{"gene":"SHQ1","run_date":"2026-06-10T07:46:31","timeline":{"discoveries":[{"year":2002,"finding":"Yeast Shq1p (SHQ1 ortholog) is required for stability of box H/ACA snoRNAs; depletion causes dramatic decrease in H/ACA snoRNA levels and ribosomal RNA processing defects. Shq1p localizes to the nucleus and interacts with H/ACA core proteins Nhp2p and Cbf5p (NAP57/dyskerin ortholog). Shq1p and Naf1p form a complex but are not strongly associated with mature snoRNPs, placing them in early biogenesis steps.","method":"Yeast depletion strains, in vivo co-immunoprecipitation, nuclear localization assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, depletion phenotype with defined molecular readout, independently replicated by subsequent labs","pmids":["12228251"],"is_preprint":false},{"year":2008,"finding":"The N-terminal CS (HSP20-like) domain of yeast Shq1p adopts an anti-parallel β-sandwich fold. Deletion or point mutations (F6, Q10, K80) in the CS domain destabilize Shq1p in vivo, cause temperature-sensitive growth, and deplete H/ACA snoRNAs with rRNA processing defects, establishing the CS domain as essential for H/ACA snoRNP biogenesis. No interaction was detected between the Shq1p CS domain and yeast Hsp90 in vitro.","method":"Crystal structure determination, deletion analysis, in vivo point mutagenesis, in vitro pulldown with Hsp90 (negative)","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure plus functional mutagenesis in a single rigorous study","pmids":["19019820"],"is_preprint":false},{"year":2009,"finding":"Human SHQ1 binds NAP57/dyskerin (the major H/ACA core pseudouridine synthase) in vivo and in vitro, and this interaction precludes binding of NAF1 and other H/ACA core proteins. SHQ1 acts before NAF1 in the assembly pathway. SHQ1 localizes to the nucleoplasm and is excluded from nucleoli and Cajal bodies (sites of mature H/ACA RNPs). Knockdown of SHQ1 prevents accumulation of newly synthesized H/ACA reporter RNA and reduces endogenous H/ACA RNA levels including telomerase RNA. Excess recombinant SHQ1 interferes with NAF1-dependent in vitro assembly of functional H/ACA RNPs. The N-terminal CS domain of SHQ1 is dispensable for NAP57 binding.","method":"In vivo and in vitro co-immunoprecipitation/pulldown, siRNA knockdown, immunofluorescence localization, in vitro H/ACA RNP assembly assay with recombinant SHQ1","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (in vitro + in vivo binding, functional assembly assay, KD with defined molecular phenotype), replicated by other labs","pmids":["19383767"],"is_preprint":false},{"year":2009,"finding":"Yeast Shq1p binds the pseudouridylating enzyme Cbf5p through its C-terminal domain (with synergy from the N-terminal domain). The NMR solution structure of the N-terminal domain is homologous to the 'Chord and Sgt1' (CS) domain of Hsp90 co-chaperones, yet Shq1p does not interact with yeast Hsp90 in vitro. Shq1p has stand-alone chaperone activity in vitro, harbored mainly by the C-terminal domain but enhanced by the N-terminal domain.","method":"NMR structure determination, in vitro binding assays, in vitro chaperone activity assay","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structure combined with in vitro biochemical assays establishing chaperone activity, single lab but multiple orthogonal methods","pmids":["19426738"],"is_preprint":false},{"year":2011,"finding":"Crystal structure of the C-terminal SHQ1-specific domain (SSD) of yeast Shq1p in complex with the RNA-binding domain of Cbf5p (lacking catalytic domain) shows that SSD uses the RNA-protein-binding sites of Cbf5p via structural mimicry of H/ACA RNA, functioning as an RNA placeholder/chaperone that prevents Cbf5p from non-specific RNA binding before H/ACA RNP assembly. Mutations causing X-linked dyskeratosis congenita modulate this SHQ1-dyskerin interaction.","method":"Crystal structure determination of Shq1p SSD–Cbf5p complex, structure-based functional inference validated by mutational analysis","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure of protein complex with structural mimicry mechanism, independently corroborated by parallel structural study (PMID:22117216)","pmids":["22085966"],"is_preprint":false},{"year":2011,"finding":"Crystal structure of yeast Shq1 SSD alone and in complex with Cbf5p, Nop10, and Gar1 reveals that SSD adopts a novel helical fold and contacts the PUA domain and disordered C-terminal extension (CTE) of Cbf5p. Shq1 binds Cbf5p independently of H/ACA RNP proteins Nop10, Gar1, Nhp2, and assembly factor Naf1, but shares an overlapping binding surface with H/ACA RNA. Dyskeratosis congenita mutations in the Cbf5p CTE likely interfere with Shq1 binding. Shq1 point mutations disrupting Cbf5 interaction suppress yeast growth, especially at elevated temperatures.","method":"Crystal structure determination, in vitro binding assays, yeast growth assays with point mutants","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure of quaternary complex, corroborated by parallel structural study (PMID:22085966), multiple functional validations","pmids":["22117216"],"is_preprint":false},{"year":2014,"finding":"Crystal and NMR structures of the human SHQ1 CS domain (hCS) show an immunoglobulin-like β-sandwich fold similar to yeast CS. NMR chemical shift perturbation (CSP) experiments with peptides from Cbf5/dyskerin identified a conserved surface on the CS domain important for Cbf5/dyskerin binding, allowing construction of a HADDOCK docking model of the full SHQ1–Cbf5 pre-H/ACA RNP complex.","method":"Crystal structure, NMR structure determination, NMR chemical shift perturbation assays, HADDOCK computational docking","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR and crystal structures with direct binding experiments mapping interaction surface, single lab","pmids":["25553844"],"is_preprint":false},{"year":2017,"finding":"Two compound heterozygous mutations in SHQ1 (identified by exome sequencing) map to the SHQ1–NAP57 interface and impair interaction of recombinant SHQ1 variants with NAP57 in pulldown assays, demonstrating that SHQ1 mutations cause disease by disrupting its chaperone interaction with dyskerin/NAP57.","method":"Exome sequencing, recombinant