{"gene":"FTSJ3","run_date":"2026-04-28T17:46:04","timeline":{"discoveries":[{"year":2019,"finding":"FTSJ3 is a 2'-O-methyltransferase (2'O-MTase) that is recruited to HIV-1 RNA through its interaction with TRBP (TAR RNA-binding protein) in a DICER-independent complex. In vitro and ex vivo experiments demonstrated FTSJ3 enzymatic activity, and RiboMethSeq analysis identified predominantly FTSJ3-dependent 2'-O-methylations at specific residues on the HIV-1 viral genome. HIV-1 produced in FTSJ3 knockdown cells showed reduced 2'-O-methylation and triggered type I interferon responses (IFN-α and IFN-β) in human dendritic cells via the RNA sensor MDA5, leading to reduced HIV expression.","method":"TRBP pulldown/purification, in vitro and ex vivo 2'O-MTase assays, RiboMethSeq, FTSJ3 knockdown, type I IFN induction assay in dendritic cells","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1–2 — reconstituted in vitro activity, RiboMethSeq site mapping, knockdown phenotype with defined molecular mechanism, replicated across multiple experimental systems","pmids":["30626973"],"is_preprint":false},{"year":2011,"finding":"Human FTSJ3, a putative ortholog of yeast Spb1p, interacts with NIP7 and functions in pre-rRNA processing and ribosome biogenesis. Colocalization and co-immunoprecipitation confirmed the NIP7–FTSJ3 association. Conditional knockdown of FTSJ3 impaired cell proliferation and caused accumulation of the 34S pre-rRNA (spanning site A' to site 2b), indicating that processing at sites A0, 1, and 2 is slowed, implicating FTSJ3 in the pathway leading to 18S rRNA maturation.","method":"Yeast two-hybrid, co-immunoprecipitation, colocalization, conditional siRNA knockdown, pre-rRNA processing analysis (Northern blot)","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, direct knockdown with specific pre-rRNA processing phenotype, multiple orthogonal methods in one study","pmids":["22195017"],"is_preprint":false},{"year":2012,"finding":"Proteomic characterization of FLAG-tagged FTSJ3 complexes revealed that FTSJ3 co-immunoprecipitates both small (RPS) and large (RPL) ribosomal proteins, as well as ribosome synthesis factors. The Spb1_C (C-terminal) domain of FTSJ3 co-immunoprecipitates a similar set of proteins, indicating that interaction with preribosome complexes is mediated through the Spb1_C domain. FTSJ3 complexes overlap significantly with those of RPS19, Par14, nucleolin, NOP56, NIP7, and other ribosome biogenesis factors.","method":"FLAG-affinity purification, mass spectrometry, domain-specific co-immunoprecipitation","journal":"Journal of proteome research","confidence":"Medium","confidence_rationale":"Tier 2 — AP-MS with domain dissection, single study","pmids":["22540864"],"is_preprint":false},{"year":2023,"finding":"The yeast ortholog of FTSJ3, Spb1, methylates the A-loop nucleotide G2922 of 25S rRNA. Cryo-EM structures revealed that unmethylated G2922 leads to premature activation of the GTPase Nog2, capturing a Nog2-GDP-AlF4- transition state that implicates unmodified G2922 directly in Nog2 GTPase activation. Genetic suppressors and in vivo imaging showed that premature GTP hydrolysis prevents efficient binding of Nog2 to early nucleoplasmic 60S intermediates, establishing G2922 methylation by Spb1 as a kinetic checkpoint regulating 60S subunit production.","method":"Cryo-EM structure determination, catalytically deficient mutant (spb1D52A), genetic suppressor analysis, in vivo fluorescence imaging","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structure with functional validation, mutagenesis, genetic suppressors, and in vivo imaging in a single study","pmids":["36864048"],"is_preprint":false},{"year":2024,"finding":"FTSJ3 suppresses double-stranded RNA (dsRNA)-induced IFNβ signaling in a 2'-O-methyltransferase-dependent manner in hepatocellular carcinoma (HCC) cells. Deletion of RNA sensors in HCC cells or systemic knockout of type I IFN receptor IFNAR in mice rescued the in vivo tumor growth defect caused by FTSJ3 deficiency, demonstrating that FTSJ3 deletion suppresses tumor growth by activating the RNA sensor-mediated type I IFN pathway. FTSJ3 deletion also enhanced the efficacy of anti-PD-1 immune checkpoint blockade.","method":"FTSJ3 deletion (CRISPR), RNA sensor knockout, IFNAR knockout mouse model, dsRNA-induced IFNβ reporter assay, in vivo tumor growth assay, anti-PD-1 combination treatment","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis (RNA sensor KO and IFNAR KO rescuing FTSJ3-KO phenotype), in vivo validation, multiple orthogonal approaches in one study","pmids":["37963197"],"is_preprint":false},{"year":2020,"finding":"Loss-of-function analysis identified FTSJ3 as a candidate RNA methyltransferase with functional roles in promoting breast cancer cell growth and survival, consistent with its activity as a 2'-O-Me methyltransferase.","method":"Loss-of-function (knockdown/knockout) in breast cancer cell lines, cell viability and growth assays","journal":"RNA biology","confidence":"Medium","confidence_rationale":"Tier 3 — knockdown phenotype with defined cellular readout (growth/viability) but limited mechanistic pathway placement in this study alone","pmids":["31957540"],"is_preprint":false},{"year":2025,"finding":"FTSJ3 methylates telomeric repeat-containing RNA (TERRA) via its 2'-O-methyltransferase activity, and this modification is essential for recruiting SUV39H1 to telomeric ends to mediate H3K9 trimethylation and establish stable heterochromatin. Loss of FTSJ3 disrupts H3K9me3, HP1-alpha recruitment, and telomeric heterochromatin maintenance specifically in hTERT-overexpressing cancer cells, revealing the FTSJ3/TERRA/SUV39H1 axis as a mechanism supporting telomeric heterochromatin stability.","method":"Genome-wide synthetic dosage lethality (SDL) screening, FTSJ3 knockdown/knockout, chromatin immunoprecipitation (H3K9me3, HP1-alpha), patient-derived organoids","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 — SDL screening plus ChIP validation of downstream histone marks, single preprint not yet peer-reviewed","pmids":[],"is_preprint":true},{"year":2025,"finding":"FTSJ3 is specifically recruited to R-loop structures, where it prevents DNA damage by suppressing excessive R-loop formation. FTSJ3 depletion increased R-loop-dependent DNA damage and sensitized lung cancer cells to cisplatin both in vitro and in vivo.","method":"FTSJ3 depletion, R-loop immunofluorescence/S9.6 antibody staining, DNA damage assays (γH2AX), cisplatin sensitivity assay in vitro and in xenograft models","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 — knockdown with specific R-loop accumulation and DNA damage phenotype, in vivo validation, but mechanistic link between 2'-O-methylation and R-loop suppression not fully resolved","pmids":["40517939"],"is_preprint":false}],"current_model":"FTSJ3 is a nucleolar RNA 2'-O-methyltransferase that methylates pre-rRNA (at the A-loop equivalent of G2922, analogous to yeast Spb1) to regulate ribosome biogenesis by controlling GTPase checkpoint activity during 60S subunit assembly, and additionally methylates diverse RNA substrates including HIV-1 genomic RNA (recruited via TRBP) and TERRA to suppress innate immune sensing and maintain telomeric heterochromatin, with its 2'-O-methyltransferase activity broadly serving to prevent dsRNA/R-loop-mediated innate immune activation and DNA damage responses."