{"gene":"MED31","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2004,"finding":"Soh1/MED31 protein is a stable component of the Mediator complex isolated from both Schizosaccharomyces pombe and Saccharomyces cerevisiae, and bioinformatic analysis places MED31 family members as ancient Mediator subunits present before the appearance of the canonical RNA polymerase II CTD heptapeptide repeat structure.","method":"Biochemical isolation of Mediator complex; bioinformatic analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct biochemical isolation of the complex from two yeast species, single lab, supported by bioinformatic conservation analysis","pmids":["15356001"],"is_preprint":false},{"year":2007,"finding":"In Schizosaccharomyces pombe, Med31 (encoded by sep10+) controls large sets of genes including cell separation genes regulated by the transcription factors Sep1 and Ace2; Med31 acts as a coactivator of Sep1-Ace2-dependent cell separation genes, linking the Mediator complex to the regulation of the cell separation phase of cell division.","method":"Genome-wide gene expression profiling of med31 (sep10) loss-of-function mutants; genetic epistasis with sep1 and ace2","journal":"Molecular genetics and genomics : MGG","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide expression profiling of mutants with epistasis analysis; single lab, two complementary approaches","pmids":["17922236"],"is_preprint":false},{"year":2010,"finding":"Mouse Med31 is required for embryonic cell proliferation; a mutation causing Med31 protein degradation results in fewer proliferating cells in rapidly expanding tissues (e.g., forelimb buds), severe proliferation defect in embryonic fibroblasts, reduced Cdc2 protein levels, and defective chondrogenesis with loss of Sox9 and Col2a1 expression, while target genes of other Mediator proteins remain normally expressed, indicating Med31 has distinct transcriptional targets.","method":"ENU mutagenesis screen; loss-of-function mouse mutant analysis; cell proliferation assays in embryonic fibroblasts; Western blot for Cdc2; gene expression analysis","journal":"Developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo loss-of-function with multiple cellular and molecular readouts in a single lab study","pmids":["20347762"],"is_preprint":false},{"year":2012,"finding":"Elmo1 physically binds Med31; Elmo1 increases the cytoplasmic localization of endogenous Med31 (which is predominantly nuclear); Elmo1 promotes monoubiquitination of Med31 in the cytoplasm; during Salmonella infection in primary macrophages, Elmo1 and Med31 together specifically affect expression of cytokine genes Il10 and Il33.","method":"Co-immunoprecipitation (Co-IP) of Elmo1 and Med31; subcellular fractionation/localization; ubiquitination assay; cytokine gene expression monitoring in primary macrophages","journal":"Current biology : CB","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, subcellular localization with functional consequence, PTM identification; single lab with multiple orthogonal methods","pmids":["23273896"],"is_preprint":false},{"year":2014,"finding":"MED31 is a direct target of miR-1 in osteosarcoma cells, as validated by luciferase reporter assay; knockdown of Med31 suppresses osteosarcoma cell proliferation and reduces expression of MET proto-oncogene and its downstream signaling in response to HGF; overexpression of Med31 abrogates the anti-proliferative effects of miR-1.","method":"Luciferase reporter assay; siRNA knockdown; overexpression rescue; cell proliferation assay; Western blot/gene expression for MET signaling","journal":"Oncology reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase reporter validates direct targeting, functional rescue experiment; single lab, multiple methods","pmids":["24969180"],"is_preprint":false},{"year":2018,"finding":"siRNA-mediated knockdown of MED31 in human mesenchymal stem cells (hMSCs) reduces self-renewal and impairs adipogenesis, as evidenced by decreased lipid vesicle formation and reduced expression of adipogenic markers.","method":"siRNA knockdown; cell self-renewal assays; adipogenesis assay (lipid staining, adipogenic marker gene expression)","journal":"Molecular biology reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single knockdown approach with phenotypic readouts but no pathway placement or mechanistic follow-up","pmids":["30006772"],"is_preprint":false},{"year":2019,"finding":"In Tetrahymena thermophila, Med31 physically interacts with >20 proteins including subunits sharing similarities to canonical Mediator subunits from yeast and humans; Med31 