{"gene":"RNF187","run_date":"2026-06-10T06:43:37","timeline":{"discoveries":[{"year":2013,"finding":"RACO-1 (RNF187) is a substrate of arginine methyltransferase PRMT1, which methylates RACO-1 on two arginine residues; this methylation promotes a conformational change that stabilizes RACO-1 by facilitating K63-linked ubiquitin chain formation, enables RACO-1 dimerization, and enables interaction with c-Jun, all required for c-Jun/AP-1 transcriptional activation.","method":"Mass spectrometry identification of methylation sites, in vitro methylation assay, mutagenesis of arginine residues, Co-IP for dimerization and c-Jun interaction, AP-1 reporter assay, PRMT1 knockdown","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (MS, in vitro assay, mutagenesis, Co-IP, reporter assay) in a single rigorous study establishing mechanistic pathway","pmids":["23624934"],"is_preprint":false},{"year":2020,"finding":"RNF187 associates with YAP and promotes its degradation via K48-linked polyubiquitination, acting as a negative regulator of Hippo signaling in TNBC cells; RNF187 depletion increases YAP protein levels and expression of Hippo target genes (CTGF, CYR61), and the migration/invasion phenotype caused by RNF187 depletion is rescued by further YAP depletion.","method":"Co-immunoprecipitation, ubiquitination assay, RNAi knockdown with epistasis rescue (YAP depletion), western blot for target gene expression","journal":"Oncogenesis","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — reciprocal Co-IP and functional epistasis (YAP rescue) in a single lab, corroborated by independent ESCC study (PMID:32896069)","pmids":["32198343","32896069"],"is_preprint":false},{"year":2020,"finding":"RACO-1 (RNF187) associates with YAP in oesophageal squamous cell carcinoma cells and promotes K48-linked polyubiquitination and degradation of YAP; RACO-1 silencing increases YAP protein level and YAP/TEAD target gene expression, promoting invasion and migration, an effect rescued by YAP depletion.","method":"Co-immunoprecipitation, ubiquitination assay, RNAi knockdown with YAP depletion rescue, western blot","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP and functional epistasis in single lab, independently corroborated by PMID:32198343","pmids":["32896069"],"is_preprint":false},{"year":2022,"finding":"RNF187 interacts with P53 and promotes its polyubiquitination and degradation in breast cancer cells; an in vitro ubiquitin assay demonstrated that RNF187 can directly ubiquitinate P53 in an MDM2-independent manner, inhibiting P53 target genes (IGFBP3, FAS) and facilitating breast cancer cell growth while inhibiting apoptosis.","method":"Co-immunoprecipitation, in vitro ubiquitination assay, RNAi knockdown, RNA sequencing, western blot","journal":"Cell death & disease","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro ubiquitination reconstitution plus Co-IP and RNA-seq in a single study with multiple orthogonal methods","pmids":["35165289"],"is_preprint":false},{"year":2019,"finding":"RNF187 is a direct transcriptional target of Notch1 in hepatocellular carcinoma; Notch1 activates the RNF187 promoter (confirmed by luciferase reporter assay and ChIP), and RNF187 is required downstream of Notch1 to promote EMT, invasion, and metastasis, as RNF187 knockdown attenuates Notch1-dependent pro-migratory effects and overexpression of RNF187 rescues Notch1 knockdown phenotypes.","method":"Luciferase reporter assay, chromatin immunoprecipitation (ChIP), RNA-seq, gain- and loss-of-function epistasis experiments","journal":"Journal of experimental & clinical cancer research : CR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and reporter assay establish direct transcriptional regulation; functional epistasis with reciprocal rescue; single lab","pmids":["31477177"],"is_preprint":false},{"year":2023,"finding":"RNF187 interacts with Keratin 36 (KRT36) and Keratin 84 (KRT84) and promotes their degradation via K48-linked polyubiquitination, thereby promoting proliferation and migration of mouse spermatogonia GC-1 cells; overexpression of KRT36 or KRT84 attenuates the pro-proliferative and pro-migratory effects of RNF187 overexpression.","method":"Co-immunoprecipitation, mass spectrometry, K48-linked ubiquitination assay, RNAi and overexpression in GC-1 cells, rescue experiment with KRT36/KRT84 overexpression","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP/MS identification of substrates plus functional rescue; single lab, multiple methods","pmids":["37738023"],"is_preprint":false},{"year":2023,"finding":"RNF187 interacts with histone H3 and mediates its ubiquitination at lysine 57 (K57) and lysine 80 (K80) in mouse spermatocyte-derived GC-2 cells, resulting in increased cellular transcription and