{"gene":"RCL1","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2000,"finding":"Rcl1p (yeast RCL1 ortholog) is an essential nucleolar protein required for pre-rRNA processing at sites A0, A1, and A2; its depletion leads to a strong decrease in 18S rRNA and 40S ribosomal subunit levels. Rcl1p co-immunoprecipitates with U3 snoRNP components but is not a structural component of U3 snoRNP; most Rcl1p sediments with 70–80S pre-ribosomal particles.","method":"Genetic depletion/inactivation in yeast, immunoprecipitation, sucrose gradient sedimentation, nucleolar localization by microscopy","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (genetic depletion, Co-IP, gradient analysis, localization), replicated across species (mouse ortholog complements yeast)","pmids":["10790377"],"is_preprint":false},{"year":2005,"finding":"Bms1 (an essential GTPase) delivers Rcl1 to pre-ribosomes in a GTP-dependent manner. Rcl1 binding to Bms1 is thermodynamically coupled to GTP and U3 snoRNA binding; a Bms1 mutant defective for Rcl1 binding severely limits Rcl1 recruitment to pre-ribosomes. The C-terminal domain of Bms1 acts as an intramolecular GTPase-activating protein.","method":"Thermodynamic binding assays, yeast genetics with Bms1 mutants, pre-ribosome association assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — thermodynamic coupling measured quantitatively, Bms1 mutant defective for Rcl1 binding validated in vivo, multiple orthogonal methods in a single rigorous study","pmids":["16307926"],"is_preprint":false},{"year":2005,"finding":"Bms1, Rcl1, and U3 snoRNA form a stable GTP-dependent subcomplex; Rcl1 activates Bms1 by promoting GDP/GTP exchange, analogous to ribosome-promoted nucleotide exchange in translation elongation factor EF-G. GTP binding (but not GDP) is required for stable subcomplex formation.","method":"Quantitative thermodynamic analysis of GTP-dependent subcomplex formation in vitro","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with complete thermodynamic analysis, single lab but multiple binding measurements","pmids":["16376378"],"is_preprint":false},{"year":2011,"finding":"Recombinant Rcl1 cleaves pre-rRNA at site A2 in vitro in an endonucleolytic reaction sensitive to nearby RNA mutations that inhibit cleavage in vivo. Mutations in Rcl1 disrupt rRNA processing at site A2 both in vivo and in vitro, establishing Rcl1 as the endonuclease responsible for the A2 cleavage that co-transcriptionally separates rRNAs destined for the small and large ribosomal subunits. Rcl1 defines a novel class of nucleases with no homology to other known endonucleases.","method":"In vitro endonuclease assay with recombinant Rcl1, site-directed mutagenesis, in vivo rRNA processing assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of endonuclease activity, active-site mutagenesis with in vivo validation, multiple orthogonal methods","pmids":["21849504"],"is_preprint":false},{"year":2011,"finding":"Crystal structure of yeast Rcl1 at 2.6 Å resolution reveals a modular 4-domain architecture with overall homology to RNA cyclase (Rtc) enzymes but local differences that explain why Rcl1 lacks the metal-dependent adenylyltransferase activity of Rtc enzymes. Mutations in and around a conserved oxyanion-binding site did not affect Rcl1 activity in vivo, arguing against a catalytic or RNA-binding role for this site.","method":"X-ray crystallography, in vivo mutagenesis of putative active-site residues","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with functional mutagenesis validation, single lab","pmids":["21367972"],"is_preprint":false},{"year":2009,"finding":"In human cells, the BMS1/RCL1 subcomplex is a component of the SSU processome, a large machine required for 18S rRNA processing. The BMS1/RCL1 subcomplex is absent from a novel 50S U3 snoRNP assembly intermediate that accumulates when pre-rRNA transcription is blocked or tUTP proteins are depleted, indicating BMS1/RCL1 join the processome after initial pre-rRNA association.","method":"Co-immunoprecipitation, sucrose gradient sedimentation, siRNA depletion","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and gradient analysis, human cell system, single lab with orthogonal depletion experiments","pmids":["19332556"],"is_preprint":false},{"year":2014,"finding":"Knockdown of mouse Rcl1 impairs endonucleolytic cleavages of pre-rRNA in the ITS1 region required for small ribosomal subunit maturation, as characterized by RAMP (Ratio Analysis of Multiple Precursors) profiling. The data suggest that completion of early small-subunit maturation (requiring Rcl1) triggers release from the common pre-rRNA transcript by stimulating cleavage at the proximal ITS1 site.","method":"siRNA knockdown, RAMP pre-rRNA ratio analysis by Northern blotting in mouse cells and tissues","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — quantitative rRNA precursor analysis with defined knockdown, single lab, novel RAMP method","pmids":["25190460"],"is_preprint":false},{"year":2016,"finding":"Cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome identifies the Bms1–Rcl1 module as one of five major modules organized around 5'-ETS and partially folded 18S rRNA within the 90S particle architecture.","method":"Cryo-EM structure determination of the 90S pre-ribosome","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure of the complete 90S pre-ribosome, Bms1–Rcl1 module directly visualized in structural context","pmids":["27419870"],"is_preprint":false},{"year":2016,"finding":"In human cells, mutation of the potential A2-site endonuclease RCL1 did not affect 18S rRNA production, whereas an intact PIN domain in UTP24 was required for accurate cleavages at sites 1 and 2a. This negative result for human RCL1 contrasts with yeast data where Rcl1 is the A2 endonuclease.","method":"In vivo mutagenesis of human RCL1 active-site residues, pre-rRNA processing analysis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct in vivo mutagenesis experiment, single lab; finding is a negative result for human RCL1 specifically","pmids":["27034467"],"is_preprint":false},{"year":2019,"finding":"Rrp5 blocks Rcl1 access to the nascent pre-rRNA cleavage site early during ribosome assembly, thereby delaying separation of small and large subunit pre-rRNAs until domain I of 25S rRNA is transcribed. Upon transcription of domain I, 60S assembly factors Noc1/Noc2 bind both this RNA and Rrp5, changing Rrp5's RNA-binding mode to permit Rcl1-mediated cleavage. Overexpression of wild-type but not catalytically inactive Rcl1 rescues subunit separation defects caused by Noc1 HEAT-repeat mutants in vivo.","method":"Quantitative RNA binding assays, in vitro cleavage assays, genetic epistasis with Noc1 mutants and Rcl1 overexpression in yeast","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro quantitative binding and cleavage combined with in vivo genetic rescue, multiple orthogonal methods, clear epistasis established","pmids":["31217256"],"is_preprint":false},{"year":2021,"finding":"In zebrafish, depletion of Rcl1 mainly impairs cleavage at the