ChIP-seq shows a global role in transcription regulation; Med31 localizes to meiotic micronuclei; MED31 knockdown causes ectopic expression of developmental genes important for programmed DNA rearrangements.","method":"Affinity purification coupled with mass spectrometry (AP-MS); ChIP-seq; indirect immunofluorescence; MED31 knockdown with gene expression analysis","journal":"Current biology : CB","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — AP-MS interactome, ChIP-seq, localization, and loss-of-function phenotype; multiple orthogonal methods in a single study","pmids":["31280994"],"is_preprint":false},{"year":2026,"finding":"ELMO1 methylation interacts with Med31 (detected by co-immunoprecipitation) and this interaction promotes M2 macrophage polarization, EMT, and intestinal metaplasia in H. pylori-infected gastric cancer cells.","method":"Co-immunoprecipitation; methylation-specific PCR; Western blot; co-culture experiments; cell viability/migration assays","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, Co-IP supports interaction but mechanistic pathway placement is limited and study is recent with no replication","pmids":["41535333"],"is_preprint":false}],"current_model":"MED31 (also known as Soh1/CGI-125) is the smallest and most evolutionarily conserved subunit of the Mediator complex, physically incorporated into Mediator to bridge transcription factors with the RNA polymerase II machinery; it is predominantly nuclear but can be redistributed to the cytoplasm and monoubiquitinated by the cytoplasmic engulfment protein Elmo1, and loss of Med31 function causes defective cell proliferation (with reduced Cdc2), impaired chondrogenesis, reduced adipogenesis of stem cells, and dysregulation of specific cytokine and developmental gene programs, collectively indicating that Med31 is a context-specific transcriptional co-activator required for normal cell cycle progression, differentiation, and tissue development."},"narrative":{"mechanistic_narrative":"MED31 is an ancient, stably incorporated subunit of the RNA polymerase II Mediator complex that functions as a context-specific transcriptional co-activator linking sequence-specific transcription factors to gene-expression programs governing proliferation, differentiation, and development [PMID:15356001, PMID:31280994]. Biochemical isolation of Mediator from two yeast species established MED31 as a bona fide complex component conserved among the oldest Mediator subunits [PMID:15356001], and affinity purification in Tetrahymena recovered a Mediator-like interactome together with a genome-wide chromatin-binding role demonstrated by ChIP-seq [PMID:31280994]. Rather than regulating Mediator targets globally, MED31 acts on distinct gene sets: in fission yeast it coactivates Sep1/Ace2-dependent cell-separation genes [PMID:17922236], and in mouse it is required for embryonic cell proliferation and chondrogenesis, with loss reducing Cdc2 and Sox9/Col2a1 expression while other Mediator targets remain unaffected [PMID:20347762]. MED31 is predominantly nuclear, but the cytoplasmic engulfment protein Elmo1 binds MED31, drives its cytoplasmic redistribution and monoubiquitination, and together with MED31 shapes Il10 and Il33 cytokine expression during macrophage infection [PMID:23273896]. Its proliferative function extends to disease contexts, where MED31 is a direct miR-1 target that supports osteosarcoma cell proliferation via MET signaling [PMID:24969180]. Beyond these contexts, the structural basis of MED31's selective target specificity within Mediator has not been characterized in the available corpus.","teleology":[{"year":2004,"claim":"Establishing whether MED31 is a genuine Mediator subunit was prerequisite to any functional interpretation; biochemical isolation defined it as a stable, deeply conserved component of the complex.","evidence":"Biochemical isolation of Mediator from S. pombe and S. cerevisiae plus bioinformatic conservation analysis","pmids":["15356001"],"confidence":"Medium","gaps":["Did not define which transcription factors or genes MED31 regulates","No structural placement of MED31 within the complex"]},{"year":2007,"claim":"Whether MED31 has selective rather than global transcriptional roles was unknown; expression profiling showed it coactivates a specific Sep1/Ace2-dependent cell-separation program, linking Mediator to a defined phase of cell division.","evidence":"Genome-wide expression profiling of med31 (sep10) mutants with sep1/ace2 epistasis in S. pombe","pmids":["17922236"],"confidence":"Medium","gaps":["Did not show direct physical contact