{"gene":"FAM98B","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2014,"finding":"FAM98B is a component of the human tRNA splicing ligase complex (tRNA-LC), which contains RTCB (HSPC117) as the catalytic subunit. FAM98B was identified as part of this multimeric complex required for tRNA splicing and RNA ligation.","method":"Biochemical purification and identification of complex components; co-purification with RTCB","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — complex composition established biochemically, replicated across multiple subsequent studies in independent labs","pmids":["24870230"],"is_preprint":false},{"year":2014,"finding":"FAM98B co-purifies with DDX1, HSPC117 (RTCB), and hCLE (C14orf166) in both nuclear and cytoplasmic fractions, forming a complex that shuttles between nucleus and cytoplasm. Nuclear import of FAM98B requires active transcription, and silencing of hCLE downregulates nuclear and cytosolic accumulation of FAM98B.","method":"Nuclear/cytoplasmic fractionation, co-immunoprecipitation, photoactivatable GFP-hCLE live imaging, RNA silencing","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP and fractionation with live imaging, single lab, multiple orthogonal methods","pmids":["24608264"],"is_preprint":false},{"year":2019,"finding":"FAM98B associates with hCLE (C14orf166), DDX1, and HSPC117 in a cap-binding complex; all four proteins bind cap analog-containing resins. This complex modulates mRNA translation, as hCLE silencing reduces accumulation of all four proteins and decreases mRNA translation.","method":"Cap analog affinity resin pulldown, competition/elution experiments, RNA silencing, polysome analysis","journal":"Frontiers in physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cap-binding affinity pulldown plus functional translation assay, single lab, two orthogonal methods","pmids":["30833903"],"is_preprint":false},{"year":2016,"finding":"FAM98B, along with its structural homolog FAM98A, forms a novel complex with DDX1 and C14orf166 that is required for PRMT1 expression in colorectal cancer cells. Knockdown of FAM98B suppresses cellular proliferation and colony formation. Knockdown of both FAM98A and FAM98B together does not cause additional reduction compared to single knockdowns, indicating they function in the same pathway axis.","method":"Co-immunoprecipitation, shRNA knockdown, cell proliferation and colony formation assays, epistasis by double knockdown","journal":"The international journal of biochemistry & cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis by double knockdown plus functional cellular assays, single lab, multiple methods","pmids":["28040436"],"is_preprint":false},{"year":2021,"finding":"The core of the human tRNA-LC is assembled from RTCB and the C-terminal alpha-helical regions of DDX1, CGI-99, and FAM98B, all of which are required for complex integrity. CGI-99 and FAM98B associate via their N-terminal domains to form a stable subcomplex. Crystal structure of GMP-bound RTCB reveals divalent metal coordination in the active site.","method":"Biochemical analysis of inter-subunit interactions, crystal structure determination of RTCB and CGI-99 N-terminal domain, deletion mutagenesis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure determination combined with biochemical mutagenesis defining subunit interactions; multiple orthogonal methods in a single rigorous study","pmids":["34854379"],"is_preprint":false},{"year":2025,"finding":"FAM98B contains the most glycine-rich intrinsically disordered region (IDR) in the human proteome. In GGC repeat expansion disorders, polyglycine aggregates sequester and deplete FAM98B through this glycine-rich IDR, disrupting tRNA-LC function and tRNA processing. Fam98b depletion in adult mice causes progressive motor coordination deficits and hindbrain pathology.","method":"Biochemical aggregation assays, patient tissue analysis, FISH for tRNA splicing intermediates, in vivo mouse knockdown with behavioral and histological readouts","journal":"Science (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (biochemical, patient tissue, in vivo mouse model) with defined molecular mechanism linking FAM98B IDR to tRNA processing disruption","pmids":["40674500"],"is_preprint":false},{"year":2020,"finding":"FAM98B binds to the major allele of the rs11466313 variant in the 5' regulatory region of TGFB1; knockdown of FAM98B attenuates the enhanced TGFB1 promoter activity driven by the major allele, indicating FAM98B functions as a transcriptional activator of TGFB1 through this regulatory element.","method":"DNA pull-down assay, mass spectrometry identification, luciferase reporter assay, siRNA knockdown","journal":"Breast cancer research and treatment","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — DNA pulldown plus reporter assay plus knockdown, single lab, mechanistically specific but not replicated","pmids":["32757134"],"is_preprint":false},{"year":2025,"finding":"FAM98B depletion by shRNA in osteoclast precursors specifically disrupts lysosome trafficking and bone resorption