protein pulldown assays","journal":"Molecular genetics & genomic medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct in vitro pulldown with recombinant proteins, single lab single method","pmids":["29178645"],"is_preprint":false},{"year":2018,"finding":"In T-ALL cells, oncogenic NOTCH1 directly binds the SHQ1 promoter and activates its transcription. SHQ1 depletion impairs widespread RNA splicing and prominently downregulates MYC through inefficient splicing. MYC overexpression rescues T-ALL cell death caused by SHQ1 inactivation, placing SHQ1 in a NOTCH1→SHQ1→MYC splicing axis required for T-ALL survival.","method":"ChIP (NOTCH1 at SHQ1 promoter), shRNA/siRNA knockdown, RNA-Seq splicing analysis, rescue by MYC overexpression, murine T-ALL xenograft model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (ChIP, RNA-seq, genetic epistasis rescue), in vivo model validation, single lab","pmids":["30323192"],"is_preprint":false},{"year":2020,"finding":"SHQ1 is regulated as an ER stress response gene by p50ATF6 and XBP1s acting through an ER-stress-response-like element on the SHQ1 promoter. SHQ1 interacts with the ER chaperone GRP78 and, upon binding, releases ER sensors PERK/IRE1α/ATF6 from GRP78 complexes, leading to hyper-activation of the unfolded protein response (UPR) and apoptosis under persistent ER stress.","method":"Promoter reporter assays, co-immunoprecipitation (SHQ1–GRP78), western blot of UPR sensors, HCC xenograft model with SHQ1 restoration","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP plus functional xenograft experiments, single lab, multiple readouts but no reconstitution","pmids":["32522979"],"is_preprint":false},{"year":2023,"finding":"Human SHQ1 variants R335C and A426V expressed in a conditional yeast strain progressively depleted of endogenous Shq1 fail to maintain H/ACA snoRNA levels and cause accumulation of unprocessed pre-rRNAs and reduced ribosome production. Immunoprecipitation showed that interaction of Cbf5 (dyskerin ortholog) with SHQ1 variants was weakened but not abolished; yeast two-hybrid confirmed R335C is more deleterious than A426V. Wild-type human SHQ1 complements the Shq1-depleted yeast strain.","method":"Conditional yeast depletion strain complementation, northern blot for snoRNAs and pre-rRNAs, polysome/ribosome profiling, co-immunoprecipitation, yeast two-hybrid","journal":"Frontiers in genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (genetic complementation, Co-IP, Y2H) in a single study, single lab","pmids":["37818102"],"is_preprint":false},{"year":2024,"finding":"SHQ1 knockdown in cortical neurons impairs neuronal migration and neurite morphology in vivo (in utero electroporation) and neurite growth and glutamate sensitivity in vitro. Co-immunoprecipitation confirmed SHQ1 interacts with DKC1 (dyskerin), and most pathogenic SHQ1 variants attenuate this interaction. SHQ1 knockdown also increases dopaminergic pathway activity, potentially underlying enhanced glutamate toxicity.","method":"shRNA knockdown, in utero electroporation, co-immunoprecipitation (SHQ1–DKC1), neuronal morphology quantification, dopaminergic function assay","journal":"Experimental neurology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct Co-IP plus loss-of-function with defined cellular phenotypes in vitro and in vivo, single lab","pmids":["39326821"],"is_preprint":false},{"year":2025,"finding":"VIRMA-mediated m6A modification of SHQ1 mRNA stabilizes it via the m6A reader HNRNPA2B1; Virma knockout reduces m6A on Shq1 mRNA, decreases HNRNPA2B1 binding, lowers Shq1 mRNA stability and protein levels, and impairs PI3K/AKT signaling and cell proliferation in liver regeneration. Shq1 supplementation rescues the liver regeneration defect caused by Virma deficiency.","method":"MeRIP-seq (m6A mapping), liver-specific Virma knockout (Cre-loxP), RIP assay (HNRNPA2B1–Shq1 mRNA), mRNA stability assay, in vivo rescue with Shq1, AKT inhibitor experiments","journal":"Acta pharmaceutica Sinica. B","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (MeRIP-seq, RIP, KO, in vivo rescue), single lab","pmids":["41132854"],"is_preprint":false},{"year":2025,"finding":"Wild-type SHQ1 enhances caspase-3 cleavage, TUNEL signals, ER stress proteins, and ROS production in SH-SY5Y neuroblastoma cells, leading to apoptosis. Three neurodevelopmental SHQ1 variants (Y65X, V271E, L333V) attenuate apoptosis, ER stress protein expression, and ROS production compared to wild-type. Despite functional differences, binding of SHQ1 variants to GRP78 remains unchanged, dissociating GRP78 binding from the apoptotic/ER-stress function.","method":"Transfection of WT and variant SHQ1 in SH-SY5Y cells, caspase-3 cleavage assay, TUNEL, western blot for ER stress markers, ROS measurement, co-immunoprecipitation (SHQ1–GRP78)","journal":"Neuroscience","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — multiple functional readouts with matched Co-IP, single lab","pmids":["40967470"],"is_preprint":false}],"current_model":"SHQ1 is a two-domain (N-terminal CS/HSP20-like + C-terminal SHQ1-specific domain) chaperone that binds dyskerin/NAP57 (Cbf5p in yeast) through structural RNA mimicry at the RNA-binding surface, acting as an RNA placeholder to prevent non-specific RNA binding before H/ACA RNP assembly; it acts upstream of NAF1, localizes to the nucleoplasm (excluded from nucleoli and Cajal bodies), and is required for stable accumulation of H/ACA snoRNAs (and telomerase RNA), ribosomal RNA processing, and spliceosomal snRNA pseudouridylation, while additionally interacting with GRP78 to modulate ER stress/UPR signaling and apoptosis, and functioning downstream of oncogenic NOTCH1 to support MYC mRNA splicing in T-ALL."