{"gene":"RTRAF","run_date":"2026-06-10T07:46:28","timeline":{"discoveries":[{"year":2006,"finding":"hCLE/CGI-99 (RTRAF) co-immunoprecipitates with different phosphorylated forms of RNA polymerase II (RNAP II) largest subunit and colocalizes with RNAP II by confocal microscopy. hCLE localizes to nuclear sites of active mRNA synthesis (colocalization with Br-UTP incorporation sites). RNAi-mediated silencing of hCLE reduced RNAP II transcript synthesis by ~50%, and microarray analysis showed >90% of differentially expressed genes were downregulated, establishing hCLE as a positive modulator of RNAP II transcriptional activity.","method":"Co-immunoprecipitation, confocal microscopy colocalization, in situ Br-UTP incorporation, RNAi knockdown, microarray expression profiling","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP and orthogonal localization/functional assays in single lab study","pmids":["16950395"],"is_preprint":false},{"year":2004,"finding":"CGI-99 (RTRAF) physically interacts with the C-terminal domain of human ninein (hNinein), as demonstrated by yeast two-hybrid screening and in vitro GST pull-down assay. CGI-99 forms homodimers via its C-terminal domain (which overlaps with the hNinein binding site). In a kinase assay, CGI-99 binding to hNinein completely blocks phosphorylation of hNinein by GSK3beta. The N-terminal region of CGI-99 harbors transcriptional activity.","method":"Yeast two-hybrid screening, GST pull-down assay, in vitro kinase assay, transcriptional activity assay","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid confirmed by GST pull-down and kinase assay, single lab with multiple orthogonal methods","pmids":["15147888"],"is_preprint":false},{"year":2011,"finding":"hCLE/C14orf166 (RTRAF) interacts with the influenza A virus polymerase complex (not just PA subunit alone) and colocalizes with viral ribonucleoproteins in infected cells. Silencing of hCLE reduces viral polymerase activity, viral RNA transcription, viral RNA replication, virus titer, and viral particle production, establishing hCLE as a host cellular factor required for influenza virus replication.","method":"Co-immunoprecipitation, confocal microscopy colocalization, siRNA knockdown with viral polymerase activity assay, viral titer measurement","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus functional knockdown with multiple viral replication readouts, single lab","pmids":["21900157"],"is_preprint":false},{"year":2012,"finding":"PTPIP51 (regulator of microtubule dynamics protein 3) interacts with CGI-99 (RTRAF) both in vitro and in vivo. The PTPIP51/CGI-99 complex localizes to the equatorial region during mitosis. Duolink proximity ligation assays confirmed in-cell association of PTPIP51 with CGI-99.","method":"In vitro binding assay, in vivo co-immunoprecipitation, Duolink proximity ligation assay, confocal microscopy","journal":"Biomolecules","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, limited mechanistic follow-up beyond localization of complex at equatorial plate","pmids":["24970130"],"is_preprint":false},{"year":2017,"finding":"CGI-99 (RTRAF) activates autocrine IL-6/STAT3 signaling in breast cancer cells by increasing accumulation and activity of RNA polymerase II and the p300 cofactor at the proximal promoter of IL-6. This mechanism drives breast cancer stem cell properties and lung colonization in vivo. The IL-6 receptor antibody tocilizumab abrogates CGI-99-induced metastasis in vivo, placing CGI-99 upstream of the IL-6/STAT3 axis.","method":"ChIP (RNA Pol II and p300 at IL-6 promoter), in vivo tumor colonization assay, STAT3 activity assay, siRNA knockdown, tocilizumab rescue experiment","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP mechanistic evidence plus in vivo rescue experiment, single lab with multiple orthogonal methods","pmids":["28166202"],"is_preprint":false},{"year":2019,"finding":"hCLE/RTRAF forms a cap-binding complex with DDX1, HSPC117, and FAM98B in HEK293T cells. All four proteins bind to cap analog-containing resins. Competition and elution experiments show that hCLE complex binding to cap resins is independent of eIF4E. Purified hCLE alone binds cap with low affinity, indicating that interacting proteins modulate its cap association. hCLE silencing reduces accumulation of complex partners and decreases mRNA translation. RNAs associated with hCLE are enriched for mRNAs involved in translation.","method":"Co-immunoprecipitation, cap analog resin pulldown, competition/elution binding assay, purified protein cap-binding assay, siRNA knockdown with translation assay, RNA immunoprecipitation and sequencing","journal":"Frontiers in physiology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal biochemical methods (co-IP, cap resin pulldown with competition, purified protein binding, functional translation assay, RNA-seq), single lab but rigorous mechanistic dissection","pmids":["30833903"],"is_preprint":false}],"current_model":"RTRAF (hCLE/CGI-99/C14orf166) is a positive modulator of RNA polymerase II transcription that forms a cap-binding complex with DDX1, HSPC117, and FAM98B to promote mRNA translation; it physically interacts with ninein and blocks its phosphorylation by GSK3beta at the centrosome, co-immunoprecipitates with the influenza virus polymerase complex to support viral replication, and in cancer cells drives autocrine IL-6/STAT3 signaling by enhancing RNA Pol II and p300 activity at the IL-6 promoter."},"narrative":{"mechanistic_narrative":"RTRAF (hCLE/CGI-99/C14orf166) is a multifunctional positive modulator of gene expression that acts at both the transcriptional and translational levels [PMID:16950395, PMID:30833903]. In the nucleus it co-immunoprecipitates with multiple phosphorylated forms of the RNA polymerase II largest subunit, localizes to sites of active mRNA synthesis, and is required for normal Pol II transcript output, with its silencing causing broad downregulation of gene expression [PMID:16950395]. In the cytoplasm it assembles a cap-binding complex with DDX1, HSPC117, and FAM98B that associates with the mRNA cap independently of eIF4E and promotes translation, with the partner proteins stabilizing each other and enhancing RTRAF's intrinsically low cap affinity [PMID:30833903]. RTRAF also engages the influenza A virus polymerase complex and is required for viral RNA transcription, replication, and particle production, indicating that its gene-expression machinery is co-opted during infection [PMID:21900157]. Through its C-terminal domain it homodimerizes and binds the centrosomal protein ninein, blocking ninein phosphorylation by GSK3beta, while its N-terminal region carries transcriptional activity [PMID:15147888]. In breast cancer cells RTRAF drives autocrine IL-6/STAT3 signaling by increasing Pol II and p300 occupancy at the IL-6 promoter, promoting cancer stem cell properties and metastasis [PMID:28166202].","teleology":[{"year":2004,"claim":"Established the first physical partner and domain architecture of RTRAF, defining a C-terminal homodimerization/ninein-binding region and an N-terminal region with transcriptional activity, and showing RTRAF can shield a substrate from GSK3beta phosphorylation.","evidence":"Yeast two-hybrid screen, GST pull-down, in vitro kinase assay, and transcriptional activity assay","pmids":["15147888"],"confidence":"Medium","gaps":["Functional consequence of blocking ninein phosphorylation in cells not established","No structural model of the homodimer or ninein interface","Link between centrosomal role and transcriptional/translational roles unresolved"]},{"year":2006,"claim":"Defined RTRAF as a positive modulator of RNA polymerase II transcription, answering whether its nuclear localization reflects a functional role in mRNA synthesis.","evidence":"Co-IP with Pol II, confocal colocalization, Br-UTP incorporation, RNAi knockdown with microarray profiling","pmids":["16950395"],"confidence":"Medium","gaps":["Direct mechanism by which RTRAF enhances Pol II activity not defined","Whether RTRAF binds Pol II directly or through other factors unknown","No genome-wide occupancy data for RTRAF itself"]},{"year":2011,"claim":"Showed RTRAF is a host factor co-opted by influenza virus, linking its gene-expression function to support of viral polymerase activity.","evidence":"Co-IP with viral polymerase complex, confocal colocalization with viral RNPs, siRNA knockdown with viral activity, titer, and replication readouts","pmids":["21900157"],"confidence":"Medium","gaps":["Whether RTRAF acts on viral transcription via its cellular Pol II/translation roles or independently unclear","Direct binding contact with viral polymerase subunits not mapped"]},{"year":2012,"claim":"Identified PTPIP51 as a RTRAF partner with a mitotic equatorial-plate localization, extending the protein's interactome to mitotic/cytoskeletal contexts.","evidence":"In vitro binding, in vivo co-IP, Duolink proximity ligation assay, confocal microscopy","pmids":["24970130"],"confidence":"Low","gaps":["Single lab with limited mechanistic follow-up beyond complex localization","Functional consequence of the PTPIP51 interaction not established","No connection drawn to RTRAF's transcription or translation functions"]},{"year":2017,"claim":"Connected RTRAF's transcriptional modulator activity to a disease-relevant program by showing it drives autocrine IL-6/STAT3 signaling and metastasis in breast cancer.","evidence":"ChIP for Pol II and p300 at the IL-6 promoter, STAT3 activity assay, siRNA knockdown, in vivo colonization, and tocilizumab rescue","pmids":["28166202"],"confidence":"Medium","gaps":["Whether RTRAF acts directly at the IL-6 promoter or via Pol II/p300 recruitment indirectly not resolved","Selectivity for IL-6 versus genome-wide promoters not addressed"]},{"year":2019,"claim":"Defined RTRAF's cytoplasmic role by establishing it as a subunit of an eIF4E-independent cap-binding complex that promotes translation, answering how RTRAF contributes to gene expression beyond transcription.","evidence":"Co-IP, cap-analog resin pulldown with competition/elution, purified-protein cap-binding, siRNA knockdown with translation assay, RIP-seq","pmids":["30833903"],"confidence":"High","gaps":["Stoichiometry and structure of the DDX1/HSPC117/FAM98B/RTRAF complex not solved","How nuclear transcription and cytoplasmic translation roles are coordinated unknown","Mechanism by which partners boost RTRAF cap affinity not defined at atomic level"]},{"year":null,"claim":"How RTRAF's distinct nuclear (Pol II transcription), cytoplasmic (cap-binding translation), centrosomal (ninein/GSK3beta), and mitotic (PTPIP51) activities are integrated into a single coherent cellular function remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying structural or regulatory model links the transcription, translation, and centrosomal functions","Spatiotemporal partitioning of RTRAF among its complexes not characterized","No structure of any RTRAF complex available"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,4]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[5]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[5]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,4]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[5]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[5]}],"complexes":["hCLE/DDX1/HSPC117/FAM98B cap-binding complex"],"partners":["DDX1","HSPC117","FAM98B","NINEIN","PTPIP51","POLR2A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y224","full_name":"tRNA-splicing ligase complex subunit RTRAF","aliases":["CLE7 homolog","CLE","hCLE","RNA transcription, translation and transport factor protein"],"length_aa":244,"mass_kda":28.1,"function":"Accessory subunit of the tRNA-splicing ligase complex that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester (PubMed:21311021, PubMed:24870230). RNA-binding protein involved in modulation of mRNA transcription by Polymerase II (PubMed:16950395). Could also play a role in RNA transport (PubMed:24608264) (Microbial infection) In case of infection by influenza virus A (IVA), is involved in viral replication (PubMed:21900157)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9Y224/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RTRAF","classification":"Common Essential","n_dependent_lines":567,"n_total_lines":1208,"dependency_fraction":0.4693708609271523},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"RTCB","stoichiometry":10.0},{"gene":"BYSL","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"CLNS1A","stoichiometry":0.2},{"gene":"G3BP2","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RTRAF","total_profiled":1310},"omim":[{"mim_id":"610858","title":"RNA TRANSCRIPTION, TRANSLATION, AND TRANSPORT FACTOR; RTRAF","url":"https://www.omim.org/entry/610858"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RTRAF"},"hgnc":{"alias_symbol":["CGI-99","RLLM1","CLE","CLE7","LCRP369","hCLE1"],"prev_symbol":["C14orf166"]},"alphafold":{"accession":"Q9Y224","domains":[{"cath_id":"-","chopping":"1-100","consensus_level":"high","plddt":75.4008,"start":1,"end":100},{"cath_id":"-","chopping":"123-174","consensus_level":"medium","plddt":75.1262,"start":123,"end":174},{"cath_id":"-","chopping":"182-234","consensus_level":"medium","plddt":79.7802,"start":182,"end":234}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y224","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y224-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y224-F1-predicted_aligned_error_v6.png","plddt_mean":71.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RTRAF","jax_strain_url":"https://www.jax.org/strain/search?query=RTRAF"},"sequence":{"accession":"Q9Y224","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y224.