{"gene":"MARCHF7","run_date":"2026-04-28T18:30:28","timeline":{"discoveries":[{"year":2008,"finding":"MARCH7 undergoes autoubiquitylation and associates with deubiquitylating enzymes USP9X (in the cytosol) and USP7 (in the nucleus), which stabilize MARCH7 by deubiquitylating it in a compartment-specific manner.","method":"Co-immunoprecipitation, siRNA depletion, exogenous expression, subcellular fractionation","journal":"Traffic","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP with functional rescue, replicated with orthogonal siRNA and overexpression experiments","pmids":["18410486"],"is_preprint":false},{"year":2014,"finding":"MARCH7/axotrophin interacts with tau protein via its RING-variant domain (aa 552–682) and catalyzes mono-ubiquitination of tau in vitro, which diminishes tau's microtubule-binding activity; the interaction was validated by yeast two-hybrid, co-immunoprecipitation, and co-localization.","method":"Yeast two-hybrid, co-immunoprecipitation, co-localization, in vitro ubiquitination assay, microtubule-binding assay","journal":"Biochimica et biophysica acta","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with functional (microtubule binding) readout, confirmed by Co-IP","pmids":["24905733"],"is_preprint":false},{"year":2012,"finding":"MARCH7 catalyzes K48-linked ubiquitination and localizes to the caudal end of the developing acrosome in spermatids (co-localizing with β-actin/acroplaxome) and to developing flagella, implicating it in spermiogenesis and sperm head/tail formation.","method":"In situ hybridization, immunohistochemistry, immunolocalization, linkage-specific ubiquitin assay","journal":"Histochemistry and cell biology","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization with linkage-specific ubiquitination assay; single lab","pmids":["23104140"],"is_preprint":false},{"year":2017,"finding":"MARCH7 directly binds NPHP5 and K48-ubiquitinates it, triggering NPHP5 degradation and cilia loss; USP9X sequesters MARCH7 away from the centrosome during interphase, and USP9X depletion allows centrosomal accumulation of MARCH7 which degrades NPHP5 to disrupt ciliogenesis.","method":"Co-immunoprecipitation, siRNA depletion, linkage-specific ubiquitin assay, confocal localization, cell cycle staging","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP with defined linkage specificity, functional ciliogenesis readout, and epistatic placement with USP9X and BBS11","pmids":["28498859"],"is_preprint":false},{"year":2018,"finding":"MARCH7 physically interacts with Mdm2 and catalyzes K63-linked polyubiquitination of Mdm2, which blocks Mdm2 autoubiquitination and degradation, thereby stabilizing Mdm2 and promoting Mdm2-dependent K48-linked polyubiquitination and proteasomal degradation of p53.","method":"Co-immunoprecipitation, in vitro ubiquitination assay, linkage-specific ubiquitin assay, siRNA knockdown, overexpression","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1 — in vitro ubiquitination assay plus multiple orthogonal cellular experiments defining mechanism","pmids":["29295817"],"is_preprint":false},{"year":2018,"finding":"MARCH7 interacts with TGFβR2, activates the TGF-β–Smad2/3 pathway, and promotes autophagy and invasion in ovarian cancer cells; MARCH7 also functions as a ceRNA competing with miR-200a to regulate ATG7 expression in conjunction with lncRNA MALAT1.","method":"Co-immunoprecipitation, ChIP assay, luciferase reporter assay, siRNA knockdown, overexpression, in vivo xenograft","journal":"Cellular physiology and biochemistry","confidence":"Medium","confidence_rationale":"Tier 2/3 — Co-IP for TGFβR2 interaction, functional rescue experiments; single lab","pmids":["29794480"],"is_preprint":false},{"year":2018,"finding":"MARCH7 interacts with VAV2 and activates the VAV2–RAC1–CDC42 signaling pathway to promote proliferation and invasion of cervical cancer cells.","method":"Co-immunoprecipitation, siRNA knockdown, signaling pathway analysis","journal":"Oncology letters","confidence":"Low","confidence_rationale":"Tier 3 — single Co-IP with pathway analysis; single lab","pmids":["30008934"],"is_preprint":false},{"year":2023,"finding":"MARCH7 ubiquitinates ATG14 via mixed K6-, K11-, and K63-linked polyubiquitin chains, causing ATG14 aggregation, reduced solubility, decreased interaction with STX17, and inhibition of autophagy flux; MARCH7 depletion reduces aggresome-like induced structures (ALISs).","method":"In vitro ubiquitination assay, linkage-specific ubiquitin mutants, Co-immunoprecipitation, MARCH7 knockout cells, autophagy flux assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 — in vitro ubiquitination with multiple linkage validations, KO rescue, functional autophagy flux readout","pmids":["37632749"],"is_preprint":false},{"year":2023,"finding":"MARCH7 interacts with NLRP3 and promotes its proteasomal degradation via ubiquitination; an E3 ligase-inactive MARCH7 mutant (W589A/I556A) fails to inhibit NAFLD development, establishing catalytic