},"narrative":{"mechanistic_narrative":"SHQ1 is a two-domain molecular chaperone that functions as an early-acting assembly factor for box H/ACA ribonucleoproteins, controlling the stable accumulation of H/ACA snoRNAs and telomerase RNA and thereby supporting ribosomal RNA processing [PMID:12228251, PMID:19383767]. Its C-terminal SHQ1-specific domain (SSD) binds the pseudouridine synthase dyskerin/NAP57 (yeast Cbf5p) by structurally mimicking H/ACA RNA and occupying the enzyme's RNA-binding surface, acting as an RNA placeholder that prevents non-specific RNA binding before RNP assembly [PMID:22085966, PMID:22117216]. SHQ1 acts upstream of NAF1: its dyskerin engagement is mutually exclusive with NAF1 and other core proteins, and excess SHQ1 blocks NAF1-dependent in vitro RNP assembly [PMID:19383767]. The N-terminal CS (HSP20-like) domain adopts a β-sandwich fold, is dispensable for dyskerin binding yet essential for SHQ1 stability and H/ACA snoRNP biogenesis, and provides an additional conserved dyskerin-contacting surface, while the protein possesses stand-alone chaperone activity but does not engage Hsp90 [PMID:19019820, PMID:19426738, PMID:25553844]. SHQ1 localizes to the nucleoplasm, excluded from nucleoli and Cajal bodies where mature RNPs reside [PMID:19383767]. Compound heterozygous SHQ1 mutations mapping to the SHQ1–dyskerin interface impair this interaction and cause neurodevelopmental disease, with loss of function impairing cortical neuronal migration and neurite morphology [PMID:29178645, PMID:39326821]. Beyond its core RNP role, SHQ1 operates downstream of oncogenic NOTCH1, which activates its transcription to support MYC mRNA splicing required for T-ALL survival [PMID:30323192], and participates in ER stress responses through interaction with GRP78 to modulate the unfolded protein response and apoptosis [PMID:32522979, PMID:40967470].","teleology":[{"year":2002,"claim":"Established that SHQ1's ortholog is a required early biogenesis factor for box H/ACA snoRNAs rather than a stable component of mature RNPs, defining its place upstream in the assembly pathway.","evidence":"Yeast depletion strains, in vivo co-immunoprecipitation with Nhp2p/Cbf5p, and nuclear localization","pmids":["12228251"],"confidence":"High","gaps":["Molecular basis of Cbf5p engagement not resolved","Order relative to other assembly factors not yet defined"]},{"year":2008,"claim":"Defined the N-terminal CS domain fold and showed it is essential for SHQ1 stability and H/ACA snoRNP biogenesis while ruling out an Hsp90 co-chaperone role.","evidence":"Crystal structure, in vivo point mutagenesis, and negative Hsp90 pulldown in yeast","pmids":["19019820"],"confidence":"High","gaps":["Mechanistic contribution of CS domain to dyskerin binding not yet mapped","Whether CS domain functions in RNA mimicry unknown"]},{"year":2009,"claim":"Mapped the dyskerin-binding activity to the SHQ1 C-terminal domain, demonstrated stand-alone chaperone activity, and showed that dyskerin engagement is mutually exclusive with NAF1, placing SHQ1 before NAF1 in assembly.","evidence":"Human and yeast in vitro/in vivo binding assays, NMR structure of N-terminal domain, in vitro chaperone and RNP assembly assays, siRNA knockdown with H/ACA RNA readouts","pmids":["19383767","19426738"],"confidence":"High","gaps":["Structural mechanism of how SHQ1 prevents NAF1 binding not yet shown","Telomerase RNA dependence shown by accumulation but downstream consequences untested"]},{"year":2011,"claim":"Revealed at atomic resolution that the SHQ1-specific domain occupies dyskerin's RNA-binding surface by mimicking H/ACA RNA, providing the structural basis for SHQ1 acting as an RNA placeholder chaperone.","evidence":"Crystal structures of Shq1 SSD with Cbf5p RNA-binding domain and with the Cbf5p–Nop10–Gar1 complex, plus functional mutagenesis","pmids":["22085966","22117216"],"confidence":"High","gaps":["Mechanism of transfer from SHQ1 to NAF1/RNA not directly visualized","Catalytic domain of dyskerin not included in structures"]},{"year":2014,"claim":"Resolved the human CS domain structure and mapped a conserved CS surface contacting dyskerin, enabling a docking model of the full pre-H/ACA RNP complex.","evidence":"Crystal and NMR structures with chemical shift perturbation mapping and HADDOCK docking","pmids":["25553844"],"confidence":"High","gaps":["Docking model not validated by experimental complex structure","Functional role of CS-dyskerin contact in vivo not tested in this study"]},{"year":2017,"claim":"Linked human SHQ1 mutations to disease by showing interface-mapping variants impair dyskerin binding, establishing disruption of the chaperone interaction as a pathogenic mechanism.","evidence":"Exome sequencing and recombinant protein pulldown assays","pmids":["29178645"],"confidence":"Medium","gaps":["Single in vitro method without cellular RNP phenotype","No reciprocal validation of binding loss"]},{"year":2018,"claim":"Uncovered a transcriptional and functional role beyond RNP biogenesis, placing SHQ1 in a NOTCH1→SHQ1→MYC splicing axis required for T-ALL survival.","evidence":"ChIP, shRNA knockdown, RNA-Seq splicing analysis, MYC-rescue genetic epistasis, murine xenograft","pmids":["30323192"],"confidence":"High","gaps":["Direct biochemical role of SHQ1 in spliceosome not defined","Connection between H/ACA chaperone activity and splicing function unresolved"]},{"year":2020,"claim":"Implicated SHQ1 in ER stress signaling by showing it binds GRP78 and releases UPR sensors to drive UPR hyperactivation and apoptosis.","evidence":"Promoter reporter assays, SHQ1–GRP78 Co-IP, UPR sensor western blots, HCC xenograft","pmids":["32522979"],"confidence":"Medium","gaps":["No reconstitution of GRP78 sensor release","Relationship to nuclear RNP role unclear"]},{"year":2023,"claim":"Demonstrated functionally that disease variants impair H/ACA snoRNA maintenance and ribosome production, connecting weakened dyskerin binding to the cellular RNP defect.","evidence":"Conditional yeast complementation, northern blot, ribosome profiling, Co-IP, yeast two-hybrid","pmids":["37818102"],"confidence":"Medium","gaps":["Variant effects assessed in yeast surrogate not human cells","Quantitative severity-to-binding correlation incomplete"]},{"year":2024,"claim":"Extended SHQ1 function to neurodevelopment, showing knockdown impairs neuronal migration and neurite morphology and confirming SHQ1–DKC1 interaction attenuated by pathogenic variants.","evidence":"shRNA knockdown, in utero electroporation, SHQ1–DKC1 Co-IP, neuronal morphology and dopaminergic assays","pmids":["39326821"],"confidence":"Medium","gaps":["Mechanism linking H/ACA chaperone role to migration not