{"gene":"MXD1","run_date":"2026-06-10T05:19:51","timeline":{"discoveries":[{"year":2016,"finding":"MXD1 localizes to the nucleolus in multiple cell lines and primary cells (neurons, Sertoli cells), interacts with UBF (confirmed by co-immunoprecipitation and proximity ligation assay), binds transcribed rDNA chromatin and ribosomal intergenic regions (ChIP), and represses rRNA synthesis: siRNA knockdown of MXD1 increases pre-rRNA synthesis while enforced MXD1 expression reduces it.","method":"Co-immunoprecipitation, proximity ligation assay, chromatin immunoprecipitation, siRNA knockdown, co-localization imaging","journal":"Oncotarget","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Co-IP, PLA, ChIP, siRNA KD, overexpression) in a single focused study establishing both localization and functional consequence","pmids":["27588501"],"is_preprint":false},{"year":2007,"finding":"Structural determinants in the leucine zipper of Mxd1 (D112a) and Max (N78a, H81d) dictate specificity of Mxd1/Max heterodimerization and whether the Mxd1/Max/DNA complex forms; heterodimerization must precede DNA binding in vivo.","method":"Mutagenesis of leucine zipper residues, DNA-binding assays","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct mutagenesis of key residues with in vitro and in vivo DNA-binding functional readouts in a single dedicated structural/mechanistic study","pmids":["18155722"],"is_preprint":false},{"year":2011,"finding":"The PAH2 domain of mSin3A interacts with the SID1 motif of Pf1 in a manner structurally reminiscent of the Mad1/Mxd1–Sin3 interaction; MRG15 competes with Sin3 for the same Pf1 segment, implying competitive regulation within the Rpd3S/Sin3S complex.","method":"NMR solution structure, mutagenesis, competitive binding assays","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structure with mutagenesis and functional binding validation; directly characterizes the Mxd1-type SID–Sin3 PAH2 interaction mechanism","pmids":["21440557"],"is_preprint":false},{"year":2012,"finding":"1,25-dihydroxyvitamin D (1,25D)/VDR signaling enhances MXD1 expression and protein stability while inhibiting c-MYC expression and accelerating its turnover; the E3-ubiquitin ligase FBW7 controls stability of both c-MYC and MXD1, and FBW7 ablation attenuates 1,25D-mediated regulation of their turnover, dramatically altering the ratio of DNA-bound c-MYC vs. MXD1.","method":"Cell- and animal-based studies, mathematical modeling, VDR/FBW7 knockdown, protein stability assays, ChIP","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (KD, in vivo mouse, ChIP, stability assays) across cell and animal models, single lab but highly rigorous","pmids":["23112173"],"is_preprint":false},{"year":2015,"finding":"Increased Mxd1 recruits the Sin3A repressor complex via enhanced binding with HDAC-2, resulting in increased HDAC activity and transcriptional repression; Mxd1 represses hTERT mRNA expression through direct binding to the hTERT promoter (confirmed by ChIP), reducing telomerase activity; these effects require Mxd1 dimerization with Max.","method":"Co-immunoprecipitation (Mxd1–Sin3A–HDAC-2), HDAC activity assay, ChIP at hTERT promoter, luciferase reporter, western blot","journal":"Cancer biology & therapy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and ChIP in a single lab with functional readouts (HDAC activity, telomerase activity)","pmids":["25611699"],"is_preprint":false},{"year":2017,"finding":"HIF-1α-induced Mxd1 directly binds E-box sites within the PTEN promoter (confirmed by luciferase reporter and ChIP), repressing PTEN transcription; this suppression activates PI3K/AKT signaling and promotes cisplatin resistance in hypoxic osteosarcoma cells.","method":"Luciferase reporter assay, ChIP, siRNA knockdown, western blot, cell viability assay","journal":"Molecular carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and reporter assay establishing direct promoter binding, with functional rescue experiments; single lab","pmids":["28543796"],"is_preprint":false},{"year":2017,"finding":"SIRT1 targets the Mxd1 locus in concert with DNMT3B; SIRT1 silencing increases Mxd1 mRNA expression, and DNMT inhibitor 5AzaCdR reverses Mxd1 silencing, indicating that SIRT1-DNMT3B-mediated DNA methylation suppresses Mxd1 expression during melanoma progression.","method":"ChIP-seq (SIRT1 binding at Mxd1 locus), Co-immunoprecipitation (SIRT1–DNMT3B), stable SIRT1 knockdown, 5AzaCdR treatment, qPCR","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP-seq plus Co-IP plus pharmacological reversal in single lab; establishes SIRT1/DNMT3B as writers silencing Mxd1","pmids":["29383100"],"is_preprint":false},{"year":2020,"finding":"MXD1 competes with MYC for binding to MAX; the MAGI2-AS3 lncRNA sequesters miR-525-5p, relieving miR-525-5p-mediated repression of MXD1, thereby increasing MXD1 availability to compete with MYC for MAX binding and suppress MYC-driven proliferation in ovarian cancer cells.","method":"RNA pull-down, luciferase reporter, western blot, rescue/overexpression assays","journal":"Cancer medicine","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, RNA pull-down and reporter assays without direct structural evidence of MXD1–MAX competition in this context","pmids":["32681706"],"is_preprint":false},{"year":2020,"finding":"The SIN3-interacting domain (SID) derived from MXD1 functions as a potent transcriptional repressor domain when fused to dCas9 (CRISPRi), outperforming the KRAB domain in lymphoid cell lines; the SID domain can be fused to the MS2 aptamer-binding protein MCP for doxycycline-regulated CRISPRi.","method":"CRISPRi library screen, RT-qPCR, competition assay with GFP-expressing sgRNA constructs, chromatin immunoprecipitation (MYC at lncRNA promoters)","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional CRISPRi screen with independent validation; directly demonstrates SID domain repressor activity in cells","pmids":["32156728"],"is_preprint":false},{"year":2020,"finding":"A mini-protein (Mad) derived from MXD1 interacts with MAX and with the nucleolar upstream binding factor (UBF), binds E-box DNA in MYC target gene promoters, and represses MYC-mediated transcription; Mad is 10-fold more potent than the MYC inhibitor Omomyc in inhibiting MYC-driven cell proliferation.","method":"Co-immunoprecipitation (Mad–MAX, Mad–UBF), E-box DNA-binding assay, cell proliferation assay, transcriptional reporter assay","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and functional assays in single lab; directly demonstrates binding partners and transcriptional repression by MXD1-derived domain","pmids":["32053209"],"is_preprint":false},{"year":2020,"finding":"Mxd1 is induced during maturation of Batf3-dependent cDC1 dendritic cells; Mxd1-deficient mature cDC1s exhibit impaired ability to inhibit the MYCL-supported transcriptional program, establishing reciprocal MYCL/MXD1 regulation of biosynthetic gene expression during cDC1 maturation.","method":"Mxd1 knockout mice, gene expression profiling, epistasis analysis with Mycl-deficient mice","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined transcriptional phenotype and epistasis, single lab","pmids":["32071205"],"is_preprint":false},{"year":2018,"finding":"MXD1 directly inhibits the transcriptional activity of the BCR-ABL1 gene