{"gene":"LSM8","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":1998,"finding":"Lsm8p is a novel component of the yeast U6 snRNP; lsm8-1 mutant cells have drastically reduced levels of mature U6 snRNP, implicating Lsm8p as a key component in the early steps of U6 snRNP assembly.","method":"Yeast genetics (lsm8-1 mutant isolation), Northern blot analysis of U6 snRNA levels","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic mutant with defined molecular phenotype (reduced U6 snRNP), replicated in subsequent studies","pmids":["9857199"],"is_preprint":false},{"year":2001,"finding":"Lsm2p and Lsm4p contact Lsm8p within the Lsm2-8 ring; LSM2 and LSM4 act as allele-specific low-copy suppressors of lsm8 mutations. Overexpression of U6 snRNA bypasses the requirement for LSM8, indicating that the only essential function of LSM8 is in U6 RNA biogenesis or function.","method":"Yeast genetic suppression analysis, overexpression rescue experiments, immunoprecipitation","journal":"Genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with allele-specificity, multiple suppressor and overexpression experiments, consistent with structural data","pmids":["11333229"],"is_preprint":false},{"year":2004,"finding":"The Lsm2-8 complex (containing Lsm8) binds and stabilizes spliceosomal U6 snRNA in the nucleus, while a separate Lsm2-7 complex (lacking Lsm8) associates with the snoRNA snR5 and is present in nucleoli.","method":"Immunoprecipitation, glycerol gradient sedimentation, in vitro reconstitution of Lsm binding to snR5","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Co-IP, sedimentation, in vitro reconstitution) replicated across studies","pmids":["15075370"],"is_preprint":false},{"year":2009,"finding":"The N-terminal region of Lsm8p contributes to nuclear accumulation of the Lsm2-8 complex; no single domain is essential or sufficient for localization, but the shorter Lsm8p N-terminus (relative to Lsm1p) promotes nuclear retention of the complex.","method":"Analysis of mutant and hybrid Lsm1/Lsm8 proteins by fluorescence microscopy in budding yeast","journal":"The FEBS journal","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization experiment with domain-swap mutants, single lab, microscopy-based","pmids":["19490016"],"is_preprint":false},{"year":2013,"finding":"Crystal structure of the heptameric Lsm2-8 complex bound to the 3' end of U6 snRNA at 2.8 Å resolution reveals that Lsm proteins arrange in the order Lsm3-2-8-4-7-5-6. Lsm8 directly contacts the U6 snRNA 3' end: four uridine nucleotides are modularly recognized by Lsm3, Lsm2, Lsm8, and Lsm4, with uracil-base specificity conferred by a conserved asparagine residue in each subunit.","method":"X-ray crystallography (2.8 Å), biochemical binding assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structure with biochemical validation, published in Nature","pmids":["24240276"],"is_preprint":false},{"year":2018,"finding":"Cryo-EM structure of the yeast U6 snRNP reveals that the Lsm2-8 heteroheptameric ring is positioned in close proximity to the chaperone active site of Prp24, and that the Lsm2-8 ring specifically recognizes post-transcriptionally 3'-end-processed U6 snRNA. The C-terminal region of Lsm8 shows unanticipated homology to cytoplasmic Lsm1.","method":"Cryo-EM structural determination of U6 snRNP from Saccharomyces cerevisiae","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure with functional interpretation, reveals mechanism of 3'-end-processed U6 snRNA recognition","pmids":["29717126"],"is_preprint":false},{"year":2018,"finding":"Lethal deletions of LSM8 (as well as lsm2Δ, lsm3Δ, lsm4Δ, lsm5Δ) are rescued by overexpression of U6 snRNA or overexpression of the U6 snRNP protein Prp24, demonstrating that supporting U6 snRNA is the only essential function of the yeast Lsm2-8 proteins including Lsm8.","method":"Yeast genetics: gene deletion rescue by high-copy U6 snRNA or Prp24 overexpression; alanine scanning mutagenesis of RNA-binding and intersubunit interface residues","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with clean deletion rescue, multiple combinatorial deletions tested, consistent with structural data","pmids":["29615482"],"is_preprint":false},{"year":2020,"finding":"In C. elegans, the LSM2-8 complex (including lsm-8) contributes to repression of Polycomb/H3K27me3-marked heterochromatic loci; loss of lsm-8 causes selective mRNA stabilization at these loci and a localized drop in H3K27me3 levels. LSM2-8 works cooperatively with the 5'-3' exoribonuclease XRN-2 to degrade these RNAs.","method":"C. elegans genetic