{"gene":"MKRN1","run_date":"2026-04-28T18:30:28","timeline":{"discoveries":[{"year":2005,"finding":"MKRN1 is an E3 ubiquitin ligase that directly ubiquitinates hTERT, promoting its proteasome-mediated degradation and reducing telomerase activity and telomere length; MKRN1-hTERT interaction was identified by yeast two-hybrid.","method":"Yeast two-hybrid, overexpression ubiquitination assay, proteasome degradation assay, telomerase activity assay","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Y2H, ubiquitination, proteasomal degradation, telomerase assay), highly cited foundational paper","pmids":["15805468"],"is_preprint":false},{"year":2009,"finding":"MKRN1 functions as an E3 ubiquitin ligase that ubiquitinates and degrades p53 (at novel sites K291/K292) and p21 via the proteasome under normal conditions; under DNA damage stress, MKRN1 preferentially degrades p21 to promote apoptosis while p53 is stabilized.","method":"Ubiquitination assay, proteasome degradation assay, site-directed mutagenesis (K291/K292), siRNA knockdown, ectopic overexpression, apoptosis assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods including mutagenesis of ubiquitination sites, highly cited, replicated in multiple cellular contexts","pmids":["19536131"],"is_preprint":false},{"year":2012,"finding":"MKRN1 is an E3 ubiquitin ligase that ubiquitinates p14ARF (human)/p19ARF (mouse), targeting it for proteasome-dependent degradation, thereby promoting cellular bypass of senescence and gastric tumorigenesis.","method":"Ubiquitination assay, proteasome degradation assay, siRNA/shRNA knockdown, MKRN1 knockout MEFs, xenograft mouse model, immunohistochemistry","journal":"Journal of the National Cancer Institute","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods, in vivo validation, epistasis via double knockdown","pmids":["23104211"],"is_preprint":false},{"year":2013,"finding":"MKRN1 is an E3 ubiquitin ligase for PPARγ, ubiquitinating it at lysines 184 and 185 and promoting proteasome-dependent degradation, thereby suppressing adipocyte differentiation.","method":"Ubiquitination assay, site-directed mutagenesis (K184/K185), stable overexpression/knockdown, MKRN1 knockout MEFs, adipocyte differentiation assay","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 1–2 — mutagenesis of ubiquitination sites, genetic KO validation, multiple cell models","pmids":["24336050"],"is_preprint":false},{"year":2018,"finding":"MKRN1 ubiquitinates and promotes proteasomal degradation of AMPKα, and its depletion stabilizes AMPK leading to chronic AMPK activation in liver and adipose tissue, suppressing diet-induced metabolic syndrome in mice.","method":"Co-immunoprecipitation, ubiquitination assay, MKRN1 knockout mice, shRNA delivery in obese mice, AMPK activity assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, genetic KO with defined metabolic phenotype, in vivo therapeutic validation","pmids":["30143610"],"is_preprint":false},{"year":2018,"finding":"MKRN1 directly interacts with and ubiquitylates APC (adenomatous polyposis coli), promoting its proteasomal degradation and thereby positively regulating Wnt/β-catenin signaling; E3 ligase-defective MKRN1 mutant cannot regulate APC.","method":"Co-immunoprecipitation, ubiquitylation assay, E3 ligase-dead mutant, siRNA knockdown, β-catenin reporter assay, cell migration/invasion assays","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, catalytic mutant validation, epistasis via double knockdown","pmids":["29713058"],"is_preprint":false},{"year":2019,"finding":"MKRN1 directly binds PABPC1 (cytoplasmic poly(A)-binding protein) in an RNA-independent manner and associates with polysomes; MKRN1 is positioned upstream of poly(A) tails in an mRNA in a PABPC1-dependent manner and ubiquitylates PABPC1 and ribosomal protein RPS10, promoting ribosome stalling at poly(A) sequences during ribosome-associated quality control (RQC).","method":"Co-immunoprecipitation, in vitro ubiquitylation assay, ubiquitin remnant profiling (mass spectrometry), polysome association assay, iCLIP/PAR-CLIP for RNA binding","journal":"Genome biology","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro ubiquitylation, proteome-wide ubiquitin remnant profiling, RNA-binding mapping, multiple orthogonal methods","pmids":["31640799"],"is_preprint":false},{"year":2010,"finding":"MKRN1 functions as an E3 ubiquitin ligase for West Nile virus capsid protein (WNVCp), ubiquitinating it at lysines 101, 103, and 104 via interaction between the C-terminus of MKRN1 and the N-terminus of WNVCp, promoting proteasome-dependent WNVCp degradation and protecting cells from WNV cytotoxicity.","method":"Co-immunoprecipitation, ubiquitination assay, site-directed mutagenesis (K101/103/104 of WNVCp), domain mapping, stable cell lines, viral replication assay","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 1–2 — mutagenesis of ubiquitination sites, domain mapping, multiple functional readouts","pmids":["19846531"],"is_preprint":false},{"year":2006,"finding":"MKRN1 acts as a transcriptional repressor of c-Jun, androgen receptor, and retinoic acid receptors, and as a transcriptional activator when fused to GAL4-DBD; both N- and C-termini are required for transcriptional activity; E3 ligase activity is not required for transcriptional repression.","method":"Reporter gene assay, truncation analysis, RING finger mutant (E3 ligase-dead), overexpression in mammalian cells","journal":"Endocrine","confidence":"Medium","confidence_rationale":"Tier 2 — truncation and catalytic mutant analysis with reporter assay, single lab","pmids":["16785614"],"is_preprint":false},{"year":2011,"finding":"MKRN1-short isoform binds PABP in an RNA-independent manner in rat neurons, co-localizes with PABP in dendritic granule-like structures, associates with dendritic mRNAs, and when tethered to a reporter mRNA stimulates translation; MKRN1-short accumulates in activated dendritic laminae after synaptic plasticity induction.","method":"Co-immunoprecipitation (RNA-independent), tethering assay (reporter translation), in vivo perforant path stimulation, co-localization by immunofluorescence","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — tethering assay for translation, RNA-independent Co-IP, in vivo neuronal stimulation; single lab, moderate orthogonal methods","pmids":["22128154"],"is_preprint":false},{"year":2015,"finding":"MKRN1 associates with RNA-binding proteins and stress granule components in embryonic stem cells and localizes to stress granules under stress, but is not required for stress granule formation; identified as a ribonucleoprotein component of the ESC gene regulatory network.","method":"Proteomic interactome (mass spectrometry), RIP-chip (RNA immunoprecipitation-microarray), live-cell imaging of stress granules, KO/KD analysis","journal":"EMBO reports","confidence":"Medium","confidence_rationale":"Tier 2–3 — proteomic interactome plus RIP-chip plus localization; single lab","pmids":["26265008"],"is_preprint":false},{"year":2018,"finding":"MKRN1 interacts with and promotes proteasomal degradation of AMPKα1 and α2 via ubiquitination; MKRN1 KO MEFs show stabilized AMPK with suppressed lipogenesis and increased mitochondrial biogenesis.","method":"Co-immunoprecipitation, ubiquitination assay, MEF knockout cells, metabolic flux assays","journal":"Cell stress","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP, ubiquitination, KO cells; single lab, consistent with companion Nature Communications paper","pmids":["31225456"],"is_preprint":false},{"year":2021,"finding":"MKRN1 is a second E3 ubiquitin ligase for Eag1 voltage-gated K+ channels, interacting primarily with the carboxyl-terminal region of Eag1; MKRN1 promotes polyubiquitination and ER-associated proteasomal degradation of immature (core-glycosylated