promoter (reporter gene assay), reducing BCR-ABL1 mRNA and protein, thereby suppressing proliferation and sensitizing imatinib-resistant CML cells to imatinib.","method":"Reporter gene assay, overexpression, western blot, qPCR, cell proliferation assay","journal":"Leukemia research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single reporter assay without ChIP confirmation of direct promoter binding","pmids":["30419548"],"is_preprint":false},{"year":2016,"finding":"MXD1 knockdown in CD34+ hematopoietic stem/progenitor cells mimics miR-382-5p overexpression, promoting granulocyte expansion and impairing megakaryocyte commitment; MXD1 was validated as a direct target of miR-382-5p by luciferase reporter assay.","method":"siRNA knockdown of MXD1 in CD34+ HSPCs, luciferase reporter assay, colony assays","journal":"Stem cells and development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct KD with defined lineage-commitment phenotype plus reporter validation; single lab","pmids":["27520398"],"is_preprint":false},{"year":2020,"finding":"MXD1 directly binds the CXCL10 promoter in influenza-infected human macrophages (EMSA), and MXD1 knockdown significantly attenuates H1N1- and H9N2/G1-induced CXCL10 expression; MXD1 knockdown also decreases H9N2 replication but not H1N1 replication; MXD1 induction is dependent on MEK1/2 activation.","method":"EMSA, siRNA knockdown, qPCR, viral replication assay, MEK1/2 inhibitor treatment","journal":"Journal of leukocyte biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — EMSA plus functional KD with specific readouts; single lab","pmids":["32794336"],"is_preprint":false},{"year":2021,"finding":"MXD1 protein stability is enhanced by the deubiquitinase USP36, and MXD1 transcription is promoted by up-regulation of the transcription factor c-JUN; MXD1 in turn up-regulates lnc-HZ01 stability via increased m6A RNA methylation, forming a positive feedback loop that promotes EIF4E transcription and inhibits trophoblast cell proliferation.","method":"Western blot, co-immunoprecipitation, luciferase reporter, siRNA knockdown, m6A methylation assay","journal":"The Science of the total environment","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mechanistic claims about USP36 deubiquitination and c-JUN transcription inferred from western blot/reporter without direct ubiquitination reconstitution","pmids":["33647641"],"is_preprint":false},{"year":2025,"finding":"In trametinib-resistant PDAC, MXD1 acts as a cofactor of the histone methyltransferase MLL1 to increase H3K4 trimethylation at transposable element loci, enhancing chromatin accessibility and transcription of transposable elements, which produces dsRNAs that activate viral mimicry response and downstream oncogenic interferon-stimulated genes.","method":"scRNA-seq, ATAC-seq, CUT&TAG, patient-derived xenograft models, MXD1 inhibition experiments","journal":"Gut","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal genomic methods (ATAC-seq, CUT&TAG, scRNA-seq) with PDX functional validation; single lab","pmids":["39819860"],"is_preprint":false},{"year":2025,"finding":"METTL14-mediated m6A modification of MXD1 mRNA is recognized by the m6A reader YTHDF2; this modification alters MXD1 expression, and increased MXD1 modulates VEGFA and VCAM1 expression, promoting retinal neovascularization in an OIR model.","method":"MeRIP-seq, RIP assay, dual-luciferase reporter, ChIP-qPCR, METTL14 conditional KO mouse, co-culture angiogenesis assay","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MeRIP-seq plus RIP and in vivo KO with functional readout; single lab","pmids":["40303324"],"is_preprint":false},{"year":2025,"finding":"In microglia, VitD/VDR transcriptionally activates FTO; upregulated FTO reduces m6A methylation on Mxd1 mRNA in a YTHDF2-dependent manner, enhancing Mxd1 mRNA stability and protein expression; increased Mxd1 then binds and represses the PTEN promoter, activating PI3K/AKT and facilitating nuclear translocation of PGC-1α to promote M2 microglial polarization.","method":"VDR ChIP at FTO promoter, m6A methylation assay, YTHDF2 knockdown, Mxd1 ChIP at PTEN promoter, luciferase reporter, in vitro and in vivo polarization assays","journal":"Inflammation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (ChIP, m6A assay, reporter, KD) in single lab; mechanistic chain includes direct promoter-binding evidence","pmids":["41632223"],"is_preprint":false}],"current_model":"MXD1 (MAD1) is a bHLH-LZ transcriptional repressor that heterodimerizes with MAX (heterodimerization preceding DNA binding and requiring specific leucine-zipper residues) to bind E-box sequences and recruit the Sin3A–HDAC corepressor complex via its SID domain, thereby antagonizing MYC–MAX-driven transcription; beyond E-box gene repression, MXD1 uniquely localizes to the nucleolus where it interacts with UBF and binds rDNA chromatin to suppress ribosome biogenesis, and it represses specific target gene promoters (PTEN, hTERT, BCR-ABL1, CXCL10) by direct binding; its activity is regulated post-translationally by FBW7-mediated ubiquitination (shared with MYC), USP36-mediated stabilization, SIRT1/DNMT3B-dependent epigenetic silencing, and m6A modification of its mRNA recognized by YTHDF2, while in context-specific settings MXD1 can act as a cofactor of MLL1 to promote H3K4me3 at transposable elements."},"narrative":{"mechanistic_narrative":"MXD1 is a bHLH-LZ transcriptional repressor that antagonizes MYC-driven gene programs by heterodimerizing with MAX and competing with MYC for the shared MAX partner [PMID:32681706, PMID:32053209]. Heterodimerization with MAX is governed by defined leucine-zipper residues and must precede DNA binding, after which the MXD1/MAX complex engages E-box elements [PMID:18155722]. Repression is executed through the MXD1 SIN3-interacting domain (SID), which recruits the Sin3A corepressor and HDAC-2 to increase histone deacetylase activity at target loci; the isolated SID is a potent portable repressor domain in synthetic CRISPRi contexts [PMID:25611699, PMID:32156728]. Through MAX-dependent E-box binding, MXD1 directly represses specific promoters including hTERT, PTEN, BCR-ABL1, and CXCL10, with functional consequences for telomerase activity, PI3K/AKT signaling, and inflammatory and oncogenic outputs [PMID:25611699, PMID:28543796, PMID:30419548, PMID:32794336]. Beyond E-box gene repression, MXD1 localizes to the nucleolus, interacts with UBF, binds rDNA chromatin, and suppresses pre-rRNA synthesis, coupling it to control of ribosome biogenesis [PMID:27588501, PMID:32053209]. MXD1 abundance is heavily regulated post-translationally and post-transcriptionally: FBW7 controls its turnover in parallel with MYC under 1,25D/VDR signaling, USP36 deubiquitination stabilizes it, SIRT1/DNMT3B-mediated DNA methylation silences its locus, and m6A modification of MXD1 mRNA read by YTHDF2 tunes its expression [PMID:23112173, PMID:29383100, PMID:33647641, PMID:40303324, PMID:41632223]. In context-specific settings MXD1 acts as a cofactor of the methyltransferase MLL1 to deposit H3K4me3 at transposable elements, linking it to chromatin accessibility and a viral-mimicry response [PMID:39819860].","teleology":[{"year":2007,"claim":"Established the structural logic of MXD1 function by defining which leucine-zipper residues