between MED31 and Sep1/Ace2","Conservation of this selectivity to metazoans untested"]},{"year":2010,"claim":"Whether MED31's selective regulation matters in a vertebrate was open; a mouse loss-of-function mutant showed it is required for embryonic proliferation and chondrogenesis through a distinct set of targets, not the whole Mediator program.","evidence":"ENU mutant mouse analysis, fibroblast proliferation assays, Cdc2 Western blot, Sox9/Col2a1 expression","pmids":["20347762"],"confidence":"Medium","gaps":["Direct vs indirect regulation of Cdc2 and Sox9 not resolved","Transcription factors recruiting MED31 to these targets unidentified"]},{"year":2012,"claim":"Whether MED31 has functions outside the nuclear Mediator complex was unexplored; Elmo1 was shown to bind MED31, drive its cytoplasmic relocation and monoubiquitination, and tune specific cytokine genes during infection.","evidence":"Reciprocal Co-IP, subcellular fractionation, ubiquitination assay, cytokine expression in primary macrophages","pmids":["23273896"],"confidence":"Medium","gaps":["Function of cytoplasmic monoubiquitinated MED31 not defined","Whether cytoplasmic redistribution is regulatory or degradative unclear"]},{"year":2014,"claim":"Whether MED31's proliferative role is exploited in cancer was unknown; it was identified as a direct miR-1 target whose levels drive osteosarcoma proliferation through MET signaling.","evidence":"Luciferase reporter validation of miR-1 targeting, siRNA knockdown, overexpression rescue, MET signaling readouts","pmids":["24969180"],"confidence":"Medium","gaps":["Mechanism by which MED31 controls MET expression not established","Whether MET regulation is Mediator-dependent untested"]},{"year":2018,"claim":"Whether MED31 contributes to adult stem-cell differentiation was untested; knockdown impaired hMSC self-renewal and adipogenesis.","evidence":"siRNA knockdown with self-renewal and adipogenesis (lipid staining, marker expression) assays in hMSCs","pmids":["30006772"],"confidence":"Low","gaps":["Single knockdown approach with no rescue or pathway placement","Direct adipogenic targets of MED31 unidentified"]},{"year":2019,"claim":"Whether MED31's Mediator-associated and genome-wide regulatory roles are conserved in a distant eukaryote was open; AP-MS, ChIP-seq, and knockdown in Tetrahymena demonstrated a Mediator-like interactome, global chromatin binding, and control of developmental DNA-rearrangement genes.","evidence":"AP-MS interactome, ChIP-seq, immunofluorescence localization to meiotic micronuclei, knockdown gene expression analysis","pmids":["31280994"],"confidence":"Medium","gaps":["Direct vs indirect repression of developmental genes not resolved","Functional significance of micronuclear localization unclear"]},{"year":2026,"claim":"Whether the MED31-ELMO1 axis operates in human cancer pathophysiology was untested; a methylation-dependent ELMO1-MED31 interaction was linked to M2 macrophage polarization and EMT in H. pylori-infected gastric cancer cells.","evidence":"Co-IP, methylation-specific PCR, Western blot, co-culture, viability/migration assays","pmids":["41535333"],"confidence":"Low","gaps":["Single Co-IP-based interaction with limited mechanistic pathway placement","No replication and causal role of MED31 versus ELMO1 not separated"]},{"year":null,"claim":"The structural and molecular basis for how MED31 confers selectivity for distinct target-gene programs within an otherwise general Mediator complex remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of MED31 within Mediator","Transcription-factor interfaces that direct MED31 to specific genes unidentified","Relationship between nuclear Mediator role and cytoplasmic Elmo1-dependent function unclear"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,2,6]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,1,6]}],"complexes":["Mediator complex"],"partners":["ELMO1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y3C7","full_name":"Mediator of RNA polymerase II transcription subunit 31","aliases":["Mediator complex subunit 31","Mediator complex subunit SOH1","hSOH1"],"length_aa":131,"mass_kda":15.8,"function":"Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9Y3C7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/MED31","classification":"Common