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y224/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y224"}},"corpus_meta":[{"pmid":"16902140","id":"PMC_16902140","title":"Dodeca-CLE peptides as suppressors of plant stem cell differentiation.","date":"2006","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/16902140","citation_count":491,"is_preprint":false},{"pmid":"18812507","id":"PMC_18812507","title":"Non-cell-autonomous control of vascular stem cell fate by a CLE peptide/receptor system.","date":"2008","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/18812507","citation_count":410,"is_preprint":false},{"pmid":"33619356","id":"PMC_33619356","title":"Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes.","date":"2021","source":"Nature plants","url":"https://pubmed.ncbi.nlm.nih.gov/33619356","citation_count":282,"is_preprint":false},{"pmid":"19074184","id":"PMC_19074184","title":"Nod factor/nitrate-induced CLE genes that drive HAR1-mediated systemic regulation of nodulation.","date":"2008","source":"Plant & cell physiology","url":"https://pubmed.ncbi.nlm.nih.gov/19074184","citation_count":280,"is_preprint":false},{"pmid":"23934307","id":"PMC_23934307","title":"Root-derived CLE glycopeptides control nodulation by direct binding to HAR1 receptor kinase.","date":"2013","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/23934307","citation_count":260,"is_preprint":false},{"pmid":"24449877","id":"PMC_24449877","title":"CLE-CLAVATA1 peptide-receptor signaling module regulates the expansion of plant root systems in a nitrogen-dependent manner.","date":"2014","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/24449877","citation_count":242,"is_preprint":false},{"pmid":"20348212","id":"PMC_20348212","title":"CLE peptides control Medicago truncatula nodulation locally and systemically.","date":"2010","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/20348212","citation_count":241,"is_preprint":false},{"pmid":"21198362","id":"PMC_21198362","title":"Inoculation- and nitrate-induced CLE peptides of soybean control NARK-dependent nodule formation.","date":"2011","source":"Molecular plant-microbe interactions : MPMI","url":"https://pubmed.ncbi.nlm.nih.gov/21198362","citation_count":208,"is_preprint":false},{"pmid":"19011104","id":"PMC_19011104","title":"Plant CLE peptides from two distinct functional classes synergistically induce division of vascular cells.","date":"2008","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/19011104","citation_count":173,"is_preprint":false},{"pmid":"16407446","id":"PMC_16407446","title":"Evidence for functional conservation, sufficiency, and proteolytic processing of the CLAVATA3 CLE domain.","date":"2006","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/16407446","citation_count":138,"is_preprint":false},{"pmid":"23371950","id":"PMC_23371950","title":"WUSCHEL-RELATED HOMEOBOX4 is involved in meristem maintenance and is negatively regulated by the CLE gene FCP1 in rice.","date":"2013","source":"The Plant cell","url":"https://pubmed.ncbi.nlm.nih.gov/23371950","citation_count":120,"is_preprint":false},{"pmid":"27229733","id":"PMC_27229733","title":"CLE peptides and their signaling pathways in plant development.","date":"2016","source":"Journal of experimental botany","url":"https://pubmed.ncbi.nlm.nih.gov/27229733","citation_count":119,"is_preprint":false},{"pmid":"27055373","id":"PMC_27055373","title":"Crystal structure of PXY-TDIF complex reveals a conserved recognition mechanism among CLE peptide-receptor pairs.","date":"2016","source":"Cell research","url":"https://pubmed.ncbi.nlm.nih.gov/27055373","citation_count":111,"is_preprint":false},{"pmid":"23370719","id":"PMC_23370719","title":"Transcriptional and functional classification of the GOLVEN/ROOT GROWTH FACTOR/CLE-like signaling peptides reveals their role in lateral root and hair formation.","date":"2012","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/23370719","citation_count":111,"is_preprint":false},{"pmid":"20802224","id":"PMC_20802224","title":"CLE peptides can negatively regulate protoxylem vessel formation via cytokinin signaling.","date":"2010","source":"Plant & cell physiology","url":"https://pubmed.ncbi.nlm.nih.gov/20802224","citation_count":98,"is_preprint":false},{"pmid":"22168914","id":"PMC_22168914","title":"Nodule numbers are governed by interaction between CLE peptides and cytokinin signaling.","date":"2012","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/22168914","citation_count":98,"is_preprint":false},{"pmid":"18676878","id":"PMC_18676878","title":"Functional diversification of CLAVATA3-related CLE proteins in meristem maintenance in rice.","date":"2008","source":"The Plant cell","url":"https://pubmed.ncbi.nlm.nih.gov/18676878","citation_count":96,"is_preprint":false},{"pmid":"32576831","id":"PMC_32576831","title":"The NIN transcription factor coordinates CEP and CLE signaling peptides that regulate nodulation antagonistically.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32576831","citation_count":95,"is_preprint":false},{"pmid":"20497349","id":"PMC_20497349","title":"Dual roles for the variable domain in protein trafficking and host-specific recognition of Heterodera glycines CLE effector proteins.","date":"2010","source":"The New phytologist","url":"https://pubmed.ncbi.nlm.nih.gov/20497349","citation_count":91,"is_preprint":false},{"pmid":"21757457","id":"PMC_21757457","title":"Soybean nodule-enhanced CLE peptides in roots act as signals in GmNARK-mediated nodulation suppression.","date":"2011","source":"Plant & cell physiology","url":"https://pubmed.ncbi.nlm.nih.gov/21757457","citation_count":84,"is_preprint":false},{"pmid":"29543153","id":"PMC_29543153","title":"The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors.","date":"2018","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/29543153","citation_count":83,"is_preprint":false},{"pmid":"28607033","id":"PMC_28607033","title":"Perception of root-active CLE peptides requires CORYNE function in the phloem vasculature.","date":"2017","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/28607033","citation_count":83,"is_preprint":false},{"pmid":"18034320","id":"PMC_18034320","title":"The CLE family of plant polypeptide signaling molecules.","date":"2008","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/18034320","citation_count":79,"is_preprint":false},{"pmid":"19656047","id":"PMC_19656047","title":"Structural and functional diversity of CLAVATA3/ESR (CLE)-like genes from the potato cyst nematode Globodera rostochiensis.","date":"2009","source":"Molecular plant-microbe interactions : MPMI","url":"https://pubmed.ncbi.nlm.nih.gov/19656047","citation_count":78,"is_preprint":false},{"pmid":"22303273","id":"PMC_22303273","title":"The Function of the CLE Peptides in Plant Development and Plant-Microbe Interactions.","date":"2011","source":"The arabidopsis book","url":"https://pubmed.ncbi.nlm.nih.gov/22303273","citation_count":75,"is_preprint":false},{"pmid":"31477892","id":"PMC_31477892","title":"A