dictate MXD1/MAX heterodimer specificity and showing heterodimerization is obligatory before DNA binding.","evidence":"Mutagenesis of leucine-zipper residues with in vitro and in vivo DNA-binding readouts","pmids":["18155722"],"confidence":"High","gaps":["Does not address how heterodimer choice is regulated in vivo","No structure of the full repressive complex on chromatin"]},{"year":2011,"claim":"Characterized the MXD1-type SID–Sin3 PAH2 interaction and revealed competitive regulation within Sin3-class corepressor assemblies, clarifying how SID engages the repressor machinery.","evidence":"NMR solution structure, mutagenesis, and competitive binding assays (Pf1/MRG15 system)","pmids":["21440557"],"confidence":"High","gaps":["Structural work on a related SID-bearing protein rather than MXD1 directly","Does not quantify MXD1 SID affinity in cells"]},{"year":2012,"claim":"Showed that MXD1 and MYC share the FBW7 ubiquitin ligase and are reciprocally regulated by 1,25D/VDR, explaining how upstream signals reset the DNA-bound MYC:MXD1 ratio.","evidence":"Cell and mouse studies with VDR/FBW7 knockdown, protein stability assays, ChIP, and mathematical modeling","pmids":["23112173"],"confidence":"High","gaps":["Does not define FBW7 phosphodegron on MXD1 directly","Tissue specificity of this regulation not mapped"]},{"year":2015,"claim":"Connected MXD1 corepressor recruitment to a defined target output by showing MXD1–Sin3A–HDAC-2 assembly represses hTERT via direct promoter binding in a MAX-dimerization-dependent manner.","evidence":"Reciprocal Co-IP, HDAC activity assay, ChIP at hTERT promoter, luciferase reporter","pmids":["25611699"],"confidence":"Medium","gaps":["Single lab","Generality of HDAC-2 selectivity across MXD1 targets unknown"]},{"year":2016,"claim":"Defined a non-canonical nucleolar role: MXD1 binds UBF and rDNA chromatin to repress rRNA synthesis, extending its function beyond classic E-box gene repression to ribosome biogenesis.","evidence":"Co-IP, proximity ligation assay, ChIP at rDNA, siRNA knockdown, and overexpression in multiple cell types","pmids":["27588501"],"confidence":"High","gaps":["Whether MAX is required for nucleolar localization is not resolved","Mechanism of UBF-directed recruitment to rDNA undefined"]},{"year":2016,"claim":"Linked MXD1 dosage to hematopoietic lineage decisions, showing its knockdown skews CD34+ progenitors toward granulocytes at the expense of megakaryocytes and identifying it as a miR-382-5p target.","evidence":"siRNA knockdown in CD34+ HSPCs, colony assays, luciferase reporter validation","pmids":["27520398"],"confidence":"Medium","gaps":["Transcriptional targets driving lineage skew not defined","Single lab"]},{"year":2017,"claim":"Extended the MXD1 target repertoire to PTEN, showing HIF-1α-induced MXD1 binds PTEN E-boxes to derepress PI3K/AKT and drive chemoresistance.","evidence":"Luciferase reporter, ChIP, siRNA knockdown, cell viability assays in hypoxic osteosarcoma","pmids":["28543796"],"confidence":"Medium","gaps":["MAX-dependence of PTEN binding not directly tested here","Single context"]},{"year":2017,"claim":"Identified an epigenetic silencing mechanism whereby SIRT1 acting with DNMT3B methylates the MXD1 locus to suppress its expression during melanoma progression.","evidence":"ChIP-seq, SIRT1–DNMT3B Co-IP, SIRT1 knockdown, 5AzaCdR pharmacological reversal, qPCR","pmids":["29383100"],"confidence":"Medium","gaps":["Specific methylated CpGs not mapped","Generality beyond melanoma untested"]},{"year":2018,"claim":"Proposed MXD1 repression of the BCR-ABL1 promoter as a route to imatinib re-sensitization in CML.","evidence":"Reporter gene assay, overexpression, qPCR, proliferation assays","pmids":["30419548"],"confidence":"Low","gaps":["No ChIP confirmation of direct promoter binding","Single lab, single assay class"]},{"year":2020,"claim":"Demonstrated MXD1 competes with MYC for MAX and that this balance is tuned by a lncRNA/miRNA axis to suppress MYC-driven proliferation.","evidence":"RNA pull-down, luciferase reporter, rescue/overexpression in ovarian cancer cells","pmids":["32681706"],"confidence":"Low","gaps":["No direct structural evidence of MXD1–MAX competition in this context","Single lab"]},{"year":2020,"claim":"Validated the MXD1 SID as a portable, potent repressor domain, providing functional proof that SID drives transcriptional silencing in cells beyond KRAB.","evidence":"dCas9-SID CRISPRi library screen, RT-qPCR, competition assays, MYC ChIP at lncRNA promoters","pmids":["32156728"],"confidence":"Medium","gaps":["Synthetic context; does not measure endogenous MXD1 occupancy","Corepressor recruitment by fused SID not directly mapped"]},{"year":2020,"claim":"Showed an MXD1-derived mini-protein engages both MAX and UBF and binds E-box promoters, recapitulating dual transcriptional and potentially nucleolar inhibition of MYC with high potency.","evidence":"Co-IP (Mad–MAX, Mad–UBF), E-box binding assay, proliferation and reporter assays","pmids":["32053209"],"confidence":"Medium","gaps":["Engineered mini-protein, not full-length endogenous MXD1","Single lab"]},{"year":2020,"claim":"Established a physiological MYCL/MXD1 antagonism, where induced Mxd1 restrains the MYCL biosynthetic program during cDC1 dendritic cell maturation.","evidence":"Mxd1 knockout mice, expression profiling, epistasis with Mycl-deficient mice","pmids":["32071205"],"confidence":"Medium","gaps":["Direct Mxd1 target genes in cDC1 not enumerated","Single lab"]},{"year":2020,"claim":"Implicated MXD1 in antiviral transcription by showing it binds the CXCL10 promoter and is required for influenza-induced CXCL10, with MEK1/2-dependent induction.","evidence":"EMSA, siRNA knockdown, qPCR, viral replication assay, MEK inhibitor treatment in macrophages","pmids":["32794336"],"confidence":"Medium","gaps":["How a repressor drives CXCL10 induction mechanistically unresolved","Strain-specific replication effects unexplained"]},{"year":2021,"claim":"Placed MXD1 in a regulatory feedback loop involving USP36 stabilization, c-JUN-driven transcription, and m6A-dependent lncRNA control affecting trophoblast proliferation.","evidence":"Western blot, Co-IP, luciferase reporter, m6A assay, siRNA knockdown","pmids":["33647641"],"confidence":"Low","gaps":["USP36 deubiquitination of MXD1 not reconstituted directly","Single lab, correlational mechanistic chain"]},{"year":2025,"claim":"Revealed a chromatin-activating role distinct from canonical repression: MXD1 partners with MLL1 to deposit H3K4me3 at transposable elements, triggering viral mimicry in drug-resistant PDAC.","evidence":"scRNA-seq, ATAC-seq, CUT&TAG, PDX models, MXD1 inhibition","pmids":["39819860"],"confidence":"Medium","gaps":["How MXD1 switches from Sin3-repression to MLL1-coactivation unknown","Direct MXD1–MLL1 interaction not biochemically resolved"]},{"year":2025,"claim":"Defined m6A control of MXD1 mRNA via METTL14 writing and YTHDF2 reading, linking MXD1 dosage to VEGFA/VCAM1 and pathological retinal neovascularization.","evidence":"MeRIP-seq, RIP, dual-luciferase, ChIP-qPCR, METTL14 conditional KO mouse, angiogenesis co-culture","pmids":["40303324"],"confidence":"Medium","gaps":["Direction of YTHDF2 effect on MXD1 stability not fully reconciled across studies","Single tissue context"]},{"year":2025,"claim":"Connected