{"gene":"RNF145","run_date":"2026-04-28T19:45:45","timeline":{"discoveries":[{"year":2018,"finding":"RNF145 is a sterol-responsive ER-resident E3 ubiquitin ligase that mediates sterol-accelerated HMGCR degradation by being recruited to HMGCR via Insig proteins upon sterol addition, promoting HMGCR ubiquitination and proteasome-mediated degradation. RNF145 acts independently and in parallel with gp78; in the absence of both, Hrd1 (a third UBE2G2-dependent E3) partially regulates HMGCR.","method":"CRISPR/Cas9 genome-wide screens with endogenous HMGCR reporter, Co-IP, epistasis (double KO), proteasome inhibitor assays","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — genome-wide unbiased screen, reciprocal Co-IP, multiple KO combinations, replicated across two labs (PMID:30543180 and PMID:29374057)","pmids":["30543180"],"is_preprint":false},{"year":2018,"finding":"RNF145 interacts with Insig-1 and Insig-2 proteins via its sterol-sensing domain tetrapeptide YLYF sequence, and its RING finger domain Cys-537 residue is essential for E3 ubiquitin ligase catalytic activity. Mutations in YLYF or Cys-537 abolish RNF145-mediated HMGCR ubiquitination and degradation.","method":"Co-IP, site-directed mutagenesis, in vitro ubiquitination assay, shRNA knockdown in CHO cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — active-site mutagenesis combined with binding assay and functional degradation readout in one study","pmids":["29374057"],"is_preprint":false},{"year":2017,"finding":"RNF145 is transcriptionally induced by LXR activation (via a functional LXR response element in its proximal promoter) and is localized to the ER where it possesses intrinsic E3 ubiquitin ligase activity. This regulation is lost in Lxrαβ(-/-) macrophages/fibroblasts and in livers of Lxrα(-/-) mice.","method":"Global transcriptional analysis, luciferase reporter assay (LXR element), ER localization by microscopy, in vitro ubiquitination assay, Lxr knockout mice","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1-2 — transcriptional mechanism confirmed with LXR element reporter, intrinsic E3 activity validated in vitro, in vivo genetic confirmation","pmids":["28231341"],"is_preprint":false},{"year":2017,"finding":"RNF145, induced by LXR activation and high-cholesterol diet, ubiquitinates SCAP on lysine residues within a cytoplasmic loop essential for COPII binding, potentially inhibiting SCAP transport to the Golgi and subsequent SREBP-2 processing, thereby inhibiting cholesterol biosynthetic gene expression and reducing plasma cholesterol.","method":"Adenoviral RNF145 transduction in mouse liver, shRNA knockdown, RNF145 genetic deletion, Co-IP, ubiquitination assay, SCAP-COPII binding assay","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — in vivo genetic models (KO and shRNA), mechanistic ubiquitination site mapping, functional COPII binding assay, multiple orthogonal approaches","pmids":["29068315"],"is_preprint":false},{"year":2022,"finding":"RNF145 acts as a fatty acid (FA)-responsive E3 ubiquitin ligase that senses membrane lipid saturation. In unsaturated lipid membranes, RNF145 is stable and ubiquitinates ADIPOR2 (a lipid hydrolase), promoting its degradation. When membranes become enriched in saturated FAs, RNF145 undergoes auto-ubiquitination and self-degradation, stabilizing ADIPOR2, which then restores lipid homeostasis and prevents lipotoxicity.","method":"Quantitative proteomics (saturated vs. unsaturated FA feeding), Co-IP, ubiquitination assays, RNF145 KO cells, ADIPOR2 functional readouts, lipid composition analysis","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — systematic proteomics discovery, functional KO validation, direct ubiquitination assays, multiple orthogonal methods in one study","pmids":["35993436"],"is_preprint":false},{"year":2025,"finding":"RNF145 senses cholesterol levels in the ER membrane, altering its oligomerization and E3 ligase activity. Together with the membrane-anchored E2 UBE2J2 (which senses lipid packing), RNF145 participates in an ERAD ubiquitination cascade targeting substrates including squalene monooxygenase. Reconstitution with purified components demonstrated direct functional interaction.","method":"Reconstituted in vitro ubiquitination system with purified ERAD factors, membrane composition assays, E2-E3 interaction assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — fully reconstituted in vitro system with purified components, direct mechanistic demonstration","pmids":["41068091"],"is_preprint":false},{"year":2020,"finding":"In C. elegans, the RNF145 ortholog rnf-145 localizes to the cis-Golgi at early developmental stages