{"gene":"EXOSC7","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":1997,"finding":"Rrp42p (yeast ortholog of EXOSC7) is an essential component of the yeast exosome, a multi-subunit 3'→5' exoribonuclease complex required for 3' processing of 5.8S rRNA. Rrp42p shares homology with bacterial RNase PH phosphorolytic ribonucleases.","method":"Mass spectrometry-based complex purification, genetic depletion, in vitro exoribonuclease assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — complex reconstitution, in vitro activity assays, genetic complementation, replicated across labs","pmids":["9390555"],"is_preprint":false},{"year":2002,"finding":"Human hRrp42p (EXOSC7) is a genuine component of the human exosome complex. hCsl4p directly interacts with hRrp42p as demonstrated by mammalian two-hybrid and GST pull-down assays, and this interaction mediates hCsl4p association with the exosome in vivo.","method":"Co-immunoprecipitation, mammalian two-hybrid assay, GST pull-down","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — reciprocal interaction shown by two methods (two-hybrid + GST pulldown) in a single lab","pmids":["11812149"],"is_preprint":false},{"year":2001,"finding":"Human hRrp42p (EXOSC7) is an autoantigenic component of the PM/Scl complex (human exosome), recognized by autoantibodies in patients with idiopathic inflammatory myopathy, and is one of the most frequently targeted exosome components by autoantibodies.","method":"ELISA and western blotting using affinity-purified recombinant hRrp42p protein with patient sera","journal":"Arthritis research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct protein identification as exosome component confirmed with recombinant protein; single lab","pmids":["11879549"],"is_preprint":false},{"year":2005,"finding":"In the archaeal exosome, the Rrp41-Rrp42 heterodimer forms a hexameric ring (three heterodimers). Rrp42 adopts the RNase PH fold but is catalytically inactive; it contributes to structuring the active site of the adjacent catalytic Rrp41 subunit. Structure-guided mutagenesis confirmed that catalytic activity resides exclusively in Rrp41.","method":"X-ray crystallography at 2.8 Å resolution, structure-guided mutagenesis, in vitro ribonuclease assay","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with mutagenesis and in vitro activity assays in one rigorous study","pmids":["15951817"],"is_preprint":false},{"year":2005,"finding":"Crystal structures of the Rrp41-Rrp42 core bound to short single-stranded RNAs and ADP revealed: the RNA-binding cleft recognizes four nucleotides in a sequence-unspecific manner primarily via phosphate backbone interactions; 2'-OH specificity distinguishes RNA from DNA; structures of both bound substrate and cleaved product defined the catalytic mechanism of 3'→5' phosphorolytic activity.","method":"X-ray crystallography with RNA and ADP ligands","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures of substrate-bound and product-bound states in a single rigorous study defining catalytic mechanism","pmids":["16285928"],"is_preprint":false},{"year":2007,"finding":"The nine-subunit archaeal exosome channels RNA through a central pore; RNA binds at the active site on one side and at the narrowest constriction of the central channel on the opposite side. This entrapment in the channel provides a mechanistic basis for processive degradation of extended RNAs and stalling at structured RNAs.","method":"X-ray crystallography at 1.6 Å (apo) and 2.3 Å (RNA-bound) resolution","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structures of RNA-bound complex directly demonstrating channeling mechanism","pmids":["17380186"],"is_preprint":false},{"year":2008,"finding":"Structural studies of the Pyrococcus abyssi RNase PH ring revealed that residues from all three Rrp41-Rrp42 heterodimers contact a single RNA molecule within the catalytic chamber, providing mechanistic evidence for the functional role of the ring assembly in RNA processivity. An ADP-bound structure demonstrated rearrangement at the N1 site, suggesting a mechanism for nucleoside diphosphate elimination after catalysis.","method":"High-resolution X-ray crystallography, RNA degradation assays with active-site mutants","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple crystal structures combined with mutagenesis and RNA degradation assays","pmids":["18353775"],"is_preprint":false},{"year":2006,"finding":"The catalytic activity of the archaeal exosome resides in the Rrp41-Rrp42 hexameric ring, which degrades RNA phosphorolytically. Rrp4 and Csl4 cap subunits do not exhibit hydrolytic RNase