CLE-SUNN module regulates strigolactone content and fungal colonization in arbuscular mycorrhiza.","date":"2019","source":"Nature plants","url":"https://pubmed.ncbi.nlm.nih.gov/31477892","citation_count":74,"is_preprint":false},{"pmid":"21052783","id":"PMC_21052783","title":"Characterization of a CLE processing activity.","date":"2010","source":"Plant molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/21052783","citation_count":71,"is_preprint":false},{"pmid":"28158306","id":"PMC_28158306","title":"Identification of cyst nematode B-type CLE peptides and modulation of the vascular stem cell pathway for feeding cell formation.","date":"2017","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/28158306","citation_count":67,"is_preprint":false},{"pmid":"18078779","id":"PMC_18078779","title":"Diverse and conserved roles of CLE peptides.","date":"2007","source":"Current opinion in plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/18078779","citation_count":64,"is_preprint":false},{"pmid":"21750229","id":"PMC_21750229","title":"Mechanisms of molecular mimicry of plant CLE peptide ligands by the parasitic nematode Globodera rostochiensis.","date":"2011","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/21750229","citation_count":64,"is_preprint":false},{"pmid":"26779239","id":"PMC_26779239","title":"CLE Peptide Signaling and Crosstalk with Phytohormones and Environmental Stimuli.","date":"2016","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/26779239","citation_count":63,"is_preprint":false},{"pmid":"20016993","id":"PMC_20016993","title":"CLE peptide signaling during plant development.","date":"2009","source":"Protoplasma","url":"https://pubmed.ncbi.nlm.nih.gov/20016993","citation_count":61,"is_preprint":false},{"pmid":"30845139","id":"PMC_30845139","title":"Control of proliferation in the haploid meristem by CLE peptide signaling in Marchantia polymorpha.","date":"2019","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30845139","citation_count":61,"is_preprint":false},{"pmid":"27294965","id":"PMC_27294965","title":"Expression of the CLE-RS3 gene suppresses root nodulation in Lotus japonicus.","date":"2016","source":"Journal of plant research","url":"https://pubmed.ncbi.nlm.nih.gov/27294965","citation_count":60,"is_preprint":false},{"pmid":"17129751","id":"PMC_17129751","title":"CLE peptide ligands and their roles in establishing meristems.","date":"2006","source":"Current opinion in plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/17129751","citation_count":60,"is_preprint":false},{"pmid":"25040127","id":"PMC_25040127","title":"The soybean (Glycine max) nodulation-suppressive CLE peptide, GmRIC1, functions interspecifically in common white bean (Phaseolus vulgaris), but not in a supernodulating line mutated in the receptor PvNARK.","date":"2014","source":"Plant biotechnology journal","url":"https://pubmed.ncbi.nlm.nih.gov/25040127","citation_count":60,"is_preprint":false},{"pmid":"12698867","id":"PMC_12698867","title":"Epidemiology of reflux disease and CLE in East Asia.","date":"2003","source":"Journal of gastroenterology","url":"https://pubmed.ncbi.nlm.nih.gov/12698867","citation_count":55,"is_preprint":false},{"pmid":"20074136","id":"PMC_20074136","title":"Regulation of vascular development by CLE peptide-receptor systems.","date":"2010","source":"Journal of integrative plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/20074136","citation_count":54,"is_preprint":false},{"pmid":"25581705","id":"PMC_25581705","title":"Enhanced resistance to soybean cyst nematode Heterodera glycines in transgenic soybean by silencing putative CLE receptors.","date":"2015","source":"Plant biotechnology journal","url":"https://pubmed.ncbi.nlm.nih.gov/25581705","citation_count":53,"is_preprint":false},{"pmid":"29393515","id":"PMC_29393515","title":"CLE peptide tri-arabinosylation and peptide domain sequence composition are essential for SUNN-dependent autoregulation of nodulation in Medicago truncatula.","date":"2018","source":"The New phytologist","url":"https://pubmed.ncbi.nlm.nih.gov/29393515","citation_count":50,"is_preprint":false},{"pmid":"24035739","id":"PMC_24035739","title":"Evolutionarily conserved CLE peptide signaling in plant development, symbiosis, and parasitism.","date":"2013","source":"Current opinion in plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/24035739","citation_count":49,"is_preprint":false},{"pmid":"34077886","id":"PMC_34077886","title":"WOX going on: CLE peptides in plant development.","date":"2021","source":"Current opinion in plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/34077886","citation_count":47,"is_preprint":false},{"pmid":"35817820","id":"PMC_35817820","title":"A Dof-CLE circuit controls phloem organization.","date":"2022","source":"Nature plants","url":"https://pubmed.ncbi.nlm.nih.gov/35817820","citation_count":46,"is_preprint":false},{"pmid":"16950395","id":"PMC_16950395","title":"hCLE/CGI-99, a human protein that interacts with the influenza virus polymerase, is a mRNA transcription modulator.","date":"2006","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16950395","citation_count":43,"is_preprint":false},{"pmid":"24529101","id":"PMC_24529101","title":"Bioinformatic and phylogenetic analysis of the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) and the CLE-LIKE signal peptide genes in the Pinophyta.","date":"2014","source":"BMC plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/24529101","citation_count":40,"is_preprint":false},{"pmid":"18848920","id":"PMC_18848920","title":"Dual assay for MCLV3 activity reveals structure-activity relationship of CLE peptides.","date":"2008","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/18848920","citation_count":40,"is_preprint":false},{"pmid":"24043854","id":"PMC_24043854","title":"A CLE-WOX signalling module regulates root meristem maintenance and vascular tissue development in rice.","date":"2013","source":"Journal of experimental botany","url":"https://pubmed.ncbi.nlm.nih.gov/24043854","citation_count":39,"is_preprint":false},{"pmid":"21900157","id":"PMC_21900157","title":"Cellular human CLE/C14orf166 protein interacts with influenza virus polymerase and is required for viral replication.","date":"2011","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/21900157","citation_count":38,"is_preprint":false},{"pmid":"23386683","id":"PMC_23386683","title":"Structure-function analysis of the GmRIC1 signal peptide and CLE domain required for nodulation control in soybean.","date":"2013","source":"Journal of experimental botany","url":"https://pubmed.ncbi.nlm.nih.gov/23386683","citation_count":38,"is_preprint":false},{"pmid":"15147888","id":"PMC_15147888","title":"A novel ninein-interaction protein, CGI-99, blocks ninein phosphorylation by GSK3beta and is highly expressed in brain