VitD/VDR signaling to an FTO/YTHDF2 m6A axis that stabilizes Mxd1, which then represses PTEN to activate PI3K/AKT and drive M2 microglial polarization.","evidence":"VDR ChIP at FTO, m6A assay, YTHDF2 knockdown, Mxd1 ChIP at PTEN, reporter and polarization assays in vitro and in vivo","pmids":["41632223"],"confidence":"Medium","gaps":["Reconciliation of m6A removal (FTO) increasing stability with YTHDF2 dependence","Single lab"]},{"year":null,"claim":"How MXD1 is partitioned between its canonical MAX/Sin3-HDAC repressive function, its nucleolar UBF/rDNA role, and its MLL1-associated coactivator role at transposable elements remains mechanistically unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No model explains the repressor-to-coactivator switch","Determinants of nucleolar versus nucleoplasmic targeting unknown","Genome-wide endogenous MXD1 occupancy not integrated across contexts"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,4,5,8,9]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[1,5,9,13]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[4,8]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[0,9]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1,5]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,4,5,8]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[4,15]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0]}],"complexes":["Sin3A-HDAC corepressor complex","MXD1/MAX heterodimer"],"partners":["MAX","SIN3A","HDAC2","UBF","MLL1","FBW7","USP36","YTHDF2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q05195","full_name":"Max dimerization protein 1","aliases":["Protein MAD"],"length_aa":221,"mass_kda":25.3,"function":"Component of a transcriptional repressor complex together with MAX (PubMed:8425218). In complex with MAX binds to the core DNA sequence 5'-CAC[GA]TG-3' (PubMed:8425218). Antagonizes MYC transcriptional activity by competing with MYC for MAX binding (PubMed:8425218). Binds to the TERT promoter and represses telomerase expression, possibly by interfering with MYC binding (PubMed:12837246)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q05195/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/MXD1","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/MXD1","total_profiled":1310},"omim":[{"mim_id":"614352","title":"NUCLEOPORIN, 205-KD; NUP205","url":"https://www.omim.org/entry/614352"},{"mim_id":"614351","title":"NUCLEOPORIN, 93-KD; NUP93","url":"https://www.omim.org/entry/614351"},{"mim_id":"608140","title":"NUCLEOPORIN, 35-KD; NUP35","url":"https://www.omim.org/entry/608140"},{"mim_id":"606694","title":"NUCLEOPORIN, 155-KD; NUP155","url":"https://www.omim.org/entry/606694"},{"mim_id":"600021","title":"MAX DIMERIZATION PROTEIN 1; MXD1","url":"https://www.omim.org/entry/600021"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Uncertain","locations":[{"location":"Nucleoplasm","reliability":"Uncertain"},{"location":"Mitochondria","reliability":"Uncertain"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"bone marrow","ntpm":163.8},{"tissue":"esophagus","ntpm":125.8}],"url":"https://www.proteinatlas.org/search/MXD1"},"hgnc":{"alias_symbol":["MAD1","bHLHc58"],"prev_symbol":["MAD"]},"alphafold":{"accession":"Q05195","domains":[{"cath_id":"4.10.280.10","chopping":"60-144","consensus_level":"medium","plddt":91.3027,"start":60,"end":144}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q05195","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q05195-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q05195-F1-predicted_aligned_error_v6.png","plddt_mean":72.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MXD1","jax_strain_url":"https://www.jax.org/strain/search?query=MXD1"},"sequence":{"accession":"Q05195","fasta_url":"https://rest.uniprot.org/uniprotkb/Q05195.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q05195/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q05195"}},"corpus_meta":[{"pmid":"24675462","id":"PMC_24675462","title":"MiR-19a/b modulate the metastasis of gastric cancer cells by targeting the tumour suppressor MXD1.","date":"2014","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/24675462","citation_count":104,"is_preprint":false},{"pmid":"23112173","id":"PMC_23112173","title":"Vitamin D receptor as a master regulator of the c-MYC/MXD1 network.","date":"2012","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/23112173","citation_count":98,"is_preprint":false},{"pmid":"33647641","id":"PMC_33647641","title":"Lnc-HZ01 with m6A RNA methylation inhibits human trophoblast cell proliferation and induces miscarriage by up-regulating BPDE-activated lnc-HZ01/MXD1 positive feedback loop.","date":"2021","source":"The Science of the total environment","url":"https://pubmed.ncbi.nlm.nih.gov/33647641","citation_count":54,"is_preprint":false},{"pmid":"32156728","id":"PMC_32156728","title":"An MXD1-derived repressor peptide identifies noncoding mediators of MYC-driven cell proliferation.","date":"2020","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/32156728","citation_count":35,"is_preprint":false},{"pmid":"25611699","id":"PMC_25611699","title":"Down regulation of miR-202 modulates Mxd1 and Sin3A repressor complexes to induce apoptosis of pancreatic cancer cells.","date":"2015","source":"Cancer biology & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/25611699","citation_count":35,"is_preprint":false},{"pmid":"21440557","id":"PMC_21440557","title":"Solution structure of the mSin3A PAH2-Pf1 SID1 complex: a Mad1/Mxd1-like interaction disrupted by MRG15 in the Rpd3S/Sin3S complex.","date":"2011","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/21440557","citation_count":28,"is_preprint":false},{"pmid":"32681706","id":"PMC_32681706","title":"MAGI2-AS3 suppresses MYC signaling to inhibit cell proliferation and migration in ovarian cancer through targeting miR-525-5p/MXD1 axis.","date":"2020","source":"Cancer medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32681706","citation_count":26,"is_preprint":false},{"pmid":"32071205","id":"PMC_32071205","title":"The MYCL and MXD1 transcription factors regulate the fitness of murine dendritic cells.","date":"2020","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/32071205","citation_count":23,"is_preprint":false},{"pmid":"28543796","id":"PMC_28543796","title":"Mxd1 mediates hypoxia-induced cisplatin resistance in osteosarcoma cells by repression of the PTEN tumor suppressor gene.","date":"2017","source":"Molecular carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/28543796","citation_count":23,"is_preprint":false},{"pmid":"27520398","id":"PMC_27520398","title":"miR-382-5p Controls Hematopoietic Stem Cell Differentiation Through the Downregulation of MXD1.","date":"2016","source":"Stem cells and development","url":"https://pubmed.ncbi.nlm.nih.gov/27520398","citation_count":22,"is_preprint":false},{"pmid":"32053209","id":"PMC_32053209","title":"Inhibition of Myc transcriptional activity by a mini-protein based upon Mxd1.","date":"2020","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/32053209","citation_count":21,"is_preprint":false},{"pmid":"27588137","id":"PMC_27588137","title":"miR-19a/b modulates lung cancer cells metastasis through suppression of MXD1 expression.","date":"2016","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/27588137","citation_count":19,"is_preprint":false},{"pmid":"27588501","id":"PMC_27588501","title":"MXD1 localizes in the nucleolus, binds UBF and impairs rRNA synthesis.