{"gene":"NOP56","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2018,"finding":"The intron-hosted box C/D snoRNA snoRD86 acts in cis as a sensor controlling NOP56 levels: excess snoRNP core proteins cause snoRD86 to adopt alternative RNP conformations that dictate usage of nearby alternative splice donors in the NOP56 pre-mRNA, triggering generation of a cytoplasmic snoRD86-containing NOP56-derived lncRNA via the nonsense-mediated decay pathway — a feedback mechanism that couples snoRNP core protein availability to NOP56 production.","method":"Alternative splicing analysis, NMD reporter assays, RNA structure probing, overexpression/depletion of snoRNP core proteins with functional readouts in human cells","journal":"Molecular Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (splicing analysis, NMD pathway, RNA structure), clear functional mechanism demonstrated in one rigorous study","pmids":["30220559"],"is_preprint":false},{"year":2009,"finding":"Fibrillarin and NOP56 directly interact in vivo prior to assembly into box C/D snoRNPs; this interaction requires the alpha-helix domain of fibrillarin (not the GAR or RNA-binding domain) and does not require RNA. Disrupting either protein's localization impairs their association with box C/D snoRNPs.","method":"Relocalization/affinity-tag delocalization of core box C/D proteins followed by co-immunoprecipitation and localization analysis in mammalian cells","journal":"Experimental Cell Research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal localization experiments and domain mapping, single lab, two orthogonal approaches","pmids":["19331828"],"is_preprint":false},{"year":2021,"finding":"High-resolution crystal structure of eukaryotic Nop1 (fibrillarin) from S. cerevisiae bound to the amino-terminal domain of Nop56 was solved; the interaction interface differs substantially from the archaeal orthologs, demonstrating that eukaryotic Nop56 recruits the methyltransferase to the box C/D RNP through a protein-protein interface distinct from that in archaea.","method":"X-ray crystallography with functional comparison to archaeal structures","journal":"RNA","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with functional validation by comparison to mutagenesis data from archaeal studies, single lab","pmids":["33483369"],"is_preprint":false},{"year":2007,"finding":"Crystal structure of archaeal Nop56/58-fibrillarin complex from Pyrococcus furiosus (at 2.7 Å) bound to S-adenosyl-L-methionine confirmed the generality of the bipartite/symmetric dimer arrangement; the distinct conformation of Nop56/58 compared to the Archaeoglobus fulgidus structure revealed flexibility via hinge motion, repositioning fibrillarin catalytic sites, suggesting simultaneous positioning of two catalytic sites at two target sites of a bipartite guide RNA.","method":"X-ray crystallography and computational normal mode analysis","journal":"Journal of Molecular Biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — two independent crystal structures from different archaeal species with computational validation, revealing conserved architecture and flexibility","pmids":["17617422"],"is_preprint":false},{"year":2006,"finding":"In archaeal box C/D sRNPs, the coiled-coil domain of Nop56/58 is dispensable for core protein binding and sRNP assembly but is required for sRNP-guided nucleotide 2'-O-methylation; Nop56/58 self-dimerization and Nop56/58-fibrillarin dimerization are mutually exclusive interactions; deletion of the coiled-coil domain disrupts RNP structure essential for methylation without preventing assembly.","method":"Site-directed mutagenesis, protein pull-down assays, in vitro methylation assays, nuclease probing of sRNP structure","journal":"RNA","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstitution with mutagenesis, in vitro methylation assay, and structural probing in one study","pmids":["16601205"],"is_preprint":false},{"year":2012,"finding":"The N-terminal domain (NTD) of archaeal Nop56/58 mediates an exceptionally stable interaction with fibrillarin; mutations that did not affect fibrillarin binding or sRNP assembly still disrupted sRNP-guided nucleotide modification, revealing a direct role for Nop56/58 in methyltransferase activity beyond scaffolding. Cross-linking confirmed Nop56/58 contacts the target RNA substrate. The NTD crystal structure (1.7 Å) showed conservation despite low sequence identity among archaeal homologs.","method":"Site-directed mutagenesis, in vitro methylation assay, chemical and thermal denaturation, RNA cross-linking, X-ray crystallography","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple orthogonal methods including structure, mutagenesis, in vitro assay, and cross-linking in one rigorous study","pmids":["22496443"],"is_preprint":false},{"year":2002,"finding":"Xenopus laevis NOP56 (XNop56p) was identified as a common component of X. laevis box C/D snoRNPs; it is not essential for snoRNA stability; its transcript initiates with a pyrimidine tract and contains an intronic snoRNA, but it is not translationally regulated in a growth-dependent manner (i.e., it is not a TOP gene).","method":"cDNA cloning, co-immunoprecipitation with box C/D snoRNPs, 5' end mapping, polysome analysis","journal":"Biochimica et Biophysica Acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical fractionation and co-IP in Xenopus, single lab, two methods","pmids":["12020815"],"is_preprint":false},{"year":2013,"finding":"NOP56 (Nol5a) was identified as a gene hyperactivated by Burkitt's lymphoma-associated Myc mutants and was shown to be necessary for Myc-induced cell transformation; Nol5a/NOP56 enhances wild-type Myc-induced cell transformation and increases the size of Myc-induced tumors, placing NOP56 downstream of Myc as a rate-limiting effector for transformation.","method":"Gene expression profiling, RNAi knockdown/overexpression with transformation assays and in vivo tumor growth assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional loss-of-function and gain-of-function experiments with defined cellular and in vivo phenotypes, single lab","pmids":["24013231"],"is_preprint":false},{"year":2022,"finding":"NOP56 depletion in KRAS-mutant lung cancer cells increases ROS levels and creates synthetic lethality with mTOR inhibition; mechanistically, cells with reduced NOP56 rely on mTOR signaling to balance oxidative stress, and IRE1α-mediated unfolded protein response activates mTOR through p38 MAPK in this context. Co-targeting NOP56 and mTOR profoundly enhances tumor cell death in vitro and in vivo.","method":"RNAi/shRNA knockdown, CRISPR/Cas9 knockout, flow cytometry for ROS, Western blot, chemical inhibitor screen, xenograft models","journal":"Journal of Experimental & Clinical Cancer Research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple genetic and pharmacological methods with in vitro and in vivo validation, single lab","pmids":["35039048"],"is_preprint":false},{"year":2022,"finding":"Loss-of-function of nop56 in zebrafish causes severe neurodegeneration characterized by absence of cerebellum, reduced spinal cord neurons, high CNS apoptosis, and impaired movement, with disrupted expression of genes related to the C/D box complex, balance, and CNS development, establishing NOP56 as essential for vertebrate CNS development and function.","method":"Zebrafish loss-of-function mutant, fluorescence