and inhibits SREBP (sbp-1) nuclear activation to promote glial growth. At adult stages, eas-1/GOLT1B-dependent shuttling of rnf-145 from cis-Golgi to trans-Golgi network releases this inhibition, halting glial growth. The pathway produces LC-PUFAs (especially EPA) as downstream effectors preventing glial overgrowth.","method":"C. elegans genetics (epistasis, double mutants), live imaging of rnf-145 subcellular localization, genetic suppressor analysis, fatty acid profiling","journal":"PLoS biology","confidence":"Medium","confidence_rationale":"Tier 2 — ortholog in C. elegans with clear epistasis and localization data; applicability to mammalian RNF145-SCAP/SREBP axis is supported by conservation","pmids":["33370778"],"is_preprint":false},{"year":2026,"finding":"RNF145 promotes hepatocellular carcinoma cell migration and invasion by ubiquitinating and degrading protocadherin 9 (PCDH9). Knockdown of RNF145 abolishes metastatic capacity in HCC cells.","method":"Co-IP, ubiquitination assay, western blot, transwell migration and wound-healing assays in RNF145-knockdown HCC cells","journal":"Oncology research","confidence":"Medium","confidence_rationale":"Tier 2 — direct ubiquitination assay combined with functional KD phenotype; single lab, single study","pmids":["41613811"],"is_preprint":false}],"current_model":"RNF145 is a sterol- and lipid-responsive ER-resident E3 ubiquitin ligase that is transcriptionally induced by LXR and regulated post-translationally by membrane lipid composition; it ubiquitinates multiple substrates—HMGCR (via Insig scaffolding), SCAP (blocking COPII transport and SREBP-2 processing), ADIPOR2 (in unsaturated membranes; auto-ubiquitinated and self-degraded in saturated membranes to stabilize ADIPOR2), and PCDH9 (in cancer cells)—coordinating cholesterol biosynthesis, membrane lipid homeostasis, and ERAD through cooperation with the E2 enzyme UBE2J2 and parallel E3 ligases gp78 and Hrd1."},"narrative":{"teleology":[{"year":2017,"claim":"Establishing that RNF145 is an LXR-regulated ER E3 ligase answered the question of how the cholesterol-sensing transcription factor LXR feeds back on ER protein quality control, linking nuclear receptor signaling to ubiquitin-dependent degradation.","evidence":"Transcriptional analysis, luciferase LXR-element reporter, in vitro ubiquitination assay, and Lxrα/β knockout mice and macrophages","pmids":["28231341"],"confidence":"High","gaps":["Physiological substrates of RNF145 were not identified in this study","Mechanism linking LXR-induced RNF145 to specific cholesterol homeostatic outcomes was unknown"]},{"year":2017,"claim":"Demonstrating that RNF145 ubiquitinates SCAP on COPII-binding lysines revealed a previously missing negative-feedback arm by which LXR activation suppresses SREBP-2 processing independently of oxysterol-mediated SCAP retention.","evidence":"Adenoviral overexpression and genetic deletion of RNF145 in mouse liver, ubiquitination site mapping, SCAP-COPII binding assay","pmids":["29068315"],"confidence":"High","gaps":["Whether SCAP ubiquitination leads to ERAD or only blocks COPII sorting was not resolved","Relative contribution of RNF145 versus other E3s for SCAP regulation in vivo was unclear"]},{"year":2018,"claim":"Identification of RNF145 as a sterol-responsive HMGCR E3 ligase acting via Insig scaffolding resolved the long-standing question of which additional E3s besides gp78 mediate sterol-accelerated HMGCR degradation, and defined the catalytic requirements (YLYF motif for Insig binding, Cys-537 for RING activity).","evidence":"CRISPR genome-wide screens, site-directed mutagenesis, Co-IP with Insig-1/2, epistasis with gp78 and Hrd1 double knockouts in multiple cell types","pmids":["30543180","29374057"],"confidence":"High","gaps":["Structural basis of the RNF145–Insig–HMGCR ternary complex is unknown","How RNF145, gp78, and Hrd1 are differentially regulated to partition HMGCR degradation was not determined"]},{"year":2020,"claim":"C. elegans work showed that the RNF145 ortholog's subcellular redistribution from cis-Golgi to trans-Golgi network developmentally releases SREBP inhibition, establishing that dynamic localization — not just expression — controls RNF145 pathway output.","evidence":"C. elegans epistasis, live imaging of rnf-145 localization, suppressor genetics, and fatty acid profiling","pmids":["33370778"],"confidence":"Medium","gaps":["Whether mammalian RNF145 undergoes analogous Golgi redistribution has not been tested","The eas-1/GOLT1B-dependent shuttling mechanism has no demonstrated mammalian counterpart"]},{"year":2022,"claim":"Discovery that RNF145 senses membrane lipid