promoting GC-2 cell viability, proliferation, and migration.","method":"Co-immunoprecipitation, ubiquitination assay with site-specific mutagenesis (K57, K80), RNAi and overexpression in GC-2 cells","journal":"Asian journal of andrology","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP, ubiquitination assay with mutagenesis; single lab","pmids":["38156805"],"is_preprint":false},{"year":2025,"finding":"RNF187 interacts with WDR77 and mediates its K48-linked polyubiquitination at K118, leading to proteasomal degradation of WDR77; reduced WDR77 decreases symmetric dimethylation at H4R3 (H4R3me2s) catalyzed by PRMT5, relieving transcriptional repression of EGR1 (a positive regulator of human SSC maintenance), thereby promoting proliferation and migration of human spermatogonial stem cells.","method":"Co-immunoprecipitation, mass spectrometry, K48-linked ubiquitination assay with site-specific mutagenesis (K118), WDR77 knockdown/overexpression, H4R3me2s methylation analysis","journal":"Cell proliferation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP/MS plus ubiquitination assay with mutagenesis and pathway epistasis; single lab","pmids":["40197797"],"is_preprint":false},{"year":2025,"finding":"NEDD8 binds RNF187 and prevents its K48-linked ubiquitination-mediated degradation, thereby stabilizing and increasing RNF187 protein levels in pancreatic cancer cells. Additionally, neddylated RNF187 upregulates IQGAP1 protein through modulation of K48- and K63-linked ubiquitination of IQGAP1, which triggers actin cytoskeleton rearrangement by altering transcriptional levels of MYH9, promoting pancreatic cancer cell proliferation and invasion.","method":"Co-immunoprecipitation (NEDD8-RNF187 interaction), K48-linked ubiquitination assay, K63-linked ubiquitination assay (IQGAP1), in vitro and in vivo proliferation/invasion assays, transcriptional analysis of MYH9, actin cytoskeleton imaging","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — multiple Co-IP and ubiquitination assays establishing two distinct mechanisms; single lab","pmids":["41291066"],"is_preprint":false},{"year":2016,"finding":"RNF187 expression is downregulated in erythroblasts following pharmacological inhibition of the NF-κB pathway (using Bay 11-7082), placing RNF187 downstream of NF-κB signaling in erythroid differentiation.","method":"NF-κB pathway inhibition with Bay 11-7082 in erythroblasts, PCR array and individual qRT-PCR gene expression analysis","journal":"Biochemical genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single pharmacological inhibition experiment with gene expression readout; no direct mechanistic follow-up","pmids":["27259582"],"is_preprint":false}],"current_model":"RNF187 (RACO-1) is a RING-domain E3 ubiquitin ligase that is activated by PRMT1-mediated arginine methylation (promoting K63-linked auto-ubiquitination, dimerization, and c-Jun/AP-1 co-activation), and that targets multiple substrates for K48-linked polyubiquitination and proteasomal degradation—including YAP (suppressing Hippo signaling), P53 (in an MDM2-independent manner), KRT36/KRT84, WDR77, and IQGAP1—while its own stability is positively regulated by NEDD8 modification that prevents its K48-linked degradation."},"narrative":{"mechanistic_narrative":"RNF187 (RACO-1) is a RING-domain E3 ubiquitin ligase that regulates transcription and cell proliferation by directing both K48- and K63-linked polyubiquitination, functioning as a transcriptional co-activator and a substrate-degrading ligase in multiple cancer and germline contexts [PMID:23624934, PMID:35165289]. Its activity is gated by post-translational modification: PRMT1-mediated arginine methylation triggers a conformational change that promotes K63-linked auto-ubiquitination, dimerization, and interaction with c-Jun, all required for c-Jun/AP-1 transcriptional activation [PMID:23624934], while NEDD8 binding stabilizes RNF187 by blocking its own K48-linked degradative ubiquitination [PMID:41291066]. As a degradative ligase, RNF187 catalyzes K48-linked polyubiquitination and proteasomal turnover of YAP, restraining Hippo/YAP-TEAD target gene expression (CTGF, CYR61) and cell migration/invasion [PMID:32198343, PMID:32896069], and directly ubiquitinates P53 in an MDM2-independent manner to suppress P53 target genes and apoptosis [PMID:35165289]. In germ cell models it degrades the keratins KRT36 and KRT84 to drive proliferation [PMID:37738023] and degrades WDR77, lowering PRMT5-dependent H4R3me2s to derepress EGR1 and promote spermatogonial stem cell maintenance [PMID:40197797]. RNF187 also ubiquitinates histone H3 at K57 and K80 to increase transcription [PMID:38156805], and its expression is driven directly by Notch1 to promote EMT and metastasis [PMID:31477177].","teleology":[{"year":2013,"claim":"Established how RNF187/RACO-1 is activated as a c-Jun/AP-1 co-activator, answering what controls its transcriptional function rather than treating it as a constitutive ligase.","evidence":"MS methylation-site mapping, in vitro methylation, arginine mutagenesis, Co-IP, and AP-1 reporter assays with PRMT1 knockdown","pmids":["23624934"],"confidence":"High","gaps":["Does not identify K48 substrates degraded by activated RACO-1","Structural basis of the methylation-induced conformational change unresolved"]},{"year":2019,"claim":"Showed RNF187 acts as a direct downstream effector of Notch1, answering how the gene is transcriptionally induced and linking it to EMT and metastasis.","evidence":"Luciferase reporter, ChIP, RNA-seq, and gain/loss-of-function epistasis in hepatocellular carcinoma cells","pmids":["31477177"],"confidence":"Medium","gaps":["Does not identify the ubiquitination substrate mediating the pro-migratory effect","Single tumor context"]},{"year":2020,"claim":"Identified YAP as a degradative substrate, establishing RNF187 as a negative regulator of Hippo/YAP-TEAD signaling.","evidence":"Reciprocal Co-IP, K48 ubiquitination assays, and RNAi with YAP-depletion epistasis rescue in TNBC and ESCC cells","pmids":["32198343","32896069"],"confidence":"Medium","gaps":["Ubiquitination not reconstituted in vitro with purified components","Whether PRMT1 methylation status modulates YAP targeting unknown"]},{"year":2022,"claim":"Demonstrated direct, MDM2-independent ubiquitination of P53, broadening RNF187 substrate repertoire and linking it to apoptosis suppression.","evidence":"In vitro ubiquitination reconstitution, Co-IP, RNA-seq, and RNAi in breast cancer cells","pmids":["35165289"],"confidence":"High","gaps":["P53 lysine residues targeted not mapped","Relationship to canonical MDM2 pathway in vivo unclear"]},{"year":2023,"claim":"Extended substrate range to keratins (KRT36/KRT84) and chromatin (histone H3 K57/K80), showing RNF187 controls germ cell proliferation through both degradative and non-degradative ubiquitination.","evidence":"Co-IP/MS substrate identification, K48 and site-specific ubiquitination assays with mutagenesis, and rescue experiments in GC-1 and GC-2 cells","pmids":["37738023","38156805"],"confidence":"Medium","gaps":["Chain linkage on histone H3 not defined","Single lab; physiological role in intact spermatogenesis untested"]},{"year":2025,"claim":"Defined two new regulatory axes: WDR77 degradation feeding into PRMT5/H4R3me2s/EGR1, and NEDD8-mediated stabilization of RNF187 driving IQGAP1/MYH9-dependent cytoskeletal remodeling.","evidence":"Co-IP/MS, K48 and K63 ubiquitination assays with mutagenesis, NEDD8 interaction Co-IP, methylation and transcriptional analyses, and proliferation/invasion assays in SSCs and pancreatic cancer cells","pmids":["40197797","41291066"],"confidence":"Medium","gaps":["Direct evidence that NEDD8 covalently neddylates RNF187 versus binding not fully resolved","How RNF187 differentially assembles K48 versus K63 chains on IQGAP1 unknown"]},{"year":null,"claim":"How RNF187 selects among its diverse substrates and switches between K48-degradative and K63/non-degradative outputs in a given cell remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of substrate engagement","No unified rule linking methylation/neddylation status to chain-type choice","In vivo physiological requirement not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,2,3,5,6,7,8]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,2,3,5,7,8]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[6]}],"localization":[],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,2,3,5,7,8]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,2,4]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,6,7]}],"complexes":[],"partners":["PRMT1","YAP","TP53","KRT36","KRT84","WDR77","IQGAP1","NEDD8"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5TA31","full_name":"E3 ubiquitin-protein ligase RNF187","aliases":["RING domain AP1 coactivator 1","RACO-1","RING finger protein 187","RING-type E3 ubiquitin transferase RNF187"],"length_aa":235,"mass_kda":26.2,"function":"E3 ubiquitin-protein ligase that acts as a coactivator of JUN-mediated gene activation in response to growth factor signaling via the MAP3K1 pathway, independently from MAPK8","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q5TA31/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RNF187","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":77,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RNF187","total_profiled":1310},"omim":[{"mim_id":"613754","title":"RING FINGER PROTEIN 187; RNF187","url":"https://www.omim.org/entry/613754"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RNF187"},"hgnc":{"alias_symbol":["RACO1","RACO-1"],"prev_symbol":[]},"alphafold":{"accession":"Q5TA31","domains":[{"cath_id":"3.30.40.10","chopping":"11-61","consensus_level":"medium","plddt":69.9198,"start":11,"end":61},{"cath_id":"1.20.5","chopping":"133-199","consensus_level":"high","plddt":93.979,"start":133,"end":199}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5TA31","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5TA31-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5TA31-F1-predicted_aligned_error_v6.png","plddt_mean":70.