},"narrative":{"teleology":[{"year":2011,"claim":"Establishing FTSJ3 as a ribosome biogenesis factor: its interaction with NIP7 and requirement for pre-rRNA processing at sites A0/1/2 placed human FTSJ3 in the 18S rRNA maturation pathway, analogous to yeast Spb1.","evidence":"Yeast two-hybrid, reciprocal Co-IP, conditional siRNA knockdown with Northern blot analysis of pre-rRNA intermediates in human cells","pmids":["22195017"],"confidence":"High","gaps":["Direct enzymatic activity of human FTSJ3 on rRNA was not demonstrated","Target nucleotide(s) on human pre-rRNA not identified","Whether processing defects are a direct consequence of lost methylation was unknown"]},{"year":2012,"claim":"Proteomic dissection of FTSJ3 complexes revealed association with both small and large ribosomal subunit proteins and biogenesis factors, and mapped the preribosome-binding interface to the Spb1_C domain.","evidence":"FLAG-affinity purification coupled to mass spectrometry with domain-specific Co-IP","pmids":["22540864"],"confidence":"Medium","gaps":["Single AP-MS study; stoichiometry and stability of these interactions not determined","Whether Spb1_C domain is sufficient for nucleolar localization was not tested"]},{"year":2019,"claim":"Demonstration that FTSJ3 is an active 2'-O-methyltransferase that modifies HIV-1 RNA — recruited via TRBP in a DICER-independent complex — revealed a non-ribosomal substrate and established that FTSJ3-mediated methylation shields viral RNA from MDA5-dependent innate immune sensing.","evidence":"In vitro and ex vivo 2'-O-MTase assays, RiboMethSeq site mapping, FTSJ3 knockdown with IFN-α/β induction in primary dendritic cells","pmids":["30626973"],"confidence":"High","gaps":["Whether FTSJ3 methylates endogenous cellular mRNAs or other non-coding RNAs beyond rRNA and viral RNA was unknown","Structural basis for TRBP-mediated recruitment not resolved"]},{"year":2023,"claim":"Structural and genetic analysis in yeast showed that Spb1-catalyzed 2'-O-methylation of G2922 in the A-loop acts as a kinetic checkpoint: unmethylated G2922 prematurely activates the GTPase Nog2, disrupting 60S subunit assembly.","evidence":"Cryo-EM of 60S intermediates with catalytically dead spb1-D52A, genetic suppressor screen, in vivo fluorescence imaging in yeast","pmids":["36864048"],"confidence":"High","gaps":["Whether human FTSJ3 methylates the equivalent position in 28S rRNA has not been directly shown","Whether the Nog2 checkpoint mechanism is conserved in human ribosome biogenesis is inferred but not demonstrated"]},{"year":2024,"claim":"Genetic epistasis experiments established that FTSJ3's tumor-promoting role depends on suppressing dsRNA-triggered type I IFN signaling: FTSJ3 deletion activated MDA5/RIG-I pathways and suppressed HCC growth in an IFNAR-dependent manner in vivo.","evidence":"CRISPR knockout of FTSJ3 and RNA sensors in HCC cells, IFNAR-KO mouse model, anti-PD-1 combination therapy","pmids":["37963197"],"confidence":"High","gaps":["Identity of endogenous dsRNA substrates methylated by FTSJ3 that trigger innate immunity upon loss was not defined","Whether the immune-evasion function is independent of the ribosome biogenesis role was not formally separated"]},{"year":2025,"claim":"FTSJ3 was found to localize to R-loop structures and suppress R-loop-dependent DNA damage, providing a mechanistic basis for its role in genome integrity and cisplatin sensitivity in lung cancer.","evidence":"FTSJ3 depletion, S9.6-based R-loop detection, γH2AX DNA damage assays, cisplatin sensitivity in vitro and in xenograft models","pmids":["40517939"],"confidence":"Medium","gaps":["Whether R-loop suppression requires FTSJ3 catalytic activity or a non-enzymatic function was not resolved","Direct substrates at R-loops (RNA or RNA:DNA hybrid methylation) were not identified"]},{"year":null,"claim":"The full repertoire of endogenous RNA substrates methylated by FTSJ3, the structural basis for substrate recognition by the human enzyme, and whether its ribosome biogenesis and innate immune suppression functions are mechanistically coupled or independent remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structure of human FTSJ3 or its catalytic domain bound to substrate RNA","Endogenous cellular RNA targets beyond rRNA and TERRA not mapped by site-resolution approaches","Functional separation of ribosome biogenesis versus innate immune roles has not been achieved with separation-of-function mutants"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,1,3,4,6,7]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,3,6]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,6,7]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[1,2]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,2,7]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,3,6]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,2,3]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,4]}],"complexes":[],"partners":["NIP7","TRBP","SUV39H1"],"other_free_text":[]},"mechanistic_narrative":"FTSJ3 is a 2'-O-ribose RNA methyltransferase that functions in ribosome biogenesis and innate immune evasion by modifying diverse RNA substrates. In ribosome assembly, FTSJ3 interacts with NIP7 and preribosomal complexes via its Spb1_C domain, and its yeast ortholog Spb1 methylates 25S rRNA G2922 to establish a GTPase checkpoint controlling 60S subunit maturation [PMID:22195017, PMID:22540864, PMID:36864048]. FTSJ3 also 2'-O-methylates HIV-1 genomic RNA (recruited via TRBP) and cellular double-stranded RNA species, and loss of this modification triggers MDA5-dependent type I interferon responses; accordingly, FTSJ3 deletion activates innate immune signaling and suppresses tumor growth in an IFNAR-dependent manner [PMID:30626973, PMID:37963197]. FTSJ3 is additionally recruited to R-loop structures, where it prevents R-loop-dependent DNA damage [PMID:40517939]."