activity alone or in complex, but modulate exosome activity. Various reconstituted complexes of different compositions showed variations in RNase activity, indicating functional interdependence of subunits.","method":"Biochemical fractionation, reconstitution of defined subcomplexes, RNase activity assays with depleted extracts","journal":"Molecular microbiology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstitution of defined complexes with activity assays; single lab but multiple compositions tested","pmids":["17078816"],"is_preprint":false},{"year":2016,"finding":"The quaternary (hexameric barrel) structure of the archaeal Rrp41:Rrp42 exosome is required for efficient RNA degradation. The entrance pore of the barrel provides nM substrate affinity essential for processivity, preventing premature RNA release. NMR analysis showed the RNA 3' end remains flexible inside the lumen, jumping between three active sites; because jumping is much faster than cleavage, confinement within the lumen ensures continuous active-site engagement.","method":"Methyl TROSY NMR, in vitro RNA degradation assays, mutagenesis of pore residues","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR combined with mutagenesis and enzymatic assays in a single rigorous study","pmids":["26837575"],"is_preprint":false},{"year":2025,"finding":"In mammalian cells, EXOSC7 is one of the earliest initiating subunits in RNA exosome assembly; along with EXOSC2 and EXOSC4, it initiates complex formation and facilitates incorporation of barrel and cap subunits in a defined hierarchical order. Orphan (unassembled) EXOSC7 is degraded via the ubiquitin-proteasome system. Disease-associated variants of EXOSC7 show functional defects in yeast complementation assays, with some variants causing reduced protein levels and others being expressed normally yet functionally defective.","method":"Inducible dual-guide CRISPR/Cas9 KO in mouse embryonic stem cells, humanized yeast complementation, proteasome inhibitor experiments, mass spectrometry","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR-based systematic dissection plus yeast complementation; preprint, single lab, multiple orthogonal methods","pmids":["39982806"],"is_preprint":true},{"year":2025,"finding":"Humanized yeast expressing human EXOSC7 in place of the yeast ortholog revealed that disease-associated patient variants of EXOSC7 cause functional defects. Some patient-derived EXOSC7 variants show reduced protein levels, while others are expressed normally but are functionally impaired, suggesting direct contribution of those residues to RNA exosome function rather than destabilization.","method":"Humanized yeast complementation (replacement of yeast Rrp42 with human EXOSC7), growth assays, protein level quantification","journal":"G3 (Bethesda, Md.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic complementation with functional readout and protein level analysis; single lab, multiple variants tested","pmids":["39982806"],"is_preprint":false},{"year":2023,"finding":"EXOSC7-containing exosome complex is recruited to a ZNF692-organized nucleolar hub specialized in 18S rRNA processing and 40S ribosomal subunit maturation in the granular component of the nucleolus.","method":"Co-immunoprecipitation, proximity labeling, fluorescence microscopy, KD with ribosome biogenesis functional readout","journal":"Cell reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — EXOSC7 mentioned as part of exosome complex in hub; no EXOSC7-specific mechanistic experiment described","pmids":["37851577"],"is_preprint":false}],"current_model":"EXOSC7 (hRrp42p) is a structural, catalytically inactive RNase PH-domain subunit of the RNA exosome that forms heterodimers with the active EXOSC4 (Rrp41) subunit; three such heterodimers assemble into a hexameric ring that channels RNA through a central pore to three active sites for processive 3'→5' phosphorolytic degradation, while EXOSC7 itself contributes to structuring the active site of EXOSC4. In mammalian cells, EXOSC7 is among the earliest assembly initiators of the exosome complex and unincorporated EXOSC7 is degraded by the ubiquitin-proteasome system; disease-causing patient variants disrupt its function either by reducing protein stability or by directly impairing RNA exosome activity."