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RNF187","jax_strain_url":"https://www.jax.org/strain/search?query=RNF187"},"sequence":{"accession":"Q5TA31","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5TA31.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5TA31/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5TA31"}},"corpus_meta":[{"pmid":"32198343","id":"PMC_32198343","title":"Regulation of Hippo signaling and triple negative breast cancer progression by an ubiquitin ligase RNF187.","date":"2020","source":"Oncogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/32198343","citation_count":42,"is_preprint":false},{"pmid":"23624934","id":"PMC_23624934","title":"Arginine methylation of the c-Jun coactivator RACO-1 is required for c-Jun/AP-1 activation.","date":"2013","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/23624934","citation_count":40,"is_preprint":false},{"pmid":"35702180","id":"PMC_35702180","title":"Dysregulation of MiR-144-5p/RNF187 Axis Contributes To the Progression of Colorectal Cancer.","date":"2022","source":"Journal of translational internal medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35702180","citation_count":38,"is_preprint":false},{"pmid":"31477177","id":"PMC_31477177","title":"An essential role of RNF187 in Notch1 mediated metastasis of hepatocellular carcinoma.","date":"2019","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/31477177","citation_count":26,"is_preprint":false},{"pmid":"30624778","id":"PMC_30624778","title":"Overexpression of RNF187 induces cell EMT and apoptosis resistance in NSCLC.","date":"2019","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/30624778","citation_count":17,"is_preprint":false},{"pmid":"37738023","id":"PMC_37738023","title":"E3 ubiquitin ligase RNF187 promotes growth of spermatogonia via lysine 48-linked polyubiquitination-mediated degradation of KRT36/KRT84.","date":"2023","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/37738023","citation_count":15,"is_preprint":false},{"pmid":"32896069","id":"PMC_32896069","title":"RACO-1 modulates Hippo signalling in oesophageal squamous cell carcinoma.","date":"2020","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32896069","citation_count":12,"is_preprint":false},{"pmid":"35165289","id":"PMC_35165289","title":"Regulation of P53 signaling in breast cancer by the E3 ubiquitin ligase RNF187.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/35165289","citation_count":12,"is_preprint":false},{"pmid":"38156805","id":"PMC_38156805","title":"RNF187 governs the maintenance of mouse GC-2 cell development by facilitating histone H3 ubiquitination at K57/80.","date":"2023","source":"Asian journal of andrology","url":"https://pubmed.ncbi.nlm.nih.gov/38156805","citation_count":11,"is_preprint":false},{"pmid":"29254210","id":"PMC_29254210","title":"Up-regulation of RNF187 induces hepatocellular carcinoma cell epithelial to mesenchymal transitions.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/29254210","citation_count":11,"is_preprint":false},{"pmid":"32047542","id":"PMC_32047542","title":"High level of RNF187 contributes to the progression and drug resistance of osteosarcoma.","date":"2020","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/32047542","citation_count":6,"is_preprint":false},{"pmid":"27259582","id":"PMC_27259582","title":"RNF187 is Downregulated Following NF-κB Inhibition in Late Erythroblasts.","date":"2016","source":"Biochemical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/27259582","citation_count":5,"is_preprint":false},{"pmid":"39804497","id":"PMC_39804497","title":"A comprehensive pan-cancer analysis of RNF187 in human tumors.","date":"2025","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/39804497","citation_count":5,"is_preprint":false},{"pmid":"40197797","id":"PMC_40197797","title":"RNF187 Facilitates Proliferation and Migration of Human Spermatogonial Stem Cells Through WDR77 Polyubiquitination.","date":"2025","source":"Cell proliferation","url":"https://pubmed.ncbi.nlm.nih.gov/40197797","citation_count":4,"is_preprint":false},{"pmid":"41291066","id":"PMC_41291066","title":"RNF187 neddylation in pancreatic cancer activates malignancy via