{"gene":"SMYD3","run_date":"2026-04-28T20:42:08","timeline":{"discoveries":[{"year":2004,"finding":"SMYD3 SET domain possesses histone H3-lysine 4 (H3K4)-specific methyltransferase activity, which is enhanced by heat-shock protein HSP90A; SMYD3 forms a complex with RNA polymerase II through interaction with the RNA helicase HELZ and binds to a 5'-CCCTCC-3' promoter motif to transactivate downstream genes.","method":"In vitro methyltransferase assay, Co-immunoprecipitation, promoter binding assay, siRNA knockdown with proliferation readout","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 1–2 — original discovery with in vitro enzymatic assay, Co-IP of complex, and functional KD; highly cited foundational paper","pmids":["15235609"],"is_preprint":false},{"year":2014,"finding":"SMYD3 methylates MAP3K2 (MEKK2) at lysine 260, potentiating Ras/Raf/MEK/ERK signaling; methylation of MAP3K2 blocks binding of the PP2A phosphatase complex (a negative regulator of the MAP kinase pathway), thereby increasing ERK activation and promoting Ras-driven pancreatic and lung carcinomas.","method":"Protein array substrate identification, in vitro methyltransferase assay, Co-IP, mouse cancer models (KRAS-driven pancreatic and lung adenocarcinoma), catalytic mutant SMYD3, MEK inhibitor synergy","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods (array, in vitro assay, mouse models, mechanistic epistasis), replicated and highly cited","pmids":["24847881"],"is_preprint":false},{"year":2007,"finding":"SMYD3 methylates vascular endothelial growth factor receptor 1 (VEGFR1) at lysine 831 in its kinase domain, and this methylation enhances VEGFR1 kinase activity in cells.","method":"In vitro methyltransferase assay, mass spectrometry identification of methylated residue, cell-based kinase activity assay","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro assay with site identification and cellular functional readout, single lab","pmids":["18006819"],"is_preprint":false},{"year":2012,"finding":"SMYD3 catalyzes mono- and di-methylation of histone H4 at lysine 5 (H4K5me), a mark detectable in diverse cell types whose formation is attenuated by SMYD3 depletion; SMYD3-driven cancer cell phenotypes require its enzymatic activity.","method":"In vitro methyltransferase assay, mass spectrometry, siRNA knockdown with H4K5me detection, cell phenotype assays","journal":"Epigenetics","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro enzymatic assay with MS confirmation and functional link to enzymatic activity","pmids":["22419068"],"is_preprint":false},{"year":2011,"finding":"Crystal structure of full-length human SMYD3 in complex with S-adenosyl-L-homocysteine at 2.8 Å resolution revealed a C-terminal tetratricopeptide repeat (TPR) domain that together with the SET and post-SET domains forms the substrate binding pocket; Tyr239 hydroxyl group is critical for enzymatic activity; DNA binding stimulates SMYD3 histone methyltransferase activity, possibly mediated via the MYND domain.","method":"X-ray crystallography, mutagenesis of active site residues, in vitro histone methyltransferase assay, DNA binding biochemical assay","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with mutagenesis and biochemical validation","pmids":["21266482"],"is_preprint":false},{"year":2007,"finding":"Cleavage of the N-terminal 34 amino acids of SMYD3 in cancer cells produces a form with higher histone methyltransferase activity; substitution of conserved glycines 15 and 17 also enhances activity; the N-terminal region mediates association with HSP90α, whose binding modulates enzymatic activity.","method":"Protein biochemistry, N-terminal sequencing, site-directed mutagenesis, in vitro methyltransferase assay, Co-immunoprecipitation with HSP90α","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — mutagenesis and in vitro assay with Co-IP; single lab","pmids":["17998933"],"is_preprint":false},{"year":2009,"finding":"SMYD3 functions as a coactivator of estrogen receptor alpha (ERα) by directly interacting with the ERα ligand-binding domain; upon estrogen induction, SMYD3 is recruited to ER target gene promoters and is responsible for accumulation of H3K4me2/3, which is required for ER-regulated gene transcription.","method":"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), siRNA knockdown with gene expression readout, domain mapping","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal Co-IP, ChIP, and functional KD; single lab","pmids":["19509295"],"is_preprint":false},{"year":2013,"finding":"SMYD3 recruits the bromodomain protein BRD4 to myostatin and c-Met gene regulatory regions through protein-protein interaction; this promotes engagement of the pause-release factor p-TEFb and elongation of Ser2-phosphorylated RNA Pol II, driving transcription; reducing SMYD3 decreases myostatin and c-Met transcription and protects against glucocorticoid-induced myotube atrophy in vivo.","method":"Co-immunoprecipitation, ChIP, siRNA/shRNA knockdown, mouse model of dexamethasone-induced atrophy","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, ChIP, in vivo mouse model with clean phenotype; multiple orthogonal