activity as essential for NLRP3 suppression and pyroptosis inhibition.","method":"Co-immunoprecipitation, active-site mutagenesis, siRNA knockdown, in vivo mouse models, western blot","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 1/2 — active-site mutagenesis combined with Co-IP and in vivo functional rescue","pmids":["37337032"],"is_preprint":false},{"year":2023,"finding":"Zebrafish MARCH7 interacts with TBK1 via its C-terminal RING domain and promotes K48-linked ubiquitination and degradation of TBK1, thereby negatively regulating type I interferon antiviral responses.","method":"Co-immunoprecipitation, truncation mapping, siRNA knockdown, linkage-specific ubiquitin assay, viral replication assay","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP with domain mapping and linkage-specific ubiquitination in zebrafish ortholog; single lab","pmids":["37054851"],"is_preprint":false},{"year":2025,"finding":"Human MARCHF7 promotes K27-linked ubiquitination of SARS-CoV-2 nsp16 and its proteasomal degradation, independently suppressing viral replication in cell culture and in mice.","method":"Ubiquitination assay, proteasome inhibitor rescue, overexpression/knockdown, viral replication assay in cells and mice","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 — linkage-specific ubiquitination plus in vivo antiviral functional readout; single lab","pmids":["40358464"],"is_preprint":false},{"year":2025,"finding":"MARCHF7 binds PXMP4 and ubiquitinates it at K20 to initiate pexophagy; TBK1 (activated by ROS in PEX1-deficient cells) phosphorylates MARCHF7, and ubiquitinated PXMP4 serves as a recognition signal for NBR1 recruitment to peroxisomes.","method":"Co-immunoprecipitation, site-directed mutagenesis (K20 ubiquitination-defective mutant), siRNA knockdown, pexophagy flux assay, phosphorylation analysis","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 1/2 — site-specific mutagenesis with functional rescue assay plus epistatic pathway placement of TBK1-MARCHF7-PXMP4-NBR1","pmids":["41267209"],"is_preprint":false},{"year":2010,"finding":"MARCH7 regulates the LIF-receptor in T lymphocytes; T cells lacking MARCH7 are hyper-responsive to activation signals and show elevated LIF activity and permissive Nanog expression during G1/S cell cycle entry.","method":"Genetic knockout (MARCH7-null mice), miRNA profiling, transcript/protein analysis","journal":"Cell cycle","confidence":"Medium","confidence_rationale":"Tier 2 — clean genetic KO with specific pathway phenotype; single lab, limited mechanistic detail on ubiquitination substrate","pmids":["20962578"],"is_preprint":false}],"current_model":"MARCHF7 is a RING-variant E3 ubiquitin ligase that undergoes autoubiquitylation and is stabilized by compartment-specific deubiquitylases (USP9X in cytosol, USP7 in nucleus); it catalyzes substrate-specific ubiquitination with distinct linkages—K48 (degradative) on NPHP5, tau, and TBK1; K63 (non-degradative, stabilizing) on Mdm2; K27 on SARS-CoV-2 nsp16; and mixed K6/K11/K63 on ATG14—regulating diverse processes including ciliogenesis, p53 tumor suppression, autophagy flux, pexophagy, neuronal tau dynamics, and innate immune signaling."},"narrative":{"teleology":[{"year":2008,"claim":"Establishing that MARCHF7 is an autoubiquitylating E3 ligase whose stability is controlled by compartment-specific deubiquitylases resolved how this enzyme is itself regulated and predicted that its subcellular distribution determines substrate access.","evidence":"Co-immunoprecipitation, siRNA depletion, and subcellular fractionation in mammalian cells","pmids":["18410486"],"confidence":"High","gaps":["Structural basis for USP9X vs. USP7 selectivity unknown","Endogenous substrates not yet identified at this stage"]},{"year":2010,"claim":"Knockout studies revealed that MARCHF7 restrains T cell activation by regulating the LIF receptor, providing the first evidence of a physiological immune-regulatory role.","evidence":"MARCH7-null mouse T cells with transcript/protein profiling","pmids":["20962578"],"confidence":"Medium","gaps":["Whether LIF receptor is a direct ubiquitination substrate was not shown","Mechanism linking MARCHF7 loss to Nanog de-repression not fully resolved"]},{"year":2012,"claim":"Localization of MARCHF7 to the acrosome and developing flagella of spermatids, together with K48-linked ubiquitin catalysis, implicated the enzyme in spermiogenesis and revealed its capacity for degradative chain assembly.","evidence":"Immunohistochemistry, in situ hybridization, and linkage-specific ubiquitin assays in testis","pmids":["23104140"],"confidence":"Medium","gaps":["Spermatid-specific substrates not identified","No loss-of-function data for fertility phenotype"]},{"year":2014,"claim":"Demonstration that MARCHF7 mono-ubiquitinates tau and reduces its microtubule-binding activity established the first biochemically reconstituted substrate and connected the enzyme to neuronal cytoskeletal regulation.","evidence":"In vitro ubiquitination