A1-site (the link between 5'ETS and 18S rRNA) rather than the A2-site as in yeast. rcl1−/− mutants exhibit small liver and exocrine pancreas and die before 15 days post-fertilization. RNA-seq reveals up-regulation of a cohort of ribosome biogenesis and tRNA production genes upon Rcl1 deficiency.","method":"Zebrafish rcl1 knockout, pre-rRNA processing site mapping by primer extension/Northern blotting, RNA-seq, phenotypic characterization","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic knockout with direct rRNA processing analysis and transcriptome profiling, site-specific cleavage mapped, clear organ phenotype","pmids":["34019640"],"is_preprint":false},{"year":2022,"finding":"RCL1 protein stability and nucleolar localization depend on its physical interaction with BMS1. When this interaction is disrupted, RCL1 is degraded via the ubiquitination–proteasome pathway. Overexpression of RCL1 in BMS1-knockdown cells partially rescues defects in 18S rRNA processing and cell proliferation. Hepatocyte-specific overexpression of Rcl1 rescues zebrafish liver development in a bms1l substitution (but not knockout) mutant, attributed to residual nucleolar entry of Rcl1 in the former.","method":"Co-immunoprecipitation identifying RCL1-interacting domain in BMS1, proteasome inhibitor experiments, zebrafish genetic rescue experiments, cell proliferation and rRNA processing assays","journal":"Journal of molecular cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP identifying interaction domain, proteasome pathway validated pharmacologically, in vivo genetic rescue in zebrafish with mechanistic specificity","pmids":["37451810"],"is_preprint":false},{"year":2022,"finding":"Zebrafish Bms1 interacts with Rcl1 and also with Ttf1 (a replication fork barrier binding protein). Loss of Bms1l upregulates rDNA transcription, causes replication-fork stall, and arrests the cell cycle at S-to-G2 transition. Bms1 GTPase activity is required to disassociate the Ttf1–RFB complex, balancing rDNA transcription and replication during S-phase.","method":"Co-immunoprecipitation (Bms1–Rcl1 and Bms1–Ttf1), ChIP-seq for Ttf1 RFB sites, zebrafish loss-of-function genetic analysis, cell cycle and DNA damage marker analysis","journal":"Journal of molecular cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus ChIP-seq plus in vivo genetic data, single lab, establishes Rcl1 in context of broader Bms1 function","pmids":["34791311"],"is_preprint":false},{"year":2021,"finding":"c-Myc directly occupies predicted transcription factor binding sites in the RCL1 promoter region, as confirmed by ChIP assay in HEK293T cells overexpressing ectopic c-Myc, and dual-luciferase reporter assays demonstrated c-Myc functional relevance for RCL1 transcriptional regulation.","method":"ChIP assay, dual-luciferase reporter assay, EMSA","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and reporter assay are orthogonal methods, single lab, establishes c-Myc as a transcriptional regulator of RCL1","pmids":["27602772"],"is_preprint":false}],"current_model":"RCL1 (Rcl1) is an essential nucleolar endonuclease that cleaves pre-rRNA at a conserved site (A2 in yeast/A1 in zebrafish) to co-transcriptionally separate rRNA precursors destined for the small and large ribosomal subunits; it is recruited to pre-ribosomes as part of a GTP-regulated Bms1–Rcl1 subcomplex within the 90S SSU processome, its stability and nucleolar entry depend on physical interaction with BMS1 (with degradation via ubiquitin–proteasome if this interaction is disrupted), and its access to the cleavage site is controlled by Rrp5 as a checkpoint coupling 40S maturation to 60S assembly progression."},"narrative":{"mechanistic_narrative":"RCL1 is an essential nucleolar component of the small subunit (SSU) processome that drives pre-rRNA processing during ribosome biogenesis, where its activity co-transcriptionally separates the rRNA precursors destined for the small and large ribosomal subunits [PMID:10790377, PMID:21849504]. In yeast, recombinant Rcl1 is the endonuclease that cleaves pre-rRNA at site A2, and active-site mutations disrupt A2 processing in vitro and in vivo; its structure defines a novel nuclease class with overall homology to RNA cyclase enzymes but lacking their adenylyltransferase activity [PMID:21849504, PMID:21367972]. Rcl1 is delivered to pre-ribosomes by the essential GTPase Bms1: the two form a GTP-dependent subcomplex with U3 snoRNA in which Rcl1 promotes GDP/GTP exchange on Bms1, and this Bms1–Rcl1 module is one of the major structural modules visualized in the assembled 90S pre-ribosome [PMID:16307926, PMID:16376378, PMID:27419870]. In human cells the BMS1/RCL1 subcomplex joins the SSU processome after initial pre-rRNA association, and RCL1 protein stability and nucleolar entry depend on its physical interaction with BMS1, with loss of this interaction triggering ubiquitin–proteasome degradation [PMID:19332556, PMID:37451810]. Rcl1's access to its cleavage site is gated by Rrp5, which blocks cleavage until domain I of 25S rRNA is transcribed and Noc1/Noc2 binding switches Rrp5's RNA-binding mode, coupling 40S maturation to 60S assembly progression [PMID:31217256]. Across organisms the precise cleavage site differs—site A2 in yeast versus the A1-site in zebrafish, where rcl1 knockout causes small liver and exocrine pancreas and larval lethality—and human RCL1 active-site mutation did not impair 18S production, indicating organism-specific deployment of the enzyme [PMID:27034467, PMID:34019640]. RCL1 transcription is directly activated by c-Myc [PMID:27602772].","teleology":[{"year":2000,"claim":"Established RCL1 as an essential nucleolar factor for early pre-rRNA processing, placing it at the heart of small-subunit biogenesis rather than as a structural U3 snoRNP component.","evidence":"Genetic depletion, Co-IP, sucrose gradient sedimentation, and nucleolar localization in yeast","pmids":["10790377"],"confidence":"High","gaps":["Did not determine whether Rcl1 is itself the catalytic enzyme or a cofactor","Mechanism of recruitment to pre-ribosomes unknown"]},{"year":2005,"claim":"Defined how Rcl1 reaches pre-ribosomes by showing that the GTPase Bms1 delivers it in a GTP-dependent manner, and that Rcl1 reciprocally activates Bms1 nucleotide exchange within a U3-containing subcomplex.","evidence":"Thermodynamic binding assays, yeast Bms1 mutants, and in vitro reconstitution of the GTP-dependent subcomplex","pmids":["16307926","16376378"],"confidence":"High","gaps":["Did not establish Rcl1 catalytic function","Structural basis of the Bms1–Rcl1 interface not resolved"]},{"year":2011,"claim":"Identified Rcl1 as the A2-site endonuclease and provided its atomic structure, answering whether it is catalytic and defining it as a new nuclease class.","evidence":"In vitro endonuclease assay with recombinant Rcl1, active-site mutagenesis with in vivo validation, and X-ray crystallography in yeast","pmids":["21849504","21367972"],"confidence":"High","gaps":["Catalytic mechanism and metal/residue requirements not fully defined","Conserved oxyanion-binding