{"gene":"SURF6","run_date":"2026-04-28T21:42:57","timeline":{"discoveries":[{"year":1996,"finding":"SURF6 is a novel nucleolar protein localized predominantly in the granular component of the nucleolus, a structure involved in ribosome maturation, as determined by immunofluorescence and immunoblot analyses.","method":"Immunofluorescence, immunoblot analysis","journal":"DNA and cell biology","confidence":"Medium","confidence_rationale":"Tier 2 — direct subcellular localization by immunofluorescence and immunoblot, single lab","pmids":["8639267"],"is_preprint":false},{"year":1998,"finding":"SURF6 is a component of the nucleolar matrix and binds both DNA and RNA in vitro, with stronger preference for RNA; it co-localizes with B23 and fibrillarin in interphase and at perichromosomal layers during mitosis.","method":"Immunofluorescence, immunoblot of nucleolar subfractions, in vitro nucleic acid binding assay with endogenous and recombinant SURF6, double immunolabeling","journal":"European journal of cell biology","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods (subcellular fractionation, in vitro binding with recombinant protein, immunofluorescence co-localization), single lab but strong evidence","pmids":["9548374"],"is_preprint":false},{"year":2005,"finding":"An evolutionarily conserved SURF-6 domain is present in the carboxy-terminus of a family of eukaryotic nucleolar proteins; GFP-fusion experiments showed proteins from distantly related species containing this domain localize to the nucleolus; deletion analysis showed multiple regions of SURF6 can independently target to the nucleolus.","method":"GFP fusion protein localization, deletion analysis, bioinformatic domain identification","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2-3 — direct localization experiments with functional domain mapping, single lab","pmids":["15629442"],"is_preprint":false},{"year":2005,"finding":"In interphase mouse NIH/3T3 cells, SURF6 is associated with RNA (not DNA) in situ; during mitosis SURF6 appears in forming nucleoli after fibrillarin and B23, suggesting involvement in terminal stages of ribosomal particle assembly.","method":"Immunofluorescence with RNase A and DNase I treatment in situ, cell cycle synchronization and immunoblot","journal":"Bioorganicheskaia khimiia","confidence":"Medium","confidence_rationale":"Tier 2-3 — in situ nuclease sensitivity combined with cell cycle analysis, single lab","pmids":["16363129"],"is_preprint":false},{"year":2006,"finding":"Knockdown of Surf6 mRNA by RNAi in mouse preimplantation embryos caused developmental arrest at the 8-cell/morula stage and decreased 18S rRNA levels, demonstrating that SURF6 is essential for preimplantation development and ribosome biogenesis.","method":"RNAi knockdown, immunocytochemistry, qRT-PCR for rRNA levels","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 2 — loss-of-function with specific molecular phenotype (decreased 18S rRNA) and developmental arrest, moderate evidence","pmids":["16855206"],"is_preprint":false},{"year":2006,"finding":"Conditional antisense RNA-mediated depletion of SURF6 in NIH/3T3 cells caused cell death and apparent G1 phase arrest, demonstrating SURF6 is essential for mammalian cell viability and cell cycle progression.","method":"Tet-On antisense RNA system, flow cytometry, cell viability assay","journal":"Molecular biology reports","confidence":"Medium","confidence_rationale":"Tier 2 — conditional knockdown with defined cell cycle phenotype, single lab","pmids":["17086444"],"is_preprint":false},{"year":2010,"finding":"Overexpression of SURF6 in NIH/3T3 cells stabilized pre-rRNA intragenic transcribed spacers (ITS2 ~7-fold, 5'ETS ~2-fold) without affecting mature rRNA levels, indicating SURF6 prevents premature cleavage of pre-rRNA spacers, analogous to its yeast homologue Rrp14.","method":"Dot-hybridization of isolated RNA with biotinylated oligonucleotide probes, Western blot, doxycycline-inducible overexpression system","journal":"Bioorganicheskaia khimiia","confidence":"Medium","confidence_rationale":"Tier 2 — overexpression with specific rRNA processing phenotype quantified, single lab","pmids":["21063453"],"is_preprint":false},{"year":2014,"finding":"GST pull-down assay identified SURF6-interacting proteins in HeLa cells including B23/nucleophosmin, nucleolin, EBP2, and UBF (a cofactor of RNA polymerase I), implicating SURF6 in both rDNA transcription and rRNA processing.","method":"GST pull-down assay, mass spectrometry","journal":"Bioorganicheskaia khimiia","confidence":"Medium","confidence_rationale":"Tier 3 — pull-down with MS identification, single lab, no reciprocal validation","pmids":["25898752"],"is_preprint":false},{"year":2017,"finding":"Conditional overexpression of SURF6 in NIH/3T3 cells accelerated cell proliferation, shortened G1 phase by ~30%, and caused accumulation of rRNA species along both ribosomal subunit maturation pathways, establishing SURF6 as a positive regulator of G1/S transition and rRNA processing.","method":"Tet-On inducible overexpression, real-time cell proliferation monitoring, flow cytometry, BrdU labeling, Northern blot, qRT-PCR","journal":"Cell