and nascent non-glycosylated) Eag1 at the ER, distinct from CUL7 which also regulates peripheral quality control.","method":"Yeast two-hybrid, co-immunoprecipitation, ubiquitination assay, glycosylation analysis, proteasome inhibitor assays, domain mapping","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — Y2H, Co-IP, ubiquitination, domain mapping, differential glycosylation analysis; multiple orthogonal methods","pmids":["33647316"],"is_preprint":false},{"year":2023,"finding":"MKRN1 ubiquitinates and degrades SNIP1 via the proteasome, thereby relieving SNIP1-mediated inhibition of TGF-β signaling and promoting EMT and metastasis in colorectal cancer.","method":"Quantitative proteomics, ubiquitination modification omics, co-immunoprecipitation, in vitro ubiquitination, conditional MKRN1 knockout mice, xenograft","journal":"Journal of experimental & clinical cancer research : CR","confidence":"High","confidence_rationale":"Tier 2 — proteomics-guided substrate identification, ubiquitination assay, genetic KO in vivo validation","pmids":["37620897"],"is_preprint":false},{"year":2025,"finding":"MKRN1 promotes K48-linked ubiquitination of LKB1 at Lys146, inhibiting AMPK signaling and impairing energy homeostasis in cardiomyocytes; FOXM1 suppresses this MKRN1-dependent LKB1 ubiquitination to preserve mitochondrial bioenergetics.","method":"Proteomic and ubiquitinome profiling of Foxm1-KO mice, site-specific ubiquitination assays, CM-specific Mkrn1 KO mouse model, AMPK signaling assays","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 — ubiquitinome mass spectrometry identifies site, genetic KO validation; single lab","pmids":["40546121"],"is_preprint":false},{"year":2025,"finding":"Ebastine binds to the C-terminal domain of MKRN1 (residues R298 and K360), promoting MKRN1 self-ubiquitination and destabilization, which in turn stabilizes AMPK and alleviates metabolic steatohepatitis.","method":"Drug-protein binding assay, mutagenesis (R298, K360), self-ubiquitination assay, MKRN1 KO mice, AAV8-mediated liver-specific knockdown, metabolic phenotyping","journal":"Cellular and molecular life sciences : CMLS","confidence":"Medium","confidence_rationale":"Tier 2 — binding site mutagenesis, self-ubiquitination assay, KO/KD in vivo; single lab","pmids":["39888429"],"is_preprint":false},{"year":2026,"finding":"MKRN1 ubiquitinates and degrades MDM2 upon DNA damage (switching substrate from p53 to MDM2), thereby stabilizing and activating p53; the substrate switch is controlled by SIRT1-mediated deacetylation, placing MKRN1 as a master regulator of the p53-MDM2 feedback loop.","method":"Ubiquitination assay, co-immunoprecipitation, SIRT1 epistasis experiments, DNA damage time-course analysis, site-directed mutagenesis","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 — ubiquitination assay with substrate switch, epistasis with SIRT1; single lab, single study","pmids":["41617974"],"is_preprint":false},{"year":2025,"finding":"MKRN1 ubiquitinates AGC1 (Aspartate/Glutamate Carrier 1) via K11- and K29-linked ubiquitin chains, promoting its degradation, reprogramming mitochondrial energy metabolism and antioxidant responses, and conferring oxaliplatin resistance in colorectal cancer cells.","method":"CRISPR/Cas9 sgRNA library screen, co-immunoprecipitation, ubiquitination linkage assay (K11/K29), gain/loss-of-function, xenograft rescue experiment","journal":"Molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — genome-wide CRISPR screen for discovery, Co-IP, ubiquitin linkage assay, in vivo rescue; single lab","pmids":["40722058"],"is_preprint":false},{"year":2022,"finding":"Host macrophage MKRN1 interacts with Mycobacterium tuberculosis PPE68/Rv3873 protein and promotes K63-linked polyubiquitination at K166 of PPE68; K63-ubiquitinated PPE68 then recruits SHP1 to suppress TRAF6 ubiquitination and downstream NF-κB/AP-1 signaling, enabling mycobacterial immune escape.","method":"Co-immunoprecipitation, ubiquitination assay (K63-linkage), site-directed mutagenesis (K166), SHP1 interaction assay, NF-κB/AP-1 reporter assay","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 2 — K63-linkage-specific ubiquitination, mutagenesis, signaling pathway epistasis; single lab","pmids":["35603194"],"is_preprint":false},{"year":2018,"finding":"Human adenovirus core protein precursor pVII binds MKRN1 and promotes MKRN1 self-ubiquitination, leading to proteasomal degradation of MKRN1 during late-phase HAdV-C5 infection; the processed mature VII protein lacks this activity.","method":"Co-immunoprecipitation, ubiquitination assay, proteasome inhibitor treatment, comparison of pVII vs. VII protein activity","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP, self-ubiquitination assay, comparison of precursor vs. mature protein; single lab","pmids":["29142133"],"is_preprint":false},{"year":2025,"finding":"MKRN1 promotes RANKL-induced osteoclast differentiation by enhancing Akt phosphorylation and inhibiting AMPK phosphorylation; Mkrn1 KO mice show increased bone volume, consistent with impaired osteoclastogenesis.","method":"Retroviral overexpression, siRNA knockdown, TRAP staining, Western blot (Akt/AMPK phosphorylation), Mkrn1 KO mouse bone phenotyping","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 — gain/loss-of-function with defined signaling readouts, KO mouse phenotype; single lab","pmids":["41457534"],"is_preprint":false}],"current_model":"MKRN1 is a RING finger E3 ubiquitin ligase and RNA-binding protein that ubiquitinates and promotes proteasomal degradation of multiple substrates—including hTERT, p53 (K291/K292), p21, p14ARF, PPARγ (K184/K185), APC, AMPKα, LKB1, and MDM2—to regulate telomere homeostasis, cell cycle, apoptosis, adipogenesis, Wnt signaling, and energy metabolism; it also binds PABPC1 to position itself at poly(A) sequences on mRNAs and ubiquitinate PABPC1 and RPS10 to promote ribosome-associated quality control, and switches its substrate specificity (e.g., from p53 to MDM2, or from p53 to p21) in response to cellular stress signals including SIRT1-mediated deacetylation."},"narrative":{"teleology":[{"year":2005,"claim":"Establishing MKRN1 as a bona fide E3 ubiquitin ligase: the first substrate identified was hTERT, whose MKRN1-dependent ubiquitination and proteasomal degradation directly linked MKRN1 to telomerase regulation and telomere maintenance.","evidence":"Yeast two-hybrid identification, in vivo ubiquitination, proteasome degradation, and telomerase activity assays in human cells","pmids":["15805468"],"confidence":"High","gaps":["Physiological relevance of MKRN1–hTERT axis in primary cells or in vivo not tested","Ubiquitination sites on hTERT not mapped"]},{"year":2006,"claim":"Beyond its E3 ligase function, MKRN1 was found to act as a transcriptional co-repressor of c-Jun, androgen receptor, and retinoic acid receptors independently of its RING-finger catalytic activity, revealing a dual-function protein.","evidence":"Reporter gene assays with truncation mutants and RING-finger catalytic-dead mutant in mammalian cells","pmids":["16785614"],"confidence":"Medium","gaps":["No endogenous target gene expression data provided","Mechanism of ligase-independent transcriptional repression remains undefined","No in vivo confirmation"]},{"year":2009,"claim":"MKRN1 was shown to ubiquitinate both p53 and p21 under normal conditions, but under DNA damage stress it preferentially degrades p21, stabilizing p53 to promote apoptosis—establishing the concept of stress-regulated substrate switching.","evidence":"Ubiquitination assays, K291/K292 mutagenesis, siRNA knockdown, and apoptosis assays across multiple cell lines","pmids":["19536131"],"confidence":"High","gaps":["The signal that redirects MKRN1 from p53 to p21 during stress was not identified in this study","In vivo