},"narrative":{"mechanistic_narrative":"EXOSC7 (hRrp42p) is a structural, catalytically inactive RNase PH-domain subunit of the RNA exosome, the conserved multi-subunit 3'→5' exoribonuclease complex required for processing of rRNA and other RNA substrates [PMID:9390555]. Within the exosome core, EXOSC7 adopts an RNase PH fold but lacks intrinsic nuclease activity; it heterodimerizes with the catalytically active EXOSC4 (Rrp41) subunit and contributes to structuring the adjacent EXOSC4 active site, while three such heterodimers assemble into a hexameric ring [PMID:15951817]. This ring forms a central channel that entraps RNA, recognizing the substrate backbone sequence-unspecifically and discriminating RNA from DNA via 2'-OH contacts, thereby providing the processivity that drives continuous 3'→5' phosphorolytic degradation as the RNA 3' end shuttles among the three active sites [PMID:16285928, PMID:26837575]. EXOSC7 is also a defined component of the human exosome, where it directly interacts with the cap subunit hCsl4p (EXOSC1) to mediate cap-subunit association [PMID:11879549]. In mammalian cells EXOSC7 is one of the earliest initiating subunits of exosome assembly, nucleating complex formation together with EXOSC2 and EXOSC4 and templating the ordered incorporation of barrel and cap subunits; unincorporated orphan EXOSC7 is cleared by the ubiquitin-proteasome system [PMID:39982806]. Disease-associated patient variants disrupt EXOSC7 either by reducing protein stability or, for normally expressed variants, by directly impairing RNA exosome function, as shown by humanized yeast complementation [PMID:39982806]. EXOSC7 is additionally an autoantigen of the PM/Scl complex frequently targeted in idiopathic inflammatory myopathy [PMID:11812149].","teleology":[{"year":1997,"claim":"Established that the EXOSC7 ortholog Rrp42p is an essential subunit of the exosome, defining the complex as a 3'→5' exoribonuclease machine required for rRNA processing.","evidence":"Mass spectrometry-based complex purification, genetic depletion and in vitro exoribonuclease assays in yeast","pmids":["9390555"],"confidence":"High","gaps":["Did not resolve whether Rrp42p itself is catalytic or structural","No atomic-resolution architecture"]},{"year":2001,"claim":"Identified human EXOSC7 as a bona fide exosome component and clinically relevant autoantigen of the PM/Scl complex, linking the human protein to autoimmune disease.","evidence":"ELISA and western blotting of recombinant hRrp42p against patient sera; recombinant-protein interaction assays","pmids":["11879549","11812149"],"confidence":"Medium","gaps":["Autoantigenicity does not define molecular function","hCsl4p interaction shown in a single lab"]},{"year":2005,"claim":"Resolved that EXOSC7/Rrp42 is catalytically inactive and instead structures the active site of its heterodimer partner Rrp41 within a hexameric ring, distinguishing structural from catalytic subunits.","evidence":"X-ray crystallography of the archaeal Rrp41-Rrp42 core with structure-guided mutagenesis and in vitro RNase assays","pmids":["15951817","16285928"],"confidence":"High","gaps":["Archaeal model; mammalian-specific contributions not directly tested","How the ring achieves processivity not yet defined"]},{"year":2008,"claim":"Defined the mechanistic basis of processivity, showing the hexameric ring channels and entraps RNA so the 3' end engages active sites continuously.","evidence":"High-resolution crystallography, methyl-TROSY NMR, and RNA degradation assays with pore and active-site mutants in archaeal exosomes","pmids":["17380186","18353775","26837575"],"confidence":"High","gaps":["Substrate channeling characterized in archaeal complexes only","EXOSC7-specific residues mediating channeling not isolated in human complex"]},{"year":2025,"claim":"Placed EXOSC7 as an early assembly initiator of the mammalian exosome subject to proteasomal quality control, and connected patient variants to function via two distinct mechanisms.","evidence":"Inducible CRISPR/Cas9 KO in mouse ES cells, proteasome inhibition, mass spectrometry, and humanized yeast complementation of disease variants","pmids":["39982806"],"confidence":"Medium","gaps":["Disease mechanism inferred from yeast, not patient cells","Specific RNA substrates affected by variants not mapped","Assembly hierarchy from a single lab/preprint"]},{"year":null,"claim":"How EXOSC7 contributes to substrate selection and processing of specific human RNA targets, and the in vivo consequences of its variants in patient tissues, remain open.","evidence":"","pmids":[],"confidence":"Low","gaps":["No EXOSC7-specific substrate repertoire defined in human cells","Nucleolar recruitment role inferred only at the complex level [#11]"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[4,8]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[3]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,9]}],"complexes":["RNA exosome","PM/Scl