cycle (Georgetown, Tex.)","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (proliferation assay, flow cytometry, Northern blot, qRT-PCR) in single lab with defined molecular and cellular phenotypes","pmids":["28873013"],"is_preprint":false},{"year":2018,"finding":"Electrostatically-driven interactions between disordered regions of NPM1 and SURF6 drive liquid-liquid phase separation; heterotypic NPM1-SURF6 and homotypic NPM1-NPM1 scaffolding interactions dynamically interconvert within liquid droplets in response to molecular crowding and protein concentration changes.","method":"In vitro phase separation reconstitution, fluorescence microscopy of liquid droplets, quantitative biophysical characterization","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution of phase separation with mechanistic characterization of interconverting interaction networks, independently notable study","pmids":["30498217"],"is_preprint":false},{"year":2023,"finding":"SURF6 knockdown in HeLa and HCT116 cells shifted pre-rRNA processing from pathway 1 to pathway 2, affecting maturation of rRNAs from both small and large ribosomal subunits; SURF6 overexpression had reciprocal effects; cell cycle changes (G0/G1 elongation, G2/M shortening) were p53-independent.","method":"siRNA knockdown, overexpression, Northern blot/RT-PCR analysis of rRNA precursors, flow cytometry, p53-deficient cell lines","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 — bidirectional manipulation (KD + OE) with specific rRNA processing pathway analysis and epistasis (p53 independence) in multiple cell lines","pmids":["37450438"],"is_preprint":false},{"year":2024,"finding":"miR-3655 targets SURF6 to inhibit its transcription; SURF6 in turn inhibits nuclear translocation of IRF7, reducing IRF7-dependent activation of the IFNβ promoter and IFNβ secretion, placing SURF6 in a KRAS-miR3655-SURF6-IRF7-IFNβ signaling axis.","method":"miRNA target validation, transcriptomic sequencing, nuclear fractionation, promoter activity assay, loss-of-function experiments","journal":"Gut microbes","confidence":"Medium","confidence_rationale":"Tier 2-3 — multiple methods establishing pathway position but single lab, non-canonical function for a nucleolar protein","pmids":["39523457"],"is_preprint":false},{"year":2025,"finding":"Super-resolution microscopy revealed SURF6 and rRNA co-localize in a core sub-phase of the nucleolar granular component; in vitro reconstitution showed SURF6/rRNA-rich core and NPM1-rich shell form multiphase condensates; SURF6's association with rRNA is weakened upon ribosomal subunit assembly, enabling NPM1 to extract assembled subunits from condensates, suggesting an assembly-line mechanism for ribosomal subunit efflux.","method":"Super-resolution microscopy, in vitro condensate reconstitution, rRNA binding assays, ribosome subunit assembly assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1-2 — in vitro reconstitution with super-resolution imaging, preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.03.01.640913"],"is_preprint":true}],"current_model":"SURF6 is an essential, intrinsically disordered nucleolar matrix protein that binds RNA preferentially, drives liquid-liquid phase separation with NPM1 through electrostatic interactions between their disordered regions, participates in early pre-rRNA processing steps (stabilizing ITS2 and regulating pathway choice between the two pre-rRNA processing routes), forms SURF6/rRNA-rich core condensates within granular component sub-phases that release assembled ribosomal subunits to the NPM1-rich shell for efflux, and also functions outside the nucleolus by inhibiting IRF7 nuclear translocation and IFNβ production downstream of KRAS/miR-3655 signaling."},"narrative":{"teleology":[{"year":1996,"claim":"Establishing SURF6 as a nucleolar protein localized to the granular component provided the first subcellular context for its function in ribosome maturation.","evidence":"Immunofluorescence and immunoblot in mammalian cells","pmids":["8639267"],"confidence":"Medium","gaps":["No functional data; localization alone does not specify role in ribosome biogenesis"]},{"year":1998,"claim":"Demonstrating that SURF6 is a nucleolar matrix component that binds RNA preferentially over DNA, and co-localizes with NPM1/B23 and fibrillarin, defined it as an RNA-associated structural nucleolar protein.","evidence":"Nucleolar subfractionation, in vitro nucleic acid binding with recombinant protein, double immunolabeling","pmids":["9548374"],"confidence":"High","gaps":["Specific RNA targets not identified","No loss-of-function data"]},{"year":2005,"claim":"Identification of an evolutionarily conserved SURF-6 domain with multiple independent nucleolar targeting regions, and confirmation that SURF6 associates with RNA (not DNA) in situ, established it as a conserved nucleolar RNA-binding factor involved in late ribosome assembly steps.","evidence":"GFP-fusion localization and deletion mapping; in situ RNase/DNase sensitivity combined with cell cycle immunofluorescence","pmids":["15629442","16363129"],"confidence":"Medium","gaps":["Functional consequence of domain