assay, yeast two-hybrid, co-immunoprecipitation, microtubule-binding assay","pmids":["24905733"],"confidence":"High","gaps":["In vivo relevance in neurons or tauopathy models not tested","Ubiquitin linkage type on tau not determined"]},{"year":2017,"claim":"Identification of NPHP5 as a K48-ubiquitination target and the finding that USP9X sequesters MARCHF7 away from the centrosome during interphase explained how ciliogenesis is maintained and linked MARCHF7 to ciliopathy-related biology.","evidence":"Linkage-specific ubiquitin assays, confocal localization, siRNA epistasis with USP9X and BBS11, ciliogenesis readout","pmids":["28498859"],"confidence":"High","gaps":["Whether MARCHF7 mutations cause ciliopathies in humans is unknown","Mechanism of MARCHF7 release from USP9X during mitosis not resolved"]},{"year":2018,"claim":"The finding that MARCHF7 K63-ubiquitinates Mdm2 to block its self-degradation and thereby promotes p53 destruction revealed a non-degradative ubiquitin linkage output and placed MARCHF7 as a negative regulator of p53 signaling.","evidence":"In vitro ubiquitination assay, linkage-specific ubiquitin mutants, Co-IP, knockdown/overexpression","pmids":["29295817"],"confidence":"High","gaps":["Physiological tumor context (e.g., cancer genetics) not explored","How MARCHF7 activity on Mdm2 is itself regulated is unclear"]},{"year":2018,"claim":"Studies in ovarian and cervical cancer cells linked MARCHF7 to TGFβ–Smad and VAV2–RAC1 signaling, broadening its potential roles to invasion and proliferation, though direct ubiquitination substrates in these pathways were not fully defined.","evidence":"Co-IP with TGFβR2 and VAV2, luciferase reporters, xenograft models, siRNA knockdown","pmids":["29794480","30008934"],"confidence":"Medium","gaps":["VAV2 interaction rests on single Co-IP without reciprocal validation","Direct ubiquitination of TGFβR2 or VAV2 by MARCHF7 not demonstrated"]},{"year":2023,"claim":"Three concurrent studies defined new substrates—ATG14 (mixed K6/K11/K63 chains inhibiting autophagy flux), NLRP3 (degradative ubiquitination suppressing pyroptosis), and TBK1 (K48-linked degradation dampening type I IFN)—demonstrating MARCHF7's versatile linkage specificity and broad roles in autophagy and innate immunity.","evidence":"In vitro ubiquitination with linkage mutants, MARCHF7-KO cells, catalytic-dead mutant rescue, zebrafish viral replication assays, mouse NAFLD models","pmids":["37632749","37337032","37054851"],"confidence":"High","gaps":["TBK1 ubiquitination demonstrated only with zebrafish ortholog; human confirmation needed","Structural determinants selecting among K6/K11/K48/K63 linkages unknown","Interplay between MARCHF7-mediated ATG14 aggregation and NLRP3 inflammasome activation not addressed"]},{"year":2025,"claim":"Identification of SARS-CoV-2 nsp16 as a K27-linked ubiquitination target and PXMP4 as a pexophagy-initiating substrate (phospho-regulated by TBK1) expanded MARCHF7's linkage repertoire further and placed it upstream of selective autophagy receptor NBR1 in peroxisome turnover.","evidence":"Linkage-specific ubiquitination assays, site-directed K20 mutagenesis of PXMP4, phosphorylation analysis, pexophagy flux assays, in vivo antiviral assays in mice","pmids":["40358464","41267209"],"confidence":"High","gaps":["How TBK1 phosphorylation of MARCHF7 alters its substrate selectivity is mechanistically undefined","Relevance to peroxisomal biogenesis disorders in patients not tested"]},{"year":null,"claim":"A unifying structural and regulatory model explaining how MARCHF7 selects among at least five ubiquitin linkage types (K6, K11, K27, K48, K63) for different substrates remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No crystal or cryo-EM structure of MARCHF7 or its RING domain–E2 complex","E2 conjugating enzyme(s) partnering with MARCHF7 for each linkage type not identified","Upstream signals coordinating MARCHF7 activity across ciliogenesis, autophagy, and immune pathways not integrated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,3,4,7,8,9,10,11]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,3,4,7,8,9,10,11]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[5,7,11]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[9,10,12]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[4,8]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[3,11]}],"complexes":[],"partners":["USP9X","USP7","NPHP5","MDM2","ATG14","NLRP3","TBK1","PXMP4"],"other_free_text":[]},"mechanistic_narrative":"MARCHF7 is a RING-variant E3 ubiquitin ligase that regulates diverse cellular processes—including ciliogenesis, autophagy, pexophagy, p53 tumor suppression, and innate immune signaling—by catalyzing substrate-specific ubiquitination with distinct linkage types. It attaches K48-linked chains to NPHP5, tau, TBK1, and NLRP3 to promote their degradation [PMID:28498859, PMID:24905733, PMID:37054851, PMID:37337032], K63-linked chains to Mdm2 to stabilize it and thereby enhance p53 degradation [PMID:29295817], mixed K6/K11/K63 chains to ATG14 to inhibit autophagy flux [PMID:37632749], and K27-linked chains to SARS-CoV-2 nsp16 for antiviral defense [PMID:40358464]. MARCHF7 itself is regulated by compartment-specific deubiquitylases—USP9X in the cytosol and USP7 in the nucleus—that counteract its autoubiquitylation and control its stability and centrosomal access [PMID:18410486, PMID:28498859], and by TBK1-mediated phosphorylation that activates its pexophagy function through ubiquitination of the peroxisomal membrane protein PXMP4 [PMID:41267209]."