site mutations were dispensable, leaving catalytic residues unidentified"]},{"year":2009,"claim":"Placed the BMS1/RCL1 subcomplex within the human SSU processome and established that it associates after initial pre-rRNA assembly.","evidence":"Reciprocal Co-IP, sucrose gradient sedimentation, and siRNA depletion in human cells","pmids":["19332556"],"confidence":"Medium","gaps":["Did not test whether human RCL1 is catalytically active","Order of module recruitment relative to other processome components incomplete"]},{"year":2014,"claim":"Extended Rcl1's processing role to mammals, linking its activity to ITS1 cleavages required for small-subunit maturation.","evidence":"siRNA knockdown with RAMP pre-rRNA ratio analysis by Northern blot in mouse cells and tissues","pmids":["25190460"],"confidence":"Medium","gaps":["Did not establish whether mouse Rcl1 cleaves directly or stimulates cleavage","Precise cleavage site not mapped"]},{"year":2016,"claim":"Resolved the structural placement of the Bms1–Rcl1 module within the assembled 90S pre-ribosome, and revealed a species discrepancy by showing human RCL1 active-site mutation did not impair 18S production.","evidence":"Cryo-EM of the C. thermophilum 90S pre-ribosome; in vivo mutagenesis of human RCL1","pmids":["27419870","27034467"],"confidence":"High","gaps":["Human catalytic contribution to cleavage remains unresolved","Whether another nuclease substitutes for RCL1 in human cells not determined here"]},{"year":2019,"claim":"Explained how Rcl1 cleavage is temporally gated, showing Rrp5 blocks access until 25S domain I transcription and Noc1/Noc2 binding licenses cleavage, coupling 40S and 60S assembly.","evidence":"Quantitative RNA binding and in vitro cleavage assays with in vivo genetic epistasis (Noc1 mutants, Rcl1 overexpression rescue) in yeast","pmids":["31217256"],"confidence":"High","gaps":["Structural basis of the Rrp5 RNA-binding-mode switch not visualized","Conservation of this checkpoint beyond yeast untested"]},{"year":2021,"claim":"Demonstrated organism-specific cleavage and physiological requirement, with zebrafish Rcl1 acting at the A1-site and its loss causing organ-specific defects and lethality.","evidence":"Zebrafish rcl1 knockout, cleavage-site mapping, RNA-seq, and phenotypic analysis","pmids":["34019640"],"confidence":"High","gaps":["Mechanistic basis for A1- vs A2-site preference across species unexplained","Tissue-selective vulnerability of liver/pancreas not mechanistically dissected"]},{"year":2022,"claim":"Defined the dependence of RCL1 stability and nucleolar localization on BMS1 binding, with proteasomal turnover when the interaction is lost, and positioned Rcl1 within Bms1's broader rDNA transcription–replication balancing role.","evidence":"Co-IP mapping the interaction domain, proteasome inhibitor experiments, ChIP-seq, and zebrafish genetic rescue","pmids":["37451810","34791311"],"confidence":"Medium","gaps":["E3 ligase responsible for RCL1 degradation not identified","Direct role of Rcl1 (vs Bms1) in transcription–replication coordination unclear"]},{"year":2021,"claim":"Identified upstream transcriptional control of RCL1 by c-Myc.","evidence":"ChIP, dual-luciferase reporter, and EMSA in HEK293T cells","pmids":["27602772"],"confidence":"Medium","gaps":["Physiological conditions driving c-Myc–dependent RCL1 expression not defined","Single cell-line context"]},{"year":null,"claim":"Whether human RCL1 retains catalytic endonuclease activity or serves a non-catalytic scaffolding role within the SSU processome remains unresolved given the negative human mutagenesis result.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No human in vitro cleavage reconstitution","Identity of the functional A1/A2 endonuclease in human cells unconfirmed"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[3,9]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[0,11]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,3,5]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[7]}],"complexes":["SSU processome (90S pre-ribosome)","Bms1–Rcl1–U3 snoRNA subcomplex"],"partners":["BMS1","U3 SNORNA","RRP5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y2P8","full_name":"RNA 3'-terminal phosphate cyclase-like protein","aliases":[],"length_aa":373,"mass_kda":40.8,"function":"As part of the small subunit (SSU) processome, it plays a role in 40S-ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1 and A2 that are required for proper maturation of the 18S RNA (By similarity). Activates BMS1 by promoting GDP/GTP exchange (By similarity). Does not have cyclase activity (By similarity)","subcellular_location":"Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/Q9Y2P8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RCL1","classification":"Common Essential","n_dependent_lines":1152,"n_total_lines":1208,"dependency_fraction":0.9536423841059603},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"BMS1","stoichiometry":10.0},{"gene":"FKBP5","stoichiometry":0.2},{"gene":"NPM1","stoichiometry":0.2},{"gene":"SSRP1","stoichiometry":0.2},{"gene":"ULK3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RCL1","total_profiled":1310},"omim":[{"mim_id":"611448","title":"BMS1 RIBOSOME BIOGENESIS FACTOR; BMS1","url":"https://www.omim.org/entry/611448"},{"mim_id":"611405","title":"RNA TERMINAL PHOSPHATE CYCLASE-LIKE 1; RCL1","url":"https://www.omim.org/entry/611405"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"liver","ntpm":229.4}],"url":"https://www.proteinatlas.org/search/RCL1"},"hgnc":{"alias_symbol":["RPCL1","RNAC"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y2P8","domains":[{"cath_id":"3.30.360.20","chopping":"187-288","consensus_level":"medium","plddt":95.0424,"start":187,"end":288},{"cath_id":"3.30.1370","chopping":"293-360","consensus_level":"medium","plddt":90.8538,"start":293,"end":360},{"cath_id":"3.30.110","chopping":"1-78","consensus_level":"medium","plddt":91.7268,"start":1,"end":78}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2P8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2P8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2P8-F1-predicted_aligned_error_v6.png","plddt_mean":93.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RCL1","jax_strain_url":"https://www.jax.org/strain/search?query=RCL1"},"sequence":{"accession":"Q9Y2P8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y2P8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y2P8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2P8"}},"corpus_meta":[{"pmid":"27419870","id":"PMC_27419870","title":"Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome.","date":"2016","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/27419870","citation_count":181,"is_preprint":false},{"pmid":"10790377","id":"PMC_10790377","title":"Rcl1p, the yeast protein similar to the RNA 3'-phosphate cyclase, associates with U3 snoRNP and is required for 18S rRNA biogenesis.","date":"2000","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/10790377","citation_count":82,"is_preprint":false},{"pmid":"15701756","id":"PMC_15701756","title":"A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon.","date":"2005","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/15701756","citation_count":80,"is_preprint":false},{"pmid":"16307926","id":"PMC_16307926","title":"An essential GTPase promotes assembly of preribosomal RNA processing complexes.","date":"2005","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/16307926","citation_count":69,"is_preprint":false},{"pmid":"25462922","id":"PMC_25462922","title":"Detection and quantification of hepatitis A virus and norovirus in Spanish authorized shellfish harvesting areas.","date":"2014","source":"International journal of food microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/25462922","citation_count":64,"is_preprint":false},{"pmid":"21849504","id":"PMC_21849504","title":"Rcl1 protein, a novel nuclease for 18 S ribosomal RNA production.