microscopy, apoptosis assays, gene expression analysis","journal":"Biomedicines","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined genetic loss-of-function model with multiple specific phenotypic readouts, single lab","pmids":["36009362"],"is_preprint":false},{"year":2011,"finding":"Expansion of an intronic GGCCTG hexanucleotide repeat in NOP56 causes SCA36; RNA foci form in lymphoblastoid cells from affected subjects, and the expanded (GGCCUG)n RNA binds the RNA-binding protein SRSF2 (but not CUG6), as shown by gel-shift assay, indicating RNA gain-of-function toxicity.","method":"Genetic linkage analysis, FISH for RNA foci, gel-shift assay, segregation analysis","journal":"American Journal of Human Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and biochemical methods establishing RNA-protein interaction and RNA foci, single lab with multiple methods","pmids":["21683323"],"is_preprint":false},{"year":2020,"finding":"The intronic GGCCTG repeat expansion in NOP56 undergoes repeat-associated non-AUG (RAN) translation to produce dipeptide repeat proteins (DPRs) including poly(GP) and poly(PR); poly(GP) in SCA36 is produced via canonical AUG-mediated translation from intron-retained repeat RNAs and exists as a soluble species without TDP-43 pathology, in contrast to c9ALS/FTD where chimeric DPR species cause aggregation.","method":"RAN translation detection in patient tissue, immunoassays for DPR proteins, comparison of solubility profiles","journal":"Neuron","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct detection in patient tissue with mechanistic dissection, single study","pmids":["32375063"],"is_preprint":false},{"year":2025,"finding":"NOP56 intron 1 GGCCTG repeat RAN translation occurs in all reading frames of the sense strand; translation initiates in a 5'-cap-dependent manner from near-cognate start codons upstream of the repeat in each frame; longer GGCCTG repeats enhance RAN translation; and a frameshift occurs within the GGCCUG repeat during translation.","method":"Cell-free translation systems with reporter constructs and mutagenesis","journal":"Journal of Biological Chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — cell-free reconstitution system with multiple constructs and controls, single lab","pmids":["40015643"],"is_preprint":false},{"year":2013,"finding":"NOP56 protein levels progressively decrease selectively in large motor neurons of lumbar and cervical spinal cord in SOD1-G93A ALS model mice from the early symptomatic stage, preceding reductions in TDP-43 and FUS, implicating early NOP56 loss in motor neuron degeneration.","method":"Immunohistochemistry and protein expression analysis across disease stages in transgenic ALS mice","journal":"Neurological Research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single localization/expression study with no direct mechanistic intervention, single lab","pmids":["23582672"],"is_preprint":false},{"year":2026,"finding":"NOP56 interacts with fibrillarin (FBL) and activates the PI3K/AKT/CREB signaling pathway in hepatocellular carcinoma; NOP56 knockdown lowers FBL levels and suppresses PI3K/AKT/CREB activity, while FBL overexpression partially rescues apoptotic effects of NOP56 silencing.","method":"Co-immunoprecipitation, Western blot, RNAi knockdown, overexpression rescue, xenograft models","journal":"Frontiers in Oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP with pathway readout, single lab, no orthogonal structural validation","pmids":["41568368"],"is_preprint":false},{"year":2026,"finding":"NOP56 promotes p53 degradation in colorectal cancer through suppression of SIRT1 and activation of p300; NOP56 depletion increases p53 stability and acetylation via the SIRT1/p300 axis, as supported by evidence of direct interaction and colocalization of NOP56 with SIRT1 and p300.","method":"RNAi knockdown, co-immunoprecipitation, colocalization, Western blot, xenograft models","journal":"International Journal of Biological Sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/colocalization with pathway readout, single lab, limited mechanistic depth in abstract","pmids":["42157947"],"is_preprint":false},{"year":2026,"finding":"NOP56 activates MYC signaling by regulating IRES-dependent translation, and MYC in turn transcriptionally upregulates NOP56 expression, creating a positive feedback loop that enhances ribosome biogenesis and drives NSCLC progression; promoter hypomethylation also contributes to NOP56 upregulation.","method":"Luciferase reporter assay for IRES translation, chromatin immunoprecipitation, bisulfite DNA sequencing, RNA sequencing, functional overexpression/knockdown assays","journal":"Cancers","confidence":"Low","confidence_rationale":"Tier 3 / Moderate — multiple assays but indirect mechanism; single lab, no reconstitution of IRES regulation","pmids":["41827688"],"is_preprint":false},{"year":2021,"finding":"In miiuy croaker, NOP56 negatively regulates MyD88-mediated NF-κB signaling; the NOSIC domain of NOP56 is responsible for suppressing MyD88 protein expression; NOP56 overexpression inhibits MyD88 protein levels while NOP56 siRNA knockdown increases them.","method":"Overexpression, siRNA knockdown, Western blot, domain deletion analysis in fish cells","journal":"Fish & Shellfish Immunology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single-organism non-mammalian model, single lab, single method per experiment; mechanistic relevance to mammalian NOP56 uncertain","pmids":["34774735"],"is_preprint":false},{"year":2025,"finding":"In a preprint, NOP56 expression was downregulated by unfolded protein response (UPR) alongside FBL and NHP2L1; reduced C/D box snoRNP function during UPR alters rRNA 2'-O-methylation and translational fidelity including effects on nonsense suppression, frameshifts, ribosome pausing, and IRES-dependent translation initiation.","method":"qRT-PCR for expression, FBL knockdown with rRNA methylation assay and translational fidelity reporter assays","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, NOP56-specific mechanistic contribution not directly isolated from general snoRNP effects","pmids":[],"is_preprint":true}],"current_model":"NOP56 is a core component of box C/D snoRNP complexes that functions as a scaffold bridging L7Ae/Snu13 and fibrillarin, with its N-terminal domain mediating an exceptionally stable interaction with fibrillarin and directly contributing to sRNP-guided 2'-O-methylation of rRNA nucleotides; its coiled-coil domain is dispensable for assembly but required for proper RNP structure and methylation activity; its own levels are autoregulated by a feedback loop in which excess snoRNP proteins cause an intronic snoRNA (snoRD86) to redirect NOP56 pre-mRNA splicing toward NMD; in cancer contexts NOP56 acts downstream of Myc to support ribosome biogenesis and cell transformation, regulates ROS homeostasis and mTOR signaling in KRAS-mutant cells, and modulates p53 stability through SIRT1/p300; pathogenic intronic GGCCTG repeat expansions in NOP56 cause SCA36 through RNA gain-of-function (foci formation, SRSF2 binding) and RAN translation producing toxic dipeptide repeat proteins."