deletions unknown","No direct rRNA processing data"]},{"year":2006,"claim":"Loss-of-function studies showed SURF6 is essential for mammalian cell viability, cell cycle progression (G1 arrest), and preimplantation development, with knockdown reducing 18S rRNA levels and causing embryonic arrest.","evidence":"RNAi in mouse embryos with qRT-PCR for rRNA; conditional antisense in NIH/3T3 with flow cytometry","pmids":["16855206","17086444"],"confidence":"High","gaps":["Mechanism linking SURF6 loss to reduced 18S unclear","Whether cell death is a direct ribosome biogenesis defect or secondary stress response not resolved"]},{"year":2010,"claim":"Overexpression of SURF6 stabilized ITS2 and 5′ETS pre-rRNA spacers without altering mature rRNA, revealing a direct role in preventing premature spacer cleavage analogous to yeast Rrp14.","evidence":"Doxycycline-inducible overexpression in NIH/3T3, dot-hybridization with biotinylated probes","pmids":["21063453"],"confidence":"Medium","gaps":["Overexpression only; no complementary knockdown rRNA processing data at this time","Direct RNA binding to spacer sequences not shown"]},{"year":2014,"claim":"Identification of NPM1/B23, nucleolin, EBP2, and UBF as SURF6-interacting partners placed SURF6 at the intersection of rDNA transcription and rRNA processing.","evidence":"GST pull-down followed by mass spectrometry in HeLa cells","pmids":["25898752"],"confidence":"Medium","gaps":["No reciprocal co-IP validation","Functional significance of individual interactions not tested"]},{"year":2017,"claim":"Demonstrating that SURF6 overexpression accelerates proliferation and shortens G1 by ~30% while accumulating rRNA intermediates from both subunit maturation pathways established SURF6 as a positive regulator of G1/S transition coupled to rRNA processing.","evidence":"Tet-On overexpression, real-time proliferation monitoring, flow cytometry, BrdU labeling, Northern blot in NIH/3T3","pmids":["28873013"],"confidence":"High","gaps":["Causal link between rRNA processing and G1/S transition not mechanistically dissected","Whether effect on proliferation is cell-type specific unknown"]},{"year":2018,"claim":"Reconstituting NPM1–SURF6 liquid–liquid phase separation in vitro revealed that electrostatic interactions between their disordered regions drive nucleolar-like condensate formation, establishing a biophysical basis for nucleolar organization.","evidence":"In vitro phase separation reconstitution with fluorescence microscopy and quantitative biophysical characterization","pmids":["30498217"],"confidence":"High","gaps":["In vitro system lacks rRNA; role of RNA in modulating phase behavior not addressed","In vivo validation of interconverting scaffolding networks not performed"]},{"year":2023,"claim":"Bidirectional manipulation (knockdown and overexpression) in multiple cell lines showed SURF6 regulates the choice between pre-rRNA processing pathways 1 and 2 in a p53-independent manner, resolving its specific role in rRNA maturation.","evidence":"siRNA and overexpression in HeLa and HCT116 cells, Northern blot/RT-PCR of rRNA precursors, flow cytometry, p53-null cell lines","pmids":["37450438"],"confidence":"High","gaps":["How SURF6 mechanistically shifts pathway choice is unknown","Whether pathway shift underlies proliferative phenotype not tested"]},{"year":2024,"claim":"Placing SURF6 in a KRAS–miR-3655–SURF6–IRF7–IFNβ axis revealed an extranucleolar function in innate immune signaling, where SURF6 inhibits IRF7 nuclear translocation.","evidence":"miRNA target validation, nuclear fractionation, IFNβ promoter assays, loss-of-function experiments","pmids":["39523457"],"confidence":"Medium","gaps":["Mechanism by which SURF6 retains IRF7 in cytoplasm unknown","Whether this function is independent of nucleolar roles unresolved","Single-lab finding not yet replicated"]},{"year":null,"claim":"The mechanism by which SURF6 switches pre-rRNA processing pathway choice, the structural basis of SURF6–rRNA interactions, and whether its innate immune regulatory function is physiologically separable from its nucleolar role remain open questions.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of SURF6 or its RNA-binding mode","Specific rRNA sequences bound by SURF6 not mapped","In vivo validation of multiphase condensate assembly-line model pending peer review"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1,3,6]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[6,10]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[0,1,2,3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,11]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[4,6,8,10]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[5,8,10]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[11]}],"complexes":[],"partners":["NPM1","NCL","EBP2","UBF","IRF7"],"other_free_text":[]},"mechanistic_narrative":"SURF6 is an intrinsically disordered nucleolar matrix protein essential for ribosome biogenesis and cell proliferation. It resides in the granular component of the nucleolus, preferentially binds RNA, and stabilizes pre-rRNA intragenic transcribed spacers (particularly ITS2) while regulating the choice between the two mammalian pre-rRNA processing pathways in a p53-independent manner [PMID:21063453, PMID:37450438]. Electrostatic interactions between the disordered regions of SURF6 and NPM1 drive liquid–liquid phase separation that organizes nucleolar sub-phases, with SURF6/rRNA-rich cores releasing assembled ribosomal subunits to NPM1-rich shells for nucleolar efflux [PMID:30498217]. Beyond the nucleolus, SURF6 inhibits IRF7 nuclear translocation and thereby suppresses IFNβ production downstream of KRAS/miR-3655 signaling [PMID:39523457]."