saturation — ubiquitinating ADIPOR2 in unsaturated membranes and auto-ubiquitinating itself in saturated membranes — extended its role from sterol sensing to a broader lipid composition sensor that prevents lipotoxicity.","evidence":"Quantitative proteomics comparing saturated versus unsaturated fatty acid conditions, RNF145 KO cells, ubiquitination assays, lipid composition analysis","pmids":["35993436"],"confidence":"High","gaps":["Structural mechanism by which membrane saturation switches RNF145 from substrate to self-ubiquitination is unknown","Whether sterol and fatty acid sensing operate through the same or distinct domains was not resolved"]},{"year":2025,"claim":"Reconstitution of the RNF145–UBE2J2 ERAD cascade with purified components demonstrated that cholesterol alters RNF145 oligomerization and that UBE2J2 senses lipid packing, providing the first biochemically defined mechanism for how membrane composition is transduced into E3 ligase activity.","evidence":"Fully reconstituted in vitro ubiquitination system with purified ERAD factors and defined membrane compositions","pmids":["41068091"],"confidence":"High","gaps":["High-resolution structure of RNF145 oligomers in different lipid environments is lacking","Full substrate repertoire of the RNF145–UBE2J2 cascade beyond squalene monooxygenase and HMGCR is undefined"]},{"year":2026,"claim":"Identification of PCDH9 as an RNF145 substrate in hepatocellular carcinoma expanded the known substrate range beyond lipid-homeostatic targets to cell adhesion molecules relevant to cancer metastasis.","evidence":"Co-IP, ubiquitination assay, and transwell/wound-healing assays in RNF145-knockdown HCC cells","pmids":["41613811"],"confidence":"Medium","gaps":["Single-lab finding; independent replication is needed","Whether PCDH9 ubiquitination depends on membrane lipid status or Insig scaffolding is unknown","In vivo metastasis validation was not reported"]},{"year":null,"claim":"Open question: how the sterol-sensing domain, fatty acid sensing, and RING domain are structurally coupled to switch RNF145 between distinct substrates and self-degradation, and what the full in vivo substrate landscape is across tissues.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of RNF145 exists","Tissue-specific substrate profiling has not been performed","Relative physiological contributions of RNF145 versus gp78/Hrd1 across metabolic states are unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,3,4,5,7]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[4,5]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,1,2,4,5]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,1,2,3,4]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,3,4,5,7]}],"complexes":[],"partners":["HMGCR","INSIG1","INSIG2","SCAP","ADIPOR2","UBE2J2","PCDH9"],"other_free_text":[]},"mechanistic_narrative":"RNF145 is an ER-resident RING-type E3 ubiquitin ligase that integrates sterol and fatty acid signals to coordinate cholesterol biosynthesis, SREBP-2 activation, and membrane lipid homeostasis. Transcriptionally induced by LXR [PMID:28231341], RNF145 is recruited to HMGCR via Insig-1/2 through its sterol-sensing domain YLYF motif, and its RING finger (Cys-537) catalyzes HMGCR ubiquitination and proteasomal degradation in parallel with gp78 and Hrd1 [PMID:30543180, PMID:29374057]. RNF145 also ubiquitinates SCAP on cytoplasmic lysines required for COPII binding, thereby blocking SCAP–SREBP-2 transport to the Golgi and suppressing cholesterol biosynthetic gene expression [PMID:29068315]. Beyond sterols, RNF145 senses membrane lipid saturation: in unsaturated membranes it ubiquitinates and degrades the lipid hydrolase ADIPOR2, whereas saturated fatty acid enrichment triggers RNF145 auto-ubiquitination and self-degradation, stabilizing ADIPOR2 to restore lipid balance; this dual sensing is coupled to the membrane-anchored E2 UBE2J2, with which RNF145 forms a reconstituted ERAD ubiquitination cascade whose activity responds to cholesterol-dependent oligomerization and lipid packing [PMID:35993436, PMID:41068091]."