relevance of the substrate switch not demonstrated"]},{"year":2010,"claim":"MKRN1's substrate repertoire was extended to viral proteins: it ubiquitinates West Nile virus capsid protein at K101/K103/K104, promoting its degradation and limiting viral cytotoxicity, positioning MKRN1 as a host antiviral factor.","evidence":"Co-IP, ubiquitination assay, site-directed mutagenesis of WNV capsid lysines, domain mapping, and viral replication assays","pmids":["19846531"],"confidence":"High","gaps":["Relevance to other flaviviruses not tested","Whether viruses counter MKRN1 activity was not addressed"]},{"year":2011,"claim":"A short MKRN1 isoform in neurons was found to bind PABP in an RNA-independent manner and stimulate translation when tethered to mRNA, and to accumulate in dendritic granules following synaptic stimulation, revealing a role in local translational regulation.","evidence":"RNA-independent Co-IP, tethering reporter assay, in vivo perforant-path stimulation in rat hippocampus, immunofluorescence co-localization","pmids":["22128154"],"confidence":"Medium","gaps":["Endogenous mRNA targets in neurons not identified","Mechanism by which MKRN1-short stimulates translation is unclear","Single lab study"]},{"year":2012,"claim":"MKRN1 was identified as an E3 ligase for p14ARF, promoting senescence bypass: MKRN1 knockout MEFs showed elevated ARF and premature senescence, and high MKRN1 expression in gastric cancer correlated with low ARF levels.","evidence":"Ubiquitination assay, MKRN1 KO MEFs, xenograft model, immunohistochemistry of gastric tumors","pmids":["23104211"],"confidence":"High","gaps":["ARF ubiquitination sites not mapped","Whether ARF degradation is linked to p53 substrate switching was not tested"]},{"year":2013,"claim":"MKRN1 was shown to ubiquitinate PPARγ at K184/K185, suppressing adipocyte differentiation, which broadened its role beyond cell-cycle/apoptosis regulation to adipogenesis and metabolic control.","evidence":"K184/K185 mutagenesis, ubiquitination assay, MKRN1 KO MEF adipocyte differentiation assay","pmids":["24336050"],"confidence":"High","gaps":["Signals regulating MKRN1 activity toward PPARγ not defined","In vivo adipose tissue phenotype in MKRN1 KO mice not fully characterized at this stage"]},{"year":2018,"claim":"Three contemporaneous studies expanded MKRN1's role in signaling: ubiquitination-driven degradation of AMPKα controls metabolic syndrome in mice, ubiquitination of the tumor suppressor APC activates Wnt/β-catenin signaling, and adenovirus pVII triggers MKRN1 self-ubiquitination to evade host defense.","evidence":"AMPKα: reciprocal Co-IP, KO mice on high-fat diet, shRNA rescue in obese mice; APC: Co-IP, E3-dead mutant, β-catenin reporter; pVII: Co-IP, self-ubiquitination assay, proteasome inhibitor","pmids":["30143610","29713058","29142133"],"confidence":"High","gaps":["Relative contribution of MKRN1 versus other AMPK regulators in vivo unclear","Whether APC ubiquitination sites are shared with other E3 ligases not addressed","Whether pVII-induced MKRN1 self-destruction occurs in all adenovirus serotypes unknown"]},{"year":2019,"claim":"MKRN1 was revealed to function in ribosome-associated quality control (RQC): it binds PABPC1 in an RNA-independent manner, is positioned upstream of poly(A) sequences on mRNAs, and ubiquitinates both PABPC1 and RPS10 to promote stalling at aberrant poly(A) tracts.","evidence":"Co-IP, in vitro ubiquitination, ubiquitin-remnant mass spectrometry, polysome profiling, iCLIP/PAR-CLIP","pmids":["31640799"],"confidence":"High","gaps":["How MKRN1-mediated ubiquitination triggers downstream RQC effectors (e.g., ZNF598 coordination) not resolved","Structural basis of PABPC1–MKRN1 interaction not determined"]},{"year":2021,"claim":"MKRN1 was identified as an ER-associated E3 ligase for the Eag1 voltage-gated K+ channel, ubiquitinating immature (core-glycosylated) Eag1 for proteasomal degradation as part of ER quality control, distinct from CUL7-mediated peripheral quality control.","evidence":"Yeast two-hybrid, Co-IP, ubiquitination assay, glycosylation analysis, domain mapping","pmids":["33647316"],"confidence":"High","gaps":["Whether MKRN1 regulates other ion channels is unknown","Structural determinants on Eag1 recognized by MKRN1 not fully defined"]},{"year":2022,"claim":"MKRN1 was shown to mediate K63-linked ubiquitination of M. tuberculosis PPE68 at K166, which recruits SHP1 to suppress NF-κB/AP-1 signaling, revealing an unconventional K63-linked ligase activity co-opted by a pathogen for immune evasion.","evidence":"K63-linkage-specific ubiquitination assay, K166 mutagenesis, SHP1 interaction, NF-κB/AP-1 reporter in macrophages","pmids":["35603194"],"confidence":"Medium","gaps":["Single lab study; independent replication needed","Whether MKRN1 catalyzes K63 chains on endogenous human substrates is unclear","In vivo infection model not used"]},{"year":2023,"claim":"Quantitative proteomics identified SNIP1 as a MKRN1 substrate whose degradation relieves inhibition of TGF-β signaling, promoting EMT and metastasis in colorectal cancer, validated by conditional MKRN1 KO in mice.","evidence":"Proteomics-guided substrate discovery, ubiquitination omics, Co-IP, in vitro ubiquitination, conditional KO mice, xenograft","pmids":["37620897"],"confidence":"High","gaps":["Whether SNIP1 degradation is relevant in non-colorectal contexts not tested","Relative contribution of MKRN1 vs. other SNIP1-regulatory mechanisms unknown"]},{"year":2025,"claim":"Multiple 2025 studies extended the MKRN1–AMPK axis: MKRN1 ubiquitinates LKB1 at K146 to suppress AMPK in cardiomyocytes (regulated by FOXM1), while the drug ebastine promotes MKRN1 self-ubiquitination at R298/K360 to stabilize AMPK and alleviate metabolic steatohepatitis; additionally, MKRN1 promotes osteoclastogenesis through Akt/AMPK modulation, and ubiquitinates AGC1 via K11/K29 chains to reprogram mitochondrial metabolism and confer chemoresistance.","evidence":"Site-specific ubiquitinome profiling, cardiomyocyte-specific Mkrn1 KO, ebastine binding-site mutagenesis, AAV8 liver knockdown, RANKL-induced osteoclast assays with Mkrn1 KO mouse bone phenotyping, CRISPR screen identifying AGC1 as substrate","pmids":["40546121","39888429","41457534","40722058"],"confidence":"Medium","gaps":["LKB1 ubiquitination site confirmation limited to a single study","Ebastine selectivity for MKRN1 over other RING ligases not demonstrated","AGC1 K11/K29 chain specificity mechanism unknown","Single-lab validations for most findings"]},{"year":2026,"claim":"The molecular switch governing MKRN1 substrate specificity was elucidated: upon DNA damage, SIRT1-mediated deacetylation of MKRN1 redirects its activity from p53 to MDM2, placing MKRN1 as a master regulator of the p53–MDM2 feedback loop.","evidence":"Ubiquitination assays, Co-IP, SIRT1 epistasis, DNA-damage time-course, mutagenesis","pmids":["41617974"],"confidence":"Medium","gaps":["Acetylation sites on MKRN1 controlling the switch not mapped","In vivo validation of the substrate switch not performed","Single study from one lab"]},{"year":null,"claim":"Key unresolved questions include the structural basis for MKRN1's remarkably broad substrate selectivity, the coordination between its E3 ligase and RNA-binding/translational regulatory functions, and whether the stress-induced substrate-switching mechanism (SIRT1-dependent) extends beyond the p53/MDM2/p21 axis to its metabolic substrates.","evidence":"","pmids":[],"confidence":"Low","gaps":["No crystal or cryo-EM structure of MKRN1 or its complexes","No unified model explaining how one E3 ligase selects among >10 structurally diverse substrates","Relative physiological importance of E3 ligase vs. translational regulatory functions untested in