established","Dopaminergic effect correlative"]},{"year":2025,"claim":"Showed SHQ1 promotes apoptosis, ER stress, and ROS in neuroblastoma cells with variants attenuating these effects, while dissociating GRP78 binding from the apoptotic phenotype.","evidence":"WT/variant transfection, caspase-3/TUNEL/ROS assays, ER stress westerns, SHQ1–GRP78 Co-IP","pmids":["40967470"],"confidence":"Medium","gaps":["GRP78-independent apoptotic mechanism unidentified","Cell-line specific, no in vivo confirmation"]},{"year":2025,"claim":"Identified post-transcriptional control of SHQ1 by VIRMA-mediated m6A and the reader HNRNPA2B1, linking SHQ1 abundance to PI3K/AKT signaling and liver regeneration.","evidence":"MeRIP-seq, liver-specific Virma knockout, HNRNPA2B1 RIP, mRNA stability assay, in vivo Shq1 rescue","pmids":["41132854"],"confidence":"Medium","gaps":["Direct mechanistic link from SHQ1 to AKT not defined","Whether RNP chaperone role mediates proliferation effect unknown"]},{"year":null,"claim":"How SHQ1's core H/ACA RNP chaperone activity mechanistically connects to its diverse downstream roles in splicing, ER stress/apoptosis, and neurodevelopment remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying mechanism linking RNP biogenesis to GRP78/UPR signaling","Direct molecular role in MYC splicing undefined","Handoff from SHQ1 to NAF1/RNA not structurally captured"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0044183","term_label":"protein folding chaperone","supporting_discovery_ids":[3]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[2,4,5]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[9]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[2]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,2]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[9]}],"complexes":[],"partners":["DKC1","NAF1","NHP2","GRP78","HNRNPA2B1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6PI26","full_name":"Protein SHQ1 homolog","aliases":[],"length_aa":577,"mass_kda":65.1,"function":"Required for the quantitative accumulation of H/ACA ribonucleoproteins (RNPs), including telomerase, probably through the stabilization of DKC1, from the time of its synthesis until its association with NOP10, NHP2, and NAF1 at the nascent H/ACA RNA","subcellular_location":"Cytoplasm, cytosol; Nucleus, nucleoplasm","url":"https://www.uniprot.org/uniprotkb/Q6PI26/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SHQ1","classification":"Common Essential","n_dependent_lines":1054,"n_total_lines":1208,"dependency_fraction":0.8725165562913907},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SHQ1","total_profiled":1310},"omim":[{"mim_id":"619922","title":"NEURODEVELOPMENTAL DISORDER WITH DYSTONIA AND SEIZURES; NEDDS","url":"https://www.omim.org/entry/619922"},{"mim_id":"619921","title":"DYSTONIA 35, CHILDHOOD-ONSET; DYT35","url":"https://www.omim.org/entry/619921"},{"mim_id":"613663","title":"SHQ1, H/ACA RIBONUCLEOPROTEIN ASSEMBLY FACTOR; SHQ1","url":"https://www.omim.org/entry/613663"},{"mim_id":"609381","title":"SYNTAXIN-BINDING PROTEIN 5-LIKE; STXBP5L","url":"https://www.omim.org/entry/609381"},{"mim_id":"300126","title":"DYSKERIN; DKC1","url":"https://www.omim.org/entry/300126"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SHQ1"},"hgnc":{"alias_symbol":["FLJ10539","Shq1p"],"prev_symbol":[]},"alphafold":{"accession":"Q6PI26","domains":[{"cath_id":"2.60.40.790","chopping":"6-86","consensus_level":"high","plddt":86.8331,"start":6,"end":86},{"cath_id":"-","chopping":"192-421","consensus_level":"high","plddt":91.8095,"start":192,"end":421}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6PI26","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6PI26-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6PI26-F1-predicted_aligned_error_v6.png","plddt_mean":72.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SHQ1","jax_strain_url":"https://www.jax.org/strain/search?query=SHQ1"},"sequence":{"accession":"Q6PI26","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6PI26.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6PI26/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6PI26"}},"corpus_meta":[{"pmid":"19383767","id":"PMC_19383767","title":"SHQ1 is required prior to NAF1 for assembly of H/ACA small nucleolar and telomerase RNPs.","date":"2009","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/19383767","citation_count":96,"is_preprint":false},{"pmid":"12228251","id":"PMC_12228251","title":"The Shq1p.Naf1p complex is required for box H/ACA small nucleolar ribonucleoprotein particle biogenesis.","date":"2002","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12228251","citation_count":57,"is_preprint":false},{"pmid":"22085966","id":"PMC_22085966","title":"The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic.","date":"2011","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/22085966","citation_count":53,"is_preprint":false},{"pmid":"22117216","id":"PMC_22117216","title":"Structure of the Shq1-Cbf5-Nop10-Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita.","date":"2011","source":"The EMBO 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communications","url":"https://pubmed.ncbi.nlm.nih.gov/29057879","citation_count":23,"is_preprint":false},{"pmid":"34542157","id":"PMC_34542157","title":"Compound heterozygous variants in SHQ1 are associated with a spectrum of neurological features, including early-onset dystonia.","date":"2022","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34542157","citation_count":19,"is_preprint":false},{"pmid":"19426738","id":"PMC_19426738","title":"The box H/ACA snoRNP assembly factor Shq1p is a chaperone protein homologous to Hsp90 cochaperones that binds to the Cbf5p enzyme.","date":"2009","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/19426738","citation_count":18,"is_preprint":false},{"pmid":"29178645","id":"PMC_29178645","title":"Inherited SHQ1 mutations impair interaction with NAP57/dyskerin, a major target in dyskeratosis congenita.","date":"2017","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/29178645","citation_count":17,"is_preprint":false},{"pmid":"32522979","id":"PMC_32522979","title":"SHQ1 is an ER stress response gene that facilitates