in osteoclasts, with phenotypes similar to FAM98A knockdown. In Fam98a-null osteoclasts, increased Fam98b expression occurs as compensation.","method":"shRNA knockdown in osteoclast precursors, lysosomal trafficking assays, bone resorption assays, qPCR for compensatory expression","journal":"Biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — specific shRNA knockdown with cellular phenotypic readout (lysosome trafficking, bone resorption), single lab, single study","pmids":["39857276"],"is_preprint":false},{"year":2025,"finding":"Cryo-EM structure of the human tRNA-LC reveals that CGI-99, DDX1, and FAM98B form an alpha-helical bundle contacting RTCB. FAM98B and CGI-99 form an intricately co-folded heterodimer that clamps Ashwin in a pincer-like structure. FAM98A and FAM98C can substitute for FAM98B to underpin compositionally distinct RTCB-containing complexes that lack Ashwin and may have distinct cellular functions.","method":"Cryo-EM structure determination at atomic resolution, structure-based mutagenesis, interaction analysis","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1 / Moderate — atomic-resolution cryo-EM structure with structure-based mutagenesis and interaction validation; preprint but rigorous structural evidence","pmids":["bio_10.1101_2025.08.01.668197"],"is_preprint":true},{"year":2025,"finding":"Three forms of the tRNA-LC exist depending on which FAM98 paralog (FAM98A, FAM98B, or FAM98C) is incorporated. Ashwin interacts exclusively with the FAM98B-containing complex, enabling nuclear localization of this specific tRNA-LC form for tRNA biogenesis. The FAM98B-tRNA-LC is thus the nuclear form required for pre-tRNA splicing, while FAM98A/C-containing complexes remain cytoplasmic for XBP1 mRNA splicing during UPR.","method":"Co-immunoprecipitation, NLS disruption mutagenesis, subcellular fractionation, tRNA splicing intermediate accumulation assay, rescue experiments with RTCB-NLS fusion","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, NLS mutagenesis, functional tRNA splicing assays, and rescue experiments; multiple orthogonal methods defining FAM98B-specific nuclear complex","pmids":["bio_10.1101_2025.08.01.668163"],"is_preprint":true},{"year":2025,"finding":"Cryo-EM structure of the five-subunit Danio rerio tRNA ligase complex shows that the DDX1 helicase module is mobile and can modulate the activity of RTCB. Chemical crosslinking confirmed specific RTCB residue involvement in RNA binding.","method":"Cryo-EM structure determination, thiol-based chemical crosslinking","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — cryo-EM structure with chemical crosslinking in single study; FAM98B is a structural component of the complex but specific FAM98B function is not individually dissected","pmids":["40220997"],"is_preprint":false}],"current_model":"FAM98B is a core structural subunit of the human tRNA ligase complex (tRNA-LC), where it forms a co-folded heterodimer with CGI-99 via N-terminal domains and contributes C-terminal alpha-helical regions to an assembly that contacts the catalytic subunit RTCB; the FAM98B-containing tRNA-LC is specifically recruited to the nucleus by Ashwin for pre-tRNA splicing, while its glycine-rich intrinsically disordered region renders it susceptible to sequestration by polyglycine aggregates in GGC repeat disorders, disrupting tRNA processing; FAM98B also participates in a cap-binding mRNA transport complex with DDX1, HSPC117, and hCLE, and has roles in osteoclast lysosome trafficking and TGFB1 transcriptional regulation."},"narrative":{"mechanistic_narrative":"FAM98B is a core structural subunit of the human tRNA ligase complex (tRNA-LC), an RTCB (HSPC117)-based assembly required for tRNA splicing and RNA ligation [PMID:24870230]. Within this complex, FAM98B and CGI-99 associate through their N-terminal domains to form a stable co-folded heterodimer, and their C-terminal alpha-helical regions, together with DDX1, build the helical bundle that contacts the catalytic subunit RTCB and is required for complex integrity [PMID:34854379, PMID:bio_10.1101_2025.08.01.668197]. The FAM98B-CGI-99 heterodimer clamps the adaptor Ashwin in a pincer-like arrangement, and Ashwin engagement is specific to the FAM98B-containing complex, directing it to the nucleus for pre-tRNA splicing; the paralogous FAM98A- and FAM98C-containing complexes lack Ashwin and remain cytoplasmic, defining FAM98B as the determinant of the nuclear tRNA-biogenesis form [PMID:bio_10.1101_2025.08.01.668197, PMID:bio_10.1101_2025.08.01.668163]. FAM98B carries an exceptionally glycine-rich intrinsically disordered region that, in GGC repeat expansion disorders, is sequestered and depleted by polyglycine aggregates, disrupting tRNA-LC function and tRNA processing; Fam98b depletion in mice produces progressive motor coordination deficits and hindbrain pathology [PMID:40674500]. Beyond the tRNA-LC, FAM98B co-purifies with DDX1, RTCB, and hCLE (C14orf166) in a cap-binding complex that shuttles between nucleus and cytoplasm and modulates mRNA translation [PMID:24608264, PMID:30833903], supports PRMT1 expression and proliferation in colorectal cancer cells redundantly with FAM98A [PMID:28040436], acts as a transcriptional activator at a TGFB1 regulatory variant [PMID:32757134], and is required for lysosome trafficking and bone resorption in osteoclasts [PMID:39857276].","teleology":[{"year":2014,"claim":"Established FAM98B as a constituent of the RTCB-based tRNA splicing ligase complex, placing it in the machinery for tRNA splicing and RNA ligation.","evidence":"Biochemical purification and co-purification with RTCB","pmids":["24870230"],"confidence":"High","gaps":["Did not define FAM98B's specific role within the complex","No structural arrangement of subunits resolved"]},{"year":2014,"claim":"Showed FAM98B participates in a transcription-dependent, nucleocytoplasmic-shuttling complex with DDX1, RTCB, and hCLE, extending its associations beyond tRNA ligation.","evidence":"Nuclear/cytoplasmic fractionation, reciprocal co-IP, photoactivatable GFP live imaging, and RNA silencing","pmids":["24608264"],"confidence":"Medium","gaps":["Relationship between this shuttling complex and the tRNA-LC not resolved","Mechanism coupling FAM98B nuclear import to active transcription unknown"]},{"year":2016,"claim":"Linked the FAM98B/DDX1/C14orf166 complex to PRMT1 expression and cancer cell proliferation, and showed FAM98A and FAM98B act in the same pathway axis.","evidence":"Co-IP, shRNA knockdown, proliferation/colony assays, and double-knockdown epistasis in colorectal cancer cells","pmids":["28040436"],"confidence":"Medium","gaps":["Molecular mechanism connecting the complex to PRMT1 expression unknown","Direct vs indirect regulation not distinguished"]},{"year":2019,"claim":"Demonstrated the FAM98B-containing complex binds the mRNA cap and modulates translation, assigning a post-transcriptional gene-expression role.","evidence":"Cap-analog affinity pulldown, competition/elution, RNA silencing, and polysome analysis","pmids":["30833903"],"confidence":"Medium","gaps":["Whether FAM98B contacts the cap directly or via partners unresolved","Transcript selectivity of translational modulation not defined"]},{"year":2020,"claim":"Identified FAM98B as a transcriptional activator acting at a TGFB1 regulatory variant, a chromatin-associated role distinct from RNA ligation.","evidence":"DNA pull-down with mass spectrometry, luciferase reporter assay, and siRNA knockdown","pmids":["32757134"],"confidence":"Medium","gaps":["Not independently replicated","Mechanism of sequence-specific DNA engagement and co-activator recruitment unknown"]},{"year":2021,"claim":"Resolved the architecture of the human tRNA-LC core, showing FAM98B and CGI-99 form an N-terminal heterodimer and contribute C-terminal helices required for complex integrity around RTCB.","evidence":"Crystal structure of RTCB and the CGI-99 N-terminal domain combined with deletion mutagenesis of inter-subunit interactions","pmids":["34854379"],"confidence":"High","gaps":["Full-length FAM98B structure not determined","How the assembly is targeted to substrates not addressed"]},{"year":2025,"claim":"Defined the disease relevance of FAM98B's glycine-rich IDR, showing polyglycine aggregates sequester FAM98B to disrupt tRNA processing and cause neurological phenotypes in vivo.","evidence":"Biochemical aggregation assays, patient tissue analysis, FISH for tRNA splicing intermediates, and in vivo mouse knockdown with behavioral/histological readouts","pmids":["40674500"],"confidence":"High","gaps":["Whether IDR sequestration is the sole disease driver in GGC disorders not established","Cell-type basis of hindbrain vulnerability not defined"]},{"year":2025,"claim":"Showed FAM98B determines the nuclear, Ashwin-bound form of the tRNA-LC dedicated to pre-tRNA splicing, distinguishing it functionally from FAM98A/C-containing cytoplasmic complexes.","evidence":"Cryo-EM structure, structure-based and NLS-disruption mutagenesis, fractionation, tRNA splicing intermediate assays, and RTCB-NLS rescue (preprints)","pmids":["bio_10.1101_2025.08.01.668197","bio_10.1101_2025.08.01.668163"],"confidence":"High","gaps":["Determinants of paralog selection between FAM98A/B/C not defined","Peer-reviewed confirmation of the preprint findings pending"]},{"year":2025,"claim":"Extended FAM98B's cellular roles to osteoclast biology, showing it is required for lysosome trafficking and bone resorption with FAM98A redundancy.","evidence":"shRNA knockdown in osteoclast precursors, lysosomal trafficking and bone resorption assays, and qPCR for compensatory expression","pmids":["39857276"],"confidence":"Medium","gaps":["Mechanism linking FAM98B to lysosome trafficking unknown","Whether this role depends on tRNA-LC activity not tested"]},{"year":2025,"claim":"Cross-species structure of the five-subunit tRNA-LC revealed a mobile DDX1 helicase module that can modulate RTCB activity, framing the regulatory dynamics of the FAM98B-containing assembly.","evidence":"Cryo-EM of Danio rerio tRNA-LC and thiol-based chemical crosslinking","pmids":["40220997"],"confidence":"Medium","gaps":["Specific