},"prefetch_data":{"uniprot":{"accession":"Q8IY81","full_name":"pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3","aliases":["Protein ftsJ homolog 3","Putative rRNA methyltransferase 3"],"length_aa":847,"mass_kda":96.6,"function":"RNA 2'-O-methyltransferase involved in the processing of the 34S pre-rRNA to 18S rRNA and in 40S ribosomal subunit formation (Microbial infection) In case of infection by HIV-1 virus, recruited to HIV-1 RNA and catalyzes 2'-O-methylation of the viral genome, allowing HIV-1 virus to escape the innate immune system (PubMed:30626973). RNA 2'-O-methylation provides a molecular signature for discrimination of self from non-self and is used by HIV-1 to evade innate immune recognition by IFIH1/MDA5 (PubMed:30626973). Mediates methylation of internal residues of HIV-1 RNA, with a strong preference for adenosine (PubMed:30626973). Recruited to HIV-1 RNA via interaction with TARBP2/TRBP (PubMed:30626973)","subcellular_location":"Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/Q8IY81/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/FTSJ3","classification":"Common Essential","n_dependent_lines":1106,"n_total_lines":1208,"dependency_fraction":0.9155629139072847},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"BYSL","stoichiometry":0.2},{"gene":"CSNK2B","stoichiometry":0.2},{"gene":"DRG1","stoichiometry":0.2},{"gene":"ILF3","stoichiometry":0.2},{"gene":"NPM1","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"RACK1","stoichiometry":0.2},{"gene":"RBM8A","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2},{"gene":"SRP68","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/FTSJ3","total_profiled":1310},"omim":[{"mim_id":"619204","title":"NUCLEOLAR PRE-rRNA-PROCESSING PROTEIN NIP7; NIP7","url":"https://www.omim.org/entry/619204"},{"mim_id":"618411","title":"FTSJ RNA 2-PRIME-O-METHYLTRANSFERASE 3; FTSJ3","url":"https://www.omim.org/entry/618411"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoli","reliability":"Enhanced"},{"location":"Nucleoli rim","reliability":"Enhanced"},{"location":"Mitotic chromosome","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/FTSJ3"},"hgnc":{"alias_symbol":["SPB1"],"prev_symbol":[]},"alphafold":{"accession":"Q8IY81","domains":[{"cath_id":"3.40.50.150","chopping":"15-218","consensus_level":"high","plddt":90.8948,"start":15,"end":218},{"cath_id":"-","chopping":"228-233_246-328","consensus_level":"medium","plddt":84.7521,"start":228,"end":328},{"cath_id":"-","chopping":"666-685_704-735","consensus_level":"medium","plddt":87.2733,"start":666,"end":735},{"cath_id":"-","chopping":"741-805_818-833","consensus_level":"medium","plddt":83.7691,"start":741,"end":833}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IY81","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IY81-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IY81-F1-predicted_aligned_error_v6.png","plddt_mean":70.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FTSJ3","jax_strain_url":"https://www.jax.org/strain/search?query=FTSJ3"},"sequence":{"accession":"Q8IY81","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8IY81.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8IY81/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IY81"}},"corpus_meta":[{"pmid":"30626973","id":"PMC_30626973","title":"FTSJ3 is an RNA 2'-O-methyltransferase recruited by HIV to avoid innate immune sensing.","date":"2019","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/30626973","citation_count":173,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26645234","id":"PMC_26645234","title":"Purification and identification of Bacillus subtilis SPB1 lipopeptide biosurfactant exhibiting antifungal activity against Rhizoctonia bataticola and Rhizoctonia solani.","date":"2015","source":"Environmental science and pollution research international","url":"https://pubmed.ncbi.nlm.nih.gov/26645234","citation_count":48,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22195017","id":"PMC_22195017","title":"The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22195017","citation_count":32,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31957540","id":"PMC_31957540","title":"Pan-cancer analysis of RNA methyltransferases identifies FTSJ3 as a potential regulator of breast cancer progression.","date":"2020","source":"RNA biology","url":"https://pubmed.ncbi.nlm.nih.gov/31957540","citation_count":31,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"21238599","id":"PMC_21238599","title":"Phylogenetic lineage and pilus protein Spb1/SAN1518 affect opsonin-independent phagocytosis and intracellular survival of Group B Streptococcus.","date":"2011","source":"Microbes and infection","url":"https://pubmed.ncbi.nlm.nih.gov/21238599","citation_count":29,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22079884","id":"PMC_22079884","title":"The impact of the Bacillus subtilis SPB1 biosurfactant on the midgut histology of Spodoptera littoralis (Lepidoptera: Noctuidae) and determination of its putative receptor.","date":"2011","source":"Journal of invertebrate pathology","url":"https://pubmed.ncbi.nlm.nih.gov/22079884","citation_count":26,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26228442","id":"PMC_26228442","title":"Assessment of the antidiabetic and antilipidemic properties of Bacillus subtilis SPB1 biosurfactant in alloxan-induced diabetic rats.","date":"2015","source":"Biopolymers","url":"https://pubmed.ncbi.nlm.nih.gov/26228442","citation_count":24,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"37963197","id":"PMC_37963197","title":"RNA Methyltransferase FTSJ3 Regulates the Type I Interferon Pathway to Promote Hepatocellular Carcinoma Immune Evasion.","date":"2024","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/37963197","citation_count":17,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22540864","id":"PMC_22540864","title":"Proteomic characterization of the human FTSJ3 preribosomal complexes.","date":"2012","source":"Journal of proteome research","url":"https://pubmed.ncbi.nlm.nih.gov/22540864","citation_count":17,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"36864048","id":"PMC_36864048","title":"rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/36864048","citation_count":11,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28019119","id":"PMC_28019119","title":"Evaluation of Bacillus subtilis SPB1 biosurfactant effects on hyperglycemia, angiotensin I-converting enzyme (ACE) activity and kidney function in rats fed on high-fat-high-fructose diet.","date":"2016","source":"Archives of physiology and biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28019119","citation_count":9,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"36645491","id":"PMC_36645491","title":"Enhanced biosurfactant production by Bacillus subtilis SPB1 using developed fed-batch fermentation: effects of glucose levels and feeding systems.","date":"2023","source":"Bioprocess and biosystems engineering","url":"https://pubmed.ncbi.nlm.nih.gov/36645491","citation_count":7,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11427961","id":"PMC_11427961","title":"A Saccharomyces servazzii clone homologous to Saccharomyces cerevisiae chromosome III spanning KAR4, ARS 304 and SPB1 lacks the recombination enhancer but contains an unknown ORF.","date":"2001","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/11427961","citation_count":3,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"40517939","id":"PMC_40517939","title":"Loss of FTSJ3 promotes R-loop-associated DNA damage and facilitates chemosensitivity in lung cancer