IQGAP1-dependent actin cytoskeleton rearrangement.","date":"2025","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/41291066","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9778,"output_tokens":2825,"usd":0.035854,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9998,"output_tokens":2605,"usd":0.057557,"stage2_stop_reason":"end_turn"},"total_usd":0.093411,"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\": 2013,\n      \"finding\": \"RACO-1 (RNF187) is a substrate of arginine methyltransferase PRMT1, which methylates RACO-1 on two arginine residues; this methylation promotes a conformational change that stabilizes RACO-1 by facilitating K63-linked ubiquitin chain formation, enables RACO-1 dimerization, and enables interaction with c-Jun, all required for c-Jun/AP-1 transcriptional activation.\",\n      \"method\": \"Mass spectrometry identification of methylation sites, in vitro methylation assay, mutagenesis of arginine residues, Co-IP for dimerization and c-Jun interaction, AP-1 reporter assay, PRMT1 knockdown\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (MS, in vitro assay, mutagenesis, Co-IP, reporter assay) in a single rigorous study establishing mechanistic pathway\",\n      \"pmids\": [\"23624934\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RNF187 associates with YAP and promotes its degradation via K48-linked polyubiquitination, acting as a negative regulator of Hippo signaling in TNBC cells; RNF187 depletion increases YAP protein levels and expression of Hippo target genes (CTGF, CYR61), and the migration/invasion phenotype caused by RNF187 depletion is rescued by further YAP depletion.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, RNAi knockdown with epistasis rescue (YAP depletion), western blot for target gene expression\",\n      \"journal\": \"Oncogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — reciprocal Co-IP and functional epistasis (YAP rescue) in a single lab, corroborated by independent ESCC study (PMID:32896069)\",\n      \"pmids\": [\"32198343\", \"32896069\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RACO-1 (RNF187) associates with YAP in oesophageal squamous cell carcinoma cells and promotes K48-linked polyubiquitination and degradation of YAP; RACO-1 silencing increases YAP protein level and YAP/TEAD target gene expression, promoting invasion and migration, an effect rescued by YAP depletion.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, RNAi knockdown with YAP depletion rescue, western blot\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP and functional epistasis in single lab, independently corroborated by PMID:32198343\",\n      \"pmids\": [\"32896069\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RNF187 interacts with P53 and promotes its polyubiquitination and degradation in breast cancer cells; an in vitro ubiquitin assay demonstrated that RNF187 can directly ubiquitinate P53 in an MDM2-independent manner, inhibiting P53 target genes (IGFBP3, FAS) and facilitating breast cancer cell growth while inhibiting apoptosis.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitination assay, RNAi knockdown, RNA sequencing, western blot\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro ubiquitination reconstitution plus Co-IP and RNA-seq in a single study with multiple orthogonal methods\",\n      \"pmids\": [\"35165289\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"RNF187 is a direct transcriptional target of Notch1 in hepatocellular carcinoma; Notch1 activates the RNF187 promoter (confirmed by luciferase reporter assay and ChIP), and RNF187 is required downstream of Notch1 to promote EMT, invasion, and metastasis, as RNF187 knockdown attenuates Notch1-dependent pro-migratory effects and overexpression of RNF187 rescues Notch1 knockdown phenotypes.\",\n      \"method\": \"Luciferase reporter assay, chromatin immunoprecipitation (ChIP), RNA-seq, gain- and loss-of-function epistasis experiments\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and reporter assay establish direct transcriptional regulation; functional epistasis with reciprocal rescue; single lab\",\n      \"pmids\": [\"31477177\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RNF187 interacts with Keratin 36 (KRT36) and Keratin 84 (KRT84) and promotes their degradation via K48-linked polyubiquitination, thereby promoting proliferation and migration of mouse spermatogonia GC-1 cells; overexpression of KRT36 or KRT84 attenuates the pro-proliferative and pro-migratory effects of RNF187 overexpression.