screen, reporter assays, RNA stabilization assays, chromatin immunoprecipitation (H3K27me3)","journal":"Cold Spring Harbor symposia on quantitative biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic screen with defined molecular phenotype (RNA stabilization, H3K27me3 drop), single lab, multiple assays","pmids":["32350050"],"is_preprint":false},{"year":2022,"finding":"LSM8 (the unique subunit of the nuclear Lsm2-8 complex) promotes Hepatitis B virus RNA production; siRNA-mediated knockdown of LSM8 reduced viral RNA levels in a manner dependent on N6-adenosine methylation (m6A) of the epsilon stem-loop at the 5' end of pre-Core/pregenomic RNA. MeRIP assays showed that LSM8 knockdown reduced viral RNA m6A methylation.","method":"siRNA knockdown of LSM8 in HBV replication model, MeRIP (methylated RNA immunoprecipitation), quantitative viral RNA analysis","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — siRNA knockdown with defined molecular phenotype and MeRIP validation, single lab, two orthogonal methods","pmids":["36016928"],"is_preprint":false},{"year":2025,"finding":"Interconversion experiments between Sm and Lsm2-8 rings reveal that the SC1-SC3 interaction (between Lsm2/3 and Lsm8/4 subcomplexes) is a key determinant distinguishing Lsm-type from Sm-type ring assembly and RNA-binding mode. Strengthening SC1-SC3 interaction converted the Sm ring into an Lsm-type ring; weakening it plus introducing RNA-binding mutations converted Lsm2-8 into an Sm-type ring.","method":"Protein engineering/mutagenesis, in vitro reconstitution of hybrid rings, functional RNA-binding assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with mutagenesis and functional validation, single lab but multiple orthogonal approaches","pmids":["40433979"],"is_preprint":false}],"current_model":"LSM8 is the defining subunit of the nuclear Lsm2-8 heteroheptameric ring, which assembles in the order Lsm3-2-8-4-7-5-6 and directly contacts the 3'-oligo(U) end of U6 snRNA (with Lsm8 recognizing the third uridine via a conserved asparagine); this interaction stabilizes nascent U6 snRNA and positions the ring adjacent to the Prp24 chaperone active site, with supporting U6 snRNA being the only essential function of yeast Lsm8; additionally, the N-terminal region of Lsm8 promotes nuclear retention of the Lsm2-8 complex, and in metazoans, the LSM2-8 complex cooperates with XRN-2 to degrade RNAs at H3K27me3-marked loci and can influence viral RNA m6A methylation."},"narrative":{"mechanistic_narrative":"LSM8 is the defining subunit of the nuclear Lsm2-8 heteroheptameric ring, which binds and stabilizes spliceosomal U6 snRNA and is essential for the early steps of U6 snRNP assembly [PMID:9857199, PMID:15075370]. Within the ring, subunits arrange in the order Lsm3-2-8-4-7-5-6, and Lsm8 directly engages the 3'-oligo(U) end of U6 snRNA, contributing uracil-base recognition through a conserved asparagine residue as part of a modular four-uridine binding interface [PMID:24240276]. The ring specifically recognizes post-transcriptionally 3'-end-processed U6 snRNA and is positioned adjacent to the chaperone active site of Prp24 in the assembled U6 snRNP [PMID:29717126]. Genetic analysis establishes that support of U6 snRNA biogenesis is the sole essential function of yeast Lsm8: both lethal deletion and overexpression bypass experiments show the requirement for LSM8 is relieved by overexpression of U6 snRNA (or Prp24) [PMID:11333229, PMID:29615482]. The N-terminal region of Lsm8 promotes nuclear retention of the Lsm2-8 complex, distinguishing it from cytoplasmic Lsm1 [PMID:19490016]. In metazoan systems, the LSM2-8 complex extends beyond snRNP function: in C. elegans it cooperates with the 5'-3' exoribonuclease XRN-2 to degrade RNAs at H3K27me3-marked heterochromatic loci [PMID:32350050], and human LSM8 promotes Hepatitis B virus RNA production in an m6A-dependent manner [PMID:36016928].","teleology":[{"year":1998,"claim":"Established that Lsm8 is a required factor for U6 snRNP, answering whether this Sm-like protein has a defined role in spliceosomal RNA metabolism.","evidence":"Yeast genetics with lsm8-1 mutant and Northern analysis of U6 snRNA levels","pmids":["9857199"],"confidence":"High","gaps":["Did not define the molecular architecture of the complex","Mechanism of U6 stabilization unresolved"]},{"year":2001,"claim":"Showed that U6 snRNA biogenesis is the single essential function of Lsm8 and placed it physically within the Lsm2-8 ring via contacts with Lsm2 and Lsm4.","evidence":"Allele-specific genetic suppression, U6 overexpression rescue, and immunoprecipitation