},"prefetch_data":{"uniprot":{"accession":"O75683","full_name":"Surfeit locus protein 6","aliases":[],"length_aa":361,"mass_kda":41.5,"function":"Binds to both DNA and RNA in vitro, with a stronger binding capacity for RNA. May represent a nucleolar constitutive protein involved in ribosomal biosynthesis or assembly (By similarity)","subcellular_location":"Nucleus, nucleoplasm; Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/O75683/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SURF6","classification":"Common Essential","n_dependent_lines":1046,"n_total_lines":1208,"dependency_fraction":0.8658940397350994},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DEGS1","stoichiometry":0.2},{"gene":"HSPA14","stoichiometry":0.2},{"gene":"NPM1","stoichiometry":0.2},{"gene":"SRP68","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/SURF6","total_profiled":1310},"omim":[{"mim_id":"185642","title":"SURFEIT 6; SURF6","url":"https://www.omim.org/entry/185642"},{"mim_id":"185620","title":"SURFEIT 1; SURF1","url":"https://www.omim.org/entry/185620"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoli","reliability":"Enhanced"},{"location":"Nucleoli rim","reliability":"Enhanced"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Mitotic chromosome","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SURF6"},"hgnc":{"alias_symbol":["FLJ30322","RRP14"],"prev_symbol":[]},"alphafold":{"accession":"O75683","domains":[{"cath_id":"-","chopping":"235-285","consensus_level":"high","plddt":93.2339,"start":235,"end":285},{"cath_id":"1.20.5","chopping":"297-351","consensus_level":"high","plddt":96.2636,"start":297,"end":351}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O75683","model_url":"https://alphafold.ebi.ac.uk/files/AF-O75683-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O75683-F1-predicted_aligned_error_v6.png","plddt_mean":73.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SURF6","jax_strain_url":"https://www.jax.org/strain/search?query=SURF6"},"sequence":{"accession":"O75683","fasta_url":"https://rest.uniprot.org/uniprotkb/O75683.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O75683/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O75683"}},"corpus_meta":[{"pmid":"30498217","id":"PMC_30498217","title":"Compositional adaptability in NPM1-SURF6 scaffolding networks enabled by dynamic switching of phase separation mechanisms.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/30498217","citation_count":87,"is_preprint":false},{"pmid":"9548374","id":"PMC_9548374","title":"The SURF-6 protein is a component of the nucleolar matrix and has a high binding capacity for nucleic acids in vitro.","date":"1998","source":"European journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/9548374","citation_count":30,"is_preprint":false},{"pmid":"16855206","id":"PMC_16855206","title":"Implication of nucleolar protein SURF6 in ribosome biogenesis and preimplantation mouse development.","date":"2006","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/16855206","citation_count":27,"is_preprint":false},{"pmid":"8639267","id":"PMC_8639267","title":"The Surf-6 gene of the mouse surfeit locus encodes a novel nucleolar protein.","date":"1996","source":"DNA and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/8639267","citation_count":23,"is_preprint":false},{"pmid":"39523457","id":"PMC_39523457","title":"KRAS mutations promote the intratumoral colonization of enterotoxigenic bacteroides fragilis in colorectal cancer through the regulation of the miRNA3655/SURF6/IRF7/IFNβ axis.","date":"2024","source":"Gut microbes","url":"https://pubmed.ncbi.nlm.nih.gov/39523457","citation_count":18,"is_preprint":false},{"pmid":"28873013","id":"PMC_28873013","title":"Involvement of the specific nucleolar protein SURF6 in regulation of proliferation and ribosome biogenesis in mouse NIH/3T3 fibroblasts.","date":"2017","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/28873013","citation_count":15,"is_preprint":false},{"pmid":"15629442","id":"PMC_15629442","title":"Identification of an evolutionary conserved SURF-6 domain in a family of nucleolar proteins extending from human to yeast.","date":"2005","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/15629442","citation_count":14,"is_preprint":false},{"pmid":"10675619","id":"PMC_10675619","title":"Isolation and genomic analysis of the human surf-6 gene: a member of the Surfeit locus.","date":"2000","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/10675619","citation_count":11,"is_preprint":false},{"pmid":"17086444","id":"PMC_17086444","title":"The nucleolar protein SURF-6 