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, K48-linked ubiquitination assay, RNAi and overexpression in GC-1 cells, rescue experiment with KRT36/KRT84 overexpression\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP/MS identification of substrates plus functional rescue; single lab, multiple methods\",\n      \"pmids\": [\"37738023\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RNF187 interacts with histone H3 and mediates its ubiquitination at lysine 57 (K57) and lysine 80 (K80) in mouse spermatocyte-derived GC-2 cells, resulting in increased cellular transcription and promoting GC-2 cell viability, proliferation, and migration.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay with site-specific mutagenesis (K57, K80), RNAi and overexpression in GC-2 cells\",\n      \"journal\": \"Asian journal of andrology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP, ubiquitination assay with mutagenesis; single lab\",\n      \"pmids\": [\"38156805\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RNF187 interacts with WDR77 and mediates its K48-linked polyubiquitination at K118, leading to proteasomal degradation of WDR77; reduced WDR77 decreases symmetric dimethylation at H4R3 (H4R3me2s) catalyzed by PRMT5, relieving transcriptional repression of EGR1 (a positive regulator of human SSC maintenance), thereby promoting proliferation and migration of human spermatogonial stem cells.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, K48-linked ubiquitination assay with site-specific mutagenesis (K118), WDR77 knockdown/overexpression, H4R3me2s methylation analysis\",\n      \"journal\": \"Cell proliferation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP/MS plus ubiquitination assay with mutagenesis and pathway epistasis; single lab\",\n      \"pmids\": [\"40197797\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NEDD8 binds RNF187 and prevents its K48-linked ubiquitination-mediated degradation, thereby stabilizing and increasing RNF187 protein levels in pancreatic cancer cells. Additionally, neddylated RNF187 upregulates IQGAP1 protein through modulation of K48- and K63-linked ubiquitination of IQGAP1, which triggers actin cytoskeleton rearrangement by altering transcriptional levels of MYH9, promoting pancreatic cancer cell proliferation and invasion.\",\n      \"method\": \"Co-immunoprecipitation (NEDD8-RNF187 interaction), K48-linked ubiquitination assay, K63-linked ubiquitination assay (IQGAP1), in vitro and in vivo proliferation/invasion assays, transcriptional analysis of MYH9, actin cytoskeleton imaging\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — multiple Co-IP and ubiquitination assays establishing two distinct mechanisms; single lab\",\n      \"pmids\": [\"41291066\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RNF187 expression is downregulated in erythroblasts following pharmacological inhibition of the NF-κB pathway (using Bay 11-7082), placing RNF187 downstream of NF-κB signaling in erythroid differentiation.\",\n      \"method\": \"NF-κB pathway inhibition with Bay 11-7082 in erythroblasts, PCR array and individual qRT-PCR gene expression analysis\",\n      \"journal\": \"Biochemical genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single pharmacological inhibition experiment with gene expression readout; no direct mechanistic follow-up\",\n      \"pmids\": [\"27259582\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RNF187 (RACO-1) is a RING-domain E3 ubiquitin ligase that is activated by PRMT1-mediated arginine methylation (promoting K63-linked auto-ubiquitination, dimerization, and c-Jun/AP-1 co-activation), and that targets multiple substrates for K48-linked polyubiquitination and proteasomal degradation—including YAP (suppressing Hippo signaling), P53 (in an MDM2-independent manner), KRT36/KRT84, WDR77, and IQGAP1—while its own stability is positively regulated by NEDD8 modification that prevents its K48-linked degradation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RNF187 (RACO-1) is a RING-domain E3 ubiquitin ligase that regulates transcription and cell proliferation by directing both K48- and K63-linked polyubiquitination, functioning as a transcriptional co-activator and a substrate-degrading ligase in multiple cancer and germline contexts [#0, #3]. Its activity is gated by post-translational modification: PRMT1-mediated arginine methylation triggers a conformational change that promotes K63-linked auto-ubiquitination, dimerization, and interaction with c-Jun, all required for c-Jun/AP-1 transcriptional activation [#0], while NEDD8 binding stabilizes RNF187 by blocking its own K48-linked degradative ubiquitination [#8]. As a degradative ligase, RNF187 catalyzes K48-linked polyubiquitination and proteasomal turnover of YAP, restraining Hippo/YAP-TEAD target gene expression (CTGF, CYR61) and cell migration/invasion [#1, #2], and directly ubiquitinates P53 in an MDM2-independent manner to suppress P53 target genes and apoptosis [#3]. In germ cell models it degrades the keratins KRT36 and KRT84 to drive proliferation [#5] and degrades WDR77, lowering PRMT5-dependent H4R3me2s to derepress EGR1 and promote spermatogonial stem cell maintenance [#7]. RNF187 also ubiquitinates histone H3 at K57 and K80 to increase transcription [#6], and its expression is driven directly by Notch1 to promote EMT and metastasis [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established how RNF187/RACO-1 is activated as a c-Jun/AP-1 co-activator, answering what controls its transcriptional function rather than treating it as a constitutive ligase.