in yeast","pmids":["11333229"],"confidence":"High","gaps":["No structural detail of subunit arrangement","Did not address how the ring discriminates U6 from other RNAs"]},{"year":2004,"claim":"Distinguished the Lsm8-containing nuclear Lsm2-8 complex (U6 binding) from a separate Lsm2-7 complex, defining Lsm8 as the subunit conferring U6/spliceosomal specificity and nuclear function.","evidence":"Co-IP, glycerol gradient sedimentation, and in vitro reconstitution in yeast","pmids":["15075370"],"confidence":"High","gaps":["Did not resolve the structural basis of RNA target discrimination","Localization determinants not mapped"]},{"year":2009,"claim":"Identified the Lsm8 N-terminus as a determinant of nuclear retention, addressing why the Lsm2-8 complex accumulates in the nucleus unlike cytoplasmic Lsm1 complexes.","evidence":"Domain-swap and hybrid Lsm1/Lsm8 mutants analyzed by fluorescence microscopy in budding yeast","pmids":["19490016"],"confidence":"Medium","gaps":["No single sufficient localization domain identified","Trafficking machinery interacting with the N-terminus unknown","Single-lab microscopy evidence"]},{"year":2013,"claim":"Resolved the atomic architecture, establishing the subunit order and the modular base-specific recognition of U6 3'-oligo(U) by Lsm8 via a conserved asparagine.","evidence":"2.8 Å X-ray crystal structure of Lsm2-8 bound to U6 3' end with biochemical binding assays","pmids":["24240276"],"confidence":"High","gaps":["Did not show the ring in the context of the full U6 snRNP","Did not address recognition of processed vs unprocessed 3' ends in vivo"]},{"year":2018,"claim":"Placed the Lsm2-8 ring within the assembled U6 snRNP adjacent to the Prp24 chaperone and demonstrated specificity for 3'-end-processed U6 snRNA.","evidence":"Cryo-EM structure of the yeast U6 snRNP","pmids":["29717126"],"confidence":"High","gaps":["Functional consequence of Lsm8 C-terminal homology to Lsm1 untested","Dynamics of Prp24-Lsm2-8 coupling unresolved"]},{"year":2018,"claim":"Confirmed genetically that supporting U6 snRNA is the only essential function of Lsm8 and the other Lsm2-8 subunits, by rescuing lethal deletions with U6 or Prp24 overexpression.","evidence":"Yeast deletion rescue and alanine-scanning mutagenesis of RNA-binding/interface residues","pmids":["29615482"],"confidence":"High","gaps":["Does not exclude non-essential moonlighting roles","Metazoan-specific functions not addressed"]},{"year":2020,"claim":"Extended Lsm8/LSM2-8 function beyond splicing to chromatin-linked RNA turnover, showing cooperation with XRN-2 to degrade RNAs at H3K27me3-marked loci.","evidence":"C. elegans genetic screen, reporter and RNA-stabilization assays, and H3K27me3 ChIP","pmids":["32350050"],"confidence":"Medium","gaps":["Direct physical interaction between LSM2-8 and XRN-2 not structurally defined","How the complex is recruited to Polycomb loci unknown","Conservation to mammals untested"]},{"year":2022,"claim":"Implicated human LSM8 in viral RNA metabolism, linking it to m6A methylation of HBV pregenomic RNA.","evidence":"siRNA knockdown of LSM8 in an HBV replication model with MeRIP and viral RNA quantification","pmids":["36016928"],"confidence":"Medium","gaps":["Whether LSM8 acts directly on viral RNA or via the m6A machinery unresolved","No reciprocal or structural validation","Single-lab knockdown evidence"]},{"year":2025,"claim":"Defined the structural determinant (SC1-SC3 interaction) that distinguishes Lsm-type from Sm-type ring assembly and RNA-binding mode.","evidence":"Protein engineering, in vitro reconstitution of hybrid rings, and functional RNA-binding assays","pmids":["40433979"],"confidence":"High","gaps":["In vivo relevance of engineered conversions not tested","Does not address regulation of ring assembly in cells"]},{"year":null,"claim":"How metazoan LSM8-containing complexes are recruited to and act at chromatin and viral RNA targets, and whether these functions are mechanistically distinct from canonical U6 stabilization, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of LSM2-8 with XRN-2 or m6A machinery","Recruitment mechanism to H3K27me3 loci unknown","Direct vs indirect role in viral m6A methylation unclear"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,2,4,5]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[4,5,9]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,3]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,2,4,5]}],"complexes":["Lsm2-8 complex","U6 snRNP"],"partners":["LSM2","LSM4","PRP24","XRN-2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O95777","full_name":"U6 