tumors.","date":"2004","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/15147888","citation_count":37,"is_preprint":false},{"pmid":"19816140","id":"PMC_19816140","title":"Evolution of CLE signaling: origins of the CLV1 and SOL2/CRN receptor diversity.","date":"2009","source":"Plant signaling & behavior","url":"https://pubmed.ncbi.nlm.nih.gov/19816140","citation_count":37,"is_preprint":false},{"pmid":"34841457","id":"PMC_34841457","title":"CLE peptides: critical regulators for stem cell maintenance in plants.","date":"2021","source":"Planta","url":"https://pubmed.ncbi.nlm.nih.gov/34841457","citation_count":36,"is_preprint":false},{"pmid":"26096704","id":"PMC_26096704","title":"CLE peptide signaling in plants - the power of moving around.","date":"2015","source":"Physiologia plantarum","url":"https://pubmed.ncbi.nlm.nih.gov/26096704","citation_count":35,"is_preprint":false},{"pmid":"20428922","id":"PMC_20428922","title":"Two CLE genes are induced by phosphate in roots of Lotus japonicus.","date":"2010","source":"Journal of plant research","url":"https://pubmed.ncbi.nlm.nih.gov/20428922","citation_count":34,"is_preprint":false},{"pmid":"35854003","id":"PMC_35854003","title":"Evolution of meristem zonation by CLE gene duplication in land plants.","date":"2022","source":"Nature plants","url":"https://pubmed.ncbi.nlm.nih.gov/35854003","citation_count":33,"is_preprint":false},{"pmid":"25443828","id":"PMC_25443828","title":"Nitrate inhibits soybean nodulation by regulating expression of CLE genes.","date":"2014","source":"Plant science : an international journal of experimental plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/25443828","citation_count":33,"is_preprint":false},{"pmid":"26136270","id":"PMC_26136270","title":"Antagonistic peptide technology for functional dissection of CLE peptides revisited.","date":"2015","source":"Journal of experimental botany","url":"https://pubmed.ncbi.nlm.nih.gov/26136270","citation_count":32,"is_preprint":false},{"pmid":"32444290","id":"PMC_32444290","title":"Evolution of CLE peptide signalling.","date":"2020","source":"Seminars in cell & developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/32444290","citation_count":31,"is_preprint":false},{"pmid":"31003469","id":"PMC_31003469","title":"CLE-CLAVATA1 Signaling Pathway Modulates Lateral Root Development under Sulfur Deficiency.","date":"2019","source":"Plants (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/31003469","citation_count":31,"is_preprint":false},{"pmid":"29722016","id":"PMC_29722016","title":"Triarabinosylation is required for nodulation-suppressive CLE peptides to systemically inhibit nodulation in Pisum sativum.","date":"2018","source":"Plant, cell & environment","url":"https://pubmed.ncbi.nlm.nih.gov/29722016","citation_count":31,"is_preprint":false},{"pmid":"28166202","id":"PMC_28166202","title":"CGI-99 promotes breast cancer metastasis via autocrine interleukin-6 signaling.","date":"2017","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/28166202","citation_count":29,"is_preprint":false},{"pmid":"17304552","id":"PMC_17304552","title":"CLV3/ESR-related (CLE) peptides as intercellular signaling molecules in plants.","date":"2006","source":"Chemical record (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/17304552","citation_count":29,"is_preprint":false},{"pmid":"26935217","id":"PMC_26935217","title":"Identification and characterization of the Populus trichocarpa CLE family.","date":"2016","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/26935217","citation_count":28,"is_preprint":false},{"pmid":"28384649","id":"PMC_28384649","title":"Differential CLE peptide perception by plant receptors implicated from structural and functional analyses of TDIF-TDR interactions.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28384649","citation_count":27,"is_preprint":false},{"pmid":"23045524","id":"PMC_23045524","title":"CLE signaling systems during plant development and nematode infection.","date":"2012","source":"Plant & cell physiology","url":"https://pubmed.ncbi.nlm.nih.gov/23045524","citation_count":26,"is_preprint":false},{"pmid":"25763500","id":"PMC_25763500","title":"CLE peptides regulate lateral root development in response to nitrogen nutritional status of plants.","date":"2014","source":"Plant signaling & behavior","url":"https://pubmed.ncbi.nlm.nih.gov/25763500","citation_count":26,"is_preprint":false},{"pmid":"33045986","id":"PMC_33045986","title":"Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences.","date":"2020","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/33045986","citation_count":26,"is_preprint":false},{"pmid":"22925455","id":"PMC_22925455","title":"CLE peptides in plants: proteolytic processing, structure-activity relationship, and ligand-receptor interaction.","date":"2012","source":"Journal of integrative plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/22925455","citation_count":25,"is_preprint":false},{"pmid":"31484454","id":"PMC_31484454","title":"Identification and Functional Analysis of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) Gene Family in Wheat.","date":"2019","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/31484454","citation_count":25,"is_preprint":false},{"pmid":"32480669","id":"PMC_32480669","title":"The structure and activity of nodulation-suppressing CLE peptide hormones of legumes.","date":"2015","source":"Functional plant biology : FPB","url":"https://pubmed.ncbi.nlm.nih.gov/32480669","citation_count":25,"is_preprint":false},{"pmid":"39468296","id":"PMC_39468296","title":"Antagonistic CLE peptide pathways shape root meristem tissue patterning.","date":"2024","source":"Nature plants","url":"https://pubmed.ncbi.nlm.nih.gov/39468296","citation_count":24,"is_preprint":false},{"pmid":"21273331","id":"PMC_21273331","title":"Search for nodulation-related CLE genes in the genome of Glycine max.","date":"2011","source":"Journal of experimental botany","url":"https://pubmed.ncbi.nlm.nih.gov/21273331","citation_count":23,"is_preprint":false},{"pmid":"26994997","id":"PMC_26994997","title":"CLE peptide signaling and nitrogen interactions in plant root development.","date":"2016","source":"Plant molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/26994997","citation_count":21,"is_preprint":false},{"pmid":"37874980","id":"PMC_37874980","title":"The Role of CLE Peptides in the Suppression of Mycorrhizal Colonization of Tomato.","date":"2024","source":"Plant & cell physiology","url":"https://pubmed.ncbi.nlm.nih.gov/37874980","citation_count":21,"is_preprint":false},{"pmid":"23473393","id":"PMC_23473393","title":"CLE peptides in vascular development.","date":"2013","source":"Journal of integrative plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/23473393","citation_count":20,"is_preprint":false},{"pmid":"30833903","id":"PMC_30833903","title":"hCLE/RTRAF-HSPC117-DDX1-FAM98B: A New Cap-Binding Complex That Activates mRNA Translation.","date":"2019","source":"Frontiers in