is essential for viability in mouse NIH/3T3 cells.","date":"2006","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/17086444","citation_count":8,"is_preprint":false},{"pmid":"37450438","id":"PMC_37450438","title":"Human nucleolar protein SURF6/RRP14 participates in early steps of pre-rRNA processing.","date":"2023","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/37450438","citation_count":6,"is_preprint":false},{"pmid":"16363129","id":"PMC_16363129","title":"[Properties and functions of a new nucleolar protein, Surf-6, in 3T3 mouse cells].","date":"2005","source":"Bioorganicheskaia khimiia","url":"https://pubmed.ncbi.nlm.nih.gov/16363129","citation_count":5,"is_preprint":false},{"pmid":"19907743","id":"PMC_19907743","title":"Early expression of nucleolar SURF-6 protein in mouse spleen lymphocytes activated for proliferation in vitro.","date":"2009","source":"Bulletin of experimental biology and medicine","url":"https://pubmed.ncbi.nlm.nih.gov/19907743","citation_count":5,"is_preprint":false},{"pmid":"22316485","id":"PMC_22316485","title":"Development of novel mouse hybridomas producing monoclonal antibodies specific to human and mouse nucleolar protein SURF-6.","date":"2012","source":"Hybridoma (2005)","url":"https://pubmed.ncbi.nlm.nih.gov/22316485","citation_count":5,"is_preprint":false},{"pmid":"33119830","id":"PMC_33119830","title":"A Higher Level of Expression of the Nucleolar Protein SURF6 in Human Normal Activated Lymphocytes and in Lymphocytes of Patients with Lymphoproliferative Disorders.","date":"2020","source":"Doklady. Biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/33119830","citation_count":3,"is_preprint":false},{"pmid":"25898752","id":"PMC_25898752","title":"[Identification of the protein partners of the human nucleolar protein SURF6 in HeLa cells by GST pull-down assay].","date":"2014","source":"Bioorganicheskaia khimiia","url":"https://pubmed.ncbi.nlm.nih.gov/25898752","citation_count":1,"is_preprint":false},{"pmid":"21063453","id":"PMC_21063453","title":"[Overexpression of the nucleolar protein SURF-6 in mouse fibroblasts NIH/3T3 leads to stabilisation of intragenic transcribed spacers of the pre-rRNA].","date":"2010","source":"Bioorganicheskaia khimiia","url":"https://pubmed.ncbi.nlm.nih.gov/21063453","citation_count":1,"is_preprint":false},{"pmid":"22808736","id":"PMC_22808736","title":"[Cloning, expression, and isolation from Escherichia coli of human protein SURF-6 translationally fused to glutathione S-transferase].","date":"2011","source":"Prikladnaia biokhimiia i mikrobiologiia","url":"https://pubmed.ncbi.nlm.nih.gov/22808736","citation_count":1,"is_preprint":false},{"pmid":"12391725","id":"PMC_12391725","title":"Cloning and expression of the surfeit locus member Surf-6 during embryogenesis in Xenopus laevis.","date":"2002","source":"DNA sequence : the journal of DNA sequencing and mapping","url":"https://pubmed.ncbi.nlm.nih.gov/12391725","citation_count":1,"is_preprint":false},{"pmid":"34974803","id":"PMC_34974803","title":"Rrp14 controls rRNA transcription via facilitating the translocation of Pol5 into the nucleolus.","date":"2022","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/34974803","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.01.640913","title":"Granular component sub-phases direct ribosome biogenesis in the nucleolus","date":"2025-03-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.01.640913","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10073,"output_tokens":2931,"usd":0.037092},"stage2":{"model":"claude-opus-4-6","input_tokens":6307,"output_tokens":2366,"usd":0.136027},"total_usd":0.173119,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"SURF6 is a novel nucleolar protein localized predominantly in the granular component of the nucleolus, a structure involved in ribosome maturation, as determined by immunofluorescence and immunoblot analyses.\",\n      \"method\": \"Immunofluorescence, immunoblot analysis\",\n      \"journal\": \"DNA and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct subcellular localization by immunofluorescence and immunoblot, single lab\",\n      \"pmids\": [\"8639267\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"SURF6 is a component of the nucleolar matrix and binds both DNA and RNA in vitro, with stronger preference for RNA; it co-localizes with B23 and fibrillarin in interphase and at perichromosomal layers during mitosis.\",\n      \"method\": \"Immunofluorescence, immunoblot of nucleolar subfractions, in vitro nucleic acid binding assay with endogenous and recombinant SURF6, double immunolabeling\",\n      \"journal\": \"European journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods (subcellular fractionation, in vitro binding with recombinant protein, immunofluorescence co-localization), single lab but strong evidence\",\n      \"pmids\": [\"9548374\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"An evolutionarily conserved SURF-6 domain is present in the carboxy-terminus of a family of eukaryotic nucleolar proteins; GFP-fusion experiments showed proteins from distantly related species containing this domain localize to the nucleolus; deletion analysis showed multiple regions of SURF6 can independently target to the nucleolus.