snRNA-associated Sm-like protein LSm8","aliases":[],"length_aa":96,"mass_kda":10.4,"function":"Plays a role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/O95777/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/LSM8","classification":"Common Essential","n_dependent_lines":1204,"n_total_lines":1208,"dependency_fraction":0.9966887417218543},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"SNRPF","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/LSM8","total_profiled":1310},"omim":[{"mim_id":"607288","title":"LSM8 PROTEIN; LSM8","url":"https://www.omim.org/entry/607288"},{"mim_id":"607287","title":"LSM7 PROTEIN; LSM7","url":"https://www.omim.org/entry/607287"},{"mim_id":"607286","title":"LSM6 PROTEIN; LSM6","url":"https://www.omim.org/entry/607286"},{"mim_id":"607285","title":"LSM5 PROTEIN; LSM5","url":"https://www.omim.org/entry/607285"},{"mim_id":"607284","title":"LSM4 PROTEIN; LSM4","url":"https://www.omim.org/entry/607284"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Vesicles","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/LSM8"},"hgnc":{"alias_symbol":["YJR022W"],"prev_symbol":[]},"alphafold":{"accession":"O95777","domains":[{"cath_id":"2.30.30.100","chopping":"1-82","consensus_level":"high","plddt":95.9037,"start":1,"end":82}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O95777","model_url":"https://alphafold.ebi.ac.uk/files/AF-O95777-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O95777-F1-predicted_aligned_error_v6.png","plddt_mean":95.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LSM8","jax_strain_url":"https://www.jax.org/strain/search?query=LSM8"},"sequence":{"accession":"O95777","fasta_url":"https://rest.uniprot.org/uniprotkb/O95777.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O95777/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O95777"}},"corpus_meta":[{"pmid":"9857199","id":"PMC_9857199","title":"A role for the yeast La protein in U6 snRNP assembly: evidence that the La protein is a molecular chaperone for RNA polymerase III transcripts.","date":"1998","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/9857199","citation_count":178,"is_preprint":false},{"pmid":"21572561","id":"PMC_21572561","title":"3' processing of eukaryotic precursor tRNAs.","date":"2011","source":"Wiley interdisciplinary reviews. RNA","url":"https://pubmed.ncbi.nlm.nih.gov/21572561","citation_count":116,"is_preprint":false},{"pmid":"24240276","id":"PMC_24240276","title":"Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA.","date":"2013","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/24240276","citation_count":86,"is_preprint":false},{"pmid":"30146317","id":"PMC_30146317","title":"The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/30146317","citation_count":67,"is_preprint":false},{"pmid":"11333229","id":"PMC_11333229","title":"Multiple functional interactions between components of the Lsm2-Lsm8 complex, U6 snRNA, and the yeast La protein.","date":"2001","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/11333229","citation_count":65,"is_preprint":false},{"pmid":"33627638","id":"PMC_33627638","title":"Chronic mild stress-induced protein dysregulations correlated with susceptibility and resiliency to depression or anxiety revealed by quantitative proteomics of the rat prefrontal cortex.","date":"2021","source":"Translational psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/33627638","citation_count":45,"is_preprint":false},{"pmid":"24828406","id":"PMC_24828406","title":"RNA binding by Hfq and ring-forming (L)Sm proteins: a trade-off between optimal sequence readout and RNA backbone conformation.","date":"2014","source":"RNA biology","url":"https://pubmed.ncbi.nlm.nih.gov/24828406","citation_count":39,"is_preprint":false},{"pmid":"15075370","id":"PMC_15075370","title":"An Lsm2-Lsm7 complex in Saccharomyces cerevisiae associates with the small nucleolar RNA snR5.","date":"2004","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/15075370","citation_count":37,"is_preprint":false},{"pmid":"29717126","id":"PMC_29717126","title":"Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29717126","citation_count":23,"is_preprint":false},{"pmid":"19596813","id":"PMC_19596813","title":"LSM1 over-expression in Saccharomyces cerevisiae depletes U6 snRNA levels.","date":"2009","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/19596813","citation_count":23,"is_preprint":false},{"pmid":"30108155","id":"PMC_30108155","title":"Genome-wide association study identifies novel recessive genetic variants for high TGs in an Arab