},"narrative":{"mechanistic_narrative":"NOP56 is a core scaffolding subunit of box C/D small nucleolar ribonucleoprotein (snoRNP) complexes that guide 2'-O-methylation of rRNA [PMID:12020815, PMID:16601205]. It bridges the methyltransferase fibrillarin to the snoRNP through its N-terminal domain, which mediates an exceptionally stable, RNA-independent interaction with fibrillarin's alpha-helix domain [PMID:19331828, PMID:22496443]; crystallographic work on archaeal and eukaryotic complexes shows that this NTD interface recruits and positions fibrillarin, and that eukaryotic NOP56 engages fibrillarin through a protein-protein interface distinct from the archaeal arrangement [PMID:33483369, PMID:17617422]. Beyond scaffolding, NOP56 contributes directly to catalysis: its coiled-coil domain is dispensable for assembly but required for sRNP-guided methylation, NOP56/fibrillarin and NOP56 self-dimerization are mutually exclusive, and the protein contacts the target RNA substrate [PMID:16601205, PMID:22496443]. NOP56 production is autoregulated by a feedback loop in which excess snoRNP core proteins drive the intron-hosted snoRNA SNORD86 to redirect NOP56 pre-mRNA splicing toward a nonsense-mediated decay fate, coupling core protein availability to NOP56 levels [PMID:30220559]. The gene is essential for vertebrate CNS development, as nop56 loss in zebrafish causes cerebellar agenesis and neurodegeneration [PMID:36009362]. In cancer, NOP56 acts downstream of Myc as a rate-limiting effector of ribosome biogenesis and transformation [PMID:24013231], and NOP56 depletion in KRAS-mutant cells raises ROS and confers synthetic lethality with mTOR inhibition [PMID:35039048]. Pathogenic intronic GGCCTG hexanucleotide repeat expansions in NOP56 cause spinocerebellar ataxia type 36 (SCA36) via RNA gain-of-function, with RNA foci that sequester SRSF2 [PMID:21683323] and repeat-associated non-AUG (RAN) translation producing dipeptide repeat proteins [PMID:32375063, PMID:40015643].","teleology":[{"year":2002,"claim":"Established that NOP56 is a constitutive component of box C/D snoRNPs, defining its baseline role in the 2'-O-methylation machinery rather than in snoRNA stabilization.","evidence":"cDNA cloning, co-immunoprecipitation with box C/D snoRNPs, 5' end mapping and polysome analysis in Xenopus laevis","pmids":["12020815"],"confidence":"Medium","gaps":["Did not resolve which domains mediate snoRNP incorporation","No structural or catalytic role defined"]},{"year":2006,"claim":"Separated NOP56 assembly from catalysis by showing the coiled-coil domain is dispensable for binding but required for methylation, and that self- and fibrillarin-dimerization are mutually exclusive.","evidence":"Site-directed mutagenesis, pull-down, in vitro methylation assays and nuclease probing of archaeal box C/D sRNPs","pmids":["16601205"],"confidence":"High","gaps":["Archaeal system; eukaryotic coiled-coil requirement not directly tested","Mechanism by which coiled-coil shapes RNP structure not resolved"]},{"year":2007,"claim":"Resolved the architecture and conformational flexibility of the Nop56/58-fibrillarin complex, explaining how hinge motion could position catalytic sites at bipartite guide RNA targets.","evidence":"X-ray crystallography of Pyrococcus furiosus complex bound to SAM with normal-mode analysis","pmids":["17617422"],"confidence":"High","gaps":["Archaeal; eukaryotic dynamics not captured","Catalytic positioning inferred, not directly visualized in turnover"]},{"year":2009,"claim":"Demonstrated that NOP56 and fibrillarin interact directly in vivo before snoRNP assembly via fibrillarin's alpha-helix domain, independent of RNA, establishing the pre-assembly scaffolding step.","evidence":"Relocalization/affinity-tag delocalization with co-immunoprecipitation and localization analysis in mammalian cells","pmids":["19331828"],"confidence":"Medium","gaps":["Single lab","NOP56 domain mediating the interaction not mapped here"]},{"year":2012,"claim":"Revealed that the NOP56 N-terminal domain not only binds fibrillarin extremely stably but contributes directly to methyltransferase activity and contacts the substrate RNA, extending its role beyond passive scaffolding.","evidence":"Mutagenesis, in vitro methylation, denaturation, RNA cross-linking and 1.7 Å crystallography of archaeal NTD","pmids":["22496443"],"confidence":"High","gaps":["Archaeal NTD; eukaryotic NTD catalytic contribution inferred","Exact catalytic step NOP56 influences not defined"]},{"year":2011,"claim":"Identified the molecular basis of SCA36 as an intronic GGCCTG repeat expansion acting through RNA gain-of-function, with foci that sequester SRSF2.","evidence":"Genetic linkage, FISH for RNA foci and gel-shift assay in patient lymphoblastoid cells","pmids":["21683323"],"confidence":"Medium","gaps":["Functional consequence of SRSF2 sequestration on splicing not established","Contribution of foci versus protein loss to disease unresolved"]},{"year":2013,"claim":"Placed NOP56 downstream of Myc as a necessary, rate-limiting effector of Myc-driven transformation, connecting ribosome biogenesis machinery to oncogenesis.","evidence":"Expression profiling, RNAi/overexpression with transformation and in vivo tumor growth assays","pmids":["24013231"],"confidence":"Medium","gaps":["Whether transformation requires snoRNP/methylation activity not tested","Direct Myc regulation of NOP56 not dissected here"]},{"year":2018,"claim":"Defined the autoregulatory circuit controlling NOP56 abundance, showing the intronic snoRNA SNORD86 senses snoRNP core protein excess and redirects splicing toward NMD.","evidence":"Alternative splicing analysis, NMD reporter assays, RNA structure probing and snoRNP protein perturbation in human cells","pmids":["30220559"],"confidence":"High","gaps":["Which core proteins trigger the conformational switch not fully enumerated","Physiological conditions activating the loop in vivo unclear"]},{"year":2020,"claim":"Showed SCA36 repeats undergo RAN translation producing soluble dipeptide repeat proteins, distinguishing its molecular pathology from aggregation-prone c9ALS/FTD.","evidence":"RAN translation detection and DPR immunoassays in patient tissue with solubility profiling","pmids":["32375063"],"confidence":"Medium","gaps":["Pathogenic contribution of DPRs versus RNA foci not quantified","No model linking DPRs to neurodegeneration"]},{"year":2021,"claim":"Solved the eukaryotic Nop1/fibrillarin-Nop56 NTD structure, establishing that eukaryotic recruitment occurs through a protein interface distinct from archaea.","evidence":"X-ray crystallography of S. cerevisiae complex with comparison to archaeal structures","pmids":["33483369"],"confidence":"High","gaps":["Full eukaryotic snoRNP not crystallized","Catalytic mechanism in eukaryotes not directly tested"]},{"year":2022,"claim":"Linked NOP56 to redox and growth-signaling control in cancer, revealing synthetic lethality between NOP56 depletion and mTOR inhibition in KRAS-mutant cells.","evidence":"RNAi/CRISPR knockdown/knockout, ROS flow cytometry, inhibitor screen and xenografts","pmids":["35039048"],"confidence":"Medium","gaps":["Whether ROS effect depends on rRNA methylation not resolved","Direct molecular target connecting NOP56 to ROS unknown"]},{"year":2022,"claim":"Established NOP56 as essential for vertebrate CNS development, with loss causing cerebellar agenesis and neurodegeneration in zebrafish.","evidence":"Zebrafish loss-of-function mutant with microscopy, apoptosis assays and gene expression analysis","pmids":["36009362"],"confidence":"Medium","gaps":["Cell-autonomous versus systemic basis of neurodegeneration