contribution of FAM98B to catalytic regulation not individually dissected","Functional consequence of DDX1 mobility on substrate handling not quantified"]},{"year":null,"claim":"How FAM98B's distinct activities — nuclear tRNA splicing, cap-binding translation, DNA-associated transcriptional activation, and osteoclast lysosome trafficking — are mechanistically coordinated within or independent of the RTCB complex remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No mechanism unifying the chromatin/transcriptional role with the RNA-processing complex","Whether non-tRNA-LC functions require complex assembly is untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,4,8]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[6]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,9]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,9]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,4,9]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[6]}],"complexes":["tRNA ligase complex (tRNA-LC)","cap-binding mRNA transport/translation complex"],"partners":["RTCB","CGI-99","DDX1","C14ORF166","ASHWIN","FAM98A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q52LJ0","full_name":"tRNA-splicing ligase complex subunit FAM98B","aliases":[],"length_aa":433,"mass_kda":45.5,"function":"Accessory subunit of the tRNA-splicing ligase complex that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as an RNA ligase with broad substrate specificity and may function toward other RNAs (PubMed:21311021, PubMed:24870230). Could regulate the expression of PRMT1, a protein arginine N-methyltransferase (PubMed:28040436)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q52LJ0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FAM98B","classification":"Not Classified","n_dependent_lines":452,"n_total_lines":1208,"dependency_fraction":0.3741721854304636},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"RTCB","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/FAM98B","total_profiled":1310},"omim":[{"mim_id":"616142","title":"FAMILY WITH SEQUENCE SIMILARITY 98, MEMBER B; FAM98B","url":"https://www.omim.org/entry/616142"},{"mim_id":"615891","title":"ZINC FINGER- AND BTB DOMAIN-CONTAINING PROTEIN 8, OPPOSITE STRAND; ZBTB8OS","url":"https://www.omim.org/entry/615891"},{"mim_id":"613901","title":"RNA 2-PRIME,3-PRIME CYCLIC PHOSPHATE AND 5-PRIME-OH LIGASE; RTCB","url":"https://www.omim.org/entry/613901"},{"mim_id":"610858","title":"RNA TRANSCRIPTION, TRANSLATION, AND TRANSPORT FACTOR; RTRAF","url":"https://www.omim.org/entry/610858"},{"mim_id":"601257","title":"DEAD-BOX HELICASE 1; DDX1","url":"https://www.omim.org/entry/601257"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Vesicles","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/FAM98B"},"hgnc":{"alias_symbol":["FLJ38426"],"prev_symbol":[]},"alphafold":{"accession":"Q52LJ0","domains":[{"cath_id":"-","chopping":"141-185","consensus_level":"high","plddt":85.6587,"start":141,"end":185},{"cath_id":"1.10.418","chopping":"13-138","consensus_level":"high","plddt":87.8917,"start":13,"end":138},{"cath_id":"1.10.287","chopping":"202-276","consensus_level":"high","plddt":93.5569,"start":202,"end":276}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q52LJ0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q52LJ0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q52LJ0-F1-predicted_aligned_error_v6.png","plddt_mean":72.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FAM98B","jax_strain_url":"https://www.jax.org/strain/search?query=FAM98B"},"sequence":{"accession":"Q52LJ0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q52LJ0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q52LJ0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q52LJ0"}},"corpus_meta":[{"pmid":"33126901","id":"PMC_33126901","title":"Long non-coding RNAs (lncRNAs) in spermatogenesis and male infertility.","date":"2020","source":"Reproductive biology and endocrinology : RB&E","url":"https://pubmed.ncbi.nlm.nih.gov/33126901","citation_count":117,"is_preprint":false},{"pmid":"24870230","id":"PMC_24870230","title":"Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors.","date":"2014","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/24870230","citation_count":101,"is_preprint":false},{"pmid":"24608264","id":"PMC_24608264","title":"hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24608264","citation_count":52,"is_preprint":false},{"pmid":"28040436","id":"PMC_28040436","title":"FAM98A associates with DDX1-C14orf166-FAM98B in a novel complex involved in colorectal cancer progression.","date":"2016","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/28040436","citation_count":33,"is_preprint":false},{"pmid":"34854379","id":"PMC_34854379","title":"Molecular architecture of the human tRNA ligase complex.","date":"2021","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/34854379","citation_count":33,"is_preprint":false},{"pmid":"30833903","id":"PMC_30833903","title":"hCLE/RTRAF-HSPC117-DDX1-FAM98B: A New Cap-Binding Complex That Activates mRNA