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27588501","citation_count":18,"is_preprint":false},{"pmid":"36167790","id":"PMC_36167790","title":"HOXA5 inhibits the proliferation of extrahepatic cholangiocarcinoma cells by enhancing MXD1 expression and activating the p53 pathway.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/36167790","citation_count":17,"is_preprint":false},{"pmid":"33537096","id":"PMC_33537096","title":"Targeting miR-21 with NL101 blocks c-Myc/Mxd1 loop and inhibits the growth of B cell lymphoma.","date":"2021","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/33537096","citation_count":16,"is_preprint":false},{"pmid":"29383100","id":"PMC_29383100","title":"SIRT1 regulates Mxd1 during malignant melanoma progression.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/29383100","citation_count":16,"is_preprint":false},{"pmid":"31635836","id":"PMC_31635836","title":"The MicroRNA-382-5p/MXD1 Axis Relates to Breast Cancer Progression and Promotes Cell Malignant Phenotypes.","date":"2019","source":"The Journal of surgical research","url":"https://pubmed.ncbi.nlm.nih.gov/31635836","citation_count":10,"is_preprint":false},{"pmid":"18155722","id":"PMC_18155722","title":"Elucidation of the structural determinants responsible for the specific formation of heterodimeric Mxd1/Max b-HLH-LZ and its binding to E-box sequences.","date":"2007","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/18155722","citation_count":8,"is_preprint":false},{"pmid":"32794336","id":"PMC_32794336","title":"MXD1 regulates the H9N2 and H1N1 influenza A virus-induced chemokine expression and their replications in human macrophage.","date":"2020","source":"Journal of leukocyte biology","url":"https://pubmed.ncbi.nlm.nih.gov/32794336","citation_count":7,"is_preprint":false},{"pmid":"39819860","id":"PMC_39819860","title":"Targeting MXD1 sensitises pancreatic cancer to trametinib.","date":"2025","source":"Gut","url":"https://pubmed.ncbi.nlm.nih.gov/39819860","citation_count":4,"is_preprint":false},{"pmid":"40303324","id":"PMC_40303324","title":"BARD1-mediated stabilization of METTL14 promotes retinal neovascularization by m6A-modifying MXD1 mRNA on a YTHDF2-dependent manner.","date":"2025","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/40303324","citation_count":4,"is_preprint":false},{"pmid":"40616070","id":"PMC_40616070","title":"Study on the mechanism and clinical value of miR-210-3p and miR-582-5p in acute myocardial infarction by targeting MXD1.","date":"2025","source":"Journal of cardiothoracic surgery","url":"https://pubmed.ncbi.nlm.nih.gov/40616070","citation_count":4,"is_preprint":false},{"pmid":"30419548","id":"PMC_30419548","title":"MXD1 regulates the imatinib resistance of chronic myeloid leukemia cells by repressing BCR-ABL1 expression.","date":"2018","source":"Leukemia research","url":"https://pubmed.ncbi.nlm.nih.gov/30419548","citation_count":1,"is_preprint":false},{"pmid":"40958908","id":"PMC_40958908","title":"Identifying aging-related biomarkers in adipose tissue using integrative bioinformatics and machine-learning approaches: discovery of ELN, MXD1, and FGF21 as key genes.","date":"2025","source":"Frontiers in endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/40958908","citation_count":0,"is_preprint":false},{"pmid":"41632223","id":"PMC_41632223","title":"FTO-dependent m6A Demethylation Activates Mxd1 To Enhance Vitamin D-induced Suppression of Neuroinflammation Via PTEN/AKT/PGC-1α Signaling Pathways in Microglia.","date":"2026","source":"Inflammation","url":"https://pubmed.ncbi.nlm.nih.gov/41632223","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15561,"output_tokens":4693,"usd":0.058539,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12635,"output_tokens":5269,"usd":0.09745,"stage2_stop_reason":"end_turn"},"total_usd":0.155989,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"MXD1 localizes to the nucleolus in multiple cell lines and primary cells (neurons, Sertoli cells), interacts with UBF (confirmed by co-immunoprecipitation and proximity ligation assay), binds transcribed rDNA chromatin and ribosomal intergenic regions (ChIP), and represses rRNA synthesis: siRNA knockdown of MXD1 increases pre-rRNA synthesis while enforced MXD1 expression reduces it.\",\n      \"method\": \"Co-immunoprecipitation, proximity ligation assay, chromatin immunoprecipitation, siRNA knockdown, co-localization imaging\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Co-IP, PLA, ChIP, siRNA KD, overexpression) in a single focused study establishing both localization and functional consequence\",\n      \"pmids\": [\"27588501\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Structural determinants in the leucine zipper of Mxd1 (D112a) and Max (N78a, H81d) dictate specificity of Mxd1/Max heterodimerization and whether the Mxd1/Max/DNA complex forms; heterodimerization must precede DNA binding in vivo.\",\n      \"method\": \"Mutagenesis of leucine zipper residues, DNA-binding assays\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct mutagenesis of key residues with in vitro and in vivo DNA-binding functional readouts in a single dedicated structural/mechanistic study\",\n      \"pmids\": [\"18155722\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The PAH2 domain of mSin3A interacts with the SID1 motif of Pf1 in a manner structurally reminiscent of the Mad1/Mxd1–Sin3 interaction; MRG15 competes with Sin3 for the same Pf1 segment, implying competitive regulation within the Rpd3S/Sin3S complex.\",\n      \"method\": \"NMR solution structure, mutagenesis, competitive binding assays\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure with mutagenesis and functional binding validation; directly characterizes the Mxd1-type SID–Sin3 PAH2 interaction mechanism\",\n      \"pmids\": [\"21440557\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"1,25-dihydroxyvitamin D (1,25D)/VDR signaling enhances MXD1 expression and protein stability while inhibiting c-MYC expression and accelerating its turnover; the E3-ubiquitin ligase FBW7 controls stability of both c-MYC and MXD1, and FBW7 ablation attenuates 1,25D-mediated regulation of their turnover, dramatically altering the ratio of DNA-bound c-MYC vs. MXD1.\",\n      \"method\": \"Cell- and animal-based studies, mathematical modeling, VDR/FBW7 knockdown, protein stability assays, ChIP\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (KD, in vivo mouse, ChIP, stability assays) across cell and animal models, single lab but highly rigorous\",\n      \"pmids\": [\"23112173\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Increased Mxd1 recruits the Sin3A repressor complex via enhanced binding with HDAC-2, resulting in increased HDAC activity and transcriptional repression; Mxd1 represses hTERT mRNA expression through direct binding to the hTERT promoter (confirmed by ChIP), reducing telomerase activity; these effects require Mxd1 dimerization with Max.