physiology","url":"https://pubmed.ncbi.nlm.nih.gov/30833903","citation_count":20,"is_preprint":false},{"pmid":"33126720","id":"PMC_33126720","title":"Nitrate-Induced CLE Peptide Systemically Inhibits Nodulation in Medicago truncatula.","date":"2020","source":"Plants (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/33126720","citation_count":19,"is_preprint":false},{"pmid":"26170479","id":"PMC_26170479","title":"Sequence and Spatiotemporal Expression Analysis of CLE-Motif Containing Genes from the Reniform Nematode (Rotylenchulus reniformis Linford & Oliveira).","date":"2015","source":"Journal of nematology","url":"https://pubmed.ncbi.nlm.nih.gov/26170479","citation_count":19,"is_preprint":false},{"pmid":"30897708","id":"PMC_30897708","title":"CLE-10 from Carpesium abrotanoides L. Suppresses the Growth of Human Breast Cancer Cells (MDA-MB-231) In Vitro by Inducing Apoptosis and Pro-Death Autophagy Via the PI3K/Akt/mTOR Signaling Pathway.","date":"2019","source":"Molecules (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/30897708","citation_count":19,"is_preprint":false},{"pmid":"26821718","id":"PMC_26821718","title":"Identification, expression, and functional analysis of CLE genes in radish (Raphanus sativus L.) storage root.","date":"2016","source":"BMC plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/26821718","citation_count":18,"is_preprint":false},{"pmid":"36396987","id":"PMC_36396987","title":"Deeper genomic insights into tomato CLE genes repertoire identify new active peptides.","date":"2022","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/36396987","citation_count":17,"is_preprint":false},{"pmid":"31280129","id":"PMC_31280129","title":"Cytokinin and CLE signaling are highly intertwined developmental regulators across tissues and species.","date":"2019","source":"Current opinion in plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/31280129","citation_count":16,"is_preprint":false},{"pmid":"33931094","id":"PMC_33931094","title":"Proteome study of cutaneous lupus erythematosus (CLE) and dermatomyositis skin lesions reveals IL-16 is differentially upregulated in CLE.","date":"2021","source":"Arthritis research & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/33931094","citation_count":16,"is_preprint":false},{"pmid":"33740893","id":"PMC_33740893","title":"Genome-wide identification of CLE gene family and their potential roles in bolting and fruit bearing in cucumber (Cucumis sativus L.).","date":"2021","source":"BMC plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/33740893","citation_count":16,"is_preprint":false},{"pmid":"21150256","id":"PMC_21150256","title":"Variable domain I of nematode CLEs directs post-translational targeting of CLE peptides to the extracellular space.","date":"2010","source":"Plant signaling & behavior","url":"https://pubmed.ncbi.nlm.nih.gov/21150256","citation_count":16,"is_preprint":false},{"pmid":"21132284","id":"PMC_21132284","title":"Familial cutaneous lupus erythematosus (CLE) in the German shorthaired pointer maps to CFA18, a canine orthologue to human CLE.","date":"2010","source":"Immunogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/21132284","citation_count":15,"is_preprint":false},{"pmid":"36092449","id":"PMC_36092449","title":"Spatial range, temporal span, and promiscuity of CLE-RLK signaling.","date":"2022","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/36092449","citation_count":14,"is_preprint":false},{"pmid":"24970130","id":"PMC_24970130","title":"Interaction of PTPIP51 with Tubulin, CGI-99 and Nuf2 During Cell Cycle Progression.","date":"2012","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/24970130","citation_count":14,"is_preprint":false},{"pmid":"36702874","id":"PMC_36702874","title":"A phosphoinositide hub connects CLE peptide signaling and polar auxin efflux regulation.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/36702874","citation_count":14,"is_preprint":false},{"pmid":"31277568","id":"PMC_31277568","title":"Genome-wide identification of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family in grape (Vitis vinifera L.).","date":"2019","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/31277568","citation_count":14,"is_preprint":false},{"pmid":"31880983","id":"PMC_31880983","title":"CLE-HAR1 Systemic Signaling and NIN-Mediated Local Signaling Suppress the Increased Rhizobial Infection in the daphne Mutant of Lotus japonicus.","date":"2019","source":"Molecular plant-microbe interactions : MPMI","url":"https://pubmed.ncbi.nlm.nih.gov/31880983","citation_count":14,"is_preprint":false},{"pmid":"23356449","id":"PMC_23356449","title":"Saccharification of recalcitrant biomass and integration options for lignocellulosic sugars from Catchlight Energy's sugar process (CLE Sugar).","date":"2013","source":"Biotechnology for biofuels","url":"https://pubmed.ncbi.nlm.nih.gov/23356449","citation_count":14,"is_preprint":false},{"pmid":"32223006","id":"PMC_32223006","title":"Identification and comprehensive analysis of the CLV3/ESR-related (CLE) gene family in Brassica napus L.","date":"2020","source":"Plant biology (Stuttgart, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/32223006","citation_count":13,"is_preprint":false},{"pmid":"37554099","id":"PMC_37554099","title":"Towards a science-based testing strategy to identify maternal thyroid hormone imbalance and neurodevelopmental effects in the progeny - Part IV: the ECETOC and CLE Proposal for a Thyroid Function-Related Neurodevelopmental Toxicity Testing and Assessment Scheme (Thyroid-NDT-TAS).","date":"2023","source":"Critical reviews in toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/37554099","citation_count":13,"is_preprint":false},{"pmid":"37977139","id":"PMC_37977139","title":"Control of stem cell behavior by CLE-JINGASA signaling in the shoot apical meristem in Marchantia polymorpha.","date":"2023","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/37977139","citation_count":12,"is_preprint":false},{"pmid":"27341987","id":"PMC_27341987","title":"MicroRNA in Skeletal Muscle: Its Crucial Roles in Signal Proteins, Mus cle Fiber Type, and Muscle Protein Synthesis.","date":"2017","source":"Current protein & peptide science","url":"https://pubmed.ncbi.nlm.nih.gov/27341987","citation_count":11,"is_preprint":false},{"pmid":"37444009","id":"PMC_37444009","title":"Dairy Cow Mastitis Detection by Thermal Infrared Images Based on CLE-UNet.","date":"2023","source":"Animals : an open access journal from MDPI","url":"https://pubmed.ncbi.nlm.nih.gov/37444009","citation_count":11,"is_preprint":false},{"pmid":"38836320","id":"PMC_38836320","title":"Identification and Application of CLE Peptides for Drought Resistance in Solanaceae Crops.","date":"2024","source":"Journal of agricultural and food chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/38836320","citation_count":10,"is_preprint":false},{"pmid":"39908106","id":"PMC_39908106","title":"Ethylene-independent modulation of root development by ACC via downregulation of WOX5 and group I CLE peptide expression.","date":"2025","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/39908106","citation_count":10,"is_preprint":false},{"pmid":"16021333","id":"PMC_16021333","title":"Functional characterization of the geminiviral conserved late element (CLE) in uninfected tobacco.","date":"2005","source":"Plant molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16021333","citation_count":10,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":44470,"output_tokens":2234,"usd":0.08346,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8658,"output_tokens":2775,"usd":0.056333,"stage2_stop_reason":"end_turn"},"total_usd":0.139793,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"Looking through the abstracts, I need to identify papers about the human gene RTRAF (also known as CGI-99, C14orf166, hCLE, hCLE1, CLE7, RLLM1, LCRP369, CLE).