not separated","Link to SCA36 disease mechanism not established"]},{"year":2025,"claim":"Detailed the cap-dependent, multi-frame initiation of SCA36 RAN translation, showing near-cognate start usage and repeat-length-dependent enhancement.","evidence":"Cell-free translation with reporter constructs and mutagenesis","pmids":["40015643"],"confidence":"Medium","gaps":["In vivo relevance of frameshifting not confirmed","Cellular factors regulating initiation not identified"]},{"year":null,"claim":"How NOP56's core snoRNP/rRNA-methylation function mechanistically connects to its diverse cancer signaling roles (Myc, mTOR/ROS, SIRT1/p300-p53) and to SCA36 neuronal vulnerability remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["Cancer signaling interactions (PI3K/AKT, SIRT1/p300) rest on single Co-IP studies without reciprocal/structural validation","Whether disease phenotypes arise from snoRNP loss-of-function versus repeat RNA/DPR gain-of-function not disentangled","No structure of the intact human box C/D snoRNP"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[5,6]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,4,2]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[4,5]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[6,1]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,6,4]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[10,11]}],"complexes":["box C/D snoRNP"],"partners":["FBL","SRSF2","SNORD86"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O00567","full_name":"Nucleolar protein 56","aliases":["Nucleolar protein 5A"],"length_aa":594,"mass_kda":66.0,"function":"Involved in the early to middle stages of 60S ribosomal subunit biogenesis. Required for the biogenesis of box C/D snoRNAs such U3, U8 and U14 snoRNAs (PubMed:12777385, PubMed:15574333). Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome (PubMed:34516797). Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) complexes that function in methylation of multiple sites on ribosomal RNAs (rRNAs) and messenger RNAs (mRNAs) (PubMed:12777385, PubMed:39570315)","subcellular_location":"Nucleus, nucleolus; Cytoplasm; Nucleus, nucleoplasm","url":"https://www.uniprot.org/uniprotkb/O00567/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/NOP56","classification":"Common Essential","n_dependent_lines":1201,"n_total_lines":1208,"dependency_fraction":0.9942052980132451},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"RAB11A","stoichiometry":10.0},{"gene":"FBL","stoichiometry":4.0},{"gene":"NOP58","stoichiometry":4.0},{"gene":"NCL","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/NOP56","total_profiled":1310},"omim":[{"mim_id":"614155","title":"MICRO RNA 1292; MIR1292","url":"https://www.omim.org/entry/614155"},{"mim_id":"614154","title":"NOP56 RIBONUCLEAR PROTEIN; NOP56","url":"https://www.omim.org/entry/614154"},{"mim_id":"614153","title":"SPINOCEREBELLAR ATAXIA 36; SCA36","url":"https://www.omim.org/entry/614153"},{"mim_id":"614146","title":"DYNEIN, AXONEMAL, ASSEMBLY FACTOR 9; DNAAF9","url":"https://www.omim.org/entry/614146"},{"mim_id":"606847","title":"TREACLE RIBOSOME BIOGENESIS FACTOR 1; TCOF1","url":"https://www.omim.org/entry/606847"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoli fibrillar center","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NOP56"},"hgnc":{"alias_symbol":["SCA36"],"prev_symbol":["NOL5A"]},"alphafold":{"accession":"O00567","domains":[{"cath_id":"3.30.420.220","chopping":"4-158","consensus_level":"high","plddt":85.9999,"start":4,"end":158},{"cath_id":"1.10.287.4070","chopping":"167-282","consensus_level":"high","plddt":88.2122,"start":167,"end":282},{"cath_id":"1.10.246.90","chopping":"295-437","consensus_level":"high","plddt":88.4243,"start":295,"end":437}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O00567","model_url":"https://alphafold.ebi.ac.uk/files/AF-O00567-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O00567-F1-predicted_aligned_error_v6.png","plddt_mean":75.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NOP56","jax_strain_url":"https://www.jax.org/strain/search?query=NOP56"},"sequence":{"accession":"O00567","fasta_url":"https://rest.uniprot.org/uniprotkb/O00567.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O00567/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O00567"}},"corpus_meta":[{"pmid":"21683323","id":"PMC_21683323","title":"Expansion of intronic GGCCTG hexanucleotide repeat in NOP56 causes SCA36, a type of spinocerebellar ataxia accompanied by motor neuron involvement.","date":"2011","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/21683323","citation_count":216,"is_preprint":false},{"pmid":"22744658","id":"PMC_22744658","title":"Clinical features of SCA36: a novel spinocerebellar ataxia with motor neuron involvement (Asidan).","date":"2012","source":"Neurology","url":"https://pubmed.ncbi.nlm.nih.gov/22744658","citation_count":73,"is_preprint":false},{"pmid":"30220559","id":"PMC_30220559","title":"Box C/D snoRNP Autoregulation by a cis-Acting snoRNA in the NOP56 Pre-mRNA.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/30220559","citation_count":67,"is_preprint":false},{"pmid":"32375063","id":"PMC_32375063","title":"Chimeric Peptide Species Contribute to Divergent Dipeptide Repeat Pathology in c9ALS/FTD and SCA36.","date":"2020","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/32375063","citation_count":60,"is_preprint":false},{"pmid":"24013231","id":"PMC_24013231","title":"Burkitt's lymphoma-associated c-Myc mutations converge on a dramatically altered target gene response and implicate Nol5a/Nop56 in oncogenesis.","date":"2013","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/24013231","citation_count":44,"is_preprint":false},{"pmid":"32375043","id":"PMC_32375043","title":"Hexanucleotide Repeat Expansions in c9FTD/ALS and SCA36 Confer Selective Patterns of Neurodegeneration In Vivo.","date":"2020","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/32375043","citation_count":38,"is_preprint":false},{"pmid":"17617422","id":"PMC_17617422","title":"Alternative conformations of the archaeal Nop56/58-fibrillarin complex imply flexibility in box C/D RNPs.","date":"2007","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/17617422","citation_count":30,"is_preprint":false},{"pmid":"16601205","id":"PMC_16601205","title":"The coiled-coil domain of the Nop56/58 core protein is dispensable for sRNP assembly but is critical for archaeal box C/D sRNP-guided nucleotide methylation.","date":"2006","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/16601205","citation_count":29,"is_preprint":false},{"pmid":"35039048","id":"PMC_35039048","title":"Metabolic synthetic lethality by targeting NOP56 and mTOR in KRAS-mutant lung cancer.","date":"2022","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/35039048","citation_count":25,"is_preprint":false},{"pmid":"29281254","id":"PMC_29281254","title":"Structural and Dynamical Characterization of DNA and RNA Quadruplexes Obtained from the GGGGCC and GGGCCT Hexanucleotide Repeats Associated with C9FTD/ALS and SCA36 Diseases.","date":"2018","source":"ACS chemical neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/29281254","citation_count":24,"is_preprint":false},{"pmid":"19331828","id":"PMC_19331828","title":"Fibrillarin and Nop56 interact before being co-assembled in box C/D