\",\n      \"method\": \"Co-immunoprecipitation (Mxd1–Sin3A–HDAC-2), HDAC activity assay, ChIP at hTERT promoter, luciferase reporter, western blot\",\n      \"journal\": \"Cancer biology & therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and ChIP in a single lab with functional readouts (HDAC activity, telomerase activity)\",\n      \"pmids\": [\"25611699\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"HIF-1α-induced Mxd1 directly binds E-box sites within the PTEN promoter (confirmed by luciferase reporter and ChIP), repressing PTEN transcription; this suppression activates PI3K/AKT signaling and promotes cisplatin resistance in hypoxic osteosarcoma cells.\",\n      \"method\": \"Luciferase reporter assay, ChIP, siRNA knockdown, western blot, cell viability assay\",\n      \"journal\": \"Molecular carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and reporter assay establishing direct promoter binding, with functional rescue experiments; single lab\",\n      \"pmids\": [\"28543796\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SIRT1 targets the Mxd1 locus in concert with DNMT3B; SIRT1 silencing increases Mxd1 mRNA expression, and DNMT inhibitor 5AzaCdR reverses Mxd1 silencing, indicating that SIRT1-DNMT3B-mediated DNA methylation suppresses Mxd1 expression during melanoma progression.\",\n      \"method\": \"ChIP-seq (SIRT1 binding at Mxd1 locus), Co-immunoprecipitation (SIRT1–DNMT3B), stable SIRT1 knockdown, 5AzaCdR treatment, qPCR\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP-seq plus Co-IP plus pharmacological reversal in single lab; establishes SIRT1/DNMT3B as writers silencing Mxd1\",\n      \"pmids\": [\"29383100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"MXD1 competes with MYC for binding to MAX; the MAGI2-AS3 lncRNA sequesters miR-525-5p, relieving miR-525-5p-mediated repression of MXD1, thereby increasing MXD1 availability to compete with MYC for MAX binding and suppress MYC-driven proliferation in ovarian cancer cells.\",\n      \"method\": \"RNA pull-down, luciferase reporter, western blot, rescue/overexpression assays\",\n      \"journal\": \"Cancer medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, RNA pull-down and reporter assays without direct structural evidence of MXD1–MAX competition in this context\",\n      \"pmids\": [\"32681706\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The SIN3-interacting domain (SID) derived from MXD1 functions as a potent transcriptional repressor domain when fused to dCas9 (CRISPRi), outperforming the KRAB domain in lymphoid cell lines; the SID domain can be fused to the MS2 aptamer-binding protein MCP for doxycycline-regulated CRISPRi.\",\n      \"method\": \"CRISPRi library screen, RT-qPCR, competition assay with GFP-expressing sgRNA constructs, chromatin immunoprecipitation (MYC at lncRNA promoters)\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional CRISPRi screen with independent validation; directly demonstrates SID domain repressor activity in cells\",\n      \"pmids\": [\"32156728\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"A mini-protein (Mad) derived from MXD1 interacts with MAX and with the nucleolar upstream binding factor (UBF), binds E-box DNA in MYC target gene promoters, and represses MYC-mediated transcription; Mad is 10-fold more potent than the MYC inhibitor Omomyc in inhibiting MYC-driven cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation (Mad–MAX, Mad–UBF), E-box DNA-binding assay, cell proliferation assay, transcriptional reporter assay\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and functional assays in single lab; directly demonstrates binding partners and transcriptional repression by MXD1-derived domain\",\n      \"pmids\": [\"32053209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Mxd1 is induced during maturation of Batf3-dependent cDC1 dendritic cells; Mxd1-deficient mature cDC1s exhibit impaired ability to inhibit the MYCL-supported transcriptional program, establishing reciprocal MYCL/MXD1 regulation of biosynthetic gene expression during cDC1 maturation.\",\n      \"method\": \"Mxd1 knockout mice, gene expression profiling, epistasis analysis with Mycl-deficient mice\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined transcriptional phenotype and epistasis, single lab\",\n      \"pmids\": [\"32071205\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"MXD1 directly inhibits the transcriptional activity of the BCR-ABL1 gene promoter (reporter gene assay), reducing BCR-ABL1 mRNA and protein, thereby suppressing proliferation and sensitizing imatinib-resistant CML cells to imatinib.\",\n      \"method\": \"Reporter gene assay, overexpression, western blot, qPCR, cell proliferation assay\",\n      \"journal\": \"Leukemia research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single reporter assay without ChIP confirmation of direct promoter binding\",\n      \"pmids\": [\"30419548\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"MXD1 knockdown in CD34+ hematopoietic stem/progenitor cells mimics miR-382-5p overexpression, promoting granulocyte expansion and impairing megakaryocyte commitment; MXD1 was validated as a direct target of miR-382-5p by luciferase reporter assay.\",\n      \"method\": \"siRNA knockdown of MXD1 in CD34+ HSPCs, luciferase reporter assay, colony assays\",\n      \"journal\": \"Stem cells and development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct KD with defined lineage-commitment phenotype plus reporter validation; single lab\",\n      \"pmids\": [\"27520398\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"MXD1 directly binds the CXCL10 promoter in influenza-infected human macrophages (EMSA), and MXD1 knockdown significantly attenuates H1N1- and H9N2/G1-induced CXCL10 expression; MXD1 knockdown also decreases H9N2 replication but not H1N1 replication; MXD1 induction is dependent on MEK1/2 activation.\",\n      \"method\": \"EMSA, siRNA knockdown, qPCR, viral replication assay, MEK1/2 inhibitor treatment\",\n      \"journal\": \"Journal of leukocyte biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — EMSA plus functional KD with specific readouts; single lab\",\n      \"pmids\": [\"32794336\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"MXD1 protein stability is enhanced by the deubiquitinase USP36, and MXD1 transcription is promoted by up-regulation of the transcription factor c-JUN; MXD1 in turn up-regulates lnc-HZ01 stability via increased m6A RNA methylation, forming a positive feedback loop that promotes EIF4E transcription and inhibits trophoblast cell proliferation.\",\n      \"method\": \"Western blot, co-immunoprecipitation, luciferase reporter, siRNA knockdown, m6A methylation assay\",\n      \"journal\": \"The Science of the total environment\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mechanistic claims about USP36 deubiquitination and c-JUN transcription inferred from western blot/reporter without direct ubiquitination reconstitution\",\n      \"pmids\": [\"33647641\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In trametinib-resistant PDAC, MXD1 acts as a cofactor of the histone methyltransferase MLL1 to increase H3K4 trimethylation at transposable element loci, enhancing chromatin accessibility and transcription of transposable elements, which produces dsRNAs that activate viral mimicry response and downstream oncogenic interferon-stimulated genes.