vivo"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,3,4,5,6,7,12,13,14,16,17,18]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[6,9,10]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[8]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[6,9]},{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[6]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[12]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,2,3,4,5,6,12,13,14,16,17]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[1,16]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[5,13,14]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[3,4,11,15,17]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[6]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[18]}],"complexes":[],"partners":["PABPC1","TP53","CDKN1A","CDKN2A","PRKAA1","MDM2","APC","PPARG"],"other_free_text":[]},"mechanistic_narrative":"MKRN1 is a RING-finger E3 ubiquitin ligase and RNA-binding protein that governs diverse cellular processes—including telomere maintenance, cell-cycle control, apoptosis, energy metabolism, and ribosome-associated quality control—by ubiquitinating and targeting a broad array of substrates for proteasomal degradation. Under basal conditions MKRN1 ubiquitinates p53 (at K291/K292), p21, and p14ARF to restrain tumor-suppressor activity, whereas DNA damage triggers a SIRT1-dependent substrate switch from p53 to MDM2, thereby stabilizing p53 and promoting apoptosis [PMID:19536131, PMID:41617974]. MKRN1 also ubiquitinates AMPKα and LKB1 to suppress AMPK signaling, and genetic deletion in mice protects against diet-induced metabolic syndrome and cardiac bioenergetic impairment [PMID:30143610, PMID:40546121]. Through direct, RNA-independent binding to PABPC1, MKRN1 positions itself at poly(A) sequences on mRNAs and ubiquitinates PABPC1 and RPS10 to promote ribosome stalling during ribosome-associated quality control [PMID:31640799]."},"prefetch_data":{"uniprot":{"accession":"Q9UHC7","full_name":"E3 ubiquitin-protein ligase makorin-1","aliases":["RING finger protein 61","RING-type E3 ubiquitin transferase makorin-1"],"length_aa":482,"mass_kda":53.3,"function":"E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. These substrates include FILIP1, p53/TP53, CDKN1A and TERT. Keeps cells alive by suppressing p53/TP53 under normal conditions, but stimulates apoptosis by repressing CDKN1A under stress conditions. Acts as a negative regulator of telomerase. Has negative and positive effects on RNA polymerase II-dependent transcription","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q9UHC7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/MKRN1","classification":"Not Classified","n_dependent_lines":162,"n_total_lines":1208,"dependency_fraction":0.13410596026490065},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PABPC4","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/MKRN1","total_profiled":1310},"omim":[{"mim_id":"608426","title":"MAKORIN 2; MKRN2","url":"https://www.omim.org/entry/608426"},{"mim_id":"607754","title":"MAKORIN 1; MKRN1","url":"https://www.omim.org/entry/607754"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/MKRN1"},"hgnc":{"alias_symbol":["RNF61"],"prev_symbol":[]},"alphafold":{"accession":"Q9UHC7","domains":[{"cath_id":"-","chopping":"67-104","consensus_level":"high","plddt":76.9074,"start":67,"end":104},{"cath_id":"-","chopping":"214-256","consensus_level":"medium","plddt":87.3288,"start":214,"end":256},{"cath_id":"-","chopping":"279-368","consensus_level":"medium","plddt":90.987,"start":279,"end":368}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UHC7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UHC7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UHC7-F1-predicted_aligned_error_v6.png","plddt_mean":66.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MKRN1","jax_strain_url":"https://www.jax.org/strain/search?query=MKRN1"},"sequence":{"accession":"Q9UHC7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UHC7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UHC7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UHC7"}},"corpus_meta":[{"pmid":"15805468","id":"PMC_15805468","title":"Ubiquitin ligase MKRN1 modulates telomere length homeostasis through a proteolysis of hTERT.","date":"2005","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/15805468","citation_count":149,"is_preprint":false},{"pmid":"19536131","id":"PMC_19536131","title":"Differential regulation of p53 and p21 by MKRN1 E3 ligase controls cell cycle arrest and apoptosis.","date":"2009","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/19536131","citation_count":135,"is_preprint":false},{"pmid":"24336050","id":"PMC_24336050","title":"Suppression of PPARγ through MKRN1-mediated ubiquitination and degradation prevents adipocyte differentiation.","date":"2013","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/24336050","citation_count":90,"is_preprint":false},{"pmid":"30143610","id":"PMC_30143610","title":"Loss of the E3 ubiquitin ligase MKRN1 represses diet-induced metabolic syndrome through AMPK activation.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/30143610","citation_count":67,"is_preprint":false},{"pmid":"23104211","id":"PMC_23104211","title":"Acceleration of gastric tumorigenesis through MKRN1-mediated posttranslational regulation of p14ARF.","date":"2012","source":"Journal of the National Cancer Institute","url":"https://pubmed.ncbi.nlm.nih.gov/23104211","citation_count":60,"is_preprint":false},{"pmid":"16882727","id":"PMC_16882727","title":"The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans.","date":"2006","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/16882727","citation_count":47,"is_preprint":false},{"pmid":"38569025","id":"PMC_38569025","title":"SF3A2 promotes progression and cisplatin resistance in triple-negative breast cancer via alternative splicing of MKRN1.","date":"2024","source":"Science 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chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22128154","citation_count":30,"is_preprint":false},{"pmid":"29713058","id":"PMC_29713058","title":"Ubiquitylation and degradation of adenomatous polyposis coli by MKRN1 enhances Wnt/β-catenin signaling.","date":"2018","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/29713058","citation_count":29,"is_preprint":false},{"pmid":"26265008","id":"PMC_26265008","title":"Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network.","date":"2015","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/26265008","citation_count":28,"is_preprint":false},{"pmid":"37620897","id":"PMC_37620897","title":"MKRN1 promotes colorectal cancer metastasis by activating the TGF-β signalling pathway through SNIP1 protein degradation.","date":"2023","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/37620897","citation_count":25,"is_preprint":false},{"pmid":"35603194","id":"PMC_35603194","title":"Host MKRN1-Mediated Mycobacterial PPE Protein Ubiquitination Suppresses Innate Immune Response.