chemotherapeutics-induced apoptosis via sensitizing ER-stress response.","date":"2020","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/32522979","citation_count":16,"is_preprint":false},{"pmid":"36847845","id":"PMC_36847845","title":"Biallelic SHQ1 variants in early infantile hypotonia and paroxysmal dystonia as the leading manifestation.","date":"2023","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36847845","citation_count":9,"is_preprint":false},{"pmid":"25553844","id":"PMC_25553844","title":"Structure and interactions of the CS domain of human H/ACA RNP assembly protein Shq1.","date":"2014","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/25553844","citation_count":8,"is_preprint":false},{"pmid":"36810590","id":"PMC_36810590","title":"SHQ1-associated neurodevelopmental disorder: Report of the first homozygous variant in unrelated patients and review of the literature.","date":"2023","source":"Human genome variation","url":"https://pubmed.ncbi.nlm.nih.gov/36810590","citation_count":8,"is_preprint":false},{"pmid":"38439529","id":"PMC_38439529","title":"β-Sitosterol attenuates anlotinib resistance in non-small cell lung cancer cells by inhibiting miR-181a-3p/SHQ1 signaling.","date":"2024","source":"Chemical biology & drug design","url":"https://pubmed.ncbi.nlm.nih.gov/38439529","citation_count":6,"is_preprint":false},{"pmid":"41132854","id":"PMC_41132854","title":"VIRMA-mediated SHQ1 m6A modification enhances liver regeneration through an HNRNPA2B1-dependent mechanism.","date":"2025","source":"Acta pharmaceutica Sinica. B","url":"https://pubmed.ncbi.nlm.nih.gov/41132854","citation_count":1,"is_preprint":false},{"pmid":"39326821","id":"PMC_39326821","title":"Pathogenic SHQ1 variants result in disruptions to neuronal development and the dopaminergic pathway.","date":"2024","source":"Experimental neurology","url":"https://pubmed.ncbi.nlm.nih.gov/39326821","citation_count":1,"is_preprint":false},{"pmid":"37818102","id":"PMC_37818102","title":"Human SHQ1 variants R335C and A426V lead to severe ribosome biogenesis defects when expressed in yeast.","date":"2023","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37818102","citation_count":1,"is_preprint":false},{"pmid":"40967470","id":"PMC_40967470","title":"Neurodevelopmental SHQ1 variants navigate the control of apoptosis, endoplasmic reticulum stress, and oxidative stress in neuroblastoma cells.","date":"2025","source":"Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/40967470","citation_count":0,"is_preprint":false},{"pmid":"38482315","id":"PMC_38482315","title":"In silico characterization and identification of compound heterozygous variants in H/ACA Ribonucleoprotein Assembly Factor (SHQ1) from Indian population.","date":"2024","source":"Journal of family medicine and primary care","url":"https://pubmed.ncbi.nlm.nih.gov/38482315","citation_count":0,"is_preprint":false},{"pmid":"41885709","id":"PMC_41885709","title":"A Revealing Case of SHQ1-Related Neurodevelopmental Disorder: Expanding the Genotypic and Phenotypic Frontier.","date":"2026","source":"Journal of child neurology","url":"https://pubmed.ncbi.nlm.nih.gov/41885709","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12853,"output_tokens":4239,"usd":0.051072,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12140,"output_tokens":4040,"usd":0.08085,"stage2_stop_reason":"end_turn"},"total_usd":0.131922,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2002,\n      \"finding\": \"Yeast Shq1p (SHQ1 ortholog) is required for stability of box H/ACA snoRNAs; depletion causes dramatic decrease in H/ACA snoRNA levels and ribosomal RNA processing defects. Shq1p localizes to the nucleus and interacts with H/ACA core proteins Nhp2p and Cbf5p (NAP57/dyskerin ortholog). Shq1p and Naf1p form a complex but are not strongly associated with mature snoRNPs, placing them in early biogenesis steps.\",\n      \"method\": \"Yeast depletion strains, in vivo co-immunoprecipitation, nuclear localization assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, depletion phenotype with defined molecular readout, independently replicated by subsequent labs\",\n      \"pmids\": [\"12228251\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The N-terminal CS (HSP20-like) domain of yeast Shq1p adopts an anti-parallel β-sandwich fold. Deletion or point mutations (F6, Q10, K80) in the CS domain destabilize Shq1p in vivo, cause temperature-sensitive growth, and deplete H/ACA snoRNAs with rRNA processing defects, establishing the CS domain as essential for H/ACA snoRNP biogenesis. No interaction was detected between the Shq1p CS domain and yeast Hsp90 in vitro.\",\n      \"method\": \"Crystal structure determination, deletion analysis, in vivo point mutagenesis, in vitro pulldown with Hsp90 (negative)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure plus functional mutagenesis in a single rigorous study\",\n      \"pmids\": [\"19019820\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Human SHQ1 binds NAP57/dyskerin (the major H/ACA core pseudouridine synthase) in vivo and in vitro, and this interaction precludes binding of NAF1 and other H/ACA core proteins. SHQ1 acts before NAF1 in the assembly pathway. SHQ1 localizes to the nucleoplasm and is excluded from nucleoli and Cajal bodies (sites of mature H/ACA RNPs). Knockdown of SHQ1 prevents accumulation of newly synthesized H/ACA reporter RNA and reduces endogenous H/ACA RNA levels including telomerase RNA. Excess recombinant SHQ1 interferes with NAF1-dependent in vitro assembly of functional H/ACA RNPs. The N-terminal CS domain of SHQ1 is dispensable for NAP57 binding.\",\n      \"method\": \"In vivo and in vitro co-immunoprecipitation/pulldown, siRNA knockdown, immunofluorescence localization, in vitro H/ACA RNP assembly assay with recombinant SHQ1\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (in vitro + in vivo binding, functional assembly assay, KD with defined molecular phenotype), replicated by other labs\",\n      \"pmids\": [\"19383767\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Yeast Shq1p binds the pseudouridylating enzyme Cbf5p through its C-terminal domain (with synergy from the N-terminal domain). The NMR solution structure of the N-terminal domain is homologous to the 'Chord and Sgt1' (CS) domain of Hsp90 co-chaperones, yet Shq1p does not interact with yeast Hsp90 in vitro. Shq1p has stand-alone chaperone activity in vitro, harbored mainly by the C-terminal domain but enhanced by the N-terminal domain.