snoRNPs.","date":"2009","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/19331828","citation_count":23,"is_preprint":false},{"pmid":"29316893","id":"PMC_29316893","title":"Frequency of SCA8, SCA10, SCA12, SCA36, FXTAS and C9orf72 repeat expansions in SCA patients negative for the most common SCA subtypes.","date":"2018","source":"BMC neurology","url":"https://pubmed.ncbi.nlm.nih.gov/29316893","citation_count":23,"is_preprint":false},{"pmid":"30610877","id":"PMC_30610877","title":"Suppression of the yeast elongation factor Spt4 ortholog reduces expanded SCA36 GGCCUG repeat aggregation and cytotoxicity.","date":"2019","source":"Brain 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macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/36572080","citation_count":8,"is_preprint":false},{"pmid":"37051597","id":"PMC_37051597","title":"A Chinese SCA36 pedigree analysis of NOP56 expansion region based on long-read sequencing.","date":"2023","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37051597","citation_count":6,"is_preprint":false},{"pmid":"34774735","id":"PMC_34774735","title":"NOP56 negatively regulates MyD88-mediated NF-κB signaling in miiuy croaker, Miichthys miiuy.","date":"2021","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/34774735","citation_count":6,"is_preprint":false},{"pmid":"36368168","id":"PMC_36368168","title":"Long-read sequencing identified intronic (GGCCTG)n expansion in NOP56 in one SCA36 family and literature review.","date":"2022","source":"Clinical neurology and neurosurgery","url":"https://pubmed.ncbi.nlm.nih.gov/36368168","citation_count":5,"is_preprint":false},{"pmid":"33483369","id":"PMC_33483369","title":"High-resolution structure of eukaryotic Fibrillarin interacting with Nop56 amino-terminal domain.","date":"2021","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/33483369","citation_count":5,"is_preprint":false},{"pmid":"40015643","id":"PMC_40015643","title":"Dissecting the mechanism of NOP56 GGCCUG repeat-associated non-AUG translation using cell-free translation systems.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40015643","citation_count":4,"is_preprint":false},{"pmid":"40047221","id":"PMC_40047221","title":"Structural Insights into an Antiparallel Chair-Type G-Quadruplex From the Intron of NOP56 Oncogene.","date":"2025","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/40047221","citation_count":4,"is_preprint":false},{"pmid":"12020815","id":"PMC_12020815","title":"Characterization of the sequences encoding for Xenopus laevis box C/D snoRNP Nop56 protein.","date":"2002","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/12020815","citation_count":4,"is_preprint":false},{"pmid":"11430491","id":"PMC_11430491","title":"Dnop56, a Drosophila gene homologous to the yeast nucleolar NOP56 gene.","date":"2000","source":"Genetica","url":"https://pubmed.ncbi.nlm.nih.gov/11430491","citation_count":3,"is_preprint":false},{"pmid":"38811808","id":"PMC_38811808","title":"Hexanucleotide repeat expansion in SCA36 reduces the expression of genes involved in ribosome biosynthesis and protein translation.","date":"2024","source":"Journal of human 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Biogenesis.","date":"2026","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/41827688","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.11.27.691012","title":"Nucleolar Cdc14 Splitting Reflects Recombination Context and Meiotic Chromosome Dynamics","date":"2025-12-01","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.27.691012","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.08.11.24311662","title":"A Novel Methodology to Recalibrate Pathogenic Range of SCA36 Repeat Expansions for PGT-M","date":"2024-08-14","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.11.24311662","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.11.24.690106","title":"Cas9-enriched nanopore sequencing enables comprehensive and multiplexed detection of repeat expansions","date":"2025-11-25","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.24.690106","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.05.09.653119","title":"Regulation of translational fidelity by repression of C/D box SNoRNPs during UPR","date":"2025-05-13","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.09.653119","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":22553,"output_tokens":4753,"usd":0.069477,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12914,"output_tokens":4155,"usd":0.084223,"stage2_stop_reason":"end_turn"},"total_usd":0.1537,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"The intron-hosted box C/D snoRNA snoRD86 acts in cis as a sensor controlling NOP56 levels: excess snoRNP core proteins cause snoRD86 to adopt alternative RNP conformations that dictate usage of nearby alternative splice donors in the NOP56 pre-mRNA, triggering generation of a cytoplasmic snoRD86-containing NOP56-derived lncRNA via the nonsense-mediated decay pathway — a feedback mechanism that couples snoRNP core protein availability to NOP56 production.\",\n      \"method\": \"Alternative splicing analysis, NMD reporter assays, RNA structure probing, overexpression/depletion of snoRNP core proteins with functional readouts in human cells\",\n      \"journal\": \"Molecular Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (splicing analysis, NMD pathway, RNA structure), clear functional mechanism demonstrated in one rigorous study\",\n      \"pmids\": [\"30220559\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Fibrillarin and NOP56 directly interact in vivo prior to assembly into box C/D snoRNPs; this interaction requires the alpha-helix domain of fibrillarin (not the GAR or RNA-binding domain) and does not require RNA. Disrupting either protein's localization impairs their association with box C/D snoRNPs.\",\n      \"method\": \"Relocalization/affinity-tag delocalization of core box C/D proteins followed by co-immunoprecipitation and localization analysis in mammalian cells\",\n      \"journal\": \"Experimental Cell Research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal localization experiments and domain mapping, single lab, two orthogonal approaches\",\n      \"pmids\": [\"19331828\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"High-resolution crystal structure of eukaryotic Nop1 (fibrillarin) from S. cerevisiae bound to the amino-terminal domain of Nop56 was solved; the interaction interface differs substantially from the archaeal orthologs, demonstrating that eukaryotic Nop56 recruits the methyltransferase to the box C/D RNP through a protein-protein interface distinct from that in archaea.\",\n      \"method\": \"X-ray crystallography with functional comparison to archaeal structures\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with functional validation by comparison to mutagenesis data from archaeal studies, single lab\",\n      \"pmids\": [\"33483369\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Crystal structure of archaeal Nop56/58-fibrillarin complex from Pyrococcus furiosus (at 2.7 Å) bound to S-adenosyl-L-methionine confirmed the generality of the bipartite/symmetric dimer arrangement; the distinct conformation of Nop56/58 compared to the Archaeoglobus fulgidus structure revealed flexibility via hinge motion, repositioning fibrillarin catalytic sites, suggesting simultaneous positioning of two catalytic sites at two target sites of a bipartite guide RNA.