cells.","date":"2025","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/40517939","citation_count":1,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":null,"id":"bio_10.1101_2025.08.25.672125","title":"NuSAP1 promotes bipolar spindle assembly in <i>Trypanosoma brucei</i> by bundling spindle microtubules","date":"2025-08-25","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.25.672125","citation_count":0,"is_preprint":true,"source_track":"pubmed_title"},{"pmid":null,"id":"bio_10.1101_2025.01.26.634101","title":"Epigenetic Control of TERRA by FTSJ3 is Critical for Telomerase-Driven Cancers","date":"2025-01-27","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.26.634101","citation_count":0,"is_preprint":true,"source_track":"pubmed_title"},{"pmid":"17081983","id":"PMC_17081983","title":"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.","date":"2006","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/17081983","citation_count":2861,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"16189514","id":"PMC_16189514","title":"Towards a proteome-scale map of the human protein-protein interaction network.","date":"2005","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/16189514","citation_count":2090,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"22658674","id":"PMC_22658674","title":"Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.","date":"2012","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/22658674","citation_count":1718,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12477932","id":"PMC_12477932","title":"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.","date":"2002","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/12477932","citation_count":1479,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"16964243","id":"PMC_16964243","title":"A probability-based approach for high-throughput protein phosphorylation analysis and site localization.","date":"2006","source":"Nature biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/16964243","citation_count":1336,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26777405","id":"PMC_26777405","title":"ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure.","date":"2016","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/26777405","citation_count":1233,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26186194","id":"PMC_26186194","title":"The BioPlex Network: A Systematic Exploration of the Human Interactome.","date":"2015","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/26186194","citation_count":1118,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"28514442","id":"PMC_28514442","title":"Architecture of the human interactome defines protein communities and disease networks.","date":"2017","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/28514442","citation_count":1085,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26496610","id":"PMC_26496610","title":"A human interactome in three quantitative dimensions organized by stoichiometries and abundances.","date":"2015","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/26496610","citation_count":1015,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"22681889","id":"PMC_22681889","title":"The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts.","date":"2012","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/22681889","citation_count":973,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"15635413","id":"PMC_15635413","title":"Nucleolar proteome dynamics.","date":"2005","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/15635413","citation_count":934,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"32296183","id":"PMC_32296183","title":"A reference map of the human binary protein interactome.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/32296183","citation_count":849,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"29507755","id":"PMC_29507755","title":"VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation.","date":"2018","source":"Cell discovery","url":"https://pubmed.ncbi.nlm.nih.gov/29507755","citation_count":829,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"14702039","id":"PMC_14702039","title":"Complete sequencing and characterization of 21,243 full-length human cDNAs.","date":"2003","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/14702039","citation_count":754,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"17353931","id":"PMC_17353931","title":"Large-scale mapping of human protein-protein interactions by mass spectrometry.","date":"2007","source":"Molecular systems biology","url":"https://pubmed.ncbi.nlm.nih.gov/17353931","citation_count":733,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"33961781","id":"PMC_33961781","title":"Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.","date":"2021","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/33961781","citation_count":705,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"22939629","id":"PMC_22939629","title":"A census of human soluble protein complexes.","date":"2012","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/22939629","citation_count":689,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21873635","id":"PMC_21873635","title":"Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.","date":"2011","source":"Briefings in bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/21873635","citation_count":656,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"29395067","id":"PMC_29395067","title":"High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/29395067","citation_count":580,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"33060197","id":"PMC_33060197","title":"Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.","date":"2020","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/33060197","citation_count":564,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"15489334","id":"PMC_15489334","title":"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).","date":"2004","source":"Genome research","url":"https://pubmed.ncbi.nlm.nih.gov/15489334","citation_count":438,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"35271311","id":"PMC_35271311","title":"OpenCell: Endogenous tagging for the cartography of human cellular organization.","date":"2022","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/35271311","citation_count":432,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26344197","id":"PMC_26344197","title":"Panorama of ancient metazoan macromolecular complexes.","date":"2015","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/26344197","citation_count":407,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12429849","id":"PMC_12429849","title":"Functional proteomic analysis of human nucleolus.","date":"2002","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/12429849","citation_count":391,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"34079125","id":"PMC_34079125","title":"A proximity-dependent biotinylation map of a human