complex"],"partners":["EXOSC4","EXOSC1","EXOSC2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q15024","full_name":"Exosome complex component RRP42","aliases":["Exosome component 7","Ribosomal RNA-processing protein 42","p8"],"length_aa":291,"mass_kda":31.8,"function":"Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes","subcellular_location":"Nucleus, nucleolus; Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q15024/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/EXOSC7","classification":"Common Essential","n_dependent_lines":1135,"n_total_lines":1208,"dependency_fraction":0.9395695364238411},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DRG1","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"RACK1","stoichiometry":0.2},{"gene":"RBM7","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/EXOSC7","total_profiled":1310},"omim":[{"mim_id":"606488","title":"EXOSOME COMPONENT 7; EXOSC7","url":"https://www.omim.org/entry/606488"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nuclear speckles","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/EXOSC7"},"hgnc":{"alias_symbol":["hRrp42p","Rrp42p","RRP42","EAP1","KIAA0116","p8"],"prev_symbol":[]},"alphafold":{"accession":"Q15024","domains":[{"cath_id":"3.30.230.70","chopping":"8-280","consensus_level":"medium","plddt":85.5814,"start":8,"end":280}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15024","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q15024-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q15024-F1-predicted_aligned_error_v6.png","plddt_mean":84.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=EXOSC7","jax_strain_url":"https://www.jax.org/strain/search?query=EXOSC7"},"sequence":{"accession":"Q15024","fasta_url":"https://rest.uniprot.org/uniprotkb/Q15024.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q15024/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15024"}},"corpus_meta":[{"pmid":"9390555","id":"PMC_9390555","title":"The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases.","date":"1997","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/9390555","citation_count":808,"is_preprint":false},{"pmid":"15951817","id":"PMC_15951817","title":"The archaeal exosome core is a hexameric ring structure with three catalytic subunits.","date":"2005","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/15951817","citation_count":185,"is_preprint":false},{"pmid":"12947419","id":"PMC_12947419","title":"An exosome-like complex in Sulfolobus solfataricus.","date":"2003","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/12947419","citation_count":118,"is_preprint":false},{"pmid":"16285928","id":"PMC_16285928","title":"Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core.","date":"2005","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/16285928","citation_count":102,"is_preprint":false},{"pmid":"17380186","id":"PMC_17380186","title":"RNA channelling by the archaeal exosome.","date":"2007","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/17380186","citation_count":99,"is_preprint":false},{"pmid":"11879549","id":"PMC_11879549","title":"Autoantibodies directed to novel components of the PM/Scl complex, the human exosome.","date":"2001","source":"Arthritis research","url":"https://pubmed.ncbi.nlm.nih.gov/11879549","citation_count":72,"is_preprint":false},{"pmid":"18353775","id":"PMC_18353775","title":"Insights into the mechanism of progressive RNA degradation by the archaeal exosome.","date":"2008","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18353775","citation_count":50,"is_preprint":false},{"pmid":"17078816","id":"PMC_17078816","title":"Characterization of native and reconstituted exosome complexes from the hyperthermophilic archaeon Sulfolobus solfataricus.","date":"2006","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/17078816","citation_count":46,"is_preprint":false},{"pmid":"34182925","id":"PMC_34182925","title":"The plasma peptides of Alzheimer's disease.","date":"2021","source":"Clinical proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/34182925","citation_count":33,"is_preprint":false},{"pmid":"11812149","id":"PMC_11812149","title":"Protein-protein interactions of hCsl4p with other human exosome subunits.","date":"2002","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/11812149","citation_count":32,"is_preprint":false},{"pmid":"24789718","id":"PMC_24789718","title":"Structure and function of the archaeal exosome.","date":"2014","source":"Wiley interdisciplinary reviews. RNA","url":"https://pubmed.ncbi.nlm.nih.gov/24789718","citation_count":30,"is_preprint":false},{"pmid":"22503705","id":"PMC_22503705","title":"Heterogeneous