},"prefetch_data":{"uniprot":{"accession":"Q9H992","full_name":"E3 ubiquitin-protein ligase MARCHF7","aliases":["Axotrophin","Membrane-associated RING finger protein 7","Membrane-associated RING-CH protein VII","MARCH-VII","RING finger protein 177","RING-type E3 ubiquitin transferase MARCHF7"],"length_aa":704,"mass_kda":78.1,"function":"E3 ubiquitin-protein ligase which may specifically enhance the E2 activity of HIP2. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates (PubMed:16868077). May be involved in T-cell proliferation by regulating LIF secretion (By similarity). May play a role in lysosome homeostasis (PubMed:31270356). Promotes 'Lys-6', 'Lys-11' and 'Lys-63'-linked mixed polyubiquitination on ATG14 leading to the inhibition of autophagy by impairing the interaction between ATG14 and STX7 (PubMed:37632749). Participates in the dopamine-mediated negative regulation of the NLRP3 inflammasome by promoting its ubiquitination and subsequent degradation (PubMed:25594175)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9H992/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/MARCHF7","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1090,"dependency_fraction":0.0009174311926605505},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/MARCHF7","total_profiled":1310},"omim":[{"mim_id":"613334","title":"MEMBRANE-ASSOCIATED RING-CH FINGER PROTEIN 7; MARCHF7","url":"https://www.omim.org/entry/613334"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Basal body","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/MARCHF7"},"hgnc":{"alias_symbol":["MARCH-VII","RNF177"],"prev_symbol":["AXOT","MARCH7"]},"alphafold":{"accession":"Q9H992","domains":[{"cath_id":"3.30.40.10","chopping":"551-617","consensus_level":"medium","plddt":87.3355,"start":551,"end":617},{"cath_id":"4.10.270","chopping":"620-684","consensus_level":"medium","plddt":84.362,"start":620,"end":684}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H992","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H992-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H992-F1-predicted_aligned_error_v6.png","plddt_mean":50.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MARCHF7","jax_strain_url":"https://www.jax.org/strain/search?query=MARCHF7"},"sequence":{"accession":"Q9H992","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H992.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H992/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H992"}},"corpus_meta":[{"pmid":"18410486","id":"PMC_18410486","title":"The ubiquitin E3 ligase MARCH7 is differentially regulated by the deubiquitylating enzymes USP7 and USP9X.","date":"2008","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/18410486","citation_count":74,"is_preprint":false},{"pmid":"29295817","id":"PMC_29295817","title":"Regulation of the Mdm2-p53 pathway by the ubiquitin E3 ligase MARCH7.","date":"2018","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/29295817","citation_count":57,"is_preprint":false},{"pmid":"37337032","id":"PMC_37337032","title":"GAS5 protects against nonalcoholic fatty liver disease via miR-28a-5p/MARCH7/NLRP3 axis-mediated pyroptosis.","date":"2023","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/37337032","citation_count":54,"is_preprint":false},{"pmid":"24905733","id":"PMC_24905733","title":"Axotrophin/MARCH7 acts as an E3 ubiquitin ligase and ubiquitinates tau protein in vitro impairing microtubule binding.","date":"2014","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/24905733","citation_count":50,"is_preprint":false},{"pmid":"29794480","id":"PMC_29794480","title":"Interaction of E3 Ubiquitin Ligase MARCH7 with Long Noncoding RNA MALAT1 and Autophagy-Related Protein ATG7 Promotes Autophagy and Invasion in Ovarian Cancer.","date":"2018","source":"Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/29794480","citation_count":48,"is_preprint":false},{"pmid":"28498859","id":"PMC_28498859","title":"USP9X counteracts differential ubiquitination of NPHP5 by MARCH7 and BBS11 to regulate ciliogenesis.","date":"2017","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28498859","citation_count":35,"is_preprint":false},{"pmid":"31006800","id":"PMC_31006800","title":"miR-27b-3p/MARCH7 regulates invasion and metastasis of endometrial cancer cells through Snail-mediated pathway.","date":"2019","source":"Acta biochimica et