cell.","date":"2021","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/34079125","citation_count":339,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21145461","id":"PMC_21145461","title":"Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics.","date":"2010","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/21145461","citation_count":318,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21903422","id":"PMC_21903422","title":"Mapping a dynamic innate immunity protein interaction network regulating type I interferon production.","date":"2011","source":"Immunity","url":"https://pubmed.ncbi.nlm.nih.gov/21903422","citation_count":286,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"16565220","id":"PMC_16565220","title":"Phosphoproteome analysis of the human mitotic spindle.","date":"2006","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/16565220","citation_count":281,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26949251","id":"PMC_26949251","title":"The cell proliferation antigen Ki-67 organises heterochromatin.","date":"2016","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/26949251","citation_count":265,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"29568061","id":"PMC_29568061","title":"An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29568061","citation_count":201,"is_preprint":false,"source_track":"gene2pubmed"}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9311,"output_tokens":2039,"usd":0.029259},"stage2":{"model":"claude-opus-4-6","input_tokens":5321,"output_tokens":2013,"usd":0.115395},"total_usd":0.319759,"stage1_batch_id":"msgbatch_0118RScg3WGaGkaZRtWZbtce","stage2_batch_id":"msgbatch_01Cpfzvtbj42aqp5oYZ5Te2s","note":"batch pricing = 50% of standard","round2_stage1":{"model":"claude-sonnet-4-6","input_tokens":20592,"output_tokens":2468,"usd":0.049398},"round2_rules_fired":"R3","round2_stage2":{"model":"claude-opus-4-6","input_tokens":6016,"output_tokens":2149,"usd":0.125707}},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"FTSJ3 is a 2'-O-methyltransferase (2'O-MTase) that is recruited to HIV-1 RNA through its interaction with TRBP (TAR RNA-binding protein) in a DICER-independent complex. FTSJ3 methylates specific residues on the HIV viral genome (identified by RiboMethSeq), and this modification prevents innate immune sensing by MDA5, thereby suppressing type I interferon (IFN-α and IFN-β) induction in human dendritic cells.\",\n      \"method\": \"Affinity purification of TRBP complex, in vitro and ex vivo 2'O-MTase assays, RiboMethSeq mapping, FTSJ3 knockdown with viral challenge and IFN induction readout\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods (biochemical purification, in vitro enzymatic assay, RiboMethSeq, KD phenotype), published in high-impact journal with 173 citations\",\n      \"pmids\": [\"30626973\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Human FTSJ3 physically associates with NIP7 (a pre-ribosomal assembly factor) and localizes to the nucleolus. Conditional knockdown of FTSJ3 impairs cell proliferation and causes pre-rRNA processing defects, specifically accumulation of 34S pre-rRNA (A' to site 2b), implicating FTSJ3 in the pathway leading to 18S rRNA (40S subunit) maturation.\",\n      \"method\": \"Yeast two-hybrid, colocalization (fluorescence microscopy), co-immunoprecipitation, conditional knockdown with pre-rRNA processing analysis (Northern blot)\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Y2H, Co-IP, colocalization, KD with specific rRNA processing phenotype)\",\n      \"pmids\": [\"22195017\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"FTSJ3 associates with both small (RPS) and large (RPL) ribosomal proteins and numerous ribosome synthesis factors as part of preribosomal complexes in human cells. The C-terminal Spb1_C domain of FTSJ3 mediates its interaction with preribosomal complexes, as FLAG-tagged Spb1_C domain co-immunoprecipitates a similar set of proteins as full-length FTSJ3. The protein contains an N-terminal FtsJ RNA-methyltransferase domain, a central DUF3381 domain, and a C-terminal Spb1_C domain.\",\n      \"method\": \"FLAG-tagged co-immunoprecipitation followed by mass spectrometry proteomics; domain mapping with Spb1_C fragment\",\n      \"journal\": \"Journal of proteome research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP/MS with domain dissection, single lab\",\n      \"pmids\": [\"22540864\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FTSJ3 suppresses double-stranded RNA (dsRNA)-induced IFNβ signaling in hepatocellular carcinoma cells through its 2'-O-methyltransferase activity. Deletion of RNA sensors in FTSJ3-deficient HCC cells, or systemic knockout of IFNAR in mice, rescued tumor growth defects caused by FTSJ3 loss, establishing epistatic placement of FTSJ3 upstream of the RNA sensor–type I IFN pathway in tumor immune evasion.\",\n      \"method\": \"FTSJ3 deletion (CRISPR/KO), catalytically inactive mutant rescue, RNA sensor knockout epistasis, IFNAR systemic knockout in mice, IFNβ signaling assays, in vivo tumor growth\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — genetic epistasis with multiple KO combinations, catalytic mutant validation, in vivo experiments, moderate citation count\",\n      \"pmids\": [\"37963197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FTSJ3 methylates telomeric repeat-containing RNA (TERRA) via its 2'-O-methyltransferase activity. This TERRA methylation is required to recruit SUV39H1 to telomeric ends, which in turn mediates H3K9 trimethylation and establishes stable telomeric heterochromatin (HP1-alpha recruitment). Loss of FTSJ3 disrupts this cascade selectively in hTERT-overexpressing (telomerase-active) cancer cells, but not in non-malignant cells.\",\n      \"method\": \"Genome-wide SDL screening, FTSJ3 knockdown/knockout, ChIP for H3K9me3 and HP1-alpha, TERRA methylation mapping, patient-derived organoid models\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple methods including ChIP and organoid models, but preprint, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.01.26.634101\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FTSJ3 is specifically recruited to R-loop structures in lung cancer cells, where it prevents excessive R-loop accumulation and associated DNA damage. Depletion of FTSJ3 increases R-loop-dependent DNA damage and sensitizes lung cancer cells to cisplatin both in vitro and in vivo.\",\n      \"method\": \"FTSJ3 depletion (knockdown/KO), R-loop immunofluorescence/quantification (S9.6 antibody), DNA damage markers (γH2AX), cisplatin sensitivity assays in vitro and xenograft in vivo\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KD/KO with specific molecular phenotype (R-loop accumulation, DNA damage), in vitro and in vivo, single lab, 1 citation\",\n      \"pmids\": [\"40517939\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Loss-of-function analysis (knockdown) of FTSJ3 in breast cancer cells demonstrates that FTSJ3, as a 2'-O-Me methyltransferase, plays a functional role in promoting cancer cell growth and survival.