complexes of the RNA exosome in Sulfolobus solfataricus.","date":"2012","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/22503705","citation_count":22,"is_preprint":false},{"pmid":"20488184","id":"PMC_20488184","title":"The evolutionarily conserved subunits Rrp4 and Csl4 confer different substrate specificities to the archaeal exosome.","date":"2010","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/20488184","citation_count":22,"is_preprint":false},{"pmid":"36473392","id":"PMC_36473392","title":"The new landscape of differentially expression proteins in placenta tissues of gestational diabetes based on iTRAQ proteomics.","date":"2022","source":"Placenta","url":"https://pubmed.ncbi.nlm.nih.gov/36473392","citation_count":16,"is_preprint":false},{"pmid":"31724941","id":"PMC_31724941","title":"The RNA degradation pathway is involved in PPARα-modulated anti-oral tumorigenesis.","date":"2019","source":"BioMedicine","url":"https://pubmed.ncbi.nlm.nih.gov/31724941","citation_count":15,"is_preprint":false},{"pmid":"20488181","id":"PMC_20488181","title":"The archaeal exosome localizes to the membrane.","date":"2010","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/20488181","citation_count":15,"is_preprint":false},{"pmid":"26837575","id":"PMC_26837575","title":"The oligomeric architecture of the archaeal exosome is important for processive and efficient RNA degradation.","date":"2016","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/26837575","citation_count":13,"is_preprint":false},{"pmid":"37851577","id":"PMC_37851577","title":"ZNF692 organizes a hub specialized in 40S ribosomal subunit maturation enhancing translation in rapidly proliferating cells.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37851577","citation_count":10,"is_preprint":false},{"pmid":"34456585","id":"PMC_34456585","title":"Identification of Dysregulated Mechanisms and Potential Biomarkers in Ischemic Stroke Onset.","date":"2021","source":"International journal of general medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34456585","citation_count":8,"is_preprint":false},{"pmid":"21713675","id":"PMC_21713675","title":"The archaeal exosome.","date":"2011","source":"Advances in experimental medicine and biology","url":"https://pubmed.ncbi.nlm.nih.gov/21713675","citation_count":7,"is_preprint":false},{"pmid":"21618872","id":"PMC_21618872","title":"The archaeal exosome.","date":"2010","source":"Advances in experimental medicine and biology","url":"https://pubmed.ncbi.nlm.nih.gov/21618872","citation_count":5,"is_preprint":false},{"pmid":"39161926","id":"PMC_39161926","title":"Characterization of RNA Processing Genes in Colon Cancer for Predicting Clinical Outcomes.","date":"2024","source":"Biomarker insights","url":"https://pubmed.ncbi.nlm.nih.gov/39161926","citation_count":1,"is_preprint":false},{"pmid":"31768972","id":"PMC_31768972","title":"Enzymatic Analysis of Reconstituted Archaeal Exosomes.","date":"2020","source":"Methods in molecular biology (Clifton, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/31768972","citation_count":0,"is_preprint":false},{"pmid":"39982806","id":"PMC_39982806","title":"Humanized Saccharomyces cerevisiae provides a facile and effective tool to identify damaging human variants that cause exosomopathies.","date":"2025","source":"G3 (Bethesda, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/39982806","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.14.643291","title":"Hierarchical assembly and functional resilience of the mammalian RNA exosome","date":"2025-03-15","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.14.643291","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14021,"output_tokens":2962,"usd":0.043247,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10277,"output_tokens":2215,"usd":0.05338,"stage2_stop_reason":"end_turn"},"total_usd":0.096627,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1997,\n      \"finding\": \"Rrp42p (yeast ortholog of EXOSC7) is an essential component of the yeast exosome, a multi-subunit 3'→5' exoribonuclease complex required for 3' processing of 5.8S rRNA. Rrp42p shares homology with bacterial RNase PH phosphorolytic ribonucleases.\",\n      \"method\": \"Mass spectrometry-based complex purification, genetic depletion, in vitro exoribonuclease assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — complex reconstitution, in vitro activity assays, genetic complementation, replicated across labs\",\n      \"pmids\": [\"9390555\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Human hRrp42p (EXOSC7) is a genuine component of the human exosome complex. hCsl4p directly interacts with hRrp42p as demonstrated by mammalian two-hybrid and GST pull-down assays, and this interaction mediates hCsl4p association with the exosome in vivo.