Translation.","date":"2019","source":"Frontiers in physiology","url":"https://pubmed.ncbi.nlm.nih.gov/30833903","citation_count":20,"is_preprint":false},{"pmid":"37919785","id":"PMC_37919785","title":"LncRNA-Gm9866 promotes liver fibrosis by activating TGFβ/Smad signaling via targeting Fam98b.","date":"2023","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37919785","citation_count":9,"is_preprint":false},{"pmid":"36873459","id":"PMC_36873459","title":"Joint Secondary Transcriptomic Analysis of Non-Hodgkin's B-Cell Lymphomas Predicts Reliance on Pathways Associated with the Extracellular Matrix and Robust Diagnostic Biomarkers.","date":"2022","source":"Journal of bioinformatics and systems biology : Open access","url":"https://pubmed.ncbi.nlm.nih.gov/36873459","citation_count":9,"is_preprint":false},{"pmid":"40674500","id":"PMC_40674500","title":"Polyglycine-mediated aggregation of FAM98B disrupts tRNA processing in GGC repeat disorders.","date":"2025","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/40674500","citation_count":8,"is_preprint":false},{"pmid":"33786620","id":"PMC_33786620","title":"Role of C14orf166 in viral infection and RNA metabolism and its relationship with cancer (Review).","date":"2021","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/33786620","citation_count":3,"is_preprint":false},{"pmid":"32757134","id":"PMC_32757134","title":"Effect of functional variant rs11466313 on breast cancer susceptibility and TGFB1 promoter activity.","date":"2020","source":"Breast cancer research and treatment","url":"https://pubmed.ncbi.nlm.nih.gov/32757134","citation_count":3,"is_preprint":false},{"pmid":"40220997","id":"PMC_40220997","title":"Structural and biochemical characterization of the 3'-5' tRNA splicing ligases.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40220997","citation_count":1,"is_preprint":false},{"pmid":"39857276","id":"PMC_39857276","title":"FAM98 Family Proteins Play Distinct Roles in Osteoclastogenesis and Bone Resorption.","date":"2025","source":"Biology","url":"https://pubmed.ncbi.nlm.nih.gov/39857276","citation_count":1,"is_preprint":false},{"pmid":"18067082","id":"PMC_18067082","title":"[Gene screening in five Chinese families with hereditary spastic paraplegia with thin corpus callosum].","date":"2007","source":"Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18067082","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.01.668197","title":"Structural framework for the assembly of the human tRNA ligase complex","date":"2025-08-02","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.01.668197","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.08.01.668163","title":"Ashwin and FAM98 paralogs define nuclear and cytoplasmic RNA ligase complexes for tRNA biogenesis and the unfolded protein response","date":"2025-08-02","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.01.668163","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9851,"output_tokens":2818,"usd":0.035911,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10158,"output_tokens":3563,"usd":0.069932,"stage2_stop_reason":"end_turn"},"total_usd":0.105843,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"FAM98B is a component of the human tRNA splicing ligase complex (tRNA-LC), which contains RTCB (HSPC117) as the catalytic subunit. FAM98B was identified as part of this multimeric complex required for tRNA splicing and RNA ligation.\",\n      \"method\": \"Biochemical purification and identification of complex components; co-purification with RTCB\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — complex composition established biochemically, replicated across multiple subsequent studies in independent labs\",\n      \"pmids\": [\"24870230\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"FAM98B co-purifies with DDX1, HSPC117 (RTCB), and hCLE (C14orf166) in both nuclear and cytoplasmic fractions, forming a complex that shuttles between nucleus and cytoplasm. Nuclear import of FAM98B requires active transcription, and silencing of hCLE downregulates nuclear and cytosolic accumulation of FAM98B.\",\n      \"method\": \"Nuclear/cytoplasmic fractionation, co-immunoprecipitation, photoactivatable GFP-hCLE live imaging, RNA silencing\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP and fractionation with live imaging, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"24608264\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FAM98B associates with hCLE (C14orf166), DDX1, and HSPC117 in a cap-binding complex; all four proteins bind cap analog-containing resins. This complex modulates mRNA translation, as hCLE silencing reduces accumulation of all four proteins and decreases mRNA translation.