biophysica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/31006800","citation_count":29,"is_preprint":false},{"pmid":"23104140","id":"PMC_23104140","title":"MARCH7 E3 ubiquitin ligase is highly expressed in developing spermatids of rats and its possible involvement in head and tail formation.","date":"2012","source":"Histochemistry and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/23104140","citation_count":25,"is_preprint":false},{"pmid":"25895127","id":"PMC_25895127","title":"Ubiquitin E3 ligase MARCH7 promotes ovarian tumor growth.","date":"2015","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/25895127","citation_count":24,"is_preprint":false},{"pmid":"30008934","id":"PMC_30008934","title":"Ubiquitin E3 Ligase MARCH7 promotes proliferation and invasion of cervical cancer cells through VAV2-RAC1-CDC42 pathway.","date":"2018","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/30008934","citation_count":13,"is_preprint":false},{"pmid":"37632749","id":"PMC_37632749","title":"MARCH7-mediated ubiquitination decreases the solubility of ATG14 to inhibit autophagy.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37632749","citation_count":10,"is_preprint":false},{"pmid":"37054851","id":"PMC_37054851","title":"Zebrafish MARCH7 negatively regulates IFN antiviral response by degrading TBK1.","date":"2023","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/37054851","citation_count":10,"is_preprint":false},{"pmid":"20962578","id":"PMC_20962578","title":"A LIF/Nanog axis is revealed in T lymphocytes that lack MARCH-7, a RINGv E3 ligase that regulates the LIF-receptor.","date":"2010","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/20962578","citation_count":8,"is_preprint":false},{"pmid":"38246482","id":"PMC_38246482","title":"Jianpi Antai formula prevents miscarriage by repressing M1 polarization of decidual macrophages through ubiquitination of NLRP3 mediated by MARCH7.","date":"2024","source":"Journal of ethnopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/38246482","citation_count":6,"is_preprint":false},{"pmid":"37915253","id":"PMC_37915253","title":"Control of ATG14 solubility and autophagy by MARCHF7/MARCH7-mediated ubiquitination.","date":"2023","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/37915253","citation_count":5,"is_preprint":false},{"pmid":"36583798","id":"PMC_36583798","title":"Association of MARCH7 with tumor progression and T-cell infiltration in esophageal cancer.","date":"2022","source":"Medical oncology (Northwood, London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/36583798","citation_count":4,"is_preprint":false},{"pmid":"40358464","id":"PMC_40358464","title":"SARS-CoV-2 nsp16 is regulated by host E3 ubiquitin ligases, UBR5 and MARCHF7.","date":"2025","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/40358464","citation_count":2,"is_preprint":false},{"pmid":"41267209","id":"PMC_41267209","title":"Regulation of pexophagy by a novel TBK1-MARCHF7-PXMP4-NBR1 axis in PEX1-depleted HeLa cells.","date":"2025","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/41267209","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10337,"output_tokens":2967,"usd":0.037758},"stage2":{"model":"claude-opus-4-6","input_tokens":6362,"output_tokens":2758,"usd":0.15114},"total_usd":0.188898,"stage1_batch_id":"msgbatch_01Mgbec4vM6c9vXht7JVJzss","stage2_batch_id":"msgbatch_01JkuuH5RB2BdJNsgnhjbC6s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"MARCH7 undergoes autoubiquitylation and associates with deubiquitylating enzymes USP9X (in the cytosol) and USP7 (in the nucleus), which stabilize MARCH7 by deubiquitylating it in a compartment-specific manner.\",\n      \"method\": \"Co-immunoprecipitation, siRNA depletion, exogenous expression, subcellular fractionation\",\n      \"journal\": \"Traffic\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP with functional rescue, replicated with orthogonal siRNA and overexpression experiments\",\n      \"pmids\": [\"18410486\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"MARCH7/axotrophin interacts with tau protein via its RING-variant domain (aa 552–682) and catalyzes mono-ubiquitination of tau in vitro, which diminishes tau's microtubule-binding activity; the interaction was validated by yeast two-hybrid, co-immunoprecipitation, and co-localization.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, co-localization, in vitro ubiquitination assay, microtubule-binding assay\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with functional (microtubule binding) readout, confirmed by Co-IP\",\n      \"pmids\": [\"24905733\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"MARCH7 catalyzes K48-linked ubiquitination and localizes to the caudal end of the developing acrosome in spermatids (co-localizing with β-actin/acroplaxome) and to developing flagella, implicating it in spermiogenesis and sperm head/tail formation.