\",\n      \"method\": \"GFP fusion protein localization, deletion analysis, bioinformatic domain identification\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct localization experiments with functional domain mapping, single lab\",\n      \"pmids\": [\"15629442\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"In interphase mouse NIH/3T3 cells, SURF6 is associated with RNA (not DNA) in situ; during mitosis SURF6 appears in forming nucleoli after fibrillarin and B23, suggesting involvement in terminal stages of ribosomal particle assembly.\",\n      \"method\": \"Immunofluorescence with RNase A and DNase I treatment in situ, cell cycle synchronization and immunoblot\",\n      \"journal\": \"Bioorganicheskaia khimiia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — in situ nuclease sensitivity combined with cell cycle analysis, single lab\",\n      \"pmids\": [\"16363129\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Knockdown of Surf6 mRNA by RNAi in mouse preimplantation embryos caused developmental arrest at the 8-cell/morula stage and decreased 18S rRNA levels, demonstrating that SURF6 is essential for preimplantation development and ribosome biogenesis.\",\n      \"method\": \"RNAi knockdown, immunocytochemistry, qRT-PCR for rRNA levels\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with specific molecular phenotype (decreased 18S rRNA) and developmental arrest, moderate evidence\",\n      \"pmids\": [\"16855206\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Conditional antisense RNA-mediated depletion of SURF6 in NIH/3T3 cells caused cell death and apparent G1 phase arrest, demonstrating SURF6 is essential for mammalian cell viability and cell cycle progression.\",\n      \"method\": \"Tet-On antisense RNA system, flow cytometry, cell viability assay\",\n      \"journal\": \"Molecular biology reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — conditional knockdown with defined cell cycle phenotype, single lab\",\n      \"pmids\": [\"17086444\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Overexpression of SURF6 in NIH/3T3 cells stabilized pre-rRNA intragenic transcribed spacers (ITS2 ~7-fold, 5'ETS ~2-fold) without affecting mature rRNA levels, indicating SURF6 prevents premature cleavage of pre-rRNA spacers, analogous to its yeast homologue Rrp14.\",\n      \"method\": \"Dot-hybridization of isolated RNA with biotinylated oligonucleotide probes, Western blot, doxycycline-inducible overexpression system\",\n      \"journal\": \"Bioorganicheskaia khimiia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — overexpression with specific rRNA processing phenotype quantified, single lab\",\n      \"pmids\": [\"21063453\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"GST pull-down assay identified SURF6-interacting proteins in HeLa cells including B23/nucleophosmin, nucleolin, EBP2, and UBF (a cofactor of RNA polymerase I), implicating SURF6 in both rDNA transcription and rRNA processing.\",\n      \"method\": \"GST pull-down assay, mass spectrometry\",\n      \"journal\": \"Bioorganicheskaia khimiia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — pull-down with MS identification, single lab, no reciprocal validation\",\n      \"pmids\": [\"25898752\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Conditional overexpression of SURF6 in NIH/3T3 cells accelerated cell proliferation, shortened G1 phase by ~30%, and caused accumulation of rRNA species along both ribosomal subunit maturation pathways, establishing SURF6 as a positive regulator of G1/S transition and rRNA processing.\",\n      \"method\": \"Tet-On inducible overexpression, real-time cell proliferation monitoring, flow cytometry, BrdU labeling, Northern blot, qRT-PCR\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (proliferation assay, flow cytometry, Northern blot, qRT-PCR) in single lab with defined molecular and cellular phenotypes\",\n      \"pmids\": [\"28873013\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Electrostatically-driven interactions between disordered regions of NPM1 and SURF6 drive liquid-liquid phase separation; heterotypic NPM1-SURF6 and homotypic NPM1-NPM1 scaffolding interactions dynamically interconvert within liquid droplets in response to molecular crowding and protein concentration changes.\",\n      \"method\": \"In vitro phase separation reconstitution, fluorescence microscopy of liquid droplets, quantitative biophysical characterization\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution of phase separation with mechanistic characterization of interconverting interaction networks, independently notable study\",\n      \"pmids\": [\"30498217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SURF6 knockdown in HeLa and HCT116 cells shifted pre-rRNA processing from pathway 1 to pathway 2, affecting maturation of rRNAs from both small and large ribosomal subunits; SURF6 overexpression had reciprocal effects; cell cycle changes (G0/G1 elongation, G2/M shortening) were p53-independent.