\",\n      \"method\": \"X-ray crystallography and computational normal mode analysis\",\n      \"journal\": \"Journal of Molecular Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — two independent crystal structures from different archaeal species with computational validation, revealing conserved architecture and flexibility\",\n      \"pmids\": [\"17617422\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"In archaeal box C/D sRNPs, the coiled-coil domain of Nop56/58 is dispensable for core protein binding and sRNP assembly but is required for sRNP-guided nucleotide 2'-O-methylation; Nop56/58 self-dimerization and Nop56/58-fibrillarin dimerization are mutually exclusive interactions; deletion of the coiled-coil domain disrupts RNP structure essential for methylation without preventing assembly.\",\n      \"method\": \"Site-directed mutagenesis, protein pull-down assays, in vitro methylation assays, nuclease probing of sRNP structure\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstitution with mutagenesis, in vitro methylation assay, and structural probing in one study\",\n      \"pmids\": [\"16601205\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The N-terminal domain (NTD) of archaeal Nop56/58 mediates an exceptionally stable interaction with fibrillarin; mutations that did not affect fibrillarin binding or sRNP assembly still disrupted sRNP-guided nucleotide modification, revealing a direct role for Nop56/58 in methyltransferase activity beyond scaffolding. Cross-linking confirmed Nop56/58 contacts the target RNA substrate. The NTD crystal structure (1.7 Å) showed conservation despite low sequence identity among archaeal homologs.\",\n      \"method\": \"Site-directed mutagenesis, in vitro methylation assay, chemical and thermal denaturation, RNA cross-linking, X-ray crystallography\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple orthogonal methods including structure, mutagenesis, in vitro assay, and cross-linking in one rigorous study\",\n      \"pmids\": [\"22496443\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Xenopus laevis NOP56 (XNop56p) was identified as a common component of X. laevis box C/D snoRNPs; it is not essential for snoRNA stability; its transcript initiates with a pyrimidine tract and contains an intronic snoRNA, but it is not translationally regulated in a growth-dependent manner (i.e., it is not a TOP gene).\",\n      \"method\": \"cDNA cloning, co-immunoprecipitation with box C/D snoRNPs, 5' end mapping, polysome analysis\",\n      \"journal\": \"Biochimica et Biophysica Acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical fractionation and co-IP in Xenopus, single lab, two methods\",\n      \"pmids\": [\"12020815\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"NOP56 (Nol5a) was identified as a gene hyperactivated by Burkitt's lymphoma-associated Myc mutants and was shown to be necessary for Myc-induced cell transformation; Nol5a/NOP56 enhances wild-type Myc-induced cell transformation and increases the size of Myc-induced tumors, placing NOP56 downstream of Myc as a rate-limiting effector for transformation.\",\n      \"method\": \"Gene expression profiling, RNAi knockdown/overexpression with transformation assays and in vivo tumor growth assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional loss-of-function and gain-of-function experiments with defined cellular and in vivo phenotypes, single lab\",\n      \"pmids\": [\"24013231\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NOP56 depletion in KRAS-mutant lung cancer cells increases ROS levels and creates synthetic lethality with mTOR inhibition; mechanistically, cells with reduced NOP56 rely on mTOR signaling to balance oxidative stress, and IRE1α-mediated unfolded protein response activates mTOR through p38 MAPK in this context. Co-targeting NOP56 and mTOR profoundly enhances tumor cell death in vitro and in vivo.\",\n      \"method\": \"RNAi/shRNA knockdown, CRISPR/Cas9 knockout, flow cytometry for ROS, Western blot, chemical inhibitor screen, xenograft models\",\n      \"journal\": \"Journal of Experimental & Clinical Cancer Research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple genetic and pharmacological methods with in vitro and in vivo validation, single lab\",\n      \"pmids\": [\"35039048\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Loss-of-function of nop56 in zebrafish causes severe neurodegeneration characterized by absence of cerebellum, reduced spinal cord neurons, high CNS apoptosis, and impaired movement, with disrupted expression of genes related to the C/D box complex, balance, and CNS development, establishing NOP56 as essential for vertebrate CNS development and function.\",\n      \"method\": \"Zebrafish loss-of-function mutant, fluorescence microscopy, apoptosis assays, gene expression analysis\",\n      \"journal\": \"Biomedicines\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined genetic loss-of-function model with multiple specific phenotypic readouts, single lab\",\n      \"pmids\": [\"36009362\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Expansion of an intronic GGCCTG hexanucleotide repeat in NOP56 causes SCA36; RNA foci form in lymphoblastoid cells from affected subjects, and the expanded (GGCCUG)n RNA binds the RNA-binding protein SRSF2 (but not CUG6), as shown by gel-shift assay, indicating RNA gain-of-function toxicity.\",\n      \"method\": \"Genetic linkage analysis, FISH for RNA foci, gel-shift assay, segregation analysis\",\n      \"journal\": \"American Journal of Human Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and biochemical methods establishing RNA-protein interaction and RNA foci, single lab with multiple methods\",\n      \"pmids\": [\"21683323\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The intronic GGCCTG repeat expansion in NOP56 undergoes repeat-associated non-AUG (RAN) translation to produce dipeptide repeat proteins (DPRs) including poly(GP) and poly(PR); poly(GP) in SCA36 is produced via canonical AUG-mediated translation from intron-retained repeat RNAs and exists as a soluble species without TDP-43 pathology, in contrast to c9ALS/FTD where chimeric DPR species cause aggregation.\",\n      \"method\": \"RAN translation detection in patient tissue, immunoassays for DPR proteins, comparison of solubility profiles\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct detection in patient tissue with mechanistic dissection, single study\",\n      \"pmids\": [\"32375063\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NOP56 intron 1 GGCCTG repeat RAN translation occurs in all reading frames of the sense strand; translation initiates in a 5'-cap-dependent manner from near-cognate start codons upstream of the repeat in each frame; longer GGCCTG repeats enhance RAN translation; and a frameshift occurs within the GGCCUG repeat during translation.\",\n      \"method\": \"Cell-free translation systems with reporter constructs and mutagenesis\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cell-free reconstitution system with multiple constructs and controls, single lab\",\n      \"pmids\": [\"40015643\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"NOP56 protein levels progressively decrease selectively in large motor neurons of lumbar and cervical spinal cord in SOD1-G93A ALS model mice from the early symptomatic stage, preceding reductions in TDP-43 and FUS, implicating early NOP56 loss in motor neuron degeneration.