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/35603194","citation_count":14,"is_preprint":false},{"pmid":"29142133","id":"PMC_29142133","title":"Human Adenovirus Infection Causes Cellular E3 Ubiquitin Ligase MKRN1 Degradation Involving the Viral Core Protein pVII.","date":"2018","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/29142133","citation_count":14,"is_preprint":false},{"pmid":"34504644","id":"PMC_34504644","title":"MKRN1 Ubiquitylates p21 to Protect against Intermittent Hypoxia-Induced Myocardial Apoptosis.","date":"2021","source":"Oxidative medicine and cellular longevity","url":"https://pubmed.ncbi.nlm.nih.gov/34504644","citation_count":11,"is_preprint":false},{"pmid":"33647316","id":"PMC_33647316","title":"Identification of MKRN1 as a second E3 ligase for Eag1 potassium channels reveals regulation via differential degradation.","date":"2021","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/33647316","citation_count":10,"is_preprint":false},{"pmid":"39509788","id":"PMC_39509788","title":"Structure-Based identification of a potent KDM7A inhibitor exerts anticancer activity through transcriptionally reducing MKRN1 in taxol- resistant and -sensitive triple-negative breast cancer cells.","date":"2024","source":"Bioorganic chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/39509788","citation_count":10,"is_preprint":false},{"pmid":"31225456","id":"PMC_31225456","title":"Attenuating MKRN1 E3 ligase-mediated AMPKα suppression increases tolerance against metabolic stresses in mice.","date":"2018","source":"Cell stress","url":"https://pubmed.ncbi.nlm.nih.gov/31225456","citation_count":10,"is_preprint":false},{"pmid":"36938725","id":"PMC_36938725","title":"MKRN1/2 serve as tumor suppressors in renal clear cell carcinoma by regulating the expression of p53.","date":"2023","source":"Cancer biomarkers : section A of Disease markers","url":"https://pubmed.ncbi.nlm.nih.gov/36938725","citation_count":9,"is_preprint":false},{"pmid":"36923435","id":"PMC_36923435","title":"Overcoming CEP85L-ROS1, MKRN1-BRAF and MET amplification as rare, acquired resistance mutations to Osimertinib.","date":"2023","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/36923435","citation_count":9,"is_preprint":false},{"pmid":"39098847","id":"PMC_39098847","title":"CircVPS8 promotes the malignant phenotype and inhibits ferroptosis of glioma stem cells by acting as a scaffold for MKRN1, SOX15 and HNF4A.","date":"2024","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/39098847","citation_count":8,"is_preprint":false},{"pmid":"32246348","id":"PMC_32246348","title":"In vitro ubiquitination of Mycobacterium tuberculosis by E3 ubiquitin ligase, MKRN1.","date":"2020","source":"Biotechnology letters","url":"https://pubmed.ncbi.nlm.nih.gov/32246348","citation_count":7,"is_preprint":false},{"pmid":"39888429","id":"PMC_39888429","title":"Ebastine-mediated destabilization of E3 ligase MKRN1 protects against metabolic dysfunction-associated steatohepatitis.","date":"2025","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/39888429","citation_count":3,"is_preprint":false},{"pmid":"40546121","id":"PMC_40546121","title":"FOXM1 Protects Against Myocardial Ischemia-Reperfusion Injury in Rodent and Porcine Models by Suppressing MKRN1-Dependent LKB1 Ubiquitination.","date":"2025","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/40546121","citation_count":3,"is_preprint":false},{"pmid":"40999490","id":"PMC_40999490","title":"Salvianolic acid A inhibits PRRSV replication via binding to Keap1 to activate the MKRN1-Nrf2-NQO1 pathway.","date":"2025","source":"Veterinary research","url":"https://pubmed.ncbi.nlm.nih.gov/40999490","citation_count":2,"is_preprint":false},{"pmid":"40032982","id":"PMC_40032982","title":"Nematode serine protease inhibitor SPI-I8 negatively regulates host NF-κB signalling by hijacking MKRN1-mediated polyubiquitination of RACK1.","date":"2025","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/40032982","citation_count":2,"is_preprint":false},{"pmid":"40722058","id":"PMC_40722058","title":"MKRN1 degrades AGC1 to trigger chemotherapy resistance of colorectal Cancer.","date":"2025","source":"Molecular medicine (Cambridge, Mass.)","url":"https://pubmed.ncbi.nlm.nih.gov/40722058","citation_count":1,"is_preprint":false},{"pmid":"41254700","id":"PMC_41254700","title":"Low expression of MKRN1 promotes leukemia cell proliferation.","date":"2025","source":"European journal of medical research","url":"https://pubmed.ncbi.nlm.nih.gov/41254700","citation_count":0,"is_preprint":false},{"pmid":"41457534","id":"PMC_41457534","title":"MKRN1 Regulates RANKL-Induced Differentiation Via Akt and AMPK Pathways.","date":"2025","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/41457534","citation_count":0,"is_preprint":false},{"pmid":"41667429","id":"PMC_41667429","title":"MKRN1 as a prioritized drug target for postpartum depression: evidence from druggable proteome profiling and multi-layer validation.","date":"2026","source":"Translational 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study","date":"2025-09-02","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.28.25334625","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":21001,"output_tokens":5081,"usd":0.069609},"stage2":{"model":"claude-opus-4-6","input_tokens":8645,"output_tokens":4170,"usd":0.221213},"total_usd":0.290822,"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\": 2005,\n      \"finding\": \"MKRN1 is an E3 ubiquitin ligase that directly ubiquitinates hTERT, promoting its proteasome-mediated degradation and reducing telomerase activity and telomere length; MKRN1-hTERT interaction was identified by yeast two-hybrid.\",\n      \"method\": \"Yeast two-hybrid, overexpression ubiquitination assay, proteasome degradation assay, telomerase activity assay\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Y2H, ubiquitination, proteasomal degradation, telomerase assay), highly cited foundational paper\",\n      \"pmids\": [\"15805468\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"MKRN1 functions as an E3 ubiquitin ligase that ubiquitinates and degrades p53 (at novel sites K291/K292) and p21 via the proteasome under normal conditions; under DNA damage stress, MKRN1 preferentially degrades p21 to promote apoptosis while p53 is stabilized.\",\n      \"method\": \"Ubiquitination assay, proteasome degradation assay, site-directed mutagenesis (K291/K292), siRNA knockdown, ectopic overexpression, apoptosis assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods including mutagenesis of ubiquitination sites, highly cited, replicated in multiple cellular contexts\",\n      \"pmids\": [\"19536131\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"MKRN1 is an E3 ubiquitin ligase that ubiquitinates p14ARF (human)/p19ARF (mouse), targeting it for proteasome-dependent degradation, thereby promoting cellular bypass of senescence and gastric tumorigenesis.\",\n      \"method\": \"Ubiquitination assay, proteasome degradation assay, siRNA/shRNA knockdown, MKRN1 knockout MEFs, xenograft mouse model, immunohistochemistry\",\n      \"journal\": \"Journal of the National Cancer Institute\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods, in vivo validation, epistasis via double knockdown\",\n      \"pmids\": [\"23104211\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"MKRN1 is an E3 ubiquitin ligase for PPARγ, ubiquitinating it at lysines 184 and 185 and promoting proteasome-dependent degradation, thereby suppressing adipocyte differentiation.\",\n      \"method\": \"Ubiquitination assay, site-directed mutagenesis (K184/K185), stable overexpression/knockdown, MKRN1 knockout MEFs, adipocyte differentiation assay\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — mutagenesis of ubiquitination sites, genetic KO validation, multiple cell models\",\n      \"pmids\": [\"24336050\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"MKRN1 ubiquitinates and promotes proteasomal degradation of AMPKα, and its depletion stabilizes AMPK leading to chronic AMPK activation in liver and adipose tissue, suppressing diet-induced metabolic syndrome in mice.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, MKRN1 knockout mice, shRNA delivery in obese mice, AMPK activity assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, genetic KO with defined metabolic phenotype, in vivo therapeutic validation\",\n      \"pmids\": [\"30143610\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"MKRN1 directly interacts with and ubiquitylates APC (adenomatous polyposis coli), promoting its proteasomal degradation and thereby positively regulating Wnt/β-catenin signaling; E3 ligase-defective MKRN1 mutant cannot regulate APC.