population.","date":"2018","source":"Journal of lipid research","url":"https://pubmed.ncbi.nlm.nih.gov/30108155","citation_count":22,"is_preprint":false},{"pmid":"18334927","id":"PMC_18334927","title":"Hypoxia-regulated components of the U4/U6.U5 tri-small nuclear riboprotein complex: possible role in autosomal dominant retinitis pigmentosa.","date":"2008","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/18334927","citation_count":17,"is_preprint":false},{"pmid":"28325844","id":"PMC_28325844","title":"The sole LSm complex in Cyanidioschyzon merolae associates with pre-mRNA splicing and mRNA degradation factors.","date":"2017","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/28325844","citation_count":14,"is_preprint":false},{"pmid":"37007092","id":"PMC_37007092","title":"Identification of LSM family members as potential chemoresistance predictive and therapeutic biomarkers for gastric cancer.","date":"2023","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/37007092","citation_count":13,"is_preprint":false},{"pmid":"36016928","id":"PMC_36016928","title":"The cytoplasmic LSm1-7 and nuclear LSm2-8 complexes exert opposite effects on Hepatitis B virus biosynthesis and interferon responses.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/36016928","citation_count":9,"is_preprint":false},{"pmid":"29615482","id":"PMC_29615482","title":"Defining essential elements and genetic interactions of the yeast Lsm2-8 ring and demonstration that essentiality of Lsm2-8 is bypassed via overexpression of U6 snRNA or the U6 snRNP subunit Prp24.","date":"2018","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/29615482","citation_count":8,"is_preprint":false},{"pmid":"19490016","id":"PMC_19490016","title":"Analysis of Lsm1p and Lsm8p domains in the cellular localization of Lsm complexes in budding yeast.","date":"2009","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/19490016","citation_count":7,"is_preprint":false},{"pmid":"38694815","id":"PMC_38694815","title":"The MexTAg collaborative cross: host genetics affects asbestos related disease latency, but has little influence once tumours develop.","date":"2024","source":"Frontiers in toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/38694815","citation_count":3,"is_preprint":false},{"pmid":"40433979","id":"PMC_40433979","title":"Interconversion and mechanisms between Lsm-type and Sm-type heteroheptameric rings: implications for spliceosome evolution and RNA metabolism.","date":"2025","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/40433979","citation_count":1,"is_preprint":false},{"pmid":"40206583","id":"PMC_40206583","title":"Integrating multi-omics and machine learning methods reveals the metabolism of amino acids and derivatives-related signature in colorectal cancer.","date":"2025","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/40206583","citation_count":1,"is_preprint":false},{"pmid":"41663668","id":"PMC_41663668","title":"A conserved Lsm8-exosome module maintains RNA splicing fidelity to control fungal stress adaptation and virulence.","date":"2026","source":"Stress biology","url":"https://pubmed.ncbi.nlm.nih.gov/41663668","citation_count":0,"is_preprint":false},{"pmid":"32350050","id":"PMC_32350050","title":"A Nuclear RNA Degradation Pathway Helps Silence Polycomb/H3K27me3-Marked Loci in Caenorhabditis elegans.","date":"2020","source":"Cold Spring Harbor symposia on quantitative biology","url":"https://pubmed.ncbi.nlm.nih.gov/32350050","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13307,"output_tokens":2677,"usd":0.040038,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9791,"output_tokens":3212,"usd":0.064628,"stage2_stop_reason":"end_turn"},"total_usd":0.104666,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1998,\n      \"finding\": \"Lsm8p is a novel component of the yeast U6 snRNP; lsm8-1 mutant cells have drastically reduced levels of mature U6 snRNP, implicating Lsm8p as a key component in the early steps of U6 snRNP assembly.\",\n      \"method\": \"Yeast genetics (lsm8-1 mutant isolation), Northern blot analysis of U6 snRNA levels\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic mutant with defined molecular phenotype (reduced U6 snRNP), replicated in subsequent studies\",\n      \"pmids\": [\"9857199\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Lsm2p and Lsm4p contact Lsm8p within the Lsm2-8 ring; LSM2 and LSM4 act as allele-specific low-copy suppressors of lsm8 mutations. Overexpression of U6 snRNA bypasses the requirement for LSM8, indicating that the only essential function of LSM8 is in U6 RNA biogenesis or function.