\",\n      \"method\": \"In situ hybridization, immunohistochemistry, immunolocalization, linkage-specific ubiquitin assay\",\n      \"journal\": \"Histochemistry and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization with linkage-specific ubiquitination assay; single lab\",\n      \"pmids\": [\"23104140\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"MARCH7 directly binds NPHP5 and K48-ubiquitinates it, triggering NPHP5 degradation and cilia loss; USP9X sequesters MARCH7 away from the centrosome during interphase, and USP9X depletion allows centrosomal accumulation of MARCH7 which degrades NPHP5 to disrupt ciliogenesis.\",\n      \"method\": \"Co-immunoprecipitation, siRNA depletion, linkage-specific ubiquitin assay, confocal localization, cell cycle staging\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP with defined linkage specificity, functional ciliogenesis readout, and epistatic placement with USP9X and BBS11\",\n      \"pmids\": [\"28498859\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"MARCH7 physically interacts with Mdm2 and catalyzes K63-linked polyubiquitination of Mdm2, which blocks Mdm2 autoubiquitination and degradation, thereby stabilizing Mdm2 and promoting Mdm2-dependent K48-linked polyubiquitination and proteasomal degradation of p53.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitination assay, linkage-specific ubiquitin assay, siRNA knockdown, overexpression\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro ubiquitination assay plus multiple orthogonal cellular experiments defining mechanism\",\n      \"pmids\": [\"29295817\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"MARCH7 interacts with TGFβR2, activates the TGF-β–Smad2/3 pathway, and promotes autophagy and invasion in ovarian cancer cells; MARCH7 also functions as a ceRNA competing with miR-200a to regulate ATG7 expression in conjunction with lncRNA MALAT1.\",\n      \"method\": \"Co-immunoprecipitation, ChIP assay, luciferase reporter assay, siRNA knockdown, overexpression, in vivo xenograft\",\n      \"journal\": \"Cellular physiology and biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — Co-IP for TGFβR2 interaction, functional rescue experiments; single lab\",\n      \"pmids\": [\"29794480\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"MARCH7 interacts with VAV2 and activates the VAV2–RAC1–CDC42 signaling pathway to promote proliferation and invasion of cervical cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, signaling pathway analysis\",\n      \"journal\": \"Oncology letters\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single Co-IP with pathway analysis; single lab\",\n      \"pmids\": [\"30008934\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MARCH7 ubiquitinates ATG14 via mixed K6-, K11-, and K63-linked polyubiquitin chains, causing ATG14 aggregation, reduced solubility, decreased interaction with STX17, and inhibition of autophagy flux; MARCH7 depletion reduces aggresome-like induced structures (ALISs).\",\n      \"method\": \"In vitro ubiquitination assay, linkage-specific ubiquitin mutants, Co-immunoprecipitation, MARCH7 knockout cells, autophagy flux assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro ubiquitination with multiple linkage validations, KO rescue, functional autophagy flux readout\",\n      \"pmids\": [\"37632749\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MARCH7 interacts with NLRP3 and promotes its proteasomal degradation via ubiquitination; an E3 ligase-inactive MARCH7 mutant (W589A/I556A) fails to inhibit NAFLD development, establishing catalytic activity as essential for NLRP3 suppression and pyroptosis inhibition.\",\n      \"method\": \"Co-immunoprecipitation, active-site mutagenesis, siRNA knockdown, in vivo mouse models, western blot\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — active-site mutagenesis combined with Co-IP and in vivo functional rescue\",\n      \"pmids\": [\"37337032\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Zebrafish MARCH7 interacts with TBK1 via its C-terminal RING domain and promotes K48-linked ubiquitination and degradation of TBK1, thereby negatively regulating type I interferon antiviral responses.\",\n      \"method\": \"Co-immunoprecipitation, truncation mapping, siRNA knockdown, linkage-specific ubiquitin assay, viral replication assay\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP with domain mapping and linkage-specific ubiquitination in zebrafish ortholog; single lab\",\n      \"pmids\": [\"37054851\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Human MARCHF7 promotes K27-linked ubiquitination of SARS-CoV-2 nsp16 and its proteasomal degradation, independently suppressing viral replication in cell culture and in mice.\",\n      \"method\": \"Ubiquitination assay, proteasome inhibitor rescue, overexpression/knockdown, viral replication assay in cells and mice\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — linkage-specific ubiquitination plus in vivo antiviral functional readout; single lab\",\n      \"pmids\": [\"40358464\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"MARCHF7 binds PXMP4 and ubiquitinates it at K20 to initiate pexophagy; TBK1 (activated by ROS in PEX1-deficient cells) phosphorylates MARCHF7, and ubiquitinated PXMP4 serves as a recognition signal for NBR1 recruitment to peroxisomes.