\",\n      \"method\": \"siRNA knockdown, overexpression, Northern blot/RT-PCR analysis of rRNA precursors, flow cytometry, p53-deficient cell lines\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — bidirectional manipulation (KD + OE) with specific rRNA processing pathway analysis and epistasis (p53 independence) in multiple cell lines\",\n      \"pmids\": [\"37450438\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"miR-3655 targets SURF6 to inhibit its transcription; SURF6 in turn inhibits nuclear translocation of IRF7, reducing IRF7-dependent activation of the IFNβ promoter and IFNβ secretion, placing SURF6 in a KRAS-miR3655-SURF6-IRF7-IFNβ signaling axis.\",\n      \"method\": \"miRNA target validation, transcriptomic sequencing, nuclear fractionation, promoter activity assay, loss-of-function experiments\",\n      \"journal\": \"Gut microbes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple methods establishing pathway position but single lab, non-canonical function for a nucleolar protein\",\n      \"pmids\": [\"39523457\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Super-resolution microscopy revealed SURF6 and rRNA co-localize in a core sub-phase of the nucleolar granular component; in vitro reconstitution showed SURF6/rRNA-rich core and NPM1-rich shell form multiphase condensates; SURF6's association with rRNA is weakened upon ribosomal subunit assembly, enabling NPM1 to extract assembled subunits from condensates, suggesting an assembly-line mechanism for ribosomal subunit efflux.\",\n      \"method\": \"Super-resolution microscopy, in vitro condensate reconstitution, rRNA binding assays, ribosome subunit assembly assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro reconstitution with super-resolution imaging, preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.03.01.640913\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"SURF6 is an essential, intrinsically disordered nucleolar matrix protein that binds RNA preferentially, drives liquid-liquid phase separation with NPM1 through electrostatic interactions between their disordered regions, participates in early pre-rRNA processing steps (stabilizing ITS2 and regulating pathway choice between the two pre-rRNA processing routes), forms SURF6/rRNA-rich core condensates within granular component sub-phases that release assembled ribosomal subunits to the NPM1-rich shell for efflux, and also functions outside the nucleolus by inhibiting IRF7 nuclear translocation and IFNβ production downstream of KRAS/miR-3655 signaling.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SURF6 is an intrinsically disordered nucleolar matrix protein essential for ribosome biogenesis and cell proliferation. It resides in the granular component of the nucleolus, preferentially binds RNA, and stabilizes pre-rRNA intragenic transcribed spacers (particularly ITS2) while regulating the choice between the two mammalian pre-rRNA processing pathways in a p53-independent manner [PMID:21063453, PMID:37450438]. Electrostatic interactions between the disordered regions of SURF6 and NPM1 drive liquid–liquid phase separation that organizes nucleolar sub-phases, with SURF6/rRNA-rich cores releasing assembled ribosomal subunits to NPM1-rich shells for nucleolar efflux [PMID:30498217]. Beyond the nucleolus, SURF6 inhibits IRF7 nuclear translocation and thereby suppresses IFNβ production downstream of KRAS/miR-3655 signaling [PMID:39523457].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Establishing SURF6 as a nucleolar protein localized to the granular component provided the first subcellular context for its function in ribosome maturation.\",\n      \"evidence\": \"Immunofluorescence and immunoblot in mammalian cells\",\n      \"pmids\": [\"8639267\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional data; localization alone does not specify role in ribosome biogenesis\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Demonstrating that SURF6 is a nucleolar matrix component that binds RNA preferentially over DNA, and co-localizes with NPM1/B23 and fibrillarin, defined it as an RNA-associated structural nucleolar protein.\",\n      \"evidence\": \"Nucleolar subfractionation, in vitro nucleic acid binding with recombinant protein, double immunolabeling\",\n      \"pmids\": [\"9548374\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific RNA targets not identified\", \"No loss-of-function data\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Identification of an evolutionarily conserved SURF-6 domain with multiple independent nucleolar targeting regions, and confirmation that SURF6 associates with RNA (not DNA) in situ, established it as a conserved nucleolar RNA-binding factor involved in late ribosome assembly steps.\",\n      \"evidence\": \"GFP-fusion localization and deletion mapping; in situ RNase/DNase sensitivity combined with cell cycle immunofluorescence\",\n      \"pmids\": [\"15629442\", \"16363129\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of domain deletions unknown\", \"No direct rRNA processing data\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Loss-of-function studies showed SURF6 is essential for mammalian cell viability, cell cycle progression (G1 arrest), and preimplantation development, with knockdown reducing 18S rRNA levels and causing embryonic arrest.