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21849504","citation_count":62,"is_preprint":false},{"pmid":"19332556","id":"PMC_19332556","title":"A novel small-subunit processome assembly intermediate that contains the U3 snoRNP, nucleolin, RRP5, and DBP4.","date":"2009","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/19332556","citation_count":59,"is_preprint":false},{"pmid":"25190460","id":"PMC_25190460","title":"Two orthogonal cleavages separate subunit RNAs in mouse ribosome biogenesis.","date":"2014","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/25190460","citation_count":57,"is_preprint":false},{"pmid":"27034467","id":"PMC_27034467","title":"The PIN domain endonuclease Utp24 cleaves pre-ribosomal RNA at two coupled sites in yeast and humans.","date":"2016","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/27034467","citation_count":50,"is_preprint":false},{"pmid":"25790031","id":"PMC_25790031","title":"Small regulatory RNA-induced growth rate heterogeneity of Bacillus subtilis.","date":"2015","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/25790031","citation_count":38,"is_preprint":false},{"pmid":"23083835","id":"PMC_23083835","title":"Early and late peritoneal and hepatic changes in goats immunized with recombinant cathepsin L1 and infected with Fasciola hepatica.","date":"2012","source":"Journal of comparative pathology","url":"https://pubmed.ncbi.nlm.nih.gov/23083835","citation_count":36,"is_preprint":false},{"pmid":"16376378","id":"PMC_16376378","title":"GTP-dependent formation of a ribonucleoprotein subcomplex required for ribosome biogenesis.","date":"2005","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16376378","citation_count":34,"is_preprint":false},{"pmid":"27113935","id":"PMC_27113935","title":"Evaluation of Circulatory RNA-Based Biomarker Panel in Hepatocellular Carcinoma.","date":"2016","source":"Molecular diagnosis & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/27113935","citation_count":32,"is_preprint":false},{"pmid":"23021545","id":"PMC_23021545","title":"Ribosome biogenesis factor Bms1-like is essential for liver development in zebrafish.","date":"2012","source":"Journal of genetics and genomics = Yi chuan xue bao","url":"https://pubmed.ncbi.nlm.nih.gov/23021545","citation_count":29,"is_preprint":false},{"pmid":"28322274","id":"PMC_28322274","title":"A rare missense variant in RCL1 segregates with depression in extended families.","date":"2017","source":"Molecular psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/28322274","citation_count":28,"is_preprint":false},{"pmid":"29113909","id":"PMC_29113909","title":"The chaperone dynein LL1 mediates cytoplasmic transport of empty and mature hepatitis B virus capsids.","date":"2017","source":"Journal of hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/29113909","citation_count":28,"is_preprint":false},{"pmid":"31284466","id":"PMC_31284466","title":"Detection of Hepatitis E Virus in Shellfish Harvesting Areas from Galicia (Northwestern Spain).","date":"2019","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/31284466","citation_count":27,"is_preprint":false},{"pmid":"9461341","id":"PMC_9461341","title":"An antisense RNA in IS30 regulates the translational expression of the transposase.","date":"1997","source":"Biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9461341","citation_count":26,"is_preprint":false},{"pmid":"32395117","id":"PMC_32395117","title":"Preclinical Studies of the Off-Target Reactivity of AFP158-Specific TCR Engineered T Cells.","date":"2020","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/32395117","citation_count":24,"is_preprint":false},{"pmid":"32911699","id":"PMC_32911699","title":"An Increased Burden of Highly Active Retrotransposition Competent L1s Is Associated with Parkinson's Disease Risk and Progression in the PPMI Cohort.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32911699","citation_count":24,"is_preprint":false},{"pmid":"27602772","id":"PMC_27602772","title":"c-Myc targeted regulators of cell metabolism in a transgenic mouse model of papillary lung adenocarcinoma.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27602772","citation_count":23,"is_preprint":false},{"pmid":"21367972","id":"PMC_21367972","title":"Crystal structure of Rcl1, an essential component of the eukaryal pre-rRNA processosome implicated in 18s rRNA biogenesis.","date":"2011","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/21367972","citation_count":19,"is_preprint":false},{"pmid":"30692270","id":"PMC_30692270","title":"Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation.","date":"2019","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/30692270","citation_count":19,"is_preprint":false},{"pmid":"35167702","id":"PMC_35167702","title":"Maize RNA 3'-terminal phosphate cyclase-like protein promotes 18S pre-rRNA cleavage and is important for kernel development.","date":"2022","source":"The Plant cell","url":"https://pubmed.ncbi.nlm.nih.gov/35167702","citation_count":17,"is_preprint":false},{"pmid":"34019640","id":"PMC_34019640","title":"Rcl1 depletion impairs 18S pre-rRNA processing at the A1-site and up-regulates a cohort of ribosome biogenesis genes in zebrafish.