\",\n      \"method\": \"Immunohistochemistry and protein expression analysis across disease stages in transgenic ALS mice\",\n      \"journal\": \"Neurological Research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single localization/expression study with no direct mechanistic intervention, single lab\",\n      \"pmids\": [\"23582672\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"NOP56 interacts with fibrillarin (FBL) and activates the PI3K/AKT/CREB signaling pathway in hepatocellular carcinoma; NOP56 knockdown lowers FBL levels and suppresses PI3K/AKT/CREB activity, while FBL overexpression partially rescues apoptotic effects of NOP56 silencing.\",\n      \"method\": \"Co-immunoprecipitation, Western blot, RNAi knockdown, overexpression rescue, xenograft models\",\n      \"journal\": \"Frontiers in Oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP with pathway readout, single lab, no orthogonal structural validation\",\n      \"pmids\": [\"41568368\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"NOP56 promotes p53 degradation in colorectal cancer through suppression of SIRT1 and activation of p300; NOP56 depletion increases p53 stability and acetylation via the SIRT1/p300 axis, as supported by evidence of direct interaction and colocalization of NOP56 with SIRT1 and p300.\",\n      \"method\": \"RNAi knockdown, co-immunoprecipitation, colocalization, Western blot, xenograft models\",\n      \"journal\": \"International Journal of Biological Sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/colocalization with pathway readout, single lab, limited mechanistic depth in abstract\",\n      \"pmids\": [\"42157947\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"NOP56 activates MYC signaling by regulating IRES-dependent translation, and MYC in turn transcriptionally upregulates NOP56 expression, creating a positive feedback loop that enhances ribosome biogenesis and drives NSCLC progression; promoter hypomethylation also contributes to NOP56 upregulation.\",\n      \"method\": \"Luciferase reporter assay for IRES translation, chromatin immunoprecipitation, bisulfite DNA sequencing, RNA sequencing, functional overexpression/knockdown assays\",\n      \"journal\": \"Cancers\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — multiple assays but indirect mechanism; single lab, no reconstitution of IRES regulation\",\n      \"pmids\": [\"41827688\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In miiuy croaker, NOP56 negatively regulates MyD88-mediated NF-κB signaling; the NOSIC domain of NOP56 is responsible for suppressing MyD88 protein expression; NOP56 overexpression inhibits MyD88 protein levels while NOP56 siRNA knockdown increases them.\",\n      \"method\": \"Overexpression, siRNA knockdown, Western blot, domain deletion analysis in fish cells\",\n      \"journal\": \"Fish & Shellfish Immunology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single-organism non-mammalian model, single lab, single method per experiment; mechanistic relevance to mammalian NOP56 uncertain\",\n      \"pmids\": [\"34774735\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In a preprint, NOP56 expression was downregulated by unfolded protein response (UPR) alongside FBL and NHP2L1; reduced C/D box snoRNP function during UPR alters rRNA 2'-O-methylation and translational fidelity including effects on nonsense suppression, frameshifts, ribosome pausing, and IRES-dependent translation initiation.\",\n      \"method\": \"qRT-PCR for expression, FBL knockdown with rRNA methylation assay and translational fidelity reporter assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, NOP56-specific mechanistic contribution not directly isolated from general snoRNP effects\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"NOP56 is a core component of box C/D snoRNP complexes that functions as a scaffold bridging L7Ae/Snu13 and fibrillarin, with its N-terminal domain mediating an exceptionally stable interaction with fibrillarin and directly contributing to sRNP-guided 2'-O-methylation of rRNA nucleotides; its coiled-coil domain is dispensable for assembly but required for proper RNP structure and methylation activity; its own levels are autoregulated by a feedback loop in which excess snoRNP proteins cause an intronic snoRNA (snoRD86) to redirect NOP56 pre-mRNA splicing toward NMD; in cancer contexts NOP56 acts downstream of Myc to support ribosome biogenesis and cell transformation, regulates ROS homeostasis and mTOR signaling in KRAS-mutant cells, and modulates p53 stability through SIRT1/p300; pathogenic intronic GGCCTG repeat expansions in NOP56 cause SCA36 through RNA gain-of-function (foci formation, SRSF2 binding) and RAN translation producing toxic dipeptide repeat proteins.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NOP56 is a core scaffolding subunit of box C/D small nucleolar ribonucleoprotein (snoRNP) complexes that guide 2'-O-methylation of rRNA [#6, #4]. It bridges the methyltransferase fibrillarin to the snoRNP through its N-terminal domain, which mediates an exceptionally stable, RNA-independent interaction with fibrillarin's alpha-helix domain [#1, #5]; crystallographic work on archaeal and eukaryotic complexes shows that this NTD interface recruits and positions fibrillarin, and that eukaryotic NOP56 engages fibrillarin through a protein-protein interface distinct from the archaeal arrangement [#2, #3]. Beyond scaffolding, NOP56 contributes directly to catalysis: its coiled-coil domain is dispensable for assembly but required for sRNP-guided methylation, NOP56/fibrillarin and NOP56 self-dimerization are mutually exclusive, and the protein contacts the target RNA substrate [#4, #5]. NOP56 production is autoregulated by a feedback loop in which excess snoRNP core proteins drive the intron-hosted snoRNA SNORD86 to redirect NOP56 pre-mRNA splicing toward a nonsense-mediated decay fate, coupling core protein availability to NOP56 levels [#0]. The gene is essential for vertebrate CNS development, as nop56 loss in zebrafish causes cerebellar agenesis and neurodegeneration [#9]. In cancer, NOP56 acts downstream of Myc as a rate-limiting effector of ribosome biogenesis and transformation [#7], and NOP56 depletion in KRAS-mutant cells raises ROS and confers synthetic lethality with mTOR inhibition [#8]. Pathogenic intronic GGCCTG hexanucleotide repeat expansions in NOP56 cause spinocerebellar ataxia type 36 (SCA36) via RNA gain-of-function, with RNA foci that sequester SRSF2 [#10] and repeat-associated non-AUG (RAN) translation producing dipeptide repeat proteins [#11, #12].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Established that NOP56 is a constitutive component of box C/D snoRNPs, defining its baseline role in the 2'-O-methylation machinery rather than in snoRNA stabilization.\",\n      \"evidence\": \"cDNA cloning, co-immunoprecipitation with box C/D snoRNPs, 5' end mapping and polysome analysis in Xenopus laevis\",\n      \"pmids\": [\"12020815\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not resolve which domains mediate snoRNP incorporation\", \"No structural or catalytic role defined\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Separated NOP56 assembly from catalysis by showing the coiled-coil domain is dispensable for binding but required for methylation, and that self- and fibrillarin-dimerization are mutually exclusive.