\n\nMost of the corpus (papers 1-35, 37-43, 45-49, 51-75, 77-82, 84-87, 89-91, 93, 95, 98-100) are about plant CLE (CLAVATA3/ESR-related) peptides - these are plant signaling peptides, completely unrelated to the human RTRAF protein. These are symbol collisions (CLE as an abbreviation in plant biology context).\n\nPapers 37, 83, 86 use CLE as \"cutaneous lupus erythematosus\" - also unrelated.\nPaper 79 uses CLE-10 as a sesquiterpene lactone compound - unrelated.\nPaper 92 uses CLE as \"Catchlight Energy\" - unrelated.\nPaper 94 uses CLE as an organization acronym - unrelated.\nPaper 97 uses CLE-UNet - unrelated.\n\nThe relevant papers about RTRAF/CGI-99/hCLE/C14orf166 are:\n- Paper 44: hCLE/CGI-99 as mRNA transcription modulator\n- Paper 48: CLE/C14orf166 interacts with influenza polymerase\n- Paper 50: CGI-99 interacts with ninein/GSK3beta\n- Paper 61: CGI-99 in breast cancer via IL-6/STAT3\n- Paper 76: hCLE/RTRAF cap-binding complex\n- Paper 88: PTPIP51 interaction with CGI-99\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"hCLE/CGI-99 (RTRAF) co-immunoprecipitates with different phosphorylated forms of RNA polymerase II (RNAP II) largest subunit and colocalizes with RNAP II by confocal microscopy. hCLE localizes to nuclear sites of active mRNA synthesis (colocalization with Br-UTP incorporation sites). RNAi-mediated silencing of hCLE reduced RNAP II transcript synthesis by ~50%, and microarray analysis showed >90% of differentially expressed genes were downregulated, establishing hCLE as a positive modulator of RNAP II transcriptional activity.\",\n      \"method\": \"Co-immunoprecipitation, confocal microscopy colocalization, in situ Br-UTP incorporation, RNAi knockdown, microarray expression profiling\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP and orthogonal localization/functional assays in single lab study\",\n      \"pmids\": [\"16950395\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"CGI-99 (RTRAF) physically interacts with the C-terminal domain of human ninein (hNinein), as demonstrated by yeast two-hybrid screening and in vitro GST pull-down assay. CGI-99 forms homodimers via its C-terminal domain (which overlaps with the hNinein binding site). In a kinase assay, CGI-99 binding to hNinein completely blocks phosphorylation of hNinein by GSK3beta. The N-terminal region of CGI-99 harbors transcriptional activity.\",\n      \"method\": \"Yeast two-hybrid screening, GST pull-down assay, in vitro kinase assay, transcriptional activity assay\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid confirmed by GST pull-down and kinase assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"15147888\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"hCLE/C14orf166 (RTRAF) interacts with the influenza A virus polymerase complex (not just PA subunit alone) and colocalizes with viral ribonucleoproteins in infected cells. Silencing of hCLE reduces viral polymerase activity, viral RNA transcription, viral RNA replication, virus titer, and viral particle production, establishing hCLE as a host cellular factor required for influenza virus replication.\",\n      \"method\": \"Co-immunoprecipitation, confocal microscopy colocalization, siRNA knockdown with viral polymerase activity assay, viral titer measurement\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus functional knockdown with multiple viral replication readouts, single lab\",\n      \"pmids\": [\"21900157\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PTPIP51 (regulator of microtubule dynamics protein 3) interacts with CGI-99 (RTRAF) both in vitro and in vivo. The PTPIP51/CGI-99 complex localizes to the equatorial region during mitosis. Duolink proximity ligation assays confirmed in-cell association of PTPIP51 with CGI-99.\",\n      \"method\": \"In vitro binding assay, in vivo co-immunoprecipitation, Duolink proximity ligation assay, confocal microscopy\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, limited mechanistic follow-up beyond localization of complex at equatorial plate\",\n      \"pmids\": [\"24970130\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"CGI-99 (RTRAF) activates autocrine IL-6/STAT3 signaling in breast cancer cells by increasing accumulation and activity of RNA polymerase II and the p300 cofactor at the proximal promoter of IL-6. This mechanism drives breast cancer stem cell properties and lung colonization in vivo. The IL-6 receptor antibody tocilizumab abrogates CGI-99-induced metastasis in vivo, placing CGI-99 upstream of the IL-6/STAT3 axis.\",\n      \"method\": \"ChIP (RNA Pol II and p300 at IL-6 promoter), in vivo tumor colonization assay, STAT3 activity assay, siRNA knockdown, tocilizumab rescue experiment\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP mechanistic evidence plus in vivo rescue experiment, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"28166202\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"hCLE/RTRAF forms a cap-binding complex with DDX1, HSPC117, and FAM98B in HEK293T cells. All four proteins bind to cap analog-containing resins. Competition and elution experiments show that hCLE complex binding to cap resins is independent of eIF4E. Purified hCLE alone binds cap with low affinity, indicating that interacting proteins modulate its cap association. hCLE silencing reduces accumulation of complex partners and decreases mRNA translation. RNAs associated with hCLE are enriched for mRNAs involved in translation.