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitylation assay, E3 ligase-dead mutant, siRNA knockdown, β-catenin reporter assay, cell migration/invasion assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, catalytic mutant validation, epistasis via double knockdown\",\n      \"pmids\": [\"29713058\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"MKRN1 directly binds PABPC1 (cytoplasmic poly(A)-binding protein) in an RNA-independent manner and associates with polysomes; MKRN1 is positioned upstream of poly(A) tails in an mRNA in a PABPC1-dependent manner and ubiquitylates PABPC1 and ribosomal protein RPS10, promoting ribosome stalling at poly(A) sequences during ribosome-associated quality control (RQC).\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitylation assay, ubiquitin remnant profiling (mass spectrometry), polysome association assay, iCLIP/PAR-CLIP for RNA binding\",\n      \"journal\": \"Genome biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro ubiquitylation, proteome-wide ubiquitin remnant profiling, RNA-binding mapping, multiple orthogonal methods\",\n      \"pmids\": [\"31640799\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"MKRN1 functions as an E3 ubiquitin ligase for West Nile virus capsid protein (WNVCp), ubiquitinating it at lysines 101, 103, and 104 via interaction between the C-terminus of MKRN1 and the N-terminus of WNVCp, promoting proteasome-dependent WNVCp degradation and protecting cells from WNV cytotoxicity.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, site-directed mutagenesis (K101/103/104 of WNVCp), domain mapping, stable cell lines, viral replication assay\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — mutagenesis of ubiquitination sites, domain mapping, multiple functional readouts\",\n      \"pmids\": [\"19846531\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"MKRN1 acts as a transcriptional repressor of c-Jun, androgen receptor, and retinoic acid receptors, and as a transcriptional activator when fused to GAL4-DBD; both N- and C-termini are required for transcriptional activity; E3 ligase activity is not required for transcriptional repression.\",\n      \"method\": \"Reporter gene assay, truncation analysis, RING finger mutant (E3 ligase-dead), overexpression in mammalian cells\",\n      \"journal\": \"Endocrine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — truncation and catalytic mutant analysis with reporter assay, single lab\",\n      \"pmids\": [\"16785614\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"MKRN1-short isoform binds PABP in an RNA-independent manner in rat neurons, co-localizes with PABP in dendritic granule-like structures, associates with dendritic mRNAs, and when tethered to a reporter mRNA stimulates translation; MKRN1-short accumulates in activated dendritic laminae after synaptic plasticity induction.\",\n      \"method\": \"Co-immunoprecipitation (RNA-independent), tethering assay (reporter translation), in vivo perforant path stimulation, co-localization by immunofluorescence\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — tethering assay for translation, RNA-independent Co-IP, in vivo neuronal stimulation; single lab, moderate orthogonal methods\",\n      \"pmids\": [\"22128154\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"MKRN1 associates with RNA-binding proteins and stress granule components in embryonic stem cells and localizes to stress granules under stress, but is not required for stress granule formation; identified as a ribonucleoprotein component of the ESC gene regulatory network.\",\n      \"method\": \"Proteomic interactome (mass spectrometry), RIP-chip (RNA immunoprecipitation-microarray), live-cell imaging of stress granules, KO/KD analysis\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — proteomic interactome plus RIP-chip plus localization; single lab\",\n      \"pmids\": [\"26265008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"MKRN1 interacts with and promotes proteasomal degradation of AMPKα1 and α2 via ubiquitination; MKRN1 KO MEFs show stabilized AMPK with suppressed lipogenesis and increased mitochondrial biogenesis.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, MEF knockout cells, metabolic flux assays\",\n      \"journal\": \"Cell stress\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, ubiquitination, KO cells; single lab, consistent with companion Nature Communications paper\",\n      \"pmids\": [\"31225456\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"MKRN1 is a second E3 ubiquitin ligase for Eag1 voltage-gated K+ channels, interacting primarily with the carboxyl-terminal region of Eag1; MKRN1 promotes polyubiquitination and ER-associated proteasomal degradation of immature (core-glycosylated and nascent non-glycosylated) Eag1 at the ER, distinct from CUL7 which also regulates peripheral quality control.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, ubiquitination assay, glycosylation analysis, proteasome inhibitor assays, domain mapping\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — Y2H, Co-IP, ubiquitination, domain mapping, differential glycosylation analysis; multiple orthogonal methods\",\n      \"pmids\": [\"33647316\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MKRN1 ubiquitinates and degrades SNIP1 via the proteasome, thereby relieving SNIP1-mediated inhibition of TGF-β signaling and promoting EMT and metastasis in colorectal cancer.\",\n      \"method\": \"Quantitative proteomics, ubiquitination modification omics, co-immunoprecipitation, in vitro ubiquitination, conditional MKRN1 knockout mice, xenograft\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — proteomics-guided substrate identification, ubiquitination assay, genetic KO in vivo validation\",\n      \"pmids\": [\"37620897\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"MKRN1 promotes K48-linked ubiquitination of LKB1 at Lys146, inhibiting AMPK signaling and impairing energy homeostasis in cardiomyocytes; FOXM1 suppresses this MKRN1-dependent LKB1 ubiquitination to preserve mitochondrial bioenergetics.\",\n      \"method\": \"Proteomic and ubiquitinome profiling of Foxm1-KO mice, site-specific ubiquitination assays, CM-specific Mkrn1 KO mouse model, AMPK signaling assays\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ubiquitinome mass spectrometry identifies site, genetic KO validation; single lab\",\n      \"pmids\": [\"40546121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Ebastine binds to the C-terminal domain of MKRN1 (residues R298 and K360), promoting MKRN1 self-ubiquitination and destabilization, which in turn stabilizes AMPK and alleviates metabolic steatohepatitis.\",\n      \"method\": \"Drug-protein binding assay, mutagenesis (R298, K360), self-ubiquitination assay, MKRN1 KO mice, AAV8-mediated liver-specific knockdown, metabolic phenotyping\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — binding site mutagenesis, self-ubiquitination assay, KO/KD in vivo; single lab\",\n      \"pmids\": [\"39888429\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"MKRN1 ubiquitinates and degrades MDM2 upon DNA damage (switching substrate from p53 to MDM2), thereby stabilizing and activating p53; the substrate switch is controlled by SIRT1-mediated deacetylation, placing MKRN1 as a master regulator of the p53-MDM2 feedback loop.\",\n      \"method\": \"Ubiquitination assay, co-immunoprecipitation, SIRT1 epistasis experiments, DNA damage time-course analysis, site-directed mutagenesis\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ubiquitination assay with substrate switch, epistasis with SIRT1; single lab, single study\",\n      \"pmids\": [\"41617974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"MKRN1 ubiquitinates AGC1 (Aspartate/Glutamate Carrier 1) via K11- and K29-linked ubiquitin chains, promoting its degradation, reprogramming mitochondrial energy metabolism and antioxidant responses, and conferring oxaliplatin resistance in colorectal cancer cells.