\",\n      \"method\": \"Co-immunoprecipitation, mammalian two-hybrid assay, GST pull-down\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — reciprocal interaction shown by two methods (two-hybrid + GST pulldown) in a single lab\",\n      \"pmids\": [\"11812149\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Human hRrp42p (EXOSC7) is an autoantigenic component of the PM/Scl complex (human exosome), recognized by autoantibodies in patients with idiopathic inflammatory myopathy, and is one of the most frequently targeted exosome components by autoantibodies.\",\n      \"method\": \"ELISA and western blotting using affinity-purified recombinant hRrp42p protein with patient sera\",\n      \"journal\": \"Arthritis research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct protein identification as exosome component confirmed with recombinant protein; single lab\",\n      \"pmids\": [\"11879549\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"In the archaeal exosome, the Rrp41-Rrp42 heterodimer forms a hexameric ring (three heterodimers). Rrp42 adopts the RNase PH fold but is catalytically inactive; it contributes to structuring the active site of the adjacent catalytic Rrp41 subunit. Structure-guided mutagenesis confirmed that catalytic activity resides exclusively in Rrp41.\",\n      \"method\": \"X-ray crystallography at 2.8 Å resolution, structure-guided mutagenesis, in vitro ribonuclease assay\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with mutagenesis and in vitro activity assays in one rigorous study\",\n      \"pmids\": [\"15951817\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Crystal structures of the Rrp41-Rrp42 core bound to short single-stranded RNAs and ADP revealed: the RNA-binding cleft recognizes four nucleotides in a sequence-unspecific manner primarily via phosphate backbone interactions; 2'-OH specificity distinguishes RNA from DNA; structures of both bound substrate and cleaved product defined the catalytic mechanism of 3'→5' phosphorolytic activity.\",\n      \"method\": \"X-ray crystallography with RNA and ADP ligands\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures of substrate-bound and product-bound states in a single rigorous study defining catalytic mechanism\",\n      \"pmids\": [\"16285928\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"The nine-subunit archaeal exosome channels RNA through a central pore; RNA binds at the active site on one side and at the narrowest constriction of the central channel on the opposite side. This entrapment in the channel provides a mechanistic basis for processive degradation of extended RNAs and stalling at structured RNAs.\",\n      \"method\": \"X-ray crystallography at 1.6 Å (apo) and 2.3 Å (RNA-bound) resolution\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structures of RNA-bound complex directly demonstrating channeling mechanism\",\n      \"pmids\": [\"17380186\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Structural studies of the Pyrococcus abyssi RNase PH ring revealed that residues from all three Rrp41-Rrp42 heterodimers contact a single RNA molecule within the catalytic chamber, providing mechanistic evidence for the functional role of the ring assembly in RNA processivity. An ADP-bound structure demonstrated rearrangement at the N1 site, suggesting a mechanism for nucleoside diphosphate elimination after catalysis.\",\n      \"method\": \"High-resolution X-ray crystallography, RNA degradation assays with active-site mutants\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple crystal structures combined with mutagenesis and RNA degradation assays\",\n      \"pmids\": [\"18353775\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"The catalytic activity of the archaeal exosome resides in the Rrp41-Rrp42 hexameric ring, which degrades RNA phosphorolytically. Rrp4 and Csl4 cap subunits do not exhibit hydrolytic RNase activity alone or in complex, but modulate exosome activity. Various reconstituted complexes of different compositions showed variations in RNase activity, indicating functional interdependence of subunits.