\",\n      \"method\": \"NMR structure determination, in vitro binding assays, in vitro chaperone activity assay\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure combined with in vitro biochemical assays establishing chaperone activity, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"19426738\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Crystal structure of the C-terminal SHQ1-specific domain (SSD) of yeast Shq1p in complex with the RNA-binding domain of Cbf5p (lacking catalytic domain) shows that SSD uses the RNA-protein-binding sites of Cbf5p via structural mimicry of H/ACA RNA, functioning as an RNA placeholder/chaperone that prevents Cbf5p from non-specific RNA binding before H/ACA RNP assembly. Mutations causing X-linked dyskeratosis congenita modulate this SHQ1-dyskerin interaction.\",\n      \"method\": \"Crystal structure determination of Shq1p SSD–Cbf5p complex, structure-based functional inference validated by mutational analysis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure of protein complex with structural mimicry mechanism, independently corroborated by parallel structural study (PMID:22117216)\",\n      \"pmids\": [\"22085966\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Crystal structure of yeast Shq1 SSD alone and in complex with Cbf5p, Nop10, and Gar1 reveals that SSD adopts a novel helical fold and contacts the PUA domain and disordered C-terminal extension (CTE) of Cbf5p. Shq1 binds Cbf5p independently of H/ACA RNP proteins Nop10, Gar1, Nhp2, and assembly factor Naf1, but shares an overlapping binding surface with H/ACA RNA. Dyskeratosis congenita mutations in the Cbf5p CTE likely interfere with Shq1 binding. Shq1 point mutations disrupting Cbf5 interaction suppress yeast growth, especially at elevated temperatures.\",\n      \"method\": \"Crystal structure determination, in vitro binding assays, yeast growth assays with point mutants\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure of quaternary complex, corroborated by parallel structural study (PMID:22085966), multiple functional validations\",\n      \"pmids\": [\"22117216\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Crystal and NMR structures of the human SHQ1 CS domain (hCS) show an immunoglobulin-like β-sandwich fold similar to yeast CS. NMR chemical shift perturbation (CSP) experiments with peptides from Cbf5/dyskerin identified a conserved surface on the CS domain important for Cbf5/dyskerin binding, allowing construction of a HADDOCK docking model of the full SHQ1–Cbf5 pre-H/ACA RNP complex.\",\n      \"method\": \"Crystal structure, NMR structure determination, NMR chemical shift perturbation assays, HADDOCK computational docking\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR and crystal structures with direct binding experiments mapping interaction surface, single lab\",\n      \"pmids\": [\"25553844\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Two compound heterozygous mutations in SHQ1 (identified by exome sequencing) map to the SHQ1–NAP57 interface and impair interaction of recombinant SHQ1 variants with NAP57 in pulldown assays, demonstrating that SHQ1 mutations cause disease by disrupting its chaperone interaction with dyskerin/NAP57.\",\n      \"method\": \"Exome sequencing, recombinant protein pulldown assays\",\n      \"journal\": \"Molecular genetics & genomic medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct in vitro pulldown with recombinant proteins, single lab single method\",\n      \"pmids\": [\"29178645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In T-ALL cells, oncogenic NOTCH1 directly binds the SHQ1 promoter and activates its transcription. SHQ1 depletion impairs widespread RNA splicing and prominently downregulates MYC through inefficient splicing. MYC overexpression rescues T-ALL cell death caused by SHQ1 inactivation, placing SHQ1 in a NOTCH1→SHQ1→MYC splicing axis required for T-ALL survival.\",\n      \"method\": \"ChIP (NOTCH1 at SHQ1 promoter), shRNA/siRNA knockdown, RNA-Seq splicing analysis, rescue by MYC overexpression, murine T-ALL xenograft model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (ChIP, RNA-seq, genetic epistasis rescue), in vivo model validation, single lab\",\n      \"pmids\": [\"30323192\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"SHQ1 is regulated as an ER stress response gene by p50ATF6 and XBP1s acting through an ER-stress-response-like element on the SHQ1 promoter. SHQ1 interacts with the ER chaperone GRP78 and, upon binding, releases ER sensors PERK/IRE1α/ATF6 from GRP78 complexes, leading to hyper-activation of the unfolded protein response (UPR) and apoptosis under persistent ER stress.\",\n      \"method\": \"Promoter reporter assays, co-immunoprecipitation (SHQ1–GRP78), western blot of UPR sensors, HCC xenograft model with SHQ1 restoration\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP plus functional xenograft experiments, single lab, multiple readouts but no reconstitution\",\n      \"pmids\": [\"32522979\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Human SHQ1 variants R335C and A426V expressed in a conditional yeast strain progressively depleted of endogenous Shq1 fail to maintain H/ACA snoRNA levels and cause accumulation of unprocessed pre-rRNAs and reduced ribosome production. Immunoprecipitation showed that interaction of Cbf5 (dyskerin ortholog) with SHQ1 variants was weakened but not abolished; yeast two-hybrid confirmed R335C is more deleterious than A426V. Wild-type human SHQ1 complements the Shq1-depleted yeast strain.