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/34019640","citation_count":16,"is_preprint":false},{"pmid":"33597717","id":"PMC_33597717","title":"RCL1 copy number variants are associated with a range of neuropsychiatric phenotypes.","date":"2021","source":"Molecular psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/33597717","citation_count":15,"is_preprint":false},{"pmid":"31565884","id":"PMC_31565884","title":"Transcriptome Analysis Identifies an Attenuated Local Immune Response in Invasive Nonfunctioning Pituitary Adenomas.","date":"2019","source":"Endocrinology and metabolism (Seoul, Korea)","url":"https://pubmed.ncbi.nlm.nih.gov/31565884","citation_count":15,"is_preprint":false},{"pmid":"29199372","id":"PMC_29199372","title":"Comparative assessment of recombinant and native immunogenic forms of Fasciola hepatica proteins for serodiagnosis of sheep fasciolosis.","date":"2017","source":"Parasitology research","url":"https://pubmed.ncbi.nlm.nih.gov/29199372","citation_count":15,"is_preprint":false},{"pmid":"31217256","id":"PMC_31217256","title":"Rrp5 establishes a checkpoint for 60S assembly during 40S maturation.","date":"2019","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/31217256","citation_count":14,"is_preprint":false},{"pmid":"30454683","id":"PMC_30454683","title":"Line-1: Implications in the etiology of cancer, clinical applications, and pharmacologic targets.","date":"2018","source":"Mutation research. Reviews in mutation research","url":"https://pubmed.ncbi.nlm.nih.gov/30454683","citation_count":12,"is_preprint":false},{"pmid":"33187550","id":"PMC_33187550","title":"Frequency and methylation status of selected retrotransposition competent L1 loci in amyotrophic lateral sclerosis.","date":"2020","source":"Molecular brain","url":"https://pubmed.ncbi.nlm.nih.gov/33187550","citation_count":12,"is_preprint":false},{"pmid":"36056451","id":"PMC_36056451","title":"The expression of GapA and CrmA correlates with the Mycoplasma gallisepticum in vitro infection process in chicken TOCs.","date":"2022","source":"Veterinary research","url":"https://pubmed.ncbi.nlm.nih.gov/36056451","citation_count":9,"is_preprint":false},{"pmid":"23838471","id":"PMC_23838471","title":"Peripheral blood lymphocyte subsets in Fasciola hepatica infected and immunised goats.","date":"2013","source":"Veterinary immunology and immunopathology","url":"https://pubmed.ncbi.nlm.nih.gov/23838471","citation_count":9,"is_preprint":false},{"pmid":"37175867","id":"PMC_37175867","title":"Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging.","date":"2023","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37175867","citation_count":8,"is_preprint":false},{"pmid":"28132487","id":"PMC_28132487","title":"RNA 3'-terminal phosphate cyclases and cyclase-like proteins.","date":"2016","source":"Postepy biochemii","url":"https://pubmed.ncbi.nlm.nih.gov/28132487","citation_count":8,"is_preprint":false},{"pmid":"35053828","id":"PMC_35053828","title":"Pain-Related Abnormal Neuronal Synchronization of the Nucleus Accumbens in Parkinson's Disease.","date":"2022","source":"Brain sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35053828","citation_count":7,"is_preprint":false},{"pmid":"27401010","id":"PMC_27401010","title":"Association of BAK1 single nucleotide polymorphism with a risk for dengue hemorrhagic fever.","date":"2016","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/27401010","citation_count":7,"is_preprint":false},{"pmid":"35264160","id":"PMC_35264160","title":"Rcl1 suppresses tumor progression of hepatocellular carcinoma: a comprehensive analysis of bioinformatics and in vitro experiments.","date":"2022","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/35264160","citation_count":6,"is_preprint":false},{"pmid":"34791311","id":"PMC_34791311","title":"Nucleolar GTPase Bms1 displaces Ttf1 from RFB-sites to balance progression of rDNA transcription and replication.","date":"2022","source":"Journal of molecular cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/34791311","citation_count":6,"is_preprint":false},{"pmid":"3024712","id":"PMC_3024712","title":"Synthesis of in vitro Co1E1 transcripts with 5'-terminal ribonucleotides that exhibit noncomplementarity with the DNA template.","date":"1986","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/3024712","citation_count":6,"is_preprint":false},{"pmid":"36246620","id":"PMC_36246620","title":"Integration of three machine learning algorithms identifies characteristic RNA binding proteins linked with diagnosis, immunity and pyroptosis of IgA nephropathy.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36246620","citation_count":5,"is_preprint":false},{"pmid":"3092859","id":"PMC_3092859","title":"Mitomycin C-induced bidirectional transcription from the colicin E1 promoter region in plasmid ColE1.","date":"1986","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/3092859","citation_count":5,"is_preprint":false},{"pmid":"37451810","id":"PMC_37451810","title":"Stability and function of RCL1 are dependent on the interaction with BMS1.","date":"2024","source":"Journal of molecular cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/37451810","citation_count":4,"is_preprint":false},{"pmid":"33971667","id":"PMC_33971667","title":"Identification of multiple RNAs using feature fusion.","date":"2021","source":"Briefings in bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/33971667","citation_count":4,"is_preprint":false},{"pmid":"32655600","id":"PMC_32655600","title":"Fine Mapping to Identify the Functional Genetic Locus for Red Coloration in Pyropia yezoensis Thallus.","date":"2020","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/32655600","citation_count":4,"is_preprint":false},{"pmid":"41137173","id":"PMC_41137173","title":"Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes.","date":"2025","source":"Genome medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41137173","citation_count":3,"is_preprint":false},{"pmid":"31235766","id":"PMC_31235766","title":"Neutrophil GM-CSF signaling in inflammatory bowel disease patients is influenced by non-coding genetic variants.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/31235766","citation_count":3,"is_preprint":false},{"pmid":"39462074","id":"PMC_39462074","title":"The effects of RT-qPCR standards on reproducibility and comparability in monitoring SARS-CoV-2 levels in wastewater.","date":"2024","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39462074","citation_count":3,"is_preprint":false},{"pmid":"12643306","id":"PMC_12643306","title":"Stereochemistry of (E)- and (Z)-1,1'-dichlorobifluorenylidenes, substituted overcrowded fullerene fragments.","date":"2002","source":"Enantiomer","url":"https://pubmed.ncbi.nlm.nih.gov/12643306","citation_count":2,"is_preprint":false},{"pmid":"40196253","id":"PMC_40196253","title":"Whole-Genome Sequencing Reveals Individual and Cohort Level Insights into Chromosome 9p Syndromes.","date":"2025","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40196253","citation_count":1,"is_preprint":false},{"pmid":"38433785","id":"PMC_38433785","title":"Roles of Nucleolar Factor RCL1 in Itraconazole Resistance of Clinical Candida albicans Under Different Stress Conditions.","date":"2024","source":"Infection and drug resistance","url":"https://pubmed.ncbi.nlm.nih.gov/38433785","citation_count":0,"is_preprint":false},{"pmid":"32884958","id":"PMC_32884958","title":"Evaluation of Gelatinolytic and Collagenolytic Activity of Fasciola hepatica Recombinant Cathepsin-L1.","date":"2020","source":"Iranian journal of biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/32884958","citation_count":0,"is_preprint":false},{"pmid":"40475058","id":"PMC_40475058","title":"MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data.","date":"2025","source":"Frontiers in bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/40475058","citation_count":0,"is_preprint":false},{"pmid":"41855910","id":"PMC_41855910","title":"Bimetallic CuCo-based metal-organic framework/graphene oxide composite-modified electrode as an