\",\n      \"method\": \"Cap analog affinity resin pulldown, competition/elution experiments, RNA silencing, polysome analysis\",\n      \"journal\": \"Frontiers in physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cap-binding affinity pulldown plus functional translation assay, single lab, two orthogonal methods\",\n      \"pmids\": [\"30833903\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"FAM98B, along with its structural homolog FAM98A, forms a novel complex with DDX1 and C14orf166 that is required for PRMT1 expression in colorectal cancer cells. Knockdown of FAM98B suppresses cellular proliferation and colony formation. Knockdown of both FAM98A and FAM98B together does not cause additional reduction compared to single knockdowns, indicating they function in the same pathway axis.\",\n      \"method\": \"Co-immunoprecipitation, shRNA knockdown, cell proliferation and colony formation assays, epistasis by double knockdown\",\n      \"journal\": \"The international journal of biochemistry & cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis by double knockdown plus functional cellular assays, single lab, multiple methods\",\n      \"pmids\": [\"28040436\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The core of the human tRNA-LC is assembled from RTCB and the C-terminal alpha-helical regions of DDX1, CGI-99, and FAM98B, all of which are required for complex integrity. CGI-99 and FAM98B associate via their N-terminal domains to form a stable subcomplex. Crystal structure of GMP-bound RTCB reveals divalent metal coordination in the active site.\",\n      \"method\": \"Biochemical analysis of inter-subunit interactions, crystal structure determination of RTCB and CGI-99 N-terminal domain, deletion mutagenesis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure determination combined with biochemical mutagenesis defining subunit interactions; multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"34854379\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FAM98B contains the most glycine-rich intrinsically disordered region (IDR) in the human proteome. In GGC repeat expansion disorders, polyglycine aggregates sequester and deplete FAM98B through this glycine-rich IDR, disrupting tRNA-LC function and tRNA processing. Fam98b depletion in adult mice causes progressive motor coordination deficits and hindbrain pathology.\",\n      \"method\": \"Biochemical aggregation assays, patient tissue analysis, FISH for tRNA splicing intermediates, in vivo mouse knockdown with behavioral and histological readouts\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (biochemical, patient tissue, in vivo mouse model) with defined molecular mechanism linking FAM98B IDR to tRNA processing disruption\",\n      \"pmids\": [\"40674500\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"FAM98B binds to the major allele of the rs11466313 variant in the 5' regulatory region of TGFB1; knockdown of FAM98B attenuates the enhanced TGFB1 promoter activity driven by the major allele, indicating FAM98B functions as a transcriptional activator of TGFB1 through this regulatory element.\",\n      \"method\": \"DNA pull-down assay, mass spectrometry identification, luciferase reporter assay, siRNA knockdown\",\n      \"journal\": \"Breast cancer research and treatment\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — DNA pulldown plus reporter assay plus knockdown, single lab, mechanistically specific but not replicated\",\n      \"pmids\": [\"32757134\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FAM98B depletion by shRNA in osteoclast precursors specifically disrupts lysosome trafficking and bone resorption in osteoclasts, with phenotypes similar to FAM98A knockdown. In Fam98a-null osteoclasts, increased Fam98b expression occurs as compensation.\",\n      \"method\": \"shRNA knockdown in osteoclast precursors, lysosomal trafficking assays, bone resorption assays, qPCR for compensatory expression\",\n      \"journal\": \"Biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — specific shRNA knockdown with cellular phenotypic readout (lysosome trafficking, bone resorption), single lab, single study\",\n      \"pmids\": [\"39857276\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structure of the human tRNA-LC reveals that CGI-99, DDX1, and FAM98B form an alpha-helical bundle contacting RTCB. FAM98B and CGI-99 form an intricately co-folded heterodimer that clamps Ashwin in a pincer-like structure. FAM98A and FAM98C can substitute for FAM98B to underpin compositionally distinct RTCB-containing complexes that lack Ashwin and may have distinct cellular functions.\",\n      \"method\": \"Cryo-EM structure determination at atomic resolution, structure-based mutagenesis, interaction analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — atomic-resolution cryo-EM structure with structure-based mutagenesis and interaction validation; preprint but rigorous structural evidence\",\n      \"pmids\": [\"bio_10.1101_2025.08.01.668197\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Three forms of the tRNA-LC exist depending on which FAM98 paralog (FAM98A, FAM98B, or FAM98C) is incorporated. Ashwin interacts exclusively with the FAM98B-containing complex, enabling nuclear localization of this specific tRNA-LC form for tRNA biogenesis. The FAM98B-tRNA-LC is thus the nuclear form required for pre-tRNA splicing, while FAM98A/C-containing complexes remain cytoplasmic for XBP1 mRNA splicing during UPR.