Essential","n_dependent_lines":1158,"n_total_lines":1208,"dependency_fraction":0.9586092715231788},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000108590","cell_line_id":"CID000247","localizations":[{"compartment":"nuclear_punctae","grade":3},{"compartment":"nucleoplasm","grade":3}],"interactors":[{"gene":"MED10","stoichiometry":10.0},{"gene":"MED11","stoichiometry":10.0},{"gene":"MED14","stoichiometry":10.0},{"gene":"MED17","stoichiometry":10.0},{"gene":"MED18","stoichiometry":10.0},{"gene":"MED19","stoichiometry":10.0},{"gene":"MED20","stoichiometry":10.0},{"gene":"MED21","stoichiometry":10.0},{"gene":"MED22","stoichiometry":10.0},{"gene":"MED25","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID000247","total_profiled":1310},"omim":[{"mim_id":"621256","title":"ZINC FINGER- AND BTB DOMAIN-CONTAINING PROTEIN 45; ZBTB45","url":"https://www.omim.org/entry/621256"},{"mim_id":"620492","title":"MEDIATOR COMPLEX SUBUNIT 31; MED31","url":"https://www.omim.org/entry/620492"},{"mim_id":"612385","title":"MEDIATOR COMPLEX SUBUNIT 19; MED19","url":"https://www.omim.org/entry/612385"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/MED31"},"hgnc":{"alias_symbol":["CGI-125","Soh1"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y3C7","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y3C7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y3C7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y3C7-F1-predicted_aligned_error_v6.png","plddt_mean":92.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MED31","jax_strain_url":"https://www.jax.org/strain/search?query=MED31"},"sequence":{"accession":"Q9Y3C7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y3C7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y3C7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y3C7"}},"corpus_meta":[{"pmid":"15356001","id":"PMC_15356001","title":"The Soh1/MED31 protein is an ancient component of Schizosaccharomyces pombe and Saccharomyces cerevisiae Mediator.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15356001","citation_count":37,"is_preprint":false},{"pmid":"20347762","id":"PMC_20347762","title":"The Mediator complex protein Med31 is required for embryonic growth and cell proliferation during mammalian development.","date":"2010","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/20347762","citation_count":26,"is_preprint":false},{"pmid":"34762494","id":"PMC_34762494","title":"Exosome-Mediated Transfer of circ-GLIS3 Enhances Temozolomide Resistance in Glioma Cells Through the miR-548m/MED31 Axis.","date":"2021","source":"Cancer biotherapy & radiopharmaceuticals","url":"https://pubmed.ncbi.nlm.nih.gov/34762494","citation_count":21,"is_preprint":false},{"pmid":"17922236","id":"PMC_17922236","title":"Genomic expression patterns in cell separation mutants of Schizosaccharomyces pombe defective in the genes sep10 ( + ) and sep15 ( + ) coding for the Mediator subunits Med31 and Med8.","date":"2007","source":"Molecular genetics and genomics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/17922236","citation_count":17,"is_preprint":false},{"pmid":"24969180","id":"PMC_24969180","title":"MicroRNA-1 functions as a potential tumor suppressor in osteosarcoma by targeting Med1 and Med31.","date":"2014","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/24969180","citation_count":17,"is_preprint":false},{"pmid":"23273896","id":"PMC_23273896","title":"A link between the cytoplasmic engulfment protein Elmo1 and the Mediator complex subunit Med31.","date":"2012","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/23273896","citation_count":15,"is_preprint":false},{"pmid":"31280994","id":"PMC_31280994","title":"The Med31 Conserved Component of the Divergent Mediator Complex in Tetrahymena thermophila Participates in Developmental Regulation.","date":"2019","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/31280994","citation_count":15,"is_preprint":false},{"pmid":"30006772","id":"PMC_30006772","title":"MED31 involved in regulating self-renewal and adipogenesis of human mesenchymal stem cells.","date":"2018","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/30006772","citation_count":7,"is_preprint":false},{"pmid":"41535333","id":"PMC_41535333","title":"Interaction between ELMO1 DNA methylation and Med31 promotes H. pylori-induced gastric cancer EMT and intestinal metaplasia via M2 polarization.","date":"2026","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/41535333","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.25.24316158","title":"Gene-Excessive Sleepiness Interactions Suggest Treatment Targets for Obstructive Sleep Apnea Subtype","date":"2024-10-28","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.25.24316158","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6525,"output_tokens":2048,"usd":0.025147,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9074,"output_tokens":2875,"usd":0.058623,"stage2_stop_reason":"end_turn"},"total_usd":0.08377,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"Soh1/MED31 protein is a stable component of the Mediator complex isolated from both Schizosaccharomyces pombe and Saccharomyces cerevisiae, and bioinformatic analysis places MED31 family members as ancient Mediator subunits present before the appearance of the canonical RNA polymerase II CTD heptapeptide repeat structure.