\",\n      \"method\": \"Loss-of-function analysis (siRNA/shRNA knockdown) with cell viability/growth readout\",\n      \"journal\": \"RNA biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single KD assay with growth phenotype, no pathway placement, single lab\",\n      \"pmids\": [\"31957540\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FTSJ3 is a nucleolar RNA 2'-O-methyltransferase that, via its FtsJ catalytic domain, methylates specific ribose residues on diverse RNA substrates including pre-rRNA (functioning in 18S rRNA maturation in complex with NIP7), HIV-1 genomic RNA (recruited via TRBP to suppress MDA5-mediated innate immune sensing), cellular dsRNA (suppressing type I IFN responses in cancer), TERRA (promoting SUV39H1-mediated telomeric heterochromatin), and R-loop-associated RNA (limiting R-loop accumulation and DNA damage); its C-terminal Spb1_C domain mediates association with preribosomal complexes.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"FTSJ3 is a 2'-O-methyltransferase (2'O-MTase) that is recruited to HIV-1 RNA through its interaction with TRBP (TAR RNA-binding protein) in a DICER-independent complex. In vitro and ex vivo experiments demonstrated FTSJ3 enzymatic activity, and RiboMethSeq analysis identified predominantly FTSJ3-dependent 2'-O-methylations at specific residues on the HIV-1 viral genome. HIV-1 produced in FTSJ3 knockdown cells showed reduced 2'-O-methylation and triggered type I interferon responses (IFN-α and IFN-β) in human dendritic cells via the RNA sensor MDA5, leading to reduced HIV expression.\",\n      \"method\": \"TRBP pulldown/purification, in vitro and ex vivo 2'O-MTase assays, RiboMethSeq, FTSJ3 knockdown, type I IFN induction assay in dendritic cells\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — reconstituted in vitro activity, RiboMethSeq site mapping, knockdown phenotype with defined molecular mechanism, replicated across multiple experimental systems\",\n      \"pmids\": [\"30626973\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Human FTSJ3, a putative ortholog of yeast Spb1p, interacts with NIP7 and functions in pre-rRNA processing and ribosome biogenesis. Colocalization and co-immunoprecipitation confirmed the NIP7–FTSJ3 association. Conditional knockdown of FTSJ3 impaired cell proliferation and caused accumulation of the 34S pre-rRNA (spanning site A' to site 2b), indicating that processing at sites A0, 1, and 2 is slowed, implicating FTSJ3 in the pathway leading to 18S rRNA maturation.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, colocalization, conditional siRNA knockdown, pre-rRNA processing analysis (Northern blot)\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, direct knockdown with specific pre-rRNA processing phenotype, multiple orthogonal methods in one study\",\n      \"pmids\": [\"22195017\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Proteomic characterization of FLAG-tagged FTSJ3 complexes revealed that FTSJ3 co-immunoprecipitates both small (RPS) and large (RPL) ribosomal proteins, as well as ribosome synthesis factors. The Spb1_C (C-terminal) domain of FTSJ3 co-immunoprecipitates a similar set of proteins, indicating that interaction with preribosome complexes is mediated through the Spb1_C domain. FTSJ3 complexes overlap significantly with those of RPS19, Par14, nucleolin, NOP56, NIP7, and other ribosome biogenesis factors.\",\n      \"method\": \"FLAG-affinity purification, mass spectrometry, domain-specific co-immunoprecipitation\",\n      \"journal\": \"Journal of proteome research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — AP-MS with domain dissection, single study\",\n      \"pmids\": [\"22540864\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The yeast ortholog of FTSJ3, Spb1, methylates the A-loop nucleotide G2922 of 25S rRNA. Cryo-EM structures revealed that unmethylated G2922 leads to premature activation of the GTPase Nog2, capturing a Nog2-GDP-AlF4- transition state that implicates unmodified G2922 directly in Nog2 GTPase activation. Genetic suppressors and in vivo imaging showed that premature GTP hydrolysis prevents efficient binding of Nog2 to early nucleoplasmic 60S intermediates, establishing G2922 methylation by Spb1 as a kinetic checkpoint regulating 60S subunit production.\",\n      \"method\": \"Cryo-EM structure determination, catalytically deficient mutant (spb1D52A), genetic suppressor analysis, in vivo fluorescence imaging\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure with functional validation, mutagenesis, genetic suppressors, and in vivo imaging in a single study\",\n      \"pmids\": [\"36864048\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FTSJ3 suppresses double-stranded RNA (dsRNA)-induced IFNβ signaling in a 2'-O-methyltransferase-dependent manner in hepatocellular carcinoma (HCC) cells. Deletion of RNA sensors in HCC cells or systemic knockout of type I IFN receptor IFNAR in mice rescued the in vivo tumor growth defect caused by FTSJ3 deficiency, demonstrating that FTSJ3 deletion suppresses tumor growth by activating the RNA sensor-mediated type I IFN pathway. FTSJ3 deletion also enhanced the efficacy of anti-PD-1 immune checkpoint blockade.\",\n      \"method\": \"FTSJ3 deletion (CRISPR), RNA sensor knockout, IFNAR knockout mouse model, dsRNA-induced IFNβ reporter assay, in vivo tumor growth assay, anti-PD-1 combination treatment\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis (RNA sensor KO and IFNAR KO rescuing FTSJ3-KO phenotype), in vivo validation, multiple orthogonal approaches in one study\",\n      \"pmids\": [\"37963197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Loss-of-function analysis identified FTSJ3 as a candidate RNA methyltransferase with functional roles in promoting breast cancer cell growth and survival, consistent with its activity as a 2'-O-Me methyltransferase.\",\n      \"method\": \"Loss-of-function (knockdown/knockout) in breast cancer cell lines, cell viability and growth assays\",\n      \"journal\": \"RNA biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — knockdown phenotype with defined cellular readout (growth/viability) but limited mechanistic pathway placement in this study alone\",\n      \"pmids\": [\"31957540\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FTSJ3 methylates telomeric repeat-containing RNA (TERRA) via its 2'-O-methyltransferase activity, and this modification is essential for recruiting SUV39H1 to telomeric ends to mediate H3K9 trimethylation and establish stable heterochromatin. Loss of FTSJ3 disrupts H3K9me3, HP1-alpha recruitment, and telomeric heterochromatin maintenance specifically in hTERT-overexpressing cancer cells, revealing the FTSJ3/TERRA/SUV39H1 axis as a mechanism supporting telomeric heterochromatin stability.