},"prefetch_data":{"uniprot":{"accession":"Q96MT1","full_name":"RING finger protein 145","aliases":[],"length_aa":663,"mass_kda":75.6,"function":"E3 ubiquitin ligase that catalyzes the direct transfer of ubiquitin from E2 ubiquitin-conjugating enzyme to a specific substrate. In response to bacterial infection, negatively regulates the phagocyte oxidative burst by controlling the turnover of the NADPH oxidase complex subunits. Promotes monoubiquitination of CYBA and 'Lys-48'-linked polyubiquitination and degradation of CYBB NADPH oxidase catalytic subunits, both essential for the generation of antimicrobial reactive oxygen species. Involved in the maintenance of cholesterol homeostasis. In response to high sterol concentrations ubiquitinates HMGCR, a rate-limiting enzyme in cholesterol biosynthesis, and targets it for degradation. The interaction with INSIG1 is required for this function. In addition, triggers ubiquitination of SCAP, likely inhibiting its transport to the Golgi apparatus and the subsequent processing/maturation of SREBPF2, ultimately down-regulating cholesterol biosynthesis","subcellular_location":"Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/Q96MT1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RNF145","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":383,"dependency_fraction":0.0026109660574412533},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RNF145","total_profiled":1310},"omim":[{"mim_id":"620640","title":"RING FINGER PROTEIN 145; RNF145","url":"https://www.omim.org/entry/620640"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Plasma membrane","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RNF145"},"hgnc":{"alias_symbol":["FLJ31951"],"prev_symbol":[]},"alphafold":{"accession":"Q96MT1","domains":[{"cath_id":"-","chopping":"73-223","consensus_level":"high","plddt":86.2444,"start":73,"end":223},{"cath_id":"-","chopping":"227-440","consensus_level":"medium","plddt":89.0622,"start":227,"end":440},{"cath_id":"3.30.40.10","chopping":"523-568","consensus_level":"high","plddt":86.7041,"start":523,"end":568}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96MT1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96MT1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96MT1-F1-predicted_aligned_error_v6.png","plddt_mean":78.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RNF145","jax_strain_url":"https://www.jax.org/strain/search?query=RNF145"},"sequence":{"accession":"Q96MT1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96MT1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96MT1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96MT1"}},"corpus_meta":[{"pmid":"30543180","id":"PMC_30543180","title":"The sterol-responsive RNF145 E3 ubiquitin ligase mediates the degradation of HMG-CoA reductase together with gp78 and Hrd1.","date":"2018","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/30543180","citation_count":90,"is_preprint":false},{"pmid":"29374057","id":"PMC_29374057","title":"Ring finger protein 145 (RNF145) is a ubiquitin ligase for sterol-induced degradation of HMG-CoA reductase.","date":"2018","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29374057","citation_count":63,"is_preprint":false},{"pmid":"29068315","id":"PMC_29068315","title":"Inhibition of cholesterol biosynthesis through RNF145-dependent ubiquitination of SCAP.","date":"2017","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/29068315","citation_count":50,"is_preprint":false},{"pmid":"35047011","id":"PMC_35047011","title":"Using Machine Learning to Predict Obesity Based on Genome-Wide and Epigenome-Wide Gene-Gene and Gene-Diet Interactions.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35047011","citation_count":34,"is_preprint":false},{"pmid":"28231341","id":"PMC_28231341","title":"Identification of the ER-resident E3 ubiquitin ligase RNF145 as a novel LXR-regulated gene.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28231341","citation_count":27,"is_preprint":false},{"pmid":"35993436","id":"PMC_35993436","title":"Regulation of membrane fluidity by RNF145-triggered degradation of the lipid hydrolase ADIPOR2.","date":"2022","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/35993436","citation_count":22,"is_preprint":false},{"pmid":"35365168","id":"PMC_35365168","title":"CircZDBF2 up-regulates RNF145 by ceRNA model and recruits CEBPB to accelerate oral squamous cell carcinoma progression via NFκB signaling pathway.","date":"2022","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35365168","citation_count":20,"is_preprint":false},{"pmid":"28139377","id":"PMC_28139377","title":"CPT1A methylation is associated with plasma adiponectin.","date":"2016","source":"Nutrition, metabolism, and cardiovascular diseases : NMCD","url":"https://pubmed.ncbi.nlm.nih.gov/28139377","citation_count":19,"is_preprint":false},{"pmid":"28059166","id":"PMC_28059166","title":"Mean Platelet Volume and Arterial Stiffness - Clinical Relationship and Common Genetic Variability.