\",\n      \"method\": \"Biochemical isolation of Mediator complex; bioinformatic analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct biochemical isolation of the complex from two yeast species, single lab, supported by bioinformatic conservation analysis\",\n      \"pmids\": [\"15356001\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"In Schizosaccharomyces pombe, Med31 (encoded by sep10+) controls large sets of genes including cell separation genes regulated by the transcription factors Sep1 and Ace2; Med31 acts as a coactivator of Sep1-Ace2-dependent cell separation genes, linking the Mediator complex to the regulation of the cell separation phase of cell division.\",\n      \"method\": \"Genome-wide gene expression profiling of med31 (sep10) loss-of-function mutants; genetic epistasis with sep1 and ace2\",\n      \"journal\": \"Molecular genetics and genomics : MGG\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide expression profiling of mutants with epistasis analysis; single lab, two complementary approaches\",\n      \"pmids\": [\"17922236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Mouse Med31 is required for embryonic cell proliferation; a mutation causing Med31 protein degradation results in fewer proliferating cells in rapidly expanding tissues (e.g., forelimb buds), severe proliferation defect in embryonic fibroblasts, reduced Cdc2 protein levels, and defective chondrogenesis with loss of Sox9 and Col2a1 expression, while target genes of other Mediator proteins remain normally expressed, indicating Med31 has distinct transcriptional targets.\",\n      \"method\": \"ENU mutagenesis screen; loss-of-function mouse mutant analysis; cell proliferation assays in embryonic fibroblasts; Western blot for Cdc2; gene expression analysis\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo loss-of-function with multiple cellular and molecular readouts in a single lab study\",\n      \"pmids\": [\"20347762\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Elmo1 physically binds Med31; Elmo1 increases the cytoplasmic localization of endogenous Med31 (which is predominantly nuclear); Elmo1 promotes monoubiquitination of Med31 in the cytoplasm; during Salmonella infection in primary macrophages, Elmo1 and Med31 together specifically affect expression of cytokine genes Il10 and Il33.\",\n      \"method\": \"Co-immunoprecipitation (Co-IP) of Elmo1 and Med31; subcellular fractionation/localization; ubiquitination assay; cytokine gene expression monitoring in primary macrophages\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, subcellular localization with functional consequence, PTM identification; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"23273896\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"MED31 is a direct target of miR-1 in osteosarcoma cells, as validated by luciferase reporter assay; knockdown of Med31 suppresses osteosarcoma cell proliferation and reduces expression of MET proto-oncogene and its downstream signaling in response to HGF; overexpression of Med31 abrogates the anti-proliferative effects of miR-1.\",\n      \"method\": \"Luciferase reporter assay; siRNA knockdown; overexpression rescue; cell proliferation assay; Western blot/gene expression for MET signaling\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase reporter validates direct targeting, functional rescue experiment; single lab, multiple methods\",\n      \"pmids\": [\"24969180\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"siRNA-mediated knockdown of MED31 in human mesenchymal stem cells (hMSCs) reduces self-renewal and impairs adipogenesis, as evidenced by decreased lipid vesicle formation and reduced expression of adipogenic markers.\",\n      \"method\": \"siRNA knockdown; cell self-renewal assays; adipogenesis assay (lipid staining, adipogenic marker gene expression)\",\n      \"journal\": \"Molecular biology reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single knockdown approach with phenotypic readouts but no pathway placement or mechanistic follow-up\",\n      \"pmids\": [\"30006772\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In Tetrahymena thermophila, Med31 physically interacts with >20 proteins including subunits sharing similarities to canonical Mediator subunits from yeast and humans; Med31 ChIP-seq shows a global role in transcription regulation; Med31 localizes to meiotic micronuclei; MED31 knockdown causes ectopic expression of developmental genes important for programmed DNA rearrangements.