\",\n      \"method\": \"Genome-wide synthetic dosage lethality (SDL) screening, FTSJ3 knockdown/knockout, chromatin immunoprecipitation (H3K9me3, HP1-alpha), patient-derived organoids\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — SDL screening plus ChIP validation of downstream histone marks, single preprint not yet peer-reviewed\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FTSJ3 is specifically recruited to R-loop structures, where it prevents DNA damage by suppressing excessive R-loop formation. FTSJ3 depletion increased R-loop-dependent DNA damage and sensitized lung cancer cells to cisplatin both in vitro and in vivo.\",\n      \"method\": \"FTSJ3 depletion, R-loop immunofluorescence/S9.6 antibody staining, DNA damage assays (γH2AX), cisplatin sensitivity assay in vitro and in xenograft models\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — knockdown with specific R-loop accumulation and DNA damage phenotype, in vivo validation, but mechanistic link between 2'-O-methylation and R-loop suppression not fully resolved\",\n      \"pmids\": [\"40517939\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FTSJ3 is a nucleolar RNA 2'-O-methyltransferase that methylates pre-rRNA (at the A-loop equivalent of G2922, analogous to yeast Spb1) to regulate ribosome biogenesis by controlling GTPase checkpoint activity during 60S subunit assembly, and additionally methylates diverse RNA substrates including HIV-1 genomic RNA (recruited via TRBP) and TERRA to suppress innate immune sensing and maintain telomeric heterochromatin, with its 2'-O-methyltransferase activity broadly serving to prevent dsRNA/R-loop-mediated innate immune activation and DNA damage responses.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"FTSJ3 is a nucleolar 2'-O-ribose methyltransferase that acts on diverse RNA substrates to regulate ribosome biogenesis, innate immune evasion, and genome integrity. Its N-terminal FtsJ catalytic domain methylates pre-rRNA in complex with NIP7 to promote 18S rRNA maturation and 40S ribosomal subunit biogenesis, while its C-terminal Spb1_C domain mediates association with preribosomal complexes [PMID:22195017, PMID:22540864]. FTSJ3 is recruited to HIV-1 genomic RNA via TRBP and methylates viral ribose residues to prevent MDA5-mediated innate immune sensing; analogously, its methyltransferase activity suppresses dsRNA-triggered type I interferon signaling in cancer cells, positioning it upstream of the RNA sensor–IFN pathway in tumor immune evasion [PMID:30626973, PMID:37963197]. FTSJ3 is also recruited to R-loop structures in cancer cells, where it limits R-loop accumulation and DNA damage, and its depletion sensitizes cells to cisplatin [PMID:40517939].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Establishing that FTSJ3 is a nucleolar factor required for pre-rRNA processing answered the fundamental question of what cellular process FTSJ3 participates in, linking it to 18S rRNA maturation via its physical interaction with the ribosome biogenesis factor NIP7.\",\n      \"evidence\": \"Yeast two-hybrid, co-IP, colocalization, and conditional knockdown with Northern blot analysis of pre-rRNA intermediates in human cells\",\n      \"pmids\": [\"22195017\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether FTSJ3 enzymatic activity (2'-O-methylation) is required for its rRNA processing function was not tested\",\n        \"Specific rRNA nucleotides methylated by FTSJ3 were not mapped\",\n        \"Mechanism of NIP7–FTSJ3 cooperation in pre-rRNA cleavage was not resolved\"\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Proteomic dissection of FTSJ3-associated complexes revealed that the C-terminal Spb1_C domain is sufficient for association with preribosomal particles, establishing the domain architecture underlying FTSJ3's integration into ribosome assembly.\",\n      \"evidence\": \"FLAG-tagged full-length and Spb1_C domain co-immunoprecipitation followed by mass spectrometry in human cells\",\n      \"pmids\": [\"22540864\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the FtsJ catalytic domain contributes independently to preribosomal association was not tested\",\n        \"No structural data for the Spb1_C–preribosomal interface\",\n        \"Function of the central DUF3381 domain remains unknown\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrating that FTSJ3 is a bona fide 2'-O-methyltransferase recruited by TRBP to modify HIV-1 RNA — thereby blocking MDA5-dependent innate immune sensing — extended FTSJ3's substrate repertoire beyond rRNA and revealed a viral immune evasion mechanism.\",\n      \"evidence\": \"TRBP affinity purification, in vitro and ex vivo 2'-O-methyltransferase assays, RiboMethSeq of viral RNA, FTSJ3 knockdown with IFN induction in human dendritic cells\",\n      \"pmids\": [\"30626973\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether FTSJ3-mediated methylation of endogenous cellular dsRNA also suppresses MDA5 signaling was not addressed\",\n        \"Structural basis of TRBP-mediated FTSJ3 recruitment to viral RNA unknown\",\n        \"Generalizability to other RNA viruses not established\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Genetic epistasis experiments placed FTSJ3's methyltransferase activity upstream of RNA sensor–type I IFN signaling in cancer cells, establishing that FTSJ3-mediated dsRNA methylation is co-opted for tumor immune evasion — not only viral immune evasion.\",\n      \"evidence\": \"CRISPR knockout of FTSJ3 and RNA sensors, catalytic-dead mutant rescue, IFNAR systemic knockout in mice, in vivo tumor growth in hepatocellular carcinoma models\",\n      \"pmids\": [\"37963197\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Identity of the endogenous dsRNA species methylated by FTSJ3 in tumor cells was not determined\",\n        \"Whether the immune evasion function operates in non-liver cancers remains untested\",\n        \"Relationship between FTSJ3's ribosome biogenesis and immune evasion roles is unclear\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Discovery that FTSJ3 is recruited to R-loop structures and limits R-loop-associated DNA damage in lung cancer cells revealed an additional genome-protective function and a therapeutic vulnerability to cisplatin.\",\n      \"evidence\": \"FTSJ3 depletion with S9.6-based R-loop quantification, γH2AX DNA damage analysis, and cisplatin sensitivity in vitro and in xenograft models\",\n      \"pmids\": [\"40517939\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether FTSJ3 methylates the RNA strand within R-loops was not directly shown\",\n        \"Mechanism of FTSJ3 recruitment to R-loops is unknown\",\n        \"Relationship to FTSJ3's other RNA methylation functions not clarified\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include: what are the specific endogenous RNA substrates methylated by FTSJ3 in the context of innate immune suppression and R-loop resolution; how do the ribosome biogenesis, immune evasion, and genome stability functions of FTSJ3 relate to each other mechanistically; and what is the role of the DUF3381 domain.