\",\n      \"method\": \"CRISPR/Cas9 sgRNA library screen, co-immunoprecipitation, ubiquitination linkage assay (K11/K29), gain/loss-of-function, xenograft rescue experiment\",\n      \"journal\": \"Molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide CRISPR screen for discovery, Co-IP, ubiquitin linkage assay, in vivo rescue; single lab\",\n      \"pmids\": [\"40722058\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Host macrophage MKRN1 interacts with Mycobacterium tuberculosis PPE68/Rv3873 protein and promotes K63-linked polyubiquitination at K166 of PPE68; K63-ubiquitinated PPE68 then recruits SHP1 to suppress TRAF6 ubiquitination and downstream NF-κB/AP-1 signaling, enabling mycobacterial immune escape.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay (K63-linkage), site-directed mutagenesis (K166), SHP1 interaction assay, NF-κB/AP-1 reporter assay\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — K63-linkage-specific ubiquitination, mutagenesis, signaling pathway epistasis; single lab\",\n      \"pmids\": [\"35603194\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Human adenovirus core protein precursor pVII binds MKRN1 and promotes MKRN1 self-ubiquitination, leading to proteasomal degradation of MKRN1 during late-phase HAdV-C5 infection; the processed mature VII protein lacks this activity.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, proteasome inhibitor treatment, comparison of pVII vs. VII protein activity\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, self-ubiquitination assay, comparison of precursor vs. mature protein; single lab\",\n      \"pmids\": [\"29142133\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"MKRN1 promotes RANKL-induced osteoclast differentiation by enhancing Akt phosphorylation and inhibiting AMPK phosphorylation; Mkrn1 KO mice show increased bone volume, consistent with impaired osteoclastogenesis.\",\n      \"method\": \"Retroviral overexpression, siRNA knockdown, TRAP staining, Western blot (Akt/AMPK phosphorylation), Mkrn1 KO mouse bone phenotyping\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — gain/loss-of-function with defined signaling readouts, KO mouse phenotype; single lab\",\n      \"pmids\": [\"41457534\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MKRN1 is a RING finger E3 ubiquitin ligase and RNA-binding protein that ubiquitinates and promotes proteasomal degradation of multiple substrates—including hTERT, p53 (K291/K292), p21, p14ARF, PPARγ (K184/K185), APC, AMPKα, LKB1, and MDM2—to regulate telomere homeostasis, cell cycle, apoptosis, adipogenesis, Wnt signaling, and energy metabolism; it also binds PABPC1 to position itself at poly(A) sequences on mRNAs and ubiquitinate PABPC1 and RPS10 to promote ribosome-associated quality control, and switches its substrate specificity (e.g., from p53 to MDM2, or from p53 to p21) in response to cellular stress signals including SIRT1-mediated deacetylation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"MKRN1 is a RING-finger E3 ubiquitin ligase and RNA-binding protein that governs diverse cellular processes—including telomere maintenance, cell-cycle control, apoptosis, energy metabolism, and ribosome-associated quality control—by ubiquitinating and targeting a broad array of substrates for proteasomal degradation. Under basal conditions MKRN1 ubiquitinates p53 (at K291/K292), p21, and p14ARF to restrain tumor-suppressor activity, whereas DNA damage triggers a SIRT1-dependent substrate switch from p53 to MDM2, thereby stabilizing p53 and promoting apoptosis [PMID:19536131, PMID:41617974]. MKRN1 also ubiquitinates AMPKα and LKB1 to suppress AMPK signaling, and genetic deletion in mice protects against diet-induced metabolic syndrome and cardiac bioenergetic impairment [PMID:30143610, PMID:40546121]. Through direct, RNA-independent binding to PABPC1, MKRN1 positions itself at poly(A) sequences on mRNAs and ubiquitinates PABPC1 and RPS10 to promote ribosome stalling during ribosome-associated quality control [PMID:31640799].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Establishing MKRN1 as a bona fide E3 ubiquitin ligase: the first substrate identified was hTERT, whose MKRN1-dependent ubiquitination and proteasomal degradation directly linked MKRN1 to telomerase regulation and telomere maintenance.\",\n      \"evidence\": \"Yeast two-hybrid identification, in vivo ubiquitination, proteasome degradation, and telomerase activity assays in human cells\",\n      \"pmids\": [\"15805468\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological relevance of MKRN1–hTERT axis in primary cells or in vivo not tested\", \"Ubiquitination sites on hTERT not mapped\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Beyond its E3 ligase function, MKRN1 was found to act as a transcriptional co-repressor of c-Jun, androgen receptor, and retinoic acid receptors independently of its RING-finger catalytic activity, revealing a dual-function protein.\",\n      \"evidence\": \"Reporter gene assays with truncation mutants and RING-finger catalytic-dead mutant in mammalian cells\",\n      \"pmids\": [\"16785614\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No endogenous target gene expression data provided\", \"Mechanism of ligase-independent transcriptional repression remains undefined\", \"No in vivo confirmation\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"MKRN1 was shown to ubiquitinate both p53 and p21 under normal conditions, but under DNA damage stress it preferentially degrades p21, stabilizing p53 to promote apoptosis—establishing the concept of stress-regulated substrate switching.\",\n      \"evidence\": \"Ubiquitination assays, K291/K292 mutagenesis, siRNA knockdown, and apoptosis assays across multiple cell lines\",\n      \"pmids\": [\"19536131\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The signal that redirects MKRN1 from p53 to p21 during stress was not identified in this study\", \"In vivo relevance of the substrate switch not demonstrated\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"MKRN1's substrate repertoire was extended to viral proteins: it ubiquitinates West Nile virus capsid protein at K101/K103/K104, promoting its degradation and limiting viral cytotoxicity, positioning MKRN1 as a host antiviral factor.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, site-directed mutagenesis of WNV capsid lysines, domain mapping, and viral replication assays\",\n      \"pmids\": [\"19846531\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relevance to other flaviviruses not tested\", \"Whether viruses counter MKRN1 activity was not addressed\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"A short MKRN1 isoform in neurons was found to bind PABP in an RNA-independent manner and stimulate translation when tethered to mRNA, and to accumulate in dendritic granules following synaptic stimulation, revealing a role in local translational regulation.\",\n      \"evidence\": \"RNA-independent Co-IP, tethering reporter assay, in vivo perforant-path stimulation in rat hippocampus, immunofluorescence co-localization\",\n      \"pmids\": [\"22128154\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Endogenous mRNA targets in neurons not identified\", \"Mechanism by which MKRN1-short stimulates translation is unclear\", \"Single lab study\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"MKRN1 was identified as an E3 ligase for p14ARF, promoting senescence bypass: MKRN1 knockout MEFs showed elevated ARF and premature senescence, and high MKRN1 expression in gastric cancer correlated with low ARF levels.