\",\n      \"method\": \"Affinity purification coupled with mass spectrometry (AP-MS); ChIP-seq; indirect immunofluorescence; MED31 knockdown with gene expression analysis\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — AP-MS interactome, ChIP-seq, localization, and loss-of-function phenotype; multiple orthogonal methods in a single study\",\n      \"pmids\": [\"31280994\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ELMO1 methylation interacts with Med31 (detected by co-immunoprecipitation) and this interaction promotes M2 macrophage polarization, EMT, and intestinal metaplasia in H. pylori-infected gastric cancer cells.\",\n      \"method\": \"Co-immunoprecipitation; methylation-specific PCR; Western blot; co-culture experiments; cell viability/migration assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, Co-IP supports interaction but mechanistic pathway placement is limited and study is recent with no replication\",\n      \"pmids\": [\"41535333\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MED31 (also known as Soh1/CGI-125) is the smallest and most evolutionarily conserved subunit of the Mediator complex, physically incorporated into Mediator to bridge transcription factors with the RNA polymerase II machinery; it is predominantly nuclear but can be redistributed to the cytoplasm and monoubiquitinated by the cytoplasmic engulfment protein Elmo1, and loss of Med31 function causes defective cell proliferation (with reduced Cdc2), impaired chondrogenesis, reduced adipogenesis of stem cells, and dysregulation of specific cytokine and developmental gene programs, collectively indicating that Med31 is a context-specific transcriptional co-activator required for normal cell cycle progression, differentiation, and tissue development.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"MED31 is an ancient, stably incorporated subunit of the RNA polymerase II Mediator complex that functions as a context-specific transcriptional co-activator linking sequence-specific transcription factors to gene-expression programs governing proliferation, differentiation, and development [#0, #6]. Biochemical isolation of Mediator from two yeast species established MED31 as a bona fide complex component conserved among the oldest Mediator subunits [#0], and affinity purification in Tetrahymena recovered a Mediator-like interactome together with a genome-wide chromatin-binding role demonstrated by ChIP-seq [#6]. Rather than regulating Mediator targets globally, MED31 acts on distinct gene sets: in fission yeast it coactivates Sep1/Ace2-dependent cell-separation genes [#1], and in mouse it is required for embryonic cell proliferation and chondrogenesis, with loss reducing Cdc2 and Sox9/Col2a1 expression while other Mediator targets remain unaffected [#2]. MED31 is predominantly nuclear, but the cytoplasmic engulfment protein Elmo1 binds MED31, drives its cytoplasmic redistribution and monoubiquitination, and together with MED31 shapes Il10 and Il33 cytokine expression during macrophage infection [#3]. Its proliferative function extends to disease contexts, where MED31 is a direct miR-1 target that supports osteosarcoma cell proliferation via MET signaling [#4]. Beyond these contexts, the structural basis of MED31's selective target specificity within Mediator has not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Establishing whether MED31 is a genuine Mediator subunit was prerequisite to any functional interpretation; biochemical isolation defined it as a stable, deeply conserved component of the complex.\",\n      \"evidence\": \"Biochemical isolation of Mediator from S. pombe and S. cerevisiae plus bioinformatic conservation analysis\",\n      \"pmids\": [\"15356001\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define which transcription factors or genes MED31 regulates\", \"No structural placement of MED31 within the complex\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Whether MED31 has selective rather than global transcriptional roles was unknown; expression profiling showed it coactivates a specific Sep1/Ace2-dependent cell-separation program, linking Mediator to a defined phase of cell division.