efficient miRNA-208a detection biosensing platform.","date":"2026","source":"Journal of colloid and interface science","url":"https://pubmed.ncbi.nlm.nih.gov/41855910","citation_count":0,"is_preprint":false},{"pmid":"8284914","id":"PMC_8284914","title":"[A method of competitive dot hydridization for genotyping influenza A viruses].","date":"1993","source":"Voprosy virusologii","url":"https://pubmed.ncbi.nlm.nih.gov/8284914","citation_count":0,"is_preprint":false},{"pmid":"42135716","id":"PMC_42135716","title":"Multi-omics integration identifies ribosome biogenesis-active macrophage subpopulation and its key gene GNL2 in driving liver hepatocellular carcinoma progression and mechanisms.","date":"2026","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/42135716","citation_count":0,"is_preprint":false},{"pmid":"31376344","id":"PMC_31376344","title":"Analysis of the amino acid sequences of 18S RNA strains of Babesia canis isolated from dogs, including the analysis of serum proteome of protozoa infected dogs.","date":"2019","source":"Annals of parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/31376344","citation_count":0,"is_preprint":false},{"pmid":"8758494","id":"PMC_8758494","title":"[Resistance of cytomegalovirus to ganciclovir: rapid detection of the mutations 460 of the UL97 phosphotransferase].","date":"1996","source":"Pathologie-biologie","url":"https://pubmed.ncbi.nlm.nih.gov/8758494","citation_count":0,"is_preprint":false},{"pmid":"40576538","id":"PMC_40576538","title":"Investigation of the role of the LC3 conjugation system in autophagy for human reward system reactivity.","date":"2025","source":"The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/40576538","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":31315,"output_tokens":3844,"usd":0.075802,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11530,"output_tokens":3533,"usd":0.072987,"stage2_stop_reason":"end_turn"},"total_usd":0.148789,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"Rcl1p (yeast RCL1 ortholog) is an essential nucleolar protein required for pre-rRNA processing at sites A0, A1, and A2; its depletion leads to a strong decrease in 18S rRNA and 40S ribosomal subunit levels. Rcl1p co-immunoprecipitates with U3 snoRNP components but is not a structural component of U3 snoRNP; most Rcl1p sediments with 70–80S pre-ribosomal particles.\",\n      \"method\": \"Genetic depletion/inactivation in yeast, immunoprecipitation, sucrose gradient sedimentation, nucleolar localization by microscopy\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (genetic depletion, Co-IP, gradient analysis, localization), replicated across species (mouse ortholog complements yeast)\",\n      \"pmids\": [\"10790377\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Bms1 (an essential GTPase) delivers Rcl1 to pre-ribosomes in a GTP-dependent manner. Rcl1 binding to Bms1 is thermodynamically coupled to GTP and U3 snoRNA binding; a Bms1 mutant defective for Rcl1 binding severely limits Rcl1 recruitment to pre-ribosomes. The C-terminal domain of Bms1 acts as an intramolecular GTPase-activating protein.\",\n      \"method\": \"Thermodynamic binding assays, yeast genetics with Bms1 mutants, pre-ribosome association assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — thermodynamic coupling measured quantitatively, Bms1 mutant defective for Rcl1 binding validated in vivo, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"16307926\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Bms1, Rcl1, and U3 snoRNA form a stable GTP-dependent subcomplex; Rcl1 activates Bms1 by promoting GDP/GTP exchange, analogous to ribosome-promoted nucleotide exchange in translation elongation factor EF-G. GTP binding (but not GDP) is required for stable subcomplex formation.\",\n      \"method\": \"Quantitative thermodynamic analysis of GTP-dependent subcomplex formation in vitro\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with complete thermodynamic analysis, single lab but multiple binding measurements\",\n      \"pmids\": [\"16376378\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Recombinant Rcl1 cleaves pre-rRNA at site A2 in vitro in an endonucleolytic reaction sensitive to nearby RNA mutations that inhibit cleavage in vivo. Mutations in Rcl1 disrupt rRNA processing at site A2 both in vivo and in vitro, establishing Rcl1 as the endonuclease responsible for the A2 cleavage that co-transcriptionally separates rRNAs destined for the small and large ribosomal subunits. Rcl1 defines a novel class of nucleases with no homology to other known endonucleases.\",\n      \"method\": \"In vitro endonuclease assay with recombinant Rcl1, site-directed mutagenesis, in vivo rRNA processing assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of endonuclease activity, active-site mutagenesis with in vivo validation, multiple orthogonal methods\",\n      \"pmids\": [\"21849504\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Crystal structure of yeast Rcl1 at 2.6 Å resolution reveals a modular 4-domain architecture with overall homology to RNA cyclase (Rtc) enzymes but local differences that explain why Rcl1 lacks the metal-dependent adenylyltransferase activity of Rtc enzymes. Mutations in and around a conserved oxyanion-binding site did not affect Rcl1 activity in vivo, arguing against a catalytic or RNA-binding role for this site.\",\n      \"method\": \"X-ray crystallography, in vivo mutagenesis of putative active-site residues\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with functional mutagenesis validation, single lab\",\n      \"pmids\": [\"21367972\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"In human cells, the BMS1/RCL1 subcomplex is a component of the SSU processome, a large machine required for 18S rRNA processing. The BMS1/RCL1 subcomplex is absent from a novel 50S U3 snoRNP assembly intermediate that accumulates when pre-rRNA transcription is blocked or tUTP proteins are depleted, indicating BMS1/RCL1 join the processome after initial pre-rRNA association.\",\n      \"method\": \"Co-immunoprecipitation, sucrose gradient sedimentation, siRNA depletion\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and gradient analysis, human cell system, single lab with orthogonal depletion experiments\",\n      \"pmids\": [\"19332556\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Knockdown of mouse Rcl1 impairs endonucleolytic cleavages of pre-rRNA in the ITS1 region required for small ribosomal subunit maturation, as characterized by RAMP (Ratio Analysis of Multiple Precursors) profiling. The data suggest that completion of early small-subunit maturation (requiring Rcl1) triggers release from the common pre-rRNA transcript by stimulating cleavage at the proximal ITS1 site.\",\n      \"method\": \"siRNA knockdown, RAMP pre-rRNA ratio analysis by Northern blotting in mouse cells and tissues\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — quantitative rRNA precursor analysis with defined knockdown, single lab, novel RAMP method\",\n      \"pmids\": [\"25190460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome identifies the Bms1–Rcl1 module as one of five major modules organized around 5'-ETS and partially folded 18S rRNA within the 90S particle architecture.