\",\n      \"method\": \"scRNA-seq, ATAC-seq, CUT&TAG, patient-derived xenograft models, MXD1 inhibition experiments\",\n      \"journal\": \"Gut\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal genomic methods (ATAC-seq, CUT&TAG, scRNA-seq) with PDX functional validation; single lab\",\n      \"pmids\": [\"39819860\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"METTL14-mediated m6A modification of MXD1 mRNA is recognized by the m6A reader YTHDF2; this modification alters MXD1 expression, and increased MXD1 modulates VEGFA and VCAM1 expression, promoting retinal neovascularization in an OIR model.\",\n      \"method\": \"MeRIP-seq, RIP assay, dual-luciferase reporter, ChIP-qPCR, METTL14 conditional KO mouse, co-culture angiogenesis assay\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MeRIP-seq plus RIP and in vivo KO with functional readout; single lab\",\n      \"pmids\": [\"40303324\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In microglia, VitD/VDR transcriptionally activates FTO; upregulated FTO reduces m6A methylation on Mxd1 mRNA in a YTHDF2-dependent manner, enhancing Mxd1 mRNA stability and protein expression; increased Mxd1 then binds and represses the PTEN promoter, activating PI3K/AKT and facilitating nuclear translocation of PGC-1α to promote M2 microglial polarization.\",\n      \"method\": \"VDR ChIP at FTO promoter, m6A methylation assay, YTHDF2 knockdown, Mxd1 ChIP at PTEN promoter, luciferase reporter, in vitro and in vivo polarization assays\",\n      \"journal\": \"Inflammation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (ChIP, m6A assay, reporter, KD) in single lab; mechanistic chain includes direct promoter-binding evidence\",\n      \"pmids\": [\"41632223\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MXD1 (MAD1) is a bHLH-LZ transcriptional repressor that heterodimerizes with MAX (heterodimerization preceding DNA binding and requiring specific leucine-zipper residues) to bind E-box sequences and recruit the Sin3A–HDAC corepressor complex via its SID domain, thereby antagonizing MYC–MAX-driven transcription; beyond E-box gene repression, MXD1 uniquely localizes to the nucleolus where it interacts with UBF and binds rDNA chromatin to suppress ribosome biogenesis, and it represses specific target gene promoters (PTEN, hTERT, BCR-ABL1, CXCL10) by direct binding; its activity is regulated post-translationally by FBW7-mediated ubiquitination (shared with MYC), USP36-mediated stabilization, SIRT1/DNMT3B-dependent epigenetic silencing, and m6A modification of its mRNA recognized by YTHDF2, while in context-specific settings MXD1 can act as a cofactor of MLL1 to promote H3K4me3 at transposable elements.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"MXD1 is a bHLH-LZ transcriptional repressor that antagonizes MYC-driven gene programs by heterodimerizing with MAX and competing with MYC for the shared MAX partner [#7, #9]. Heterodimerization with MAX is governed by defined leucine-zipper residues and must precede DNA binding, after which the MXD1/MAX complex engages E-box elements [#1]. Repression is executed through the MXD1 SIN3-interacting domain (SID), which recruits the Sin3A corepressor and HDAC-2 to increase histone deacetylase activity at target loci; the isolated SID is a potent portable repressor domain in synthetic CRISPRi contexts [#4, #8]. Through MAX-dependent E-box binding, MXD1 directly represses specific promoters including hTERT, PTEN, BCR-ABL1, and CXCL10, with functional consequences for telomerase activity, PI3K/AKT signaling, and inflammatory and oncogenic outputs [#4, #5, #11, #13]. Beyond E-box gene repression, MXD1 localizes to the nucleolus, interacts with UBF, binds rDNA chromatin, and suppresses pre-rRNA synthesis, coupling it to control of ribosome biogenesis [#0, #9]. MXD1 abundance is heavily regulated post-translationally and post-transcriptionally: FBW7 controls its turnover in parallel with MYC under 1,25D/VDR signaling, USP36 deubiquitination stabilizes it, SIRT1/DNMT3B-mediated DNA methylation silences its locus, and m6A modification of MXD1 mRNA read by YTHDF2 tunes its expression [#3, #6, #14, #16, #17]. In context-specific settings MXD1 acts as a cofactor of the methyltransferase MLL1 to deposit H3K4me3 at transposable elements, linking it to chromatin accessibility and a viral-mimicry response [#15].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established the structural logic of MXD1 function by defining which leucine-zipper residues dictate MXD1/MAX heterodimer specificity and showing heterodimerization is obligatory before DNA binding.\",\n      \"evidence\": \"Mutagenesis of leucine-zipper residues with in vitro and in vivo DNA-binding readouts\",\n      \"pmids\": [\"18155722\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not address how heterodimer choice is regulated in vivo\", \"No structure of the full repressive complex on chromatin\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Characterized the MXD1-type SID–Sin3 PAH2 interaction and revealed competitive regulation within Sin3-class corepressor assemblies, clarifying how SID engages the repressor machinery.\",\n      \"evidence\": \"NMR solution structure, mutagenesis, and competitive binding assays (Pf1/MRG15 system)\",\n      \"pmids\": [\"21440557\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural work on a related SID-bearing protein rather than MXD1 directly\", \"Does not quantify MXD1 SID affinity in cells\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Showed that MXD1 and MYC share the FBW7 ubiquitin ligase and are reciprocally regulated by 1,25D/VDR, explaining how upstream signals reset the DNA-bound MYC:MXD1 ratio.\",\n      \"evidence\": \"Cell and mouse studies with VDR/FBW7 knockdown, protein stability assays, ChIP, and mathematical modeling\",\n      \"pmids\": [\"23112173\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define FBW7 phosphodegron on MXD1 directly\", \"Tissue specificity of this regulation not mapped\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Connected MXD1 corepressor recruitment to a defined target output by showing MXD1–Sin3A–HDAC-2 assembly represses hTERT via direct promoter binding in a MAX-dimerization-dependent manner.\",\n      \"evidence\": \"Reciprocal Co-IP, HDAC activity assay, ChIP at hTERT promoter, luciferase reporter\",\n      \"pmids\": [\"25611699\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Generality of HDAC-2 selectivity across MXD1 targets unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined a non-canonical nucleolar role: MXD1 binds UBF and rDNA chromatin to repress rRNA synthesis, extending its function beyond classic E-box gene repression to ribosome biogenesis.\",\n      \"evidence\": \"Co-IP, proximity ligation assay, ChIP at rDNA, siRNA knockdown, and overexpression in multiple cell types\",\n      \"pmids\": [\"27588501\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether MAX is required for nucleolar localization is not resolved\", \"Mechanism of UBF-directed recruitment to rDNA undefined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Linked MXD1 dosage to hematopoietic lineage decisions, showing its knockdown skews CD34+ progenitors toward granulocytes at the expense of megakaryocytes and identifying it as a miR-382-5p target.