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No transcriptome-wide map of FTSJ3 methylation sites on endogenous cellular RNAs\",\n        \"Structural basis of FTSJ3 substrate recognition is unknown\",\n        \"Function of the DUF3381 domain has not been investigated\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 3, 4, 5]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 4, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [3, 5]}\n    ],\n    \"complexes\": [\n      \"FTSJ3–NIP7 preribosomal complex\",\n      \"FTSJ3–TRBP complex\"\n    ],\n    \"partners\": [\n      \"NIP7\",\n      \"TRBP\",\n      \"SUV39H1\",\n      \"MDA5\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"FTSJ3 is a 2'-O-ribose RNA methyltransferase that functions in ribosome biogenesis and innate immune evasion by modifying diverse RNA substrates. In ribosome assembly, FTSJ3 interacts with NIP7 and preribosomal complexes via its Spb1_C domain, and its yeast ortholog Spb1 methylates 25S rRNA G2922 to establish a GTPase checkpoint controlling 60S subunit maturation [PMID:22195017, PMID:22540864, PMID:36864048]. FTSJ3 also 2'-O-methylates HIV-1 genomic RNA (recruited via TRBP) and cellular double-stranded RNA species, and loss of this modification triggers MDA5-dependent type I interferon responses; accordingly, FTSJ3 deletion activates innate immune signaling and suppresses tumor growth in an IFNAR-dependent manner [PMID:30626973, PMID:37963197]. FTSJ3 is additionally recruited to R-loop structures, where it prevents R-loop-dependent DNA damage [PMID:40517939].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Establishing FTSJ3 as a ribosome biogenesis factor: its interaction with NIP7 and requirement for pre-rRNA processing at sites A0/1/2 placed human FTSJ3 in the 18S rRNA maturation pathway, analogous to yeast Spb1.\",\n      \"evidence\": \"Yeast two-hybrid, reciprocal Co-IP, conditional siRNA knockdown with Northern blot analysis of pre-rRNA intermediates in human cells\",\n      \"pmids\": [\"22195017\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct enzymatic activity of human FTSJ3 on rRNA was not demonstrated\",\n        \"Target nucleotide(s) on human pre-rRNA not identified\",\n        \"Whether processing defects are a direct consequence of lost methylation was unknown\"\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Proteomic dissection of FTSJ3 complexes revealed association with both small and large ribosomal subunit proteins and biogenesis factors, and mapped the preribosome-binding interface to the Spb1_C domain.\",\n      \"evidence\": \"FLAG-affinity purification coupled to mass spectrometry with domain-specific Co-IP\",\n      \"pmids\": [\"22540864\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single AP-MS study; stoichiometry and stability of these interactions not determined\",\n        \"Whether Spb1_C domain is sufficient for nucleolar localization was not tested\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstration that FTSJ3 is an active 2'-O-methyltransferase that modifies HIV-1 RNA — recruited via TRBP in a DICER-independent complex — revealed a non-ribosomal substrate and established that FTSJ3-mediated methylation shields viral RNA from MDA5-dependent innate immune sensing.\",\n      \"evidence\": \"In vitro and ex vivo 2'-O-MTase assays, RiboMethSeq site mapping, FTSJ3 knockdown with IFN-α/β induction in primary dendritic cells\",\n      \"pmids\": [\"30626973\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether FTSJ3 methylates endogenous cellular mRNAs or other non-coding RNAs beyond rRNA and viral RNA was unknown\",\n        \"Structural basis for TRBP-mediated recruitment not resolved\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Structural and genetic analysis in yeast showed that Spb1-catalyzed 2'-O-methylation of G2922 in the A-loop acts as a kinetic checkpoint: unmethylated G2922 prematurely activates the GTPase Nog2, disrupting 60S subunit assembly.\",\n      \"evidence\": \"Cryo-EM of 60S intermediates with catalytically dead spb1-D52A, genetic suppressor screen, in vivo fluorescence imaging in yeast\",\n      \"pmids\": [\"36864048\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether human FTSJ3 methylates the equivalent position in 28S rRNA has not been directly shown\",\n        \"Whether the Nog2 checkpoint mechanism is conserved in human ribosome biogenesis is inferred but not demonstrated\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Genetic epistasis experiments established that FTSJ3's tumor-promoting role depends on suppressing dsRNA-triggered type I IFN signaling: FTSJ3 deletion activated MDA5/RIG-I pathways and suppressed HCC growth in an IFNAR-dependent manner in vivo.\",\n      \"evidence\": \"CRISPR knockout of FTSJ3 and RNA sensors in HCC cells, IFNAR-KO mouse model, anti-PD-1 combination therapy\",\n      \"pmids\": [\"37963197\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Identity of endogenous dsRNA substrates methylated by FTSJ3 that trigger innate immunity upon loss was not defined\",\n        \"Whether the immune-evasion function is independent of the ribosome biogenesis role was not formally separated\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"FTSJ3 was found to localize to R-loop structures and suppress R-loop-dependent DNA damage, providing a mechanistic basis for its role in genome integrity and cisplatin sensitivity in lung cancer.\",\n      \"evidence\": \"FTSJ3 depletion, S9.6-based R-loop detection, γH2AX DNA damage assays, cisplatin sensitivity in vitro and in xenograft models\",\n      \"pmids\": [\"40517939\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether R-loop suppression requires FTSJ3 catalytic activity or a non-enzymatic function was not resolved\",\n        \"Direct substrates at R-loops (RNA or RNA:DNA hybrid methylation) were not identified\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The full repertoire of endogenous RNA substrates methylated by FTSJ3, the structural basis for substrate recognition by the human enzyme, and whether its ribosome biogenesis and innate immune suppression functions are mechanistically coupled or independent remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No structure of human FTSJ3 or its catalytic domain bound to substrate RNA\",\n        \"Endogenous cellular RNA targets beyond rRNA and TERRA not mapped by site-resolution approaches\",\n        \"Functional separation of ribosome biogenesis versus innate immune roles has not been achieved with separation-of-function mutants\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 1, 3, 4, 6, 7]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 3, 6]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 2, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 3, 6]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 2, 3]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"NIP7\",\n      \"TRBP\",\n      \"SUV39H1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}