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28059166","citation_count":18,"is_preprint":false},{"pmid":"36797040","id":"PMC_36797040","title":"Identification of new risk loci shared across systemic vasculitides points towards potential target genes for drug repurposing.","date":"2023","source":"Annals of the rheumatic diseases","url":"https://pubmed.ncbi.nlm.nih.gov/36797040","citation_count":16,"is_preprint":false},{"pmid":"24446873","id":"PMC_24446873","title":"Identification of clinically important chromosomal aberrations in acute myeloid leukemia by array-based comparative genomic hybridization.","date":"2014","source":"Leukemia & lymphoma","url":"https://pubmed.ncbi.nlm.nih.gov/24446873","citation_count":12,"is_preprint":false},{"pmid":"34155583","id":"PMC_34155583","title":"Transcriptional Profiles Reveal Deregulation of Lipid Metabolism and Inflammatory Pathways in Neurons Exposed to Palmitic Acid.","date":"2021","source":"Molecular neurobiology","url":"https://pubmed.ncbi.nlm.nih.gov/34155583","citation_count":10,"is_preprint":false},{"pmid":"33370778","id":"PMC_33370778","title":"Regulation of glial size by eicosapentaenoic acid through a novel Golgi apparatus mechanism.","date":"2020","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/33370778","citation_count":7,"is_preprint":false},{"pmid":"33727652","id":"PMC_33727652","title":"Genetic variation of RNF145 gene and blood lipid levels in Xinjiang population, China.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33727652","citation_count":5,"is_preprint":false},{"pmid":"37987107","id":"PMC_37987107","title":"Promoter-Specific Variants in NeuroD1 and H3K4me3 Coincident Regions and Clinical Outcomes of Small Cell Lung Cancer.","date":"2023","source":"Journal of Korean medical science","url":"https://pubmed.ncbi.nlm.nih.gov/37987107","citation_count":5,"is_preprint":false},{"pmid":"40018925","id":"PMC_40018925","title":"Molecular Markers of Occult Lymph Node Metastasis in Head and Neck Squamous Cell Carcinoma (HNSCC) Patients.","date":"2025","source":"Frontiers in bioscience (Landmark edition)","url":"https://pubmed.ncbi.nlm.nih.gov/40018925","citation_count":4,"is_preprint":false},{"pmid":"39180204","id":"PMC_39180204","title":"Palmdelphin Inhibits Ovarian Cancer Cell Stem Specification via Downregulating Ring Finger Protein 145.","date":"2024","source":"Critical reviews in eukaryotic gene expression","url":"https://pubmed.ncbi.nlm.nih.gov/39180204","citation_count":1,"is_preprint":false},{"pmid":"41613811","id":"PMC_41613811","title":"RNF145 Promotes Hepatocellular Carcinoma Metastasis through Ubiquitination and Degradation of PCDH9.","date":"2026","source":"Oncology research","url":"https://pubmed.ncbi.nlm.nih.gov/41613811","citation_count":0,"is_preprint":false},{"pmid":"41233983","id":"PMC_41233983","title":"Single-cell transcriptome-wide Mendelian randomization and colocalization reveal cell-specific mechanisms in systemic lupus erythematosus.","date":"2026","source":"Rheumatology (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/41233983","citation_count":0,"is_preprint":false},{"pmid":"41068091","id":"PMC_41068091","title":"UBE2J2 sensitizes the ERAD ubiquitination cascade to changes in membrane lipid saturation.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41068091","citation_count":0,"is_preprint":false},{"pmid":"41459856","id":"PMC_41459856","title":"In Silico Analysis of the Role of Estrogen Signaling in the Expression of Metabolic Genes in Breast Cancer.","date":"2025","source":"Asian Pacific journal of cancer prevention : APJCP","url":"https://pubmed.ncbi.nlm.nih.gov/41459856","citation_count":0,"is_preprint":false},{"pmid":"37890275","id":"PMC_37890275","title":"As a matter of fat: Emerging roles of lipid-sensitive E3 ubiquitin ligases.","date":"2023","source":"BioEssays : news and reviews in molecular, cellular and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/37890275","citation_count":0,"is_preprint":false},{"pmid":"39612541","id":"PMC_39612541","title":"Multi-omics study of sex in greater amberjack (Seriola dumerili): Identifying related genes, analyzing sex-biased expression, and developing sex-specific markers.","date":"2024","source":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/39612541","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13356,"output_tokens":2260,"usd":0.036984},"stage2":{"model":"claude-opus-4-6","input_tokens":5547,"output_tokens":2441,"usd":0.13314},"total_usd":0.170124,"stage1_batch_id":"msgbatch_01SUR8NDzVrNmyszWyJeCct7","stage2_batch_id":"msgbatch_01G7Yfutko3cDWzejrwH5AMx","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"RNF145 is a sterol-responsive ER-resident E3 ubiquitin ligase that mediates sterol-accelerated HMGCR degradation by being recruited to HMGCR via Insig proteins upon sterol addition, promoting HMGCR ubiquitination and proteasome-mediated degradation. RNF145 acts independently and in parallel with gp78; in the absence of both, Hrd1 (a third UBE2G2-dependent E3) partially regulates HMGCR.