling in mouse ILPFC\",\n      \"pmids\": [\"41094471\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific Ψ targets driving memory not pinpointed\", \"Whether effect requires catalytic activity not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified PUS7 as a SARS-CoV-2 RNA-binding protein recognizing consensus motifs at viral terminal regions, raising a host-modification interface with viral RNA.\",\n      \"evidence\": \"RaPID coupled with mass spectrometry and nanopore direct RNA sequencing\",\n      \"pmids\": [\"38028201\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of binding for viral replication not established\", \"Whether PUS7 actually pseudouridylates viral RNA not demonstrated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how PUS7's catalytic (Ψ deposition on tRNA, mRNA, 7SK) and catalysis-independent (HSP90/SIRT1/ANLN scaffolding) activities are partitioned and coordinated across cell types and stress states.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model distinguishing when PUS7 acts as enzyme versus scaffold\", \"Regulation of nuclear-cytoplasmic partitioning incompletely defined\", \"Direct mRNA target rules for productive pseudouridylation in vivo not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 1, 2, 8, 9]},\n      {\"term_id\": \"GO:0016853\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 11]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [1, 4, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [9, 10]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 8, 9]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 4, 14]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [10, 14]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [2, 3, 6, 7]}\n    ],\n    \"complexes\": [\"7SK snRNP\"],\n    \"partners\": [\"SIRT1\", \"HSP90\", \"ANLN\", \"P-TEFb\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}