\",\n      \"evidence\": \"siRNA knockdown in CD34+ HSPCs, colony assays, luciferase reporter validation\",\n      \"pmids\": [\"27520398\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Transcriptional targets driving lineage skew not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Extended the MXD1 target repertoire to PTEN, showing HIF-1α-induced MXD1 binds PTEN E-boxes to derepress PI3K/AKT and drive chemoresistance.\",\n      \"evidence\": \"Luciferase reporter, ChIP, siRNA knockdown, cell viability assays in hypoxic osteosarcoma\",\n      \"pmids\": [\"28543796\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"MAX-dependence of PTEN binding not directly tested here\", \"Single context\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identified an epigenetic silencing mechanism whereby SIRT1 acting with DNMT3B methylates the MXD1 locus to suppress its expression during melanoma progression.\",\n      \"evidence\": \"ChIP-seq, SIRT1–DNMT3B Co-IP, SIRT1 knockdown, 5AzaCdR pharmacological reversal, qPCR\",\n      \"pmids\": [\"29383100\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific methylated CpGs not mapped\", \"Generality beyond melanoma untested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Proposed MXD1 repression of the BCR-ABL1 promoter as a route to imatinib re-sensitization in CML.\",\n      \"evidence\": \"Reporter gene assay, overexpression, qPCR, proliferation assays\",\n      \"pmids\": [\"30419548\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No ChIP confirmation of direct promoter binding\", \"Single lab, single assay class\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstrated MXD1 competes with MYC for MAX and that this balance is tuned by a lncRNA/miRNA axis to suppress MYC-driven proliferation.\",\n      \"evidence\": \"RNA pull-down, luciferase reporter, rescue/overexpression in ovarian cancer cells\",\n      \"pmids\": [\"32681706\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct structural evidence of MXD1–MAX competition in this context\", \"Single lab\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Validated the MXD1 SID as a portable, potent repressor domain, providing functional proof that SID drives transcriptional silencing in cells beyond KRAB.\",\n      \"evidence\": \"dCas9-SID CRISPRi library screen, RT-qPCR, competition assays, MYC ChIP at lncRNA promoters\",\n      \"pmids\": [\"32156728\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Synthetic context; does not measure endogenous MXD1 occupancy\", \"Corepressor recruitment by fused SID not directly mapped\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed an MXD1-derived mini-protein engages both MAX and UBF and binds E-box promoters, recapitulating dual transcriptional and potentially nucleolar inhibition of MYC with high potency.\",\n      \"evidence\": \"Co-IP (Mad–MAX, Mad–UBF), E-box binding assay, proliferation and reporter assays\",\n      \"pmids\": [\"32053209\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Engineered mini-protein, not full-length endogenous MXD1\", \"Single lab\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Established a physiological MYCL/MXD1 antagonism, where induced Mxd1 restrains the MYCL biosynthetic program during cDC1 dendritic cell maturation.\",\n      \"evidence\": \"Mxd1 knockout mice, expression profiling, epistasis with Mycl-deficient mice\",\n      \"pmids\": [\"32071205\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct Mxd1 target genes in cDC1 not enumerated\", \"Single lab\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Implicated MXD1 in antiviral transcription by showing it binds the CXCL10 promoter and is required for influenza-induced CXCL10, with MEK1/2-dependent induction.\",\n      \"evidence\": \"EMSA, siRNA knockdown, qPCR, viral replication assay, MEK inhibitor treatment in macrophages\",\n      \"pmids\": [\"32794336\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How a repressor drives CXCL10 induction mechanistically unresolved\", \"Strain-specific replication effects unexplained\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Placed MXD1 in a regulatory feedback loop involving USP36 stabilization, c-JUN-driven transcription, and m6A-dependent lncRNA control affecting trophoblast proliferation.\",\n      \"evidence\": \"Western blot, Co-IP, luciferase reporter, m6A assay, siRNA knockdown\",\n      \"pmids\": [\"33647641\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"USP36 deubiquitination of MXD1 not reconstituted directly\", \"Single lab, correlational mechanistic chain\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealed a chromatin-activating role distinct from canonical repression: MXD1 partners with MLL1 to deposit H3K4me3 at transposable elements, triggering viral mimicry in drug-resistant PDAC.\",\n      \"evidence\": \"scRNA-seq, ATAC-seq, CUT&TAG, PDX models, MXD1 inhibition\",\n      \"pmids\": [\"39819860\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How MXD1 switches from Sin3-repression to MLL1-coactivation unknown\", \"Direct MXD1–MLL1 interaction not biochemically resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined m6A control of MXD1 mRNA via METTL14 writing and YTHDF2 reading, linking MXD1 dosage to VEGFA/VCAM1 and pathological retinal neovascularization.\",\n      \"evidence\": \"MeRIP-seq, RIP, dual-luciferase, ChIP-qPCR, METTL14 conditional KO mouse, angiogenesis co-culture\",\n      \"pmids\": [\"40303324\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direction of YTHDF2 effect on MXD1 stability not fully reconciled across studies\", \"Single tissue context\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected VitD/VDR signaling to an FTO/YTHDF2 m6A axis that stabilizes Mxd1, which then represses PTEN to activate PI3K/AKT and drive M2 microglial polarization.\",\n      \"evidence\": \"VDR ChIP at FTO, m6A assay, YTHDF2 knockdown, Mxd1 ChIP at PTEN, reporter and polarization assays in vitro and in vivo\",\n      \"pmids\": [\"41632223\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reconciliation of m6A removal (FTO) increasing stability with YTHDF2 dependence\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How MXD1 is partitioned between its canonical MAX/Sin3-HDAC repressive function, its nucleolar UBF/rDNA role, and its MLL1-associated coactivator role at transposable elements remains mechanistically unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No model explains the repressor-to-coactivator switch\", \"Determinants of nucleolar versus nucleoplasmic targeting unknown\", \"Genome-wide endogenous MXD1 occupancy not integrated across contexts\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 4, 5, 8, 9]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [1, 5, 9, 13]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [4, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0, 9]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 4, 5, 8]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [4, 15]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"Sin3A-HDAC corepressor complex\",\n      \"MXD1/MAX heterodimer\"\n    ],\n    \"partners\": [\n      \"MAX\",\n      \"SIN3A\",\n      \"HDAC2\",\n      \"UBF\",\n      \"MLL1\",\n      \"FBW7\",\n      \"USP36\",\n      \"YTHDF2\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}