\",\n      \"evidence\": \"Site-directed mutagenesis, pull-down, in vitro methylation assays and nuclease probing of archaeal box C/D sRNPs\",\n      \"pmids\": [\"16601205\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Archaeal system; eukaryotic coiled-coil requirement not directly tested\", \"Mechanism by which coiled-coil shapes RNP structure not resolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Resolved the architecture and conformational flexibility of the Nop56/58-fibrillarin complex, explaining how hinge motion could position catalytic sites at bipartite guide RNA targets.\",\n      \"evidence\": \"X-ray crystallography of Pyrococcus furiosus complex bound to SAM with normal-mode analysis\",\n      \"pmids\": [\"17617422\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Archaeal; eukaryotic dynamics not captured\", \"Catalytic positioning inferred, not directly visualized in turnover\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstrated that NOP56 and fibrillarin interact directly in vivo before snoRNP assembly via fibrillarin's alpha-helix domain, independent of RNA, establishing the pre-assembly scaffolding step.\",\n      \"evidence\": \"Relocalization/affinity-tag delocalization with co-immunoprecipitation and localization analysis in mammalian cells\",\n      \"pmids\": [\"19331828\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"NOP56 domain mediating the interaction not mapped here\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Revealed that the NOP56 N-terminal domain not only binds fibrillarin extremely stably but contributes directly to methyltransferase activity and contacts the substrate RNA, extending its role beyond passive scaffolding.\",\n      \"evidence\": \"Mutagenesis, in vitro methylation, denaturation, RNA cross-linking and 1.7 Å crystallography of archaeal NTD\",\n      \"pmids\": [\"22496443\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Archaeal NTD; eukaryotic NTD catalytic contribution inferred\", \"Exact catalytic step NOP56 influences not defined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identified the molecular basis of SCA36 as an intronic GGCCTG repeat expansion acting through RNA gain-of-function, with foci that sequester SRSF2.\",\n      \"evidence\": \"Genetic linkage, FISH for RNA foci and gel-shift assay in patient lymphoblastoid cells\",\n      \"pmids\": [\"21683323\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of SRSF2 sequestration on splicing not established\", \"Contribution of foci versus protein loss to disease unresolved\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Placed NOP56 downstream of Myc as a necessary, rate-limiting effector of Myc-driven transformation, connecting ribosome biogenesis machinery to oncogenesis.\",\n      \"evidence\": \"Expression profiling, RNAi/overexpression with transformation and in vivo tumor growth assays\",\n      \"pmids\": [\"24013231\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether transformation requires snoRNP/methylation activity not tested\", \"Direct Myc regulation of NOP56 not dissected here\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined the autoregulatory circuit controlling NOP56 abundance, showing the intronic snoRNA SNORD86 senses snoRNP core protein excess and redirects splicing toward NMD.\",\n      \"evidence\": \"Alternative splicing analysis, NMD reporter assays, RNA structure probing and snoRNP protein perturbation in human cells\",\n      \"pmids\": [\"30220559\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which core proteins trigger the conformational switch not fully enumerated\", \"Physiological conditions activating the loop in vivo unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed SCA36 repeats undergo RAN translation producing soluble dipeptide repeat proteins, distinguishing its molecular pathology from aggregation-prone c9ALS/FTD.\",\n      \"evidence\": \"RAN translation detection and DPR immunoassays in patient tissue with solubility profiling\",\n      \"pmids\": [\"32375063\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Pathogenic contribution of DPRs versus RNA foci not quantified\", \"No model linking DPRs to neurodegeneration\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Solved the eukaryotic Nop1/fibrillarin-Nop56 NTD structure, establishing that eukaryotic recruitment occurs through a protein interface distinct from archaea.\",\n      \"evidence\": \"X-ray crystallography of S. cerevisiae complex with comparison to archaeal structures\",\n      \"pmids\": [\"33483369\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full eukaryotic snoRNP not crystallized\", \"Catalytic mechanism in eukaryotes not directly tested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked NOP56 to redox and growth-signaling control in cancer, revealing synthetic lethality between NOP56 depletion and mTOR inhibition in KRAS-mutant cells.\",\n      \"evidence\": \"RNAi/CRISPR knockdown/knockout, ROS flow cytometry, inhibitor screen and xenografts\",\n      \"pmids\": [\"35039048\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ROS effect depends on rRNA methylation not resolved\", \"Direct molecular target connecting NOP56 to ROS unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Established NOP56 as essential for vertebrate CNS development, with loss causing cerebellar agenesis and neurodegeneration in zebrafish.\",\n      \"evidence\": \"Zebrafish loss-of-function mutant with microscopy, apoptosis assays and gene expression analysis\",\n      \"pmids\": [\"36009362\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cell-autonomous versus systemic basis of neurodegeneration not separated\", \"Link to SCA36 disease mechanism not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Detailed the cap-dependent, multi-frame initiation of SCA36 RAN translation, showing near-cognate start usage and repeat-length-dependent enhancement.\",\n      \"evidence\": \"Cell-free translation with reporter constructs and mutagenesis\",\n      \"pmids\": [\"40015643\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo relevance of frameshifting not confirmed\", \"Cellular factors regulating initiation not identified\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NOP56's core snoRNP/rRNA-methylation function mechanistically connects to its diverse cancer signaling roles (Myc, mTOR/ROS, SIRT1/p300-p53) and to SCA36 neuronal vulnerability remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Cancer signaling interactions (PI3K/AKT, SIRT1/p300) rest on single Co-IP studies without reciprocal/structural validation\", \"Whether disease phenotypes arise from snoRNP loss-of-function versus repeat RNA/DPR gain-of-function not disentangled\", \"No structure of the intact human box C/D snoRNP\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [5, 6]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 4, 2]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [6, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 6, 4]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [10, 11]}\n    ],\n    \"complexes\": [\n      \"box C/D snoRNP\"\n    ],\n    \"partners\": [\n      \"FBL\",\n      \"SRSF2\",\n      \"SNORD86\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}