\",\n      \"evidence\": \"RNAi in mouse embryos with qRT-PCR for rRNA; conditional antisense in NIH/3T3 with flow cytometry\",\n      \"pmids\": [\"16855206\", \"17086444\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking SURF6 loss to reduced 18S unclear\", \"Whether cell death is a direct ribosome biogenesis defect or secondary stress response not resolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Overexpression of SURF6 stabilized ITS2 and 5′ETS pre-rRNA spacers without altering mature rRNA, revealing a direct role in preventing premature spacer cleavage analogous to yeast Rrp14.\",\n      \"evidence\": \"Doxycycline-inducible overexpression in NIH/3T3, dot-hybridization with biotinylated probes\",\n      \"pmids\": [\"21063453\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Overexpression only; no complementary knockdown rRNA processing data at this time\", \"Direct RNA binding to spacer sequences not shown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identification of NPM1/B23, nucleolin, EBP2, and UBF as SURF6-interacting partners placed SURF6 at the intersection of rDNA transcription and rRNA processing.\",\n      \"evidence\": \"GST pull-down followed by mass spectrometry in HeLa cells\",\n      \"pmids\": [\"25898752\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No reciprocal co-IP validation\", \"Functional significance of individual interactions not tested\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrating that SURF6 overexpression accelerates proliferation and shortens G1 by ~30% while accumulating rRNA intermediates from both subunit maturation pathways established SURF6 as a positive regulator of G1/S transition coupled to rRNA processing.\",\n      \"evidence\": \"Tet-On overexpression, real-time proliferation monitoring, flow cytometry, BrdU labeling, Northern blot in NIH/3T3\",\n      \"pmids\": [\"28873013\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Causal link between rRNA processing and G1/S transition not mechanistically dissected\", \"Whether effect on proliferation is cell-type specific unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Reconstituting NPM1–SURF6 liquid–liquid phase separation in vitro revealed that electrostatic interactions between their disordered regions drive nucleolar-like condensate formation, establishing a biophysical basis for nucleolar organization.\",\n      \"evidence\": \"In vitro phase separation reconstitution with fluorescence microscopy and quantitative biophysical characterization\",\n      \"pmids\": [\"30498217\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vitro system lacks rRNA; role of RNA in modulating phase behavior not addressed\", \"In vivo validation of interconverting scaffolding networks not performed\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Bidirectional manipulation (knockdown and overexpression) in multiple cell lines showed SURF6 regulates the choice between pre-rRNA processing pathways 1 and 2 in a p53-independent manner, resolving its specific role in rRNA maturation.\",\n      \"evidence\": \"siRNA and overexpression in HeLa and HCT116 cells, Northern blot/RT-PCR of rRNA precursors, flow cytometry, p53-null cell lines\",\n      \"pmids\": [\"37450438\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How SURF6 mechanistically shifts pathway choice is unknown\", \"Whether pathway shift underlies proliferative phenotype not tested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placing SURF6 in a KRAS–miR-3655–SURF6–IRF7–IFNβ axis revealed an extranucleolar function in innate immune signaling, where SURF6 inhibits IRF7 nuclear translocation.\",\n      \"evidence\": \"miRNA target validation, nuclear fractionation, IFNβ promoter assays, loss-of-function experiments\",\n      \"pmids\": [\"39523457\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which SURF6 retains IRF7 in cytoplasm unknown\", \"Whether this function is independent of nucleolar roles unresolved\", \"Single-lab finding not yet replicated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The mechanism by which SURF6 switches pre-rRNA processing pathway choice, the structural basis of SURF6–rRNA interactions, and whether its innate immune regulatory function is physiologically separable from its nucleolar role remain open questions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of SURF6 or its RNA-binding mode\", \"Specific rRNA sequences bound by SURF6 not mapped\", \"In vivo validation of multiphase condensate assembly-line model pending peer review\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1, 3, 6]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [6, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0, 1, 2, 3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [4, 6, 8, 10]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [5, 8, 10]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NPM1\", \"NCL\", \"EBP2\", \"UBF\", \"IRF7\"],\n    \"other_free_text\": []\n  }\n}\n```"}