\",\n      \"method\": \"CRISPR/Cas9 genome-wide screens with endogenous HMGCR reporter, Co-IP, epistasis (double KO), proteasome inhibitor assays\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide unbiased screen, reciprocal Co-IP, multiple KO combinations, replicated across two labs (PMID:30543180 and PMID:29374057)\",\n      \"pmids\": [\"30543180\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RNF145 interacts with Insig-1 and Insig-2 proteins via its sterol-sensing domain tetrapeptide YLYF sequence, and its RING finger domain Cys-537 residue is essential for E3 ubiquitin ligase catalytic activity. Mutations in YLYF or Cys-537 abolish RNF145-mediated HMGCR ubiquitination and degradation.\",\n      \"method\": \"Co-IP, site-directed mutagenesis, in vitro ubiquitination assay, shRNA knockdown in CHO cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — active-site mutagenesis combined with binding assay and functional degradation readout in one study\",\n      \"pmids\": [\"29374057\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"RNF145 is transcriptionally induced by LXR activation (via a functional LXR response element in its proximal promoter) and is localized to the ER where it possesses intrinsic E3 ubiquitin ligase activity. This regulation is lost in Lxrαβ(-/-) macrophages/fibroblasts and in livers of Lxrα(-/-) mice.\",\n      \"method\": \"Global transcriptional analysis, luciferase reporter assay (LXR element), ER localization by microscopy, in vitro ubiquitination assay, Lxr knockout mice\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — transcriptional mechanism confirmed with LXR element reporter, intrinsic E3 activity validated in vitro, in vivo genetic confirmation\",\n      \"pmids\": [\"28231341\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"RNF145, induced by LXR activation and high-cholesterol diet, ubiquitinates SCAP on lysine residues within a cytoplasmic loop essential for COPII binding, potentially inhibiting SCAP transport to the Golgi and subsequent SREBP-2 processing, thereby inhibiting cholesterol biosynthetic gene expression and reducing plasma cholesterol.\",\n      \"method\": \"Adenoviral RNF145 transduction in mouse liver, shRNA knockdown, RNF145 genetic deletion, Co-IP, ubiquitination assay, SCAP-COPII binding assay\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic models (KO and shRNA), mechanistic ubiquitination site mapping, functional COPII binding assay, multiple orthogonal approaches\",\n      \"pmids\": [\"29068315\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RNF145 acts as a fatty acid (FA)-responsive E3 ubiquitin ligase that senses membrane lipid saturation. In unsaturated lipid membranes, RNF145 is stable and ubiquitinates ADIPOR2 (a lipid hydrolase), promoting its degradation. When membranes become enriched in saturated FAs, RNF145 undergoes auto-ubiquitination and self-degradation, stabilizing ADIPOR2, which then restores lipid homeostasis and prevents lipotoxicity.\",\n      \"method\": \"Quantitative proteomics (saturated vs. unsaturated FA feeding), Co-IP, ubiquitination assays, RNF145 KO cells, ADIPOR2 functional readouts, lipid composition analysis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — systematic proteomics discovery, functional KO validation, direct ubiquitination assays, multiple orthogonal methods in one study\",\n      \"pmids\": [\"35993436\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RNF145 senses cholesterol levels in the ER membrane, altering its oligomerization and E3 ligase activity. Together with the membrane-anchored E2 UBE2J2 (which senses lipid packing), RNF145 participates in an ERAD ubiquitination cascade targeting substrates including squalene monooxygenase. Reconstitution with purified components demonstrated direct functional interaction.\",\n      \"method\": \"Reconstituted in vitro ubiquitination system with purified ERAD factors, membrane composition assays, E2-E3 interaction assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — fully reconstituted in vitro system with purified components, direct mechanistic demonstration\",\n      \"pmids\": [\"41068091\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In C. elegans, the RNF145 ortholog rnf-145 localizes to the cis-Golgi at early developmental stages and inhibits SREBP (sbp-1) nuclear activation to promote glial growth. At adult stages, eas-1/GOLT1B-dependent shuttling of rnf-145 from cis-Golgi to trans-Golgi network releases this inhibition, halting glial growth. The pathway produces LC-PUFAs (especially EPA) as downstream effectors preventing glial overgrowth.