\",\n      \"method\": \"Co-immunoprecipitation, site-directed mutagenesis (K20 ubiquitination-defective mutant), siRNA knockdown, pexophagy flux assay, phosphorylation analysis\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — site-specific mutagenesis with functional rescue assay plus epistatic pathway placement of TBK1-MARCHF7-PXMP4-NBR1\",\n      \"pmids\": [\"41267209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"MARCH7 regulates the LIF-receptor in T lymphocytes; T cells lacking MARCH7 are hyper-responsive to activation signals and show elevated LIF activity and permissive Nanog expression during G1/S cell cycle entry.\",\n      \"method\": \"Genetic knockout (MARCH7-null mice), miRNA profiling, transcript/protein analysis\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean genetic KO with specific pathway phenotype; single lab, limited mechanistic detail on ubiquitination substrate\",\n      \"pmids\": [\"20962578\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MARCHF7 is a RING-variant E3 ubiquitin ligase that undergoes autoubiquitylation and is stabilized by compartment-specific deubiquitylases (USP9X in cytosol, USP7 in nucleus); it catalyzes substrate-specific ubiquitination with distinct linkages—K48 (degradative) on NPHP5, tau, and TBK1; K63 (non-degradative, stabilizing) on Mdm2; K27 on SARS-CoV-2 nsp16; and mixed K6/K11/K63 on ATG14—regulating diverse processes including ciliogenesis, p53 tumor suppression, autophagy flux, pexophagy, neuronal tau dynamics, and innate immune signaling.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"MARCHF7 is a RING-variant E3 ubiquitin ligase that regulates diverse cellular processes—including ciliogenesis, autophagy, pexophagy, p53 tumor suppression, and innate immune signaling—by catalyzing substrate-specific ubiquitination with distinct linkage types. It attaches K48-linked chains to NPHP5, tau, TBK1, and NLRP3 to promote their degradation [PMID:28498859, PMID:24905733, PMID:37054851, PMID:37337032], K63-linked chains to Mdm2 to stabilize it and thereby enhance p53 degradation [PMID:29295817], mixed K6/K11/K63 chains to ATG14 to inhibit autophagy flux [PMID:37632749], and K27-linked chains to SARS-CoV-2 nsp16 for antiviral defense [PMID:40358464]. MARCHF7 itself is regulated by compartment-specific deubiquitylases—USP9X in the cytosol and USP7 in the nucleus—that counteract its autoubiquitylation and control its stability and centrosomal access [PMID:18410486, PMID:28498859], and by TBK1-mediated phosphorylation that activates its pexophagy function through ubiquitination of the peroxisomal membrane protein PXMP4 [PMID:41267209].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Establishing that MARCHF7 is an autoubiquitylating E3 ligase whose stability is controlled by compartment-specific deubiquitylases resolved how this enzyme is itself regulated and predicted that its subcellular distribution determines substrate access.\",\n      \"evidence\": \"Co-immunoprecipitation, siRNA depletion, and subcellular fractionation in mammalian cells\",\n      \"pmids\": [\"18410486\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for USP9X vs. USP7 selectivity unknown\", \"Endogenous substrates not yet identified at this stage\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Knockout studies revealed that MARCHF7 restrains T cell activation by regulating the LIF receptor, providing the first evidence of a physiological immune-regulatory role.\",\n      \"evidence\": \"MARCH7-null mouse T cells with transcript/protein profiling\",\n      \"pmids\": [\"20962578\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether LIF receptor is a direct ubiquitination substrate was not shown\", \"Mechanism linking MARCHF7 loss to Nanog de-repression not fully resolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Localization of MARCHF7 to the acrosome and developing flagella of spermatids, together with K48-linked ubiquitin catalysis, implicated the enzyme in spermiogenesis and revealed its capacity for degradative chain assembly.\",\n      \"evidence\": \"Immunohistochemistry, in situ hybridization, and linkage-specific ubiquitin assays in testis\",\n      \"pmids\": [\"23104140\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Spermatid-specific substrates not identified\", \"No loss-of-function data for fertility phenotype\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstration that MARCHF7 mono-ubiquitinates tau and reduces its microtubule-binding activity established the first biochemically reconstituted substrate and connected the enzyme to neuronal cytoskeletal regulation.