\",\n      \"method\": \"Yeast genetic suppression analysis, overexpression rescue experiments, immunoprecipitation\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with allele-specificity, multiple suppressor and overexpression experiments, consistent with structural data\",\n      \"pmids\": [\"11333229\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"The Lsm2-8 complex (containing Lsm8) binds and stabilizes spliceosomal U6 snRNA in the nucleus, while a separate Lsm2-7 complex (lacking Lsm8) associates with the snoRNA snR5 and is present in nucleoli.\",\n      \"method\": \"Immunoprecipitation, glycerol gradient sedimentation, in vitro reconstitution of Lsm binding to snR5\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Co-IP, sedimentation, in vitro reconstitution) replicated across studies\",\n      \"pmids\": [\"15075370\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The N-terminal region of Lsm8p contributes to nuclear accumulation of the Lsm2-8 complex; no single domain is essential or sufficient for localization, but the shorter Lsm8p N-terminus (relative to Lsm1p) promotes nuclear retention of the complex.\",\n      \"method\": \"Analysis of mutant and hybrid Lsm1/Lsm8 proteins by fluorescence microscopy in budding yeast\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization experiment with domain-swap mutants, single lab, microscopy-based\",\n      \"pmids\": [\"19490016\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Crystal structure of the heptameric Lsm2-8 complex bound to the 3' end of U6 snRNA at 2.8 Å resolution reveals that Lsm proteins arrange in the order Lsm3-2-8-4-7-5-6. Lsm8 directly contacts the U6 snRNA 3' end: four uridine nucleotides are modularly recognized by Lsm3, Lsm2, Lsm8, and Lsm4, with uracil-base specificity conferred by a conserved asparagine residue in each subunit.\",\n      \"method\": \"X-ray crystallography (2.8 Å), biochemical binding assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structure with biochemical validation, published in Nature\",\n      \"pmids\": [\"24240276\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Cryo-EM structure of the yeast U6 snRNP reveals that the Lsm2-8 heteroheptameric ring is positioned in close proximity to the chaperone active site of Prp24, and that the Lsm2-8 ring specifically recognizes post-transcriptionally 3'-end-processed U6 snRNA. The C-terminal region of Lsm8 shows unanticipated homology to cytoplasmic Lsm1.\",\n      \"method\": \"Cryo-EM structural determination of U6 snRNP from Saccharomyces cerevisiae\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure with functional interpretation, reveals mechanism of 3'-end-processed U6 snRNA recognition\",\n      \"pmids\": [\"29717126\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Lethal deletions of LSM8 (as well as lsm2Δ, lsm3Δ, lsm4Δ, lsm5Δ) are rescued by overexpression of U6 snRNA or overexpression of the U6 snRNP protein Prp24, demonstrating that supporting U6 snRNA is the only essential function of the yeast Lsm2-8 proteins including Lsm8.\",\n      \"method\": \"Yeast genetics: gene deletion rescue by high-copy U6 snRNA or Prp24 overexpression; alanine scanning mutagenesis of RNA-binding and intersubunit interface residues\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with clean deletion rescue, multiple combinatorial deletions tested, consistent with structural data\",\n      \"pmids\": [\"29615482\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In C. elegans, the LSM2-8 complex (including lsm-8) contributes to repression of Polycomb/H3K27me3-marked heterochromatic loci; loss of lsm-8 causes selective mRNA stabilization at these loci and a localized drop in H3K27me3 levels. LSM2-8 works cooperatively with the 5'-3' exoribonuclease XRN-2 to degrade these RNAs.\",\n      \"method\": \"C. elegans genetic screen, reporter assays, RNA stabilization assays, chromatin immunoprecipitation (H3K27me3)\",\n      \"journal\": \"Cold Spring Harbor symposia on quantitative biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic screen with defined molecular phenotype (RNA stabilization, H3K27me3 drop), single lab, multiple assays\",\n      \"pmids\": [\"32350050\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"LSM8 (the unique subunit of the nuclear Lsm2-8 complex) promotes Hepatitis B virus RNA production; siRNA-mediated knockdown of LSM8 reduced viral RNA levels in a manner dependent on N6-adenosine methylation (m6A) of the epsilon stem-loop at the 5' end of pre-Core/pregenomic RNA. MeRIP assays showed that LSM8 knockdown reduced viral RNA m6A methylation.