\",\n      \"method\": \"C. elegans genetics (epistasis, double mutants), live imaging of rnf-145 subcellular localization, genetic suppressor analysis, fatty acid profiling\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ortholog in C. elegans with clear epistasis and localization data; applicability to mammalian RNF145-SCAP/SREBP axis is supported by conservation\",\n      \"pmids\": [\"33370778\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"RNF145 promotes hepatocellular carcinoma cell migration and invasion by ubiquitinating and degrading protocadherin 9 (PCDH9). Knockdown of RNF145 abolishes metastatic capacity in HCC cells.\",\n      \"method\": \"Co-IP, ubiquitination assay, western blot, transwell migration and wound-healing assays in RNF145-knockdown HCC cells\",\n      \"journal\": \"Oncology research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct ubiquitination assay combined with functional KD phenotype; single lab, single study\",\n      \"pmids\": [\"41613811\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RNF145 is a sterol- and lipid-responsive ER-resident E3 ubiquitin ligase that is transcriptionally induced by LXR and regulated post-translationally by membrane lipid composition; it ubiquitinates multiple substrates—HMGCR (via Insig scaffolding), SCAP (blocking COPII transport and SREBP-2 processing), ADIPOR2 (in unsaturated membranes; auto-ubiquitinated and self-degraded in saturated membranes to stabilize ADIPOR2), and PCDH9 (in cancer cells)—coordinating cholesterol biosynthesis, membrane lipid homeostasis, and ERAD through cooperation with the E2 enzyme UBE2J2 and parallel E3 ligases gp78 and Hrd1.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"RNF145 is an ER-resident RING-type E3 ubiquitin ligase that integrates sterol and fatty acid signals to coordinate cholesterol biosynthesis, SREBP-2 activation, and membrane lipid homeostasis. Transcriptionally induced by LXR [PMID:28231341], RNF145 is recruited to HMGCR via Insig-1/2 through its sterol-sensing domain YLYF motif, and its RING finger (Cys-537) catalyzes HMGCR ubiquitination and proteasomal degradation in parallel with gp78 and Hrd1 [PMID:30543180, PMID:29374057]. RNF145 also ubiquitinates SCAP on cytoplasmic lysines required for COPII binding, thereby blocking SCAP–SREBP-2 transport to the Golgi and suppressing cholesterol biosynthetic gene expression [PMID:29068315]. Beyond sterols, RNF145 senses membrane lipid saturation: in unsaturated membranes it ubiquitinates and degrades the lipid hydrolase ADIPOR2, whereas saturated fatty acid enrichment triggers RNF145 auto-ubiquitination and self-degradation, stabilizing ADIPOR2 to restore lipid balance; this dual sensing is coupled to the membrane-anchored E2 UBE2J2, with which RNF145 forms a reconstituted ERAD ubiquitination cascade whose activity responds to cholesterol-dependent oligomerization and lipid packing [PMID:35993436, PMID:41068091].\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Establishing that RNF145 is an LXR-regulated ER E3 ligase answered the question of how the cholesterol-sensing transcription factor LXR feeds back on ER protein quality control, linking nuclear receptor signaling to ubiquitin-dependent degradation.\",\n      \"evidence\": \"Transcriptional analysis, luciferase LXR-element reporter, in vitro ubiquitination assay, and Lxrα/β knockout mice and macrophages\",\n      \"pmids\": [\"28231341\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Physiological substrates of RNF145 were not identified in this study\",\n        \"Mechanism linking LXR-induced RNF145 to specific cholesterol homeostatic outcomes was unknown\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrating that RNF145 ubiquitinates SCAP on COPII-binding lysines revealed a previously missing negative-feedback arm by which LXR activation suppresses SREBP-2 processing independently of oxysterol-mediated SCAP retention.\",\n      \"evidence\": \"Adenoviral overexpression and genetic deletion of RNF145 in mouse liver, ubiquitination site mapping, SCAP-COPII binding assay\",\n      \"pmids\": [\"29068315\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether SCAP ubiquitination leads to ERAD or only blocks COPII sorting was not resolved\",\n        \"Relative contribution of RNF145 versus other E3s for SCAP regulation in vivo was unclear\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identification of RNF145 as a sterol-responsive HMGCR E3 ligase acting via Insig scaffolding resolved the long-standing question of which additional E3s besides gp78 mediate sterol-accelerated HMGCR degradation, and defined the catalytic requirements (YLYF motif for Insig binding, Cys-537 for RING activity).