\",\n      \"method\": \"Conditional yeast depletion strain complementation, northern blot for snoRNAs and pre-rRNAs, polysome/ribosome profiling, co-immunoprecipitation, yeast two-hybrid\",\n      \"journal\": \"Frontiers in genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (genetic complementation, Co-IP, Y2H) in a single study, single lab\",\n      \"pmids\": [\"37818102\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SHQ1 knockdown in cortical neurons impairs neuronal migration and neurite morphology in vivo (in utero electroporation) and neurite growth and glutamate sensitivity in vitro. Co-immunoprecipitation confirmed SHQ1 interacts with DKC1 (dyskerin), and most pathogenic SHQ1 variants attenuate this interaction. SHQ1 knockdown also increases dopaminergic pathway activity, potentially underlying enhanced glutamate toxicity.\",\n      \"method\": \"shRNA knockdown, in utero electroporation, co-immunoprecipitation (SHQ1–DKC1), neuronal morphology quantification, dopaminergic function assay\",\n      \"journal\": \"Experimental neurology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct Co-IP plus loss-of-function with defined cellular phenotypes in vitro and in vivo, single lab\",\n      \"pmids\": [\"39326821\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"VIRMA-mediated m6A modification of SHQ1 mRNA stabilizes it via the m6A reader HNRNPA2B1; Virma knockout reduces m6A on Shq1 mRNA, decreases HNRNPA2B1 binding, lowers Shq1 mRNA stability and protein levels, and impairs PI3K/AKT signaling and cell proliferation in liver regeneration. Shq1 supplementation rescues the liver regeneration defect caused by Virma deficiency.\",\n      \"method\": \"MeRIP-seq (m6A mapping), liver-specific Virma knockout (Cre-loxP), RIP assay (HNRNPA2B1–Shq1 mRNA), mRNA stability assay, in vivo rescue with Shq1, AKT inhibitor experiments\",\n      \"journal\": \"Acta pharmaceutica Sinica. B\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (MeRIP-seq, RIP, KO, in vivo rescue), single lab\",\n      \"pmids\": [\"41132854\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Wild-type SHQ1 enhances caspase-3 cleavage, TUNEL signals, ER stress proteins, and ROS production in SH-SY5Y neuroblastoma cells, leading to apoptosis. Three neurodevelopmental SHQ1 variants (Y65X, V271E, L333V) attenuate apoptosis, ER stress protein expression, and ROS production compared to wild-type. Despite functional differences, binding of SHQ1 variants to GRP78 remains unchanged, dissociating GRP78 binding from the apoptotic/ER-stress function.\",\n      \"method\": \"Transfection of WT and variant SHQ1 in SH-SY5Y cells, caspase-3 cleavage assay, TUNEL, western blot for ER stress markers, ROS measurement, co-immunoprecipitation (SHQ1–GRP78)\",\n      \"journal\": \"Neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — multiple functional readouts with matched Co-IP, single lab\",\n      \"pmids\": [\"40967470\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SHQ1 is a two-domain (N-terminal CS/HSP20-like + C-terminal SHQ1-specific domain) chaperone that binds dyskerin/NAP57 (Cbf5p in yeast) through structural RNA mimicry at the RNA-binding surface, acting as an RNA placeholder to prevent non-specific RNA binding before H/ACA RNP assembly; it acts upstream of NAF1, localizes to the nucleoplasm (excluded from nucleoli and Cajal bodies), and is required for stable accumulation of H/ACA snoRNAs (and telomerase RNA), ribosomal RNA processing, and spliceosomal snRNA pseudouridylation, while additionally interacting with GRP78 to modulate ER stress/UPR signaling and apoptosis, and functioning downstream of oncogenic NOTCH1 to support MYC mRNA splicing in T-ALL.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SHQ1 is a two-domain molecular chaperone that functions as an early-acting assembly factor for box H/ACA ribonucleoproteins, controlling the stable accumulation of H/ACA snoRNAs and telomerase RNA and thereby supporting ribosomal RNA processing [#0, #2]. Its C-terminal SHQ1-specific domain (SSD) binds the pseudouridine synthase dyskerin/NAP57 (yeast Cbf5p) by structurally mimicking H/ACA RNA and occupying the enzyme's RNA-binding surface, acting as an RNA placeholder that prevents non-specific RNA binding before RNP assembly [#4, #5]. SHQ1 acts upstream of NAF1: its dyskerin engagement is mutually exclusive with NAF1 and other core proteins, and excess SHQ1 blocks NAF1-dependent in vitro RNP assembly [#2]. The N-terminal CS (HSP20-like) domain adopts a β-sandwich fold, is dispensable for dyskerin binding yet essential for SHQ1 stability and H/ACA snoRNP biogenesis, and provides an additional conserved dyskerin-contacting surface, while the protein possesses stand-alone chaperone activity but does not engage Hsp90 [#1, #3, #6]. SHQ1 localizes to the nucleoplasm, excluded from nucleoli and Cajal bodies where mature RNPs reside [#2]. Compound heterozygous SHQ1 mutations mapping to the SHQ1–dyskerin interface impair this interaction and cause neurodevelopmental disease, with loss of function impairing cortical neuronal migration and neurite morphology [#7, #11]. Beyond its core RNP role, SHQ1 operates downstream of oncogenic NOTCH1, which activates its transcription to support MYC mRNA splicing required for T-ALL survival [#8], and participates in ER stress responses through interaction with GRP78 to modulate the unfolded protein response and apoptosis [#9, #13].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Established that SHQ1's ortholog is a required early biogenesis factor for box H/ACA snoRNAs rather than a stable component of mature RNPs, defining its place upstream in the assembly pathway.\",\n      \"evidence\": \"Yeast depletion strains, in vivo co-immunoprecipitation with Nhp2p/Cbf5p, and nuclear localization\",\n      \"pmids\": [\"12228251\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of Cbf5p engagement not resolved\", \"Order relative to other assembly factors not yet defined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Defined the N-terminal CS domain fold and showed it is essential for SHQ1 stability and H/ACA snoRNP biogenesis while ruling out an Hsp90 co-chaperone role.\",\n      \"evidence\": \"Crystal structure, in vivo point mutagenesis, and negative Hsp90 pulldown in yeast\",\n      \"pmids\": [\"19019820\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic contribution of CS domain to dyskerin binding not yet mapped\", \"Whether CS domain functions in RNA mimicry unknown\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Mapped the dyskerin-binding activity to the SHQ1 C-terminal domain, demonstrated stand-alone chaperone activity, and showed that dyskerin engagement is mutually exclusive with NAF1, placing SHQ1 before NAF1 in assembly.