\",\n      \"method\": \"Co-immunoprecipitation, NLS disruption mutagenesis, subcellular fractionation, tRNA splicing intermediate accumulation assay, rescue experiments with RTCB-NLS fusion\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, NLS mutagenesis, functional tRNA splicing assays, and rescue experiments; multiple orthogonal methods defining FAM98B-specific nuclear complex\",\n      \"pmids\": [\"bio_10.1101_2025.08.01.668163\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structure of the five-subunit Danio rerio tRNA ligase complex shows that the DDX1 helicase module is mobile and can modulate the activity of RTCB. Chemical crosslinking confirmed specific RTCB residue involvement in RNA binding.\",\n      \"method\": \"Cryo-EM structure determination, thiol-based chemical crosslinking\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — cryo-EM structure with chemical crosslinking in single study; FAM98B is a structural component of the complex but specific FAM98B function is not individually dissected\",\n      \"pmids\": [\"40220997\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FAM98B is a core structural subunit of the human tRNA ligase complex (tRNA-LC), where it forms a co-folded heterodimer with CGI-99 via N-terminal domains and contributes C-terminal alpha-helical regions to an assembly that contacts the catalytic subunit RTCB; the FAM98B-containing tRNA-LC is specifically recruited to the nucleus by Ashwin for pre-tRNA splicing, while its glycine-rich intrinsically disordered region renders it susceptible to sequestration by polyglycine aggregates in GGC repeat disorders, disrupting tRNA processing; FAM98B also participates in a cap-binding mRNA transport complex with DDX1, HSPC117, and hCLE, and has roles in osteoclast lysosome trafficking and TGFB1 transcriptional regulation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FAM98B is a core structural subunit of the human tRNA ligase complex (tRNA-LC), an RTCB (HSPC117)-based assembly required for tRNA splicing and RNA ligation [#0]. Within this complex, FAM98B and CGI-99 associate through their N-terminal domains to form a stable co-folded heterodimer, and their C-terminal alpha-helical regions, together with DDX1, build the helical bundle that contacts the catalytic subunit RTCB and is required for complex integrity [#4, #8]. The FAM98B-CGI-99 heterodimer clamps the adaptor Ashwin in a pincer-like arrangement, and Ashwin engagement is specific to the FAM98B-containing complex, directing it to the nucleus for pre-tRNA splicing; the paralogous FAM98A- and FAM98C-containing complexes lack Ashwin and remain cytoplasmic, defining FAM98B as the determinant of the nuclear tRNA-biogenesis form [#8, #9]. FAM98B carries an exceptionally glycine-rich intrinsically disordered region that, in GGC repeat expansion disorders, is sequestered and depleted by polyglycine aggregates, disrupting tRNA-LC function and tRNA processing; Fam98b depletion in mice produces progressive motor coordination deficits and hindbrain pathology [#5]. Beyond the tRNA-LC, FAM98B co-purifies with DDX1, RTCB, and hCLE (C14orf166) in a cap-binding complex that shuttles between nucleus and cytoplasm and modulates mRNA translation [#1, #2], supports PRMT1 expression and proliferation in colorectal cancer cells redundantly with FAM98A [#3], acts as a transcriptional activator at a TGFB1 regulatory variant [#6], and is required for lysosome trafficking and bone resorption in osteoclasts [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Established FAM98B as a constituent of the RTCB-based tRNA splicing ligase complex, placing it in the machinery for tRNA splicing and RNA ligation.\",\n      \"evidence\": \"Biochemical purification and co-purification with RTCB\",\n      \"pmids\": [\"24870230\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define FAM98B's specific role within the complex\", \"No structural arrangement of subunits resolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showed FAM98B participates in a transcription-dependent, nucleocytoplasmic-shuttling complex with DDX1, RTCB, and hCLE, extending its associations beyond tRNA ligation.\",\n      \"evidence\": \"Nuclear/cytoplasmic fractionation, reciprocal co-IP, photoactivatable GFP live imaging, and RNA silencing\",\n      \"pmids\": [\"24608264\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relationship between this shuttling complex and the tRNA-LC not resolved\", \"Mechanism coupling FAM98B nuclear import to active transcription unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Linked the FAM98B/DDX1/C14orf166 complex to PRMT1 expression and cancer cell proliferation, and showed FAM98A and FAM98B act in the same pathway axis.\",\n      \"evidence\": \"Co-IP, shRNA knockdown, proliferation/colony assays, and double-knockdown epistasis in colorectal cancer cells\",\n      \"pmids\": [\"28040436\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism connecting the complex to PRMT1 expression unknown\", \"Direct vs indirect regulation not distinguished\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrated the FAM98B-containing complex binds the mRNA cap and modulates translation, assigning a post-transcriptional gene-expression role.