\",\n      \"method\": \"Biochemical fractionation, reconstitution of defined subcomplexes, RNase activity assays with depleted extracts\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstitution of defined complexes with activity assays; single lab but multiple compositions tested\",\n      \"pmids\": [\"17078816\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The quaternary (hexameric barrel) structure of the archaeal Rrp41:Rrp42 exosome is required for efficient RNA degradation. The entrance pore of the barrel provides nM substrate affinity essential for processivity, preventing premature RNA release. NMR analysis showed the RNA 3' end remains flexible inside the lumen, jumping between three active sites; because jumping is much faster than cleavage, confinement within the lumen ensures continuous active-site engagement.\",\n      \"method\": \"Methyl TROSY NMR, in vitro RNA degradation assays, mutagenesis of pore residues\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR combined with mutagenesis and enzymatic assays in a single rigorous study\",\n      \"pmids\": [\"26837575\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In mammalian cells, EXOSC7 is one of the earliest initiating subunits in RNA exosome assembly; along with EXOSC2 and EXOSC4, it initiates complex formation and facilitates incorporation of barrel and cap subunits in a defined hierarchical order. Orphan (unassembled) EXOSC7 is degraded via the ubiquitin-proteasome system. Disease-associated variants of EXOSC7 show functional defects in yeast complementation assays, with some variants causing reduced protein levels and others being expressed normally yet functionally defective.\",\n      \"method\": \"Inducible dual-guide CRISPR/Cas9 KO in mouse embryonic stem cells, humanized yeast complementation, proteasome inhibitor experiments, mass spectrometry\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR-based systematic dissection plus yeast complementation; preprint, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"39982806\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Humanized yeast expressing human EXOSC7 in place of the yeast ortholog revealed that disease-associated patient variants of EXOSC7 cause functional defects. Some patient-derived EXOSC7 variants show reduced protein levels, while others are expressed normally but are functionally impaired, suggesting direct contribution of those residues to RNA exosome function rather than destabilization.\",\n      \"method\": \"Humanized yeast complementation (replacement of yeast Rrp42 with human EXOSC7), growth assays, protein level quantification\",\n      \"journal\": \"G3 (Bethesda, Md.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic complementation with functional readout and protein level analysis; single lab, multiple variants tested\",\n      \"pmids\": [\"39982806\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"EXOSC7-containing exosome complex is recruited to a ZNF692-organized nucleolar hub specialized in 18S rRNA processing and 40S ribosomal subunit maturation in the granular component of the nucleolus.\",\n      \"method\": \"Co-immunoprecipitation, proximity labeling, fluorescence microscopy, KD with ribosome biogenesis functional readout\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — EXOSC7 mentioned as part of exosome complex in hub; no EXOSC7-specific mechanistic experiment described\",\n      \"pmids\": [\"37851577\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EXOSC7 (hRrp42p) is a structural, catalytically inactive RNase PH-domain subunit of the RNA exosome that forms heterodimers with the active EXOSC4 (Rrp41) subunit; three such heterodimers assemble into a hexameric ring that channels RNA through a central pore to three active sites for processive 3'→5' phosphorolytic degradation, while EXOSC7 itself contributes to structuring the active site of EXOSC4. In mammalian cells, EXOSC7 is among the earliest assembly initiators of the exosome complex and unincorporated EXOSC7 is degraded by the ubiquitin-proteasome system; disease-causing patient variants disrupt its function either by reducing protein stability or by directly impairing RNA exosome activity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"EXOSC7 (hRrp42p) is a structural, catalytically inactive RNase PH-domain subunit of the RNA exosome, the conserved multi-subunit 3'→5' exoribonuclease complex required for processing of rRNA and other RNA substrates [#0]. Within the exosome core, EXOSC7 adopts an RNase PH fold but lacks intrinsic nuclease activity; it heterodimerizes with the catalytically active EXOSC4 (Rrp41) subunit and contributes to structuring the adjacent EXOSC4 active site, while three such heterodimers assemble into a hexameric ring [#3]. This ring forms a central channel that entraps RNA, recognizing the substrate backbone sequence-unspecifically and discriminating RNA from DNA via 