\",\n      \"evidence\": \"Genome-wide expression profiling of med31 (sep10) mutants with sep1/ace2 epistasis in S. pombe\",\n      \"pmids\": [\"17922236\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not show direct physical contact between MED31 and Sep1/Ace2\", \"Conservation of this selectivity to metazoans untested\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Whether MED31's selective regulation matters in a vertebrate was open; a mouse loss-of-function mutant showed it is required for embryonic proliferation and chondrogenesis through a distinct set of targets, not the whole Mediator program.\",\n      \"evidence\": \"ENU mutant mouse analysis, fibroblast proliferation assays, Cdc2 Western blot, Sox9/Col2a1 expression\",\n      \"pmids\": [\"20347762\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect regulation of Cdc2 and Sox9 not resolved\", \"Transcription factors recruiting MED31 to these targets unidentified\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Whether MED31 has functions outside the nuclear Mediator complex was unexplored; Elmo1 was shown to bind MED31, drive its cytoplasmic relocation and monoubiquitination, and tune specific cytokine genes during infection.\",\n      \"evidence\": \"Reciprocal Co-IP, subcellular fractionation, ubiquitination assay, cytokine expression in primary macrophages\",\n      \"pmids\": [\"23273896\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Function of cytoplasmic monoubiquitinated MED31 not defined\", \"Whether cytoplasmic redistribution is regulatory or degradative unclear\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Whether MED31's proliferative role is exploited in cancer was unknown; it was identified as a direct miR-1 target whose levels drive osteosarcoma proliferation through MET signaling.\",\n      \"evidence\": \"Luciferase reporter validation of miR-1 targeting, siRNA knockdown, overexpression rescue, MET signaling readouts\",\n      \"pmids\": [\"24969180\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which MED31 controls MET expression not established\", \"Whether MET regulation is Mediator-dependent untested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Whether MED31 contributes to adult stem-cell differentiation was untested; knockdown impaired hMSC self-renewal and adipogenesis.\",\n      \"evidence\": \"siRNA knockdown with self-renewal and adipogenesis (lipid staining, marker expression) assays in hMSCs\",\n      \"pmids\": [\"30006772\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single knockdown approach with no rescue or pathway placement\", \"Direct adipogenic targets of MED31 unidentified\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Whether MED31's Mediator-associated and genome-wide regulatory roles are conserved in a distant eukaryote was open; AP-MS, ChIP-seq, and knockdown in Tetrahymena demonstrated a Mediator-like interactome, global chromatin binding, and control of developmental DNA-rearrangement genes.\",\n      \"evidence\": \"AP-MS interactome, ChIP-seq, immunofluorescence localization to meiotic micronuclei, knockdown gene expression analysis\",\n      \"pmids\": [\"31280994\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect repression of developmental genes not resolved\", \"Functional significance of micronuclear localization unclear\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Whether the MED31-ELMO1 axis operates in human cancer pathophysiology was untested; a methylation-dependent ELMO1-MED31 interaction was linked to M2 macrophage polarization and EMT in H. pylori-infected gastric cancer cells.\",\n      \"evidence\": \"Co-IP, methylation-specific PCR, Western blot, co-culture, viability/migration assays\",\n      \"pmids\": [\"41535333\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP-based interaction with limited mechanistic pathway placement\", \"No replication and causal role of MED31 versus ELMO1 not separated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural and molecular basis for how MED31 confers selectivity for distinct target-gene programs within an otherwise general Mediator complex remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of MED31 within Mediator\", \"Transcription-factor interfaces that direct MED31 to specific genes unidentified\", \"Relationship between nuclear Mediator role and cytoplasmic Elmo1-dependent function unclear\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 2, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 1, 6]}\n    ],\n    \"complexes\": [\"Mediator complex\"],\n    \"partners\": [\"ELMO1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}