\",\n      \"evidence\": \"Ubiquitination assay, MKRN1 KO MEFs, xenograft model, immunohistochemistry of gastric tumors\",\n      \"pmids\": [\"23104211\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"ARF ubiquitination sites not mapped\", \"Whether ARF degradation is linked to p53 substrate switching was not tested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"MKRN1 was shown to ubiquitinate PPARγ at K184/K185, suppressing adipocyte differentiation, which broadened its role beyond cell-cycle/apoptosis regulation to adipogenesis and metabolic control.\",\n      \"evidence\": \"K184/K185 mutagenesis, ubiquitination assay, MKRN1 KO MEF adipocyte differentiation assay\",\n      \"pmids\": [\"24336050\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signals regulating MKRN1 activity toward PPARγ not defined\", \"In vivo adipose tissue phenotype in MKRN1 KO mice not fully characterized at this stage\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Three contemporaneous studies expanded MKRN1's role in signaling: ubiquitination-driven degradation of AMPKα controls metabolic syndrome in mice, ubiquitination of the tumor suppressor APC activates Wnt/β-catenin signaling, and adenovirus pVII triggers MKRN1 self-ubiquitination to evade host defense.\",\n      \"evidence\": \"AMPKα: reciprocal Co-IP, KO mice on high-fat diet, shRNA rescue in obese mice; APC: Co-IP, E3-dead mutant, β-catenin reporter; pVII: Co-IP, self-ubiquitination assay, proteasome inhibitor\",\n      \"pmids\": [\"30143610\", \"29713058\", \"29142133\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contribution of MKRN1 versus other AMPK regulators in vivo unclear\", \"Whether APC ubiquitination sites are shared with other E3 ligases not addressed\", \"Whether pVII-induced MKRN1 self-destruction occurs in all adenovirus serotypes unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"MKRN1 was revealed to function in ribosome-associated quality control (RQC): it binds PABPC1 in an RNA-independent manner, is positioned upstream of poly(A) sequences on mRNAs, and ubiquitinates both PABPC1 and RPS10 to promote stalling at aberrant poly(A) tracts.\",\n      \"evidence\": \"Co-IP, in vitro ubiquitination, ubiquitin-remnant mass spectrometry, polysome profiling, iCLIP/PAR-CLIP\",\n      \"pmids\": [\"31640799\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How MKRN1-mediated ubiquitination triggers downstream RQC effectors (e.g., ZNF598 coordination) not resolved\", \"Structural basis of PABPC1–MKRN1 interaction not determined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"MKRN1 was identified as an ER-associated E3 ligase for the Eag1 voltage-gated K+ channel, ubiquitinating immature (core-glycosylated) Eag1 for proteasomal degradation as part of ER quality control, distinct from CUL7-mediated peripheral quality control.\",\n      \"evidence\": \"Yeast two-hybrid, Co-IP, ubiquitination assay, glycosylation analysis, domain mapping\",\n      \"pmids\": [\"33647316\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether MKRN1 regulates other ion channels is unknown\", \"Structural determinants on Eag1 recognized by MKRN1 not fully defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"MKRN1 was shown to mediate K63-linked ubiquitination of M. tuberculosis PPE68 at K166, which recruits SHP1 to suppress NF-κB/AP-1 signaling, revealing an unconventional K63-linked ligase activity co-opted by a pathogen for immune evasion.\",\n      \"evidence\": \"K63-linkage-specific ubiquitination assay, K166 mutagenesis, SHP1 interaction, NF-κB/AP-1 reporter in macrophages\",\n      \"pmids\": [\"35603194\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab study; independent replication needed\", \"Whether MKRN1 catalyzes K63 chains on endogenous human substrates is unclear\", \"In vivo infection model not used\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Quantitative proteomics identified SNIP1 as a MKRN1 substrate whose degradation relieves inhibition of TGF-β signaling, promoting EMT and metastasis in colorectal cancer, validated by conditional MKRN1 KO in mice.\",\n      \"evidence\": \"Proteomics-guided substrate discovery, ubiquitination omics, Co-IP, in vitro ubiquitination, conditional KO mice, xenograft\",\n      \"pmids\": [\"37620897\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether SNIP1 degradation is relevant in non-colorectal contexts not tested\", \"Relative contribution of MKRN1 vs. other SNIP1-regulatory mechanisms unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Multiple 2025 studies extended the MKRN1–AMPK axis: MKRN1 ubiquitinates LKB1 at K146 to suppress AMPK in cardiomyocytes (regulated by FOXM1), while the drug ebastine promotes MKRN1 self-ubiquitination at R298/K360 to stabilize AMPK and alleviate metabolic steatohepatitis; additionally, MKRN1 promotes osteoclastogenesis through Akt/AMPK modulation, and ubiquitinates AGC1 via K11/K29 chains to reprogram mitochondrial metabolism and confer chemoresistance.\",\n      \"evidence\": \"Site-specific ubiquitinome profiling, cardiomyocyte-specific Mkrn1 KO, ebastine binding-site mutagenesis, AAV8 liver knockdown, RANKL-induced osteoclast assays with Mkrn1 KO mouse bone phenotyping, CRISPR screen identifying AGC1 as substrate\",\n      \"pmids\": [\"40546121\", \"39888429\", \"41457534\", \"40722058\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"LKB1 ubiquitination site confirmation limited to a single study\", \"Ebastine selectivity for MKRN1 over other RING ligases not demonstrated\", \"AGC1 K11/K29 chain specificity mechanism unknown\", \"Single-lab validations for most findings\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"The molecular switch governing MKRN1 substrate specificity was elucidated: upon DNA damage, SIRT1-mediated deacetylation of MKRN1 redirects its activity from p53 to MDM2, placing MKRN1 as a master regulator of the p53–MDM2 feedback loop.\",\n      \"evidence\": \"Ubiquitination assays, Co-IP, SIRT1 epistasis, DNA-damage time-course, mutagenesis\",\n      \"pmids\": [\"41617974\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Acetylation sites on MKRN1 controlling the switch not mapped\", \"In vivo validation of the substrate switch not performed\", \"Single study from one lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis for MKRN1's remarkably broad substrate selectivity, the coordination between its E3 ligase and RNA-binding/translational regulatory functions, and whether the stress-induced substrate-switching mechanism (SIRT1-dependent) extends beyond the p53/MDM2/p21 axis to its metabolic substrates.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No crystal or cryo-EM structure of MKRN1 or its complexes\", \"No unified model explaining how one E3 ligase selects among >10 structurally diverse substrates\", \"Relative physiological importance of E3 ligase vs. translational regulatory functions untested in vivo\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 16, 17, 18]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [6, 9, 10]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [6, 9]},\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [12]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 16, 17]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [1, 16]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [5, 13, 14]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [3, 4, 11, 15, 17]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [18]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PABPC1\",\n      \"TP53\",\n      \"CDKN1A\",\n      \"CDKN2A\",\n      \"PRKAA1\",\n      \"MDM2\",\n      \"APC\",\n      \"PPARG\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}