2'-OH contacts, thereby providing the processivity that drives continuous 3'→5' phosphorolytic degradation as the RNA 3' end shuttles among the three active sites [#4, #8]. EXOSC7 is also a defined component of the human exosome, where it directly interacts with the cap subunit hCsl4p (EXOSC1) to mediate cap-subunit association [#2]. In mammalian cells EXOSC7 is one of the earliest initiating subunits of exosome assembly, nucleating complex formation together with EXOSC2 and EXOSC4 and templating the ordered incorporation of barrel and cap subunits; unincorporated orphan EXOSC7 is cleared by the ubiquitin-proteasome system [#9]. Disease-associated patient variants disrupt EXOSC7 either by reducing protein stability or, for normally expressed variants, by directly impairing RNA exosome function, as shown by humanized yeast complementation [#9, #10]. EXOSC7 is additionally an autoantigen of the PM/Scl complex frequently targeted in idiopathic inflammatory myopathy [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Established that the EXOSC7 ortholog Rrp42p is an essential subunit of the exosome, defining the complex as a 3'→5' exoribonuclease machine required for rRNA processing.\",\n      \"evidence\": \"Mass spectrometry-based complex purification, genetic depletion and in vitro exoribonuclease assays in yeast\",\n      \"pmids\": [\"9390555\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve whether Rrp42p itself is catalytic or structural\", \"No atomic-resolution architecture\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Identified human EXOSC7 as a bona fide exosome component and clinically relevant autoantigen of the PM/Scl complex, linking the human protein to autoimmune disease.\",\n      \"evidence\": \"ELISA and western blotting of recombinant hRrp42p against patient sera; recombinant-protein interaction assays\",\n      \"pmids\": [\"11879549\", \"11812149\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Autoantigenicity does not define molecular function\", \"hCsl4p interaction shown in a single lab\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Resolved that EXOSC7/Rrp42 is catalytically inactive and instead structures the active site of its heterodimer partner Rrp41 within a hexameric ring, distinguishing structural from catalytic subunits.\",\n      \"evidence\": \"X-ray crystallography of the archaeal Rrp41-Rrp42 core with structure-guided mutagenesis and in vitro RNase assays\",\n      \"pmids\": [\"15951817\", \"16285928\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Archaeal model; mammalian-specific contributions not directly tested\", \"How the ring achieves processivity not yet defined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Defined the mechanistic basis of processivity, showing the hexameric ring channels and entraps RNA so the 3' end engages active sites continuously.\",\n      \"evidence\": \"High-resolution crystallography, methyl-TROSY NMR, and RNA degradation assays with pore and active-site mutants in archaeal exosomes\",\n      \"pmids\": [\"17380186\", \"18353775\", \"26837575\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrate channeling characterized in archaeal complexes only\", \"EXOSC7-specific residues mediating channeling not isolated in human complex\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placed EXOSC7 as an early assembly initiator of the mammalian exosome subject to proteasomal quality control, and connected patient variants to function via two distinct mechanisms.\",\n      \"evidence\": \"Inducible CRISPR/Cas9 KO in mouse ES cells, proteasome inhibition, mass spectrometry, and humanized yeast complementation of disease variants\",\n      \"pmids\": [\"39982806\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Disease mechanism inferred from yeast, not patient cells\", \"Specific RNA substrates affected by variants not mapped\", \"Assembly hierarchy from a single lab/preprint\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How EXOSC7 contributes to substrate selection and processing of specific human RNA targets, and the in vivo consequences of its variants in patient tissues, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No EXOSC7-specific substrate repertoire defined in human cells\", \"Nucleolar recruitment role inferred only at the complex level [#11]\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [4, 8]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 9]}\n    ],\n    \"complexes\": [\"RNA exosome\", \"PM/Scl complex\"],\n    \"partners\": [\"EXOSC4\", \"EXOSC1\", \"EXOSC2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}