\",\n      \"method\": \"siRNA knockdown of LSM8 in HBV replication model, MeRIP (methylated RNA immunoprecipitation), quantitative viral RNA analysis\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — siRNA knockdown with defined molecular phenotype and MeRIP validation, single lab, two orthogonal methods\",\n      \"pmids\": [\"36016928\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Interconversion experiments between Sm and Lsm2-8 rings reveal that the SC1-SC3 interaction (between Lsm2/3 and Lsm8/4 subcomplexes) is a key determinant distinguishing Lsm-type from Sm-type ring assembly and RNA-binding mode. Strengthening SC1-SC3 interaction converted the Sm ring into an Lsm-type ring; weakening it plus introducing RNA-binding mutations converted Lsm2-8 into an Sm-type ring.\",\n      \"method\": \"Protein engineering/mutagenesis, in vitro reconstitution of hybrid rings, functional RNA-binding assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with mutagenesis and functional validation, single lab but multiple orthogonal approaches\",\n      \"pmids\": [\"40433979\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LSM8 is the defining subunit of the nuclear Lsm2-8 heteroheptameric ring, which assembles in the order Lsm3-2-8-4-7-5-6 and directly contacts the 3'-oligo(U) end of U6 snRNA (with Lsm8 recognizing the third uridine via a conserved asparagine); this interaction stabilizes nascent U6 snRNA and positions the ring adjacent to the Prp24 chaperone active site, with supporting U6 snRNA being the only essential function of yeast Lsm8; additionally, the N-terminal region of Lsm8 promotes nuclear retention of the Lsm2-8 complex, and in metazoans, the LSM2-8 complex cooperates with XRN-2 to degrade RNAs at H3K27me3-marked loci and can influence viral RNA m6A methylation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LSM8 is the defining subunit of the nuclear Lsm2-8 heteroheptameric ring, which binds and stabilizes spliceosomal U6 snRNA and is essential for the early steps of U6 snRNP assembly [#0, #2]. Within the ring, subunits arrange in the order Lsm3-2-8-4-7-5-6, and Lsm8 directly engages the 3'-oligo(U) end of U6 snRNA, contributing uracil-base recognition through a conserved asparagine residue as part of a modular four-uridine binding interface [#4]. The ring specifically recognizes post-transcriptionally 3'-end-processed U6 snRNA and is positioned adjacent to the chaperone active site of Prp24 in the assembled U6 snRNP [#5]. Genetic analysis establishes that support of U6 snRNA biogenesis is the sole essential function of yeast Lsm8: both lethal deletion and overexpression bypass experiments show the requirement for LSM8 is relieved by overexpression of U6 snRNA (or Prp24) [#1, #6]. The N-terminal region of Lsm8 promotes nuclear retention of the Lsm2-8 complex, distinguishing it from cytoplasmic Lsm1 [#3]. In metazoan systems, the LSM2-8 complex extends beyond snRNP function: in C. elegans it cooperates with the 5'-3' exoribonuclease XRN-2 to degrade RNAs at H3K27me3-marked heterochromatic loci [#7], and human LSM8 promotes Hepatitis B virus RNA production in an m6A-dependent manner [#8].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 1998,\n      \"claim\": \"Established that Lsm8 is a required factor for U6 snRNP, answering whether this Sm-like protein has a defined role in spliceosomal RNA metabolism.\",\n      \"evidence\": \"Yeast genetics with lsm8-1 mutant and Northern analysis of U6 snRNA levels\",\n      \"pmids\": [\"9857199\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the molecular architecture of the complex\", \"Mechanism of U6 stabilization unresolved\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Showed that U6 snRNA biogenesis is the single essential function of Lsm8 and placed it physically within the Lsm2-8 ring via contacts with Lsm2 and Lsm4.\",\n      \"evidence\": \"Allele-specific genetic suppression, U6 overexpression rescue, and immunoprecipitation in yeast\",\n      \"pmids\": [\"11333229\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural detail of subunit arrangement\", \"Did not address how the ring discriminates U6 from other RNAs\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Distinguished the Lsm8-containing nuclear Lsm2-8 complex (U6 binding) from a separate Lsm2-7 complex, defining Lsm8 as the subunit conferring U6/spliceosomal specificity and nuclear function.