\",\n      \"evidence\": \"In vitro ubiquitination assay, yeast two-hybrid, co-immunoprecipitation, microtubule-binding assay\",\n      \"pmids\": [\"24905733\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance in neurons or tauopathy models not tested\", \"Ubiquitin linkage type on tau not determined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identification of NPHP5 as a K48-ubiquitination target and the finding that USP9X sequesters MARCHF7 away from the centrosome during interphase explained how ciliogenesis is maintained and linked MARCHF7 to ciliopathy-related biology.\",\n      \"evidence\": \"Linkage-specific ubiquitin assays, confocal localization, siRNA epistasis with USP9X and BBS11, ciliogenesis readout\",\n      \"pmids\": [\"28498859\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether MARCHF7 mutations cause ciliopathies in humans is unknown\", \"Mechanism of MARCHF7 release from USP9X during mitosis not resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"The finding that MARCHF7 K63-ubiquitinates Mdm2 to block its self-degradation and thereby promotes p53 destruction revealed a non-degradative ubiquitin linkage output and placed MARCHF7 as a negative regulator of p53 signaling.\",\n      \"evidence\": \"In vitro ubiquitination assay, linkage-specific ubiquitin mutants, Co-IP, knockdown/overexpression\",\n      \"pmids\": [\"29295817\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological tumor context (e.g., cancer genetics) not explored\", \"How MARCHF7 activity on Mdm2 is itself regulated is unclear\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Studies in ovarian and cervical cancer cells linked MARCHF7 to TGFβ–Smad and VAV2–RAC1 signaling, broadening its potential roles to invasion and proliferation, though direct ubiquitination substrates in these pathways were not fully defined.\",\n      \"evidence\": \"Co-IP with TGFβR2 and VAV2, luciferase reporters, xenograft models, siRNA knockdown\",\n      \"pmids\": [\"29794480\", \"30008934\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"VAV2 interaction rests on single Co-IP without reciprocal validation\", \"Direct ubiquitination of TGFβR2 or VAV2 by MARCHF7 not demonstrated\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Three concurrent studies defined new substrates—ATG14 (mixed K6/K11/K63 chains inhibiting autophagy flux), NLRP3 (degradative ubiquitination suppressing pyroptosis), and TBK1 (K48-linked degradation dampening type I IFN)—demonstrating MARCHF7's versatile linkage specificity and broad roles in autophagy and innate immunity.\",\n      \"evidence\": \"In vitro ubiquitination with linkage mutants, MARCHF7-KO cells, catalytic-dead mutant rescue, zebrafish viral replication assays, mouse NAFLD models\",\n      \"pmids\": [\"37632749\", \"37337032\", \"37054851\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"TBK1 ubiquitination demonstrated only with zebrafish ortholog; human confirmation needed\", \"Structural determinants selecting among K6/K11/K48/K63 linkages unknown\", \"Interplay between MARCHF7-mediated ATG14 aggregation and NLRP3 inflammasome activation not addressed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identification of SARS-CoV-2 nsp16 as a K27-linked ubiquitination target and PXMP4 as a pexophagy-initiating substrate (phospho-regulated by TBK1) expanded MARCHF7's linkage repertoire further and placed it upstream of selective autophagy receptor NBR1 in peroxisome turnover.\",\n      \"evidence\": \"Linkage-specific ubiquitination assays, site-directed K20 mutagenesis of PXMP4, phosphorylation analysis, pexophagy flux assays, in vivo antiviral assays in mice\",\n      \"pmids\": [\"40358464\", \"41267209\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TBK1 phosphorylation of MARCHF7 alters its substrate selectivity is mechanistically undefined\", \"Relevance to peroxisomal biogenesis disorders in patients not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"A unifying structural and regulatory model explaining how MARCHF7 selects among at least five ubiquitin linkage types (K6, K11, K27, K48, K63) for different substrates remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No crystal or cryo-EM structure of MARCHF7 or its RING domain–E2 complex\", \"E2 conjugating enzyme(s) partnering with MARCHF7 for each linkage type not identified\", \"Upstream signals coordinating MARCHF7 activity across ciliogenesis, autophagy, and immune pathways not integrated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 7, 8, 9, 10, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 3, 4, 7, 8, 9, 10, 11]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [5, 7, 11]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [9, 10, 12]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [4, 8]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [3, 11]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"USP9X\",\n      \"USP7\",\n      \"NPHP5\",\n      \"MDM2\",\n      \"ATG14\",\n      \"NLRP3\",\n      \"TBK1\",\n      \"PXMP4\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}