\",\n      \"method\": \"Cryo-EM structure determination of the 90S pre-ribosome\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure of the complete 90S pre-ribosome, Bms1–Rcl1 module directly visualized in structural context\",\n      \"pmids\": [\"27419870\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"In human cells, mutation of the potential A2-site endonuclease RCL1 did not affect 18S rRNA production, whereas an intact PIN domain in UTP24 was required for accurate cleavages at sites 1 and 2a. This negative result for human RCL1 contrasts with yeast data where Rcl1 is the A2 endonuclease.\",\n      \"method\": \"In vivo mutagenesis of human RCL1 active-site residues, pre-rRNA processing analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct in vivo mutagenesis experiment, single lab; finding is a negative result for human RCL1 specifically\",\n      \"pmids\": [\"27034467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Rrp5 blocks Rcl1 access to the nascent pre-rRNA cleavage site early during ribosome assembly, thereby delaying separation of small and large subunit pre-rRNAs until domain I of 25S rRNA is transcribed. Upon transcription of domain I, 60S assembly factors Noc1/Noc2 bind both this RNA and Rrp5, changing Rrp5's RNA-binding mode to permit Rcl1-mediated cleavage. Overexpression of wild-type but not catalytically inactive Rcl1 rescues subunit separation defects caused by Noc1 HEAT-repeat mutants in vivo.\",\n      \"method\": \"Quantitative RNA binding assays, in vitro cleavage assays, genetic epistasis with Noc1 mutants and Rcl1 overexpression in yeast\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro quantitative binding and cleavage combined with in vivo genetic rescue, multiple orthogonal methods, clear epistasis established\",\n      \"pmids\": [\"31217256\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In zebrafish, depletion of Rcl1 mainly impairs cleavage at the A1-site (the link between 5'ETS and 18S rRNA) rather than the A2-site as in yeast. rcl1−/− mutants exhibit small liver and exocrine pancreas and die before 15 days post-fertilization. RNA-seq reveals up-regulation of a cohort of ribosome biogenesis and tRNA production genes upon Rcl1 deficiency.\",\n      \"method\": \"Zebrafish rcl1 knockout, pre-rRNA processing site mapping by primer extension/Northern blotting, RNA-seq, phenotypic characterization\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic knockout with direct rRNA processing analysis and transcriptome profiling, site-specific cleavage mapped, clear organ phenotype\",\n      \"pmids\": [\"34019640\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RCL1 protein stability and nucleolar localization depend on its physical interaction with BMS1. When this interaction is disrupted, RCL1 is degraded via the ubiquitination–proteasome pathway. Overexpression of RCL1 in BMS1-knockdown cells partially rescues defects in 18S rRNA processing and cell proliferation. Hepatocyte-specific overexpression of Rcl1 rescues zebrafish liver development in a bms1l substitution (but not knockout) mutant, attributed to residual nucleolar entry of Rcl1 in the former.\",\n      \"method\": \"Co-immunoprecipitation identifying RCL1-interacting domain in BMS1, proteasome inhibitor experiments, zebrafish genetic rescue experiments, cell proliferation and rRNA processing assays\",\n      \"journal\": \"Journal of molecular cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP identifying interaction domain, proteasome pathway validated pharmacologically, in vivo genetic rescue in zebrafish with mechanistic specificity\",\n      \"pmids\": [\"37451810\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Zebrafish Bms1 interacts with Rcl1 and also with Ttf1 (a replication fork barrier binding protein). Loss of Bms1l upregulates rDNA transcription, causes replication-fork stall, and arrests the cell cycle at S-to-G2 transition. Bms1 GTPase activity is required to disassociate the Ttf1–RFB complex, balancing rDNA transcription and replication during S-phase.\",\n      \"method\": \"Co-immunoprecipitation (Bms1–Rcl1 and Bms1–Ttf1), ChIP-seq for Ttf1 RFB sites, zebrafish loss-of-function genetic analysis, cell cycle and DNA damage marker analysis\",\n      \"journal\": \"Journal of molecular cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus ChIP-seq plus in vivo genetic data, single lab, establishes Rcl1 in context of broader Bms1 function\",\n      \"pmids\": [\"34791311\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"c-Myc directly occupies predicted transcription factor binding sites in the RCL1 promoter region, as confirmed by ChIP assay in HEK293T cells overexpressing ectopic c-Myc, and dual-luciferase reporter assays demonstrated c-Myc functional relevance for RCL1 transcriptional regulation.\",\n      \"method\": \"ChIP assay, dual-luciferase reporter assay, EMSA\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and reporter assay are orthogonal methods, single lab, establishes c-Myc as a transcriptional regulator of RCL1\",\n      \"pmids\": [\"27602772\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RCL1 (Rcl1) is an essential nucleolar endonuclease that cleaves pre-rRNA at a conserved site (A2 in yeast/A1 in zebrafish) to co-transcriptionally separate rRNA precursors destined for the small and large ribosomal subunits; it is recruited to pre-ribosomes as part of a GTP-regulated Bms1–Rcl1 subcomplex within the 90S SSU processome, its stability and nucleolar entry depend on physical interaction with BMS1 (with degradation via ubiquitin–proteasome if this interaction is disrupted), and its access to the cleavage site is controlled by Rrp5 as a checkpoint coupling 40S maturation to 60S assembly progression.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RCL1 is an essential nucleolar component of the small subunit (SSU) processome that drives pre-rRNA processing during ribosome biogenesis, where its activity co-transcriptionally separates the rRNA precursors destined for the small and large ribosomal subunits [#0, #3]. In yeast, recombinant Rcl1 is the endonuclease that cleaves pre-rRNA at site A2, and active-site mutations disrupt A2 processing in vitro and in vivo; its structure defines a novel nuclease class with overall homology to RNA cyclase enzymes but lacking their adenylyltransferase activity [#3, #4]. Rcl1 is delivered to pre-ribosomes by the essential GTPase Bms1: the two form a GTP-dependent subcomplex with U3 snoRNA in which Rcl1 promotes GDP/GTP exchange on Bms1, and this Bms1–Rcl1 module is one of the major structural modules visualized in the assembled 90S pre-ribosome [#1, #2, #7]. In human cells the BMS1/RCL1 subcomplex joins the SSU processome after initial pre-rRNA association, and RCL1 protein stability and nucleolar entry depend on its physical interaction with BMS1, with loss of this interaction triggering ubiquitin–proteasome degradation [#5, #11]. Rcl1's access to its cleavage site is gated by Rrp5, which blocks cleavage until domain I of 25S rRNA is transcribed and Noc1/Noc2 binding switches Rrp5's RNA-binding mode, coupling 40S maturation to 60S assembly progression [#9]. Across organisms the precise cleavage site differs—site A2 in yeast versus the A1-site in zebrafish, where rcl1 knockout causes small liver and exocrine pancreas and larval lethality—and human RCL1 active-site mutation did not impair 18S production, indicating organism-specific deployment of the enzyme [#8, #10]. RCL1 transcription is directly activated by c-Myc [#13].