\",\n      \"evidence\": \"Human and yeast in vitro/in vivo binding assays, NMR structure of N-terminal domain, in vitro chaperone and RNP assembly assays, siRNA knockdown with H/ACA RNA readouts\",\n      \"pmids\": [\"19383767\", \"19426738\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural mechanism of how SHQ1 prevents NAF1 binding not yet shown\", \"Telomerase RNA dependence shown by accumulation but downstream consequences untested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Revealed at atomic resolution that the SHQ1-specific domain occupies dyskerin's RNA-binding surface by mimicking H/ACA RNA, providing the structural basis for SHQ1 acting as an RNA placeholder chaperone.\",\n      \"evidence\": \"Crystal structures of Shq1 SSD with Cbf5p RNA-binding domain and with the Cbf5p–Nop10–Gar1 complex, plus functional mutagenesis\",\n      \"pmids\": [\"22085966\", \"22117216\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of transfer from SHQ1 to NAF1/RNA not directly visualized\", \"Catalytic domain of dyskerin not included in structures\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved the human CS domain structure and mapped a conserved CS surface contacting dyskerin, enabling a docking model of the full pre-H/ACA RNP complex.\",\n      \"evidence\": \"Crystal and NMR structures with chemical shift perturbation mapping and HADDOCK docking\",\n      \"pmids\": [\"25553844\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Docking model not validated by experimental complex structure\", \"Functional role of CS-dyskerin contact in vivo not tested in this study\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Linked human SHQ1 mutations to disease by showing interface-mapping variants impair dyskerin binding, establishing disruption of the chaperone interaction as a pathogenic mechanism.\",\n      \"evidence\": \"Exome sequencing and recombinant protein pulldown assays\",\n      \"pmids\": [\"29178645\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single in vitro method without cellular RNP phenotype\", \"No reciprocal validation of binding loss\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Uncovered a transcriptional and functional role beyond RNP biogenesis, placing SHQ1 in a NOTCH1→SHQ1→MYC splicing axis required for T-ALL survival.\",\n      \"evidence\": \"ChIP, shRNA knockdown, RNA-Seq splicing analysis, MYC-rescue genetic epistasis, murine xenograft\",\n      \"pmids\": [\"30323192\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct biochemical role of SHQ1 in spliceosome not defined\", \"Connection between H/ACA chaperone activity and splicing function unresolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Implicated SHQ1 in ER stress signaling by showing it binds GRP78 and releases UPR sensors to drive UPR hyperactivation and apoptosis.\",\n      \"evidence\": \"Promoter reporter assays, SHQ1–GRP78 Co-IP, UPR sensor western blots, HCC xenograft\",\n      \"pmids\": [\"32522979\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No reconstitution of GRP78 sensor release\", \"Relationship to nuclear RNP role unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrated functionally that disease variants impair H/ACA snoRNA maintenance and ribosome production, connecting weakened dyskerin binding to the cellular RNP defect.\",\n      \"evidence\": \"Conditional yeast complementation, northern blot, ribosome profiling, Co-IP, yeast two-hybrid\",\n      \"pmids\": [\"37818102\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Variant effects assessed in yeast surrogate not human cells\", \"Quantitative severity-to-binding correlation incomplete\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended SHQ1 function to neurodevelopment, showing knockdown impairs neuronal migration and neurite morphology and confirming SHQ1–DKC1 interaction attenuated by pathogenic variants.\",\n      \"evidence\": \"shRNA knockdown, in utero electroporation, SHQ1–DKC1 Co-IP, neuronal morphology and dopaminergic assays\",\n      \"pmids\": [\"39326821\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking H/ACA chaperone role to migration not established\", \"Dopaminergic effect correlative\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed SHQ1 promotes apoptosis, ER stress, and ROS in neuroblastoma cells with variants attenuating these effects, while dissociating GRP78 binding from the apoptotic phenotype.\",\n      \"evidence\": \"WT/variant transfection, caspase-3/TUNEL/ROS assays, ER stress westerns, SHQ1–GRP78 Co-IP\",\n      \"pmids\": [\"40967470\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"GRP78-independent apoptotic mechanism unidentified\", \"Cell-line specific, no in vivo confirmation\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified post-transcriptional control of SHQ1 by VIRMA-mediated m6A and the reader HNRNPA2B1, linking SHQ1 abundance to PI3K/AKT signaling and liver regeneration.\",\n      \"evidence\": \"MeRIP-seq, liver-specific Virma knockout, HNRNPA2B1 RIP, mRNA stability assay, in vivo Shq1 rescue\",\n      \"pmids\": [\"41132854\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct mechanistic link from SHQ1 to AKT not defined\", \"Whether RNP chaperone role mediates proliferation effect unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How SHQ1's core H/ACA RNP chaperone activity mechanistically connects to its diverse downstream roles in splicing, ER stress/apoptosis, and neurodevelopment remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying mechanism linking RNP biogenesis to GRP78/UPR signaling\", \"Direct molecular role in MYC splicing undefined\", \"Handoff from SHQ1 to NAF1/RNA not structurally captured\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0044183\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [2, 4, 5]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"DKC1\", \"NAF1\", \"NHP2\", \"GRP78\", \"HNRNPA2B1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}