\",\n      \"evidence\": \"CRISPR genome-wide screens, site-directed mutagenesis, Co-IP with Insig-1/2, epistasis with gp78 and Hrd1 double knockouts in multiple cell types\",\n      \"pmids\": [\"30543180\", \"29374057\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of the RNF145–Insig–HMGCR ternary complex is unknown\",\n        \"How RNF145, gp78, and Hrd1 are differentially regulated to partition HMGCR degradation was not determined\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"C. elegans work showed that the RNF145 ortholog's subcellular redistribution from cis-Golgi to trans-Golgi network developmentally releases SREBP inhibition, establishing that dynamic localization — not just expression — controls RNF145 pathway output.\",\n      \"evidence\": \"C. elegans epistasis, live imaging of rnf-145 localization, suppressor genetics, and fatty acid profiling\",\n      \"pmids\": [\"33370778\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether mammalian RNF145 undergoes analogous Golgi redistribution has not been tested\",\n        \"The eas-1/GOLT1B-dependent shuttling mechanism has no demonstrated mammalian counterpart\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Discovery that RNF145 senses membrane lipid saturation — ubiquitinating ADIPOR2 in unsaturated membranes and auto-ubiquitinating itself in saturated membranes — extended its role from sterol sensing to a broader lipid composition sensor that prevents lipotoxicity.\",\n      \"evidence\": \"Quantitative proteomics comparing saturated versus unsaturated fatty acid conditions, RNF145 KO cells, ubiquitination assays, lipid composition analysis\",\n      \"pmids\": [\"35993436\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural mechanism by which membrane saturation switches RNF145 from substrate to self-ubiquitination is unknown\",\n        \"Whether sterol and fatty acid sensing operate through the same or distinct domains was not resolved\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Reconstitution of the RNF145–UBE2J2 ERAD cascade with purified components demonstrated that cholesterol alters RNF145 oligomerization and that UBE2J2 senses lipid packing, providing the first biochemically defined mechanism for how membrane composition is transduced into E3 ligase activity.\",\n      \"evidence\": \"Fully reconstituted in vitro ubiquitination system with purified ERAD factors and defined membrane compositions\",\n      \"pmids\": [\"41068091\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"High-resolution structure of RNF145 oligomers in different lipid environments is lacking\",\n        \"Full substrate repertoire of the RNF145–UBE2J2 cascade beyond squalene monooxygenase and HMGCR is undefined\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identification of PCDH9 as an RNF145 substrate in hepatocellular carcinoma expanded the known substrate range beyond lipid-homeostatic targets to cell adhesion molecules relevant to cancer metastasis.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, and transwell/wound-healing assays in RNF145-knockdown HCC cells\",\n      \"pmids\": [\"41613811\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab finding; independent replication is needed\",\n        \"Whether PCDH9 ubiquitination depends on membrane lipid status or Insig scaffolding is unknown\",\n        \"In vivo metastasis validation was not reported\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Open question: how the sterol-sensing domain, fatty acid sensing, and RING domain are structurally coupled to switch RNF145 between distinct substrates and self-degradation, and what the full in vivo substrate landscape is across tissues.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No high-resolution structure of RNF145 exists\",\n        \"Tissue-specific substrate profiling has not been performed\",\n        \"Relative physiological contributions of RNF145 versus gp78/Hrd1 across metabolic states are unresolved\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 3, 4, 5, 7]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 1, 2, 4, 5]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 3, 4, 5, 7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"HMGCR\",\n      \"INSIG1\",\n      \"INSIG2\",\n      \"SCAP\",\n      \"ADIPOR2\",\n      \"UBE2J2\",\n      \"PCDH9\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}