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established RCL1 as an essential nucleolar factor for early pre-rRNA processing, placing it at the heart of small-subunit biogenesis rather than as a structural U3 snoRNP component.\",\n      \"evidence\": \"Genetic depletion, Co-IP, sucrose gradient sedimentation, and nucleolar localization in yeast\",\n      \"pmids\": [\"10790377\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not determine whether Rcl1 is itself the catalytic enzyme or a cofactor\", \"Mechanism of recruitment to pre-ribosomes unknown\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Defined how Rcl1 reaches pre-ribosomes by showing that the GTPase Bms1 delivers it in a GTP-dependent manner, and that Rcl1 reciprocally activates Bms1 nucleotide exchange within a U3-containing subcomplex.\",\n      \"evidence\": \"Thermodynamic binding assays, yeast Bms1 mutants, and in vitro reconstitution of the GTP-dependent subcomplex\",\n      \"pmids\": [\"16307926\", \"16376378\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish Rcl1 catalytic function\", \"Structural basis of the Bms1–Rcl1 interface not resolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identified Rcl1 as the A2-site endonuclease and provided its atomic structure, answering whether it is catalytic and defining it as a new nuclease class.\",\n      \"evidence\": \"In vitro endonuclease assay with recombinant Rcl1, active-site mutagenesis with in vivo validation, and X-ray crystallography in yeast\",\n      \"pmids\": [\"21849504\", \"21367972\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Catalytic mechanism and metal/residue requirements not fully defined\", \"Conserved oxyanion-binding site mutations were dispensable, leaving catalytic residues unidentified\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Placed the BMS1/RCL1 subcomplex within the human SSU processome and established that it associates after initial pre-rRNA assembly.\",\n      \"evidence\": \"Reciprocal Co-IP, sucrose gradient sedimentation, and siRNA depletion in human cells\",\n      \"pmids\": [\"19332556\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not test whether human RCL1 is catalytically active\", \"Order of module recruitment relative to other processome components incomplete\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Extended Rcl1's processing role to mammals, linking its activity to ITS1 cleavages required for small-subunit maturation.\",\n      \"evidence\": \"siRNA knockdown with RAMP pre-rRNA ratio analysis by Northern blot in mouse cells and tissues\",\n      \"pmids\": [\"25190460\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not establish whether mouse Rcl1 cleaves directly or stimulates cleavage\", \"Precise cleavage site not mapped\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Resolved the structural placement of the Bms1–Rcl1 module within the assembled 90S pre-ribosome, and revealed a species discrepancy by showing human RCL1 active-site mutation did not impair 18S production.\",\n      \"evidence\": \"Cryo-EM of the C. thermophilum 90S pre-ribosome; in vivo mutagenesis of human RCL1\",\n      \"pmids\": [\"27419870\", \"27034467\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Human catalytic contribution to cleavage remains unresolved\", \"Whether another nuclease substitutes for RCL1 in human cells not determined here\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Explained how Rcl1 cleavage is temporally gated, showing Rrp5 blocks access until 25S domain I transcription and Noc1/Noc2 binding licenses cleavage, coupling 40S and 60S assembly.\",\n      \"evidence\": \"Quantitative RNA binding and in vitro cleavage assays with in vivo genetic epistasis (Noc1 mutants, Rcl1 overexpression rescue) in yeast\",\n      \"pmids\": [\"31217256\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the Rrp5 RNA-binding-mode switch not visualized\", \"Conservation of this checkpoint beyond yeast untested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrated organism-specific cleavage and physiological requirement, with zebrafish Rcl1 acting at the A1-site and its loss causing organ-specific defects and lethality.\",\n      \"evidence\": \"Zebrafish rcl1 knockout, cleavage-site mapping, RNA-seq, and phenotypic analysis\",\n      \"pmids\": [\"34019640\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic basis for A1- vs A2-site preference across species unexplained\", \"Tissue-selective vulnerability of liver/pancreas not mechanistically dissected\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined the dependence of RCL1 stability and nucleolar localization on BMS1 binding, with proteasomal turnover when the interaction is lost, and positioned Rcl1 within Bms1's broader rDNA transcription–replication balancing role.\",\n      \"evidence\": \"Co-IP mapping the interaction domain, proteasome inhibitor experiments, ChIP-seq, and zebrafish genetic rescue\",\n      \"pmids\": [\"37451810\", \"34791311\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ligase responsible for RCL1 degradation not identified\", \"Direct role of Rcl1 (vs Bms1) in transcription–replication coordination unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified upstream transcriptional control of RCL1 by c-Myc.\",\n      \"evidence\": \"ChIP, dual-luciferase reporter, and EMSA in HEK293T cells\",\n      \"pmids\": [\"27602772\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological conditions driving c-Myc–dependent RCL1 expression not defined\", \"Single cell-line context\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether human RCL1 retains catalytic endonuclease activity or serves a non-catalytic scaffolding role within the SSU processome remains unresolved given the negative human mutagenesis result.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No human in vitro cleavage reconstitution\", \"Identity of the functional A1/A2 endonuclease in human cells unconfirmed\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [3, 9]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0, 11]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 3, 5]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"complexes\": [\"SSU processome (90S pre-ribosome)\", \"Bms1–Rcl1–U3 snoRNA subcomplex\"],\n    \"partners\": [\"BMS1\", \"U3 snoRNA\", \"RRP5\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}