\",\n      \"method\": \"Co-immunoprecipitation, cap analog resin pulldown, competition/elution binding assay, purified protein cap-binding assay, siRNA knockdown with translation assay, RNA immunoprecipitation and sequencing\",\n      \"journal\": \"Frontiers in physiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal biochemical methods (co-IP, cap resin pulldown with competition, purified protein binding, functional translation assay, RNA-seq), single lab but rigorous mechanistic dissection\",\n      \"pmids\": [\"30833903\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RTRAF (hCLE/CGI-99/C14orf166) is a positive modulator of RNA polymerase II transcription that forms a cap-binding complex with DDX1, HSPC117, and FAM98B to promote mRNA translation; it physically interacts with ninein and blocks its phosphorylation by GSK3beta at the centrosome, co-immunoprecipitates with the influenza virus polymerase complex to support viral replication, and in cancer cells drives autocrine IL-6/STAT3 signaling by enhancing RNA Pol II and p300 activity at the IL-6 promoter.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RTRAF (hCLE/CGI-99/C14orf166) is a multifunctional positive modulator of gene expression that acts at both the transcriptional and translational levels [#0, #5]. In the nucleus it co-immunoprecipitates with multiple phosphorylated forms of the RNA polymerase II largest subunit, localizes to sites of active mRNA synthesis, and is required for normal Pol II transcript output, with its silencing causing broad downregulation of gene expression [#0]. In the cytoplasm it assembles a cap-binding complex with DDX1, HSPC117, and FAM98B that associates with the mRNA cap independently of eIF4E and promotes translation, with the partner proteins stabilizing each other and enhancing RTRAF's intrinsically low cap affinity [#5]. RTRAF also engages the influenza A virus polymerase complex and is required for viral RNA transcription, replication, and particle production, indicating that its gene-expression machinery is co-opted during infection [#2]. Through its C-terminal domain it homodimerizes and binds the centrosomal protein ninein, blocking ninein phosphorylation by GSK3beta, while its N-terminal region carries transcriptional activity [#1]. In breast cancer cells RTRAF drives autocrine IL-6/STAT3 signaling by increasing Pol II and p300 occupancy at the IL-6 promoter, promoting cancer stem cell properties and metastasis [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established the first physical partner and domain architecture of RTRAF, defining a C-terminal homodimerization/ninein-binding region and an N-terminal region with transcriptional activity, and showing RTRAF can shield a substrate from GSK3beta phosphorylation.\",\n      \"evidence\": \"Yeast two-hybrid screen, GST pull-down, in vitro kinase assay, and transcriptional activity assay\",\n      \"pmids\": [\"15147888\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence of blocking ninein phosphorylation in cells not established\",\n        \"No structural model of the homodimer or ninein interface\",\n        \"Link between centrosomal role and transcriptional/translational roles unresolved\"\n      ]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Defined RTRAF as a positive modulator of RNA polymerase II transcription, answering whether its nuclear localization reflects a functional role in mRNA synthesis.\",\n      \"evidence\": \"Co-IP with Pol II, confocal colocalization, Br-UTP incorporation, RNAi knockdown with microarray profiling\",\n      \"pmids\": [\"16950395\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct mechanism by which RTRAF enhances Pol II activity not defined\",\n        \"Whether RTRAF binds Pol II directly or through other factors unknown\",\n        \"No genome-wide occupancy data for RTRAF itself\"\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Showed RTRAF is a host factor co-opted by influenza virus, linking its gene-expression function to support of viral polymerase activity.\",\n      \"evidence\": \"Co-IP with viral polymerase complex, confocal colocalization with viral RNPs, siRNA knockdown with viral activity, titer, and replication readouts\",\n      \"pmids\": [\"21900157\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether RTRAF acts on viral transcription via its cellular Pol II/translation roles or independently unclear\",\n        \"Direct binding contact with viral polymerase subunits not mapped\"\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identified PTPIP51 as a RTRAF partner with a mitotic equatorial-plate localization, extending the protein's interactome to mitotic/cytoskeletal contexts.\",\n      \"evidence\": \"In vitro binding, in vivo co-IP, Duolink proximity ligation assay, confocal microscopy\",\n      \"pmids\": [\"24970130\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single lab with limited mechanistic follow-up beyond complex localization\",\n        \"Functional consequence of the PTPIP51 interaction not established\",\n        \"No connection drawn to RTRAF's transcription or translation functions\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected RTRAF's transcriptional modulator activity to a disease-relevant program by showing it drives autocrine IL-6/STAT3 signaling and metastasis in breast cancer.\",\n      \"evidence\": \"ChIP for Pol II and p300 at the IL-6 promoter, STAT3 activity assay, siRNA knockdown, in vivo colonization, and tocilizumab rescue\",\n      \"pmids\": [\"28166202\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether RTRAF acts directly at the IL-6 promoter or via Pol II/p300 recruitment indirectly not resolved\",\n        \"Selectivity for IL-6 versus genome-wide promoters not addressed\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined RTRAF's cytoplasmic role by establishing it as a subunit of an eIF4E-independent cap-binding complex that promotes translation, answering how RTRAF contributes to gene expression beyond transcription.\",\n      \"evidence\": \"Co-IP, cap-analog resin pulldown with competition/elution, purified-protein cap-binding, siRNA knockdown with translation assay, RIP-seq\",\n      \"pmids\": [\"30833903\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Stoichiometry and structure of the DDX1/HSPC117/FAM98B/RTRAF complex not solved\",\n        \"How nuclear transcription and cytoplasmic translation roles are coordinated unknown\",\n        \"Mechanism by which partners boost RTRAF cap affinity not defined at atomic level\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RTRAF's distinct nuclear (Pol II transcription), cytoplasmic (cap-binding translation), centrosomal (ninein/GSK3beta), and mitotic (PTPIP51) activities are integrated into a single coherent cellular function remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No unifying structural or regulatory model links the transcription, translation, and centrosomal functions\",\n        \"Spatiotemporal partitioning of RTRAF among its complexes not characterized\",\n        \"No structure of any RTRAF complex available\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"complexes\": [\n      \"hCLE/DDX1/HSPC117/FAM98B cap-binding complex\"\n    ],\n    \"partners\": [\n      \"DDX1\",\n      \"HSPC117\",\n      \"FAM98B\",\n      \"ninein\",\n      \"PTPIP51\",\n      \"POLR2A\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}