\",\n      \"evidence\": \"Cap-analog affinity pulldown, competition/elution, RNA silencing, and polysome analysis\",\n      \"pmids\": [\"30833903\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether FAM98B contacts the cap directly or via partners unresolved\", \"Transcript selectivity of translational modulation not defined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified FAM98B as a transcriptional activator acting at a TGFB1 regulatory variant, a chromatin-associated role distinct from RNA ligation.\",\n      \"evidence\": \"DNA pull-down with mass spectrometry, luciferase reporter assay, and siRNA knockdown\",\n      \"pmids\": [\"32757134\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Not independently replicated\", \"Mechanism of sequence-specific DNA engagement and co-activator recruitment unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Resolved the architecture of the human tRNA-LC core, showing FAM98B and CGI-99 form an N-terminal heterodimer and contribute C-terminal helices required for complex integrity around RTCB.\",\n      \"evidence\": \"Crystal structure of RTCB and the CGI-99 N-terminal domain combined with deletion mutagenesis of inter-subunit interactions\",\n      \"pmids\": [\"34854379\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length FAM98B structure not determined\", \"How the assembly is targeted to substrates not addressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined the disease relevance of FAM98B's glycine-rich IDR, showing polyglycine aggregates sequester FAM98B to disrupt tRNA processing and cause neurological phenotypes in vivo.\",\n      \"evidence\": \"Biochemical aggregation assays, patient tissue analysis, FISH for tRNA splicing intermediates, and in vivo mouse knockdown with behavioral/histological readouts\",\n      \"pmids\": [\"40674500\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether IDR sequestration is the sole disease driver in GGC disorders not established\", \"Cell-type basis of hindbrain vulnerability not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed FAM98B determines the nuclear, Ashwin-bound form of the tRNA-LC dedicated to pre-tRNA splicing, distinguishing it functionally from FAM98A/C-containing cytoplasmic complexes.\",\n      \"evidence\": \"Cryo-EM structure, structure-based and NLS-disruption mutagenesis, fractionation, tRNA splicing intermediate assays, and RTCB-NLS rescue (preprints)\",\n      \"pmids\": [\"bio_10.1101_2025.08.01.668197\", \"bio_10.1101_2025.08.01.668163\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Determinants of paralog selection between FAM98A/B/C not defined\", \"Peer-reviewed confirmation of the preprint findings pending\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended FAM98B's cellular roles to osteoclast biology, showing it is required for lysosome trafficking and bone resorption with FAM98A redundancy.\",\n      \"evidence\": \"shRNA knockdown in osteoclast precursors, lysosomal trafficking and bone resorption assays, and qPCR for compensatory expression\",\n      \"pmids\": [\"39857276\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking FAM98B to lysosome trafficking unknown\", \"Whether this role depends on tRNA-LC activity not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Cross-species structure of the five-subunit tRNA-LC revealed a mobile DDX1 helicase module that can modulate RTCB activity, framing the regulatory dynamics of the FAM98B-containing assembly.\",\n      \"evidence\": \"Cryo-EM of Danio rerio tRNA-LC and thiol-based chemical crosslinking\",\n      \"pmids\": [\"40220997\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific contribution of FAM98B to catalytic regulation not individually dissected\", \"Functional consequence of DDX1 mobility on substrate handling not quantified\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How FAM98B's distinct activities — nuclear tRNA splicing, cap-binding translation, DNA-associated transcriptional activation, and osteoclast lysosome trafficking — are mechanistically coordinated within or independent of the RTCB complex remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No mechanism unifying the chromatin/transcriptional role with the RNA-processing complex\", \"Whether non-tRNA-LC functions require complex assembly is untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 4, 8]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 9]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 4, 9]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\n      \"tRNA ligase complex (tRNA-LC)\",\n      \"cap-binding mRNA transport/translation complex\"\n    ],\n    \"partners\": [\n      \"RTCB\",\n      \"CGI-99\",\n      \"DDX1\",\n      \"C14orf166\",\n      \"Ashwin\",\n      \"FAM98A\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}