\",\n      \"evidence\": \"Co-IP, glycerol gradient sedimentation, and in vitro reconstitution in yeast\",\n      \"pmids\": [\"15075370\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the structural basis of RNA target discrimination\", \"Localization determinants not mapped\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identified the Lsm8 N-terminus as a determinant of nuclear retention, addressing why the Lsm2-8 complex accumulates in the nucleus unlike cytoplasmic Lsm1 complexes.\",\n      \"evidence\": \"Domain-swap and hybrid Lsm1/Lsm8 mutants analyzed by fluorescence microscopy in budding yeast\",\n      \"pmids\": [\"19490016\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No single sufficient localization domain identified\", \"Trafficking machinery interacting with the N-terminus unknown\", \"Single-lab microscopy evidence\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved the atomic architecture, establishing the subunit order and the modular base-specific recognition of U6 3'-oligo(U) by Lsm8 via a conserved asparagine.\",\n      \"evidence\": \"2.8 Å X-ray crystal structure of Lsm2-8 bound to U6 3' end with biochemical binding assays\",\n      \"pmids\": [\"24240276\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not show the ring in the context of the full U6 snRNP\", \"Did not address recognition of processed vs unprocessed 3' ends in vivo\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Placed the Lsm2-8 ring within the assembled U6 snRNP adjacent to the Prp24 chaperone and demonstrated specificity for 3'-end-processed U6 snRNA.\",\n      \"evidence\": \"Cryo-EM structure of the yeast U6 snRNP\",\n      \"pmids\": [\"29717126\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of Lsm8 C-terminal homology to Lsm1 untested\", \"Dynamics of Prp24-Lsm2-8 coupling unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Confirmed genetically that supporting U6 snRNA is the only essential function of Lsm8 and the other Lsm2-8 subunits, by rescuing lethal deletions with U6 or Prp24 overexpression.\",\n      \"evidence\": \"Yeast deletion rescue and alanine-scanning mutagenesis of RNA-binding/interface residues\",\n      \"pmids\": [\"29615482\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not exclude non-essential moonlighting roles\", \"Metazoan-specific functions not addressed\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended Lsm8/LSM2-8 function beyond splicing to chromatin-linked RNA turnover, showing cooperation with XRN-2 to degrade RNAs at H3K27me3-marked loci.\",\n      \"evidence\": \"C. elegans genetic screen, reporter and RNA-stabilization assays, and H3K27me3 ChIP\",\n      \"pmids\": [\"32350050\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct physical interaction between LSM2-8 and XRN-2 not structurally defined\", \"How the complex is recruited to Polycomb loci unknown\", \"Conservation to mammals untested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Implicated human LSM8 in viral RNA metabolism, linking it to m6A methylation of HBV pregenomic RNA.\",\n      \"evidence\": \"siRNA knockdown of LSM8 in an HBV replication model with MeRIP and viral RNA quantification\",\n      \"pmids\": [\"36016928\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether LSM8 acts directly on viral RNA or via the m6A machinery unresolved\", \"No reciprocal or structural validation\", \"Single-lab knockdown evidence\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined the structural determinant (SC1-SC3 interaction) that distinguishes Lsm-type from Sm-type ring assembly and RNA-binding mode.\",\n      \"evidence\": \"Protein engineering, in vitro reconstitution of hybrid rings, and functional RNA-binding assays\",\n      \"pmids\": [\"40433979\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of engineered conversions not tested\", \"Does not address regulation of ring assembly in cells\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How metazoan LSM8-containing complexes are recruited to and act at chromatin and viral RNA targets, and whether these functions are mechanistically distinct from canonical U6 stabilization, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of LSM2-8 with XRN-2 or m6A machinery\", \"Recruitment mechanism to H3K27me3 loci unknown\", \"Direct vs indirect role in viral m6A methylation unclear\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 2, 4, 5]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [4, 5, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 2, 4, 5]}\n    ],\n    \"complexes\": [\"Lsm2-8 complex\", \"U6 snRNP\"],\n    \"partners\": [\"LSM2\", \"LSM4\", \"PRP24\", \"XRN-2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}