\",\n      \"evidence\": \"MS methylation-site mapping, in vitro methylation, arginine mutagenesis, Co-IP, and AP-1 reporter assays with PRMT1 knockdown\",\n      \"pmids\": [\"23624934\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not identify K48 substrates degraded by activated RACO-1\", \"Structural basis of the methylation-induced conformational change unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showed RNF187 acts as a direct downstream effector of Notch1, answering how the gene is transcriptionally induced and linking it to EMT and metastasis.\",\n      \"evidence\": \"Luciferase reporter, ChIP, RNA-seq, and gain/loss-of-function epistasis in hepatocellular carcinoma cells\",\n      \"pmids\": [\"31477177\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not identify the ubiquitination substrate mediating the pro-migratory effect\", \"Single tumor context\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified YAP as a degradative substrate, establishing RNF187 as a negative regulator of Hippo/YAP-TEAD signaling.\",\n      \"evidence\": \"Reciprocal Co-IP, K48 ubiquitination assays, and RNAi with YAP-depletion epistasis rescue in TNBC and ESCC cells\",\n      \"pmids\": [\"32198343\", \"32896069\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitination not reconstituted in vitro with purified components\", \"Whether PRMT1 methylation status modulates YAP targeting unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated direct, MDM2-independent ubiquitination of P53, broadening RNF187 substrate repertoire and linking it to apoptosis suppression.\",\n      \"evidence\": \"In vitro ubiquitination reconstitution, Co-IP, RNA-seq, and RNAi in breast cancer cells\",\n      \"pmids\": [\"35165289\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"P53 lysine residues targeted not mapped\", \"Relationship to canonical MDM2 pathway in vivo unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Extended substrate range to keratins (KRT36/KRT84) and chromatin (histone H3 K57/K80), showing RNF187 controls germ cell proliferation through both degradative and non-degradative ubiquitination.\",\n      \"evidence\": \"Co-IP/MS substrate identification, K48 and site-specific ubiquitination assays with mutagenesis, and rescue experiments in GC-1 and GC-2 cells\",\n      \"pmids\": [\"37738023\", \"38156805\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Chain linkage on histone H3 not defined\", \"Single lab; physiological role in intact spermatogenesis untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined two new regulatory axes: WDR77 degradation feeding into PRMT5/H4R3me2s/EGR1, and NEDD8-mediated stabilization of RNF187 driving IQGAP1/MYH9-dependent cytoskeletal remodeling.\",\n      \"evidence\": \"Co-IP/MS, K48 and K63 ubiquitination assays with mutagenesis, NEDD8 interaction Co-IP, methylation and transcriptional analyses, and proliferation/invasion assays in SSCs and pancreatic cancer cells\",\n      \"pmids\": [\"40197797\", \"41291066\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct evidence that NEDD8 covalently neddylates RNF187 versus binding not fully resolved\", \"How RNF187 differentially assembles K48 versus K63 chains on IQGAP1 unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RNF187 selects among its diverse substrates and switches between K48-degradative and K63/non-degradative outputs in a given cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of substrate engagement\", \"No unified rule linking methylation/neddylation status to chain-type choice\", \"In vivo physiological requirement not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 2, 3, 5, 6, 7, 8]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 2, 3, 5, 7, 8]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 2, 3, 5, 7, 8]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 2, 4]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 6, 7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PRMT1\", \"YAP\", \"TP53\", \"KRT36\", \"KRT84\", \"WDR77\", \"IQGAP1\", \"NEDD8\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}