methods","pmids":["23752591"],"is_preprint":false},{"year":2015,"finding":"SMYD3 interacts with PC4 (human positive coactivator 4) and cooperates with it to drive expression of proliferation- and invasion-linked genes; PC4 depletion abolishes SMYD3-mediated H3K4me3 and target gene expression; SMYD3 and PC4 recruit each other to target genes in a mutually dependent manner.","method":"Co-immunoprecipitation, ChIP, siRNA knockdown, artificial tethering with catalytic mutant","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP, ChIP, and functional depletion; single lab but multiple orthogonal methods","pmids":["26350217"],"is_preprint":false},{"year":2016,"finding":"SMYD3 methylates histone H2A.Z.1 at lysine 101 (H2A.Z.1K101me2), stabilizing H2A.Z.1 by preventing binding of the removal chaperone ANP32E and facilitating interaction with histone H3; SMYD3/H2A.Z.1K101me2 co-localizes at the cyclin A1 promoter, activates cyclin A1 expression, and promotes G1-S cell cycle progression and tumor formation.","method":"In vitro methyltransferase assay, Co-immunoprecipitation, ChIP, mutagenesis of K101, microarray, mouse tumor model","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro assay, mutagenesis, ChIP, and in vivo mouse model; multiple orthogonal methods","pmids":["27569210"],"is_preprint":false},{"year":2016,"finding":"Co-crystal structures of SMYD3 with VEGFR1 and MAP3K2 peptides revealed that MAP3K2 is a robust substrate due to a phenylalanine at the -2 position fitting a shallow hydrophobic pocket; VEGFR1 is a weaker substrate because the acceptor lysine is buried in the folded kinase domain, requiring drastic conformational rearrangement.","method":"X-ray co-crystallography, in vitro kinetic/biochemical assays, mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — co-crystal structures with biochemical validation of substrate preference determinants","pmids":["26929412"],"is_preprint":false},{"year":2016,"finding":"Co-crystal structure of SMYD3 with a MEKK2-peptide substrate and a SAM-competitive inhibitor (GSK2807, Ki = 14 nM) showed the inhibitor bridges the SAM-binding pocket and the substrate lysine tunnel; SMYD3 follows a partially processive methylation mechanism.","method":"X-ray crystallography (co-crystal with peptide substrate and inhibitor), kinetic characterization, biochemical inhibitor assays","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 — high-resolution co-crystal structure with kinetic mechanistic characterization","pmids":["27066749"],"is_preprint":false},{"year":2016,"finding":"SMYD3 interacts with H3K4me3-modified histone tails, facilitating its recruitment to core promoter regions of active genes; Smyd3 binding correlates with increased RNA polymerase II density and is required for chemically induced liver and colon cancer formation in mice.","method":"ChIP-seq, Smyd3 knockout mouse model with chemical carcinogenesis, Co-immunoprecipitation with H3K4me3","journal":"Cancer cell","confidence":"High","confidence_rationale":"Tier 2 — in vivo knockout mouse model with carcinogenesis phenotype, genome-wide ChIP-seq; multiple orthogonal methods","pmids":["26908355"],"is_preprint":false},{"year":2016,"finding":"SMYD3 methylates AKT1 at lysine 14 in its PH domain; this methylation is required for AKT1 plasma membrane accumulation and for phosphorylation at threonine 308; K14-substituted AKT1 shows reduced membrane localization and lower growth-promoting activity.","method":"In vitro methyltransferase assay, Co-immunoprecipitation, site-directed mutagenesis, subcellular fractionation/imaging, SMYD3 KD and inhibitor treatment","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro assay with mutagenesis, cellular localization, and functional readout; single lab","pmids":["27626683"],"is_preprint":false},{"year":2017,"finding":"SMYD3 trimethylates HER2 at lysine 175; this methylation promotes HER2 homodimerization; K175A substitution reduces homodimer formation and autophosphorylation; SMYD3 knockdown attenuates HER2 autophosphorylation in breast cancer cells.","method":"In vitro methyltransferase assay, Co-immunoprecipitation, site-directed mutagenesis, siRNA knockdown with phosphorylation readout","journal":"Cancer medicine","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro assay, mutagenesis, Co-IP, and cellular functional readout; single lab","pmids":["28639750"],"is_preprint":false},{"year":2019,"finding":"SMYD3 directly interacts with SMAD3 and is required for SMAD3 association to chromatin at EMT gene regulatory regions in TGFβ-induced epithelial-mesenchymal transition; SMYD3 is dispensable for SMAD2/3 phosphorylation and nuclear translocation but is essential for SMAD3 chromatin binding.","method":"Co-immunoprecipitation, ChIP, SMYD3 knockdown and pharmacological inhibition (BCI121), zebrafish xenograft invasion model","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP, ChIP, KD with clean mechanistic dissection; single lab","pmids":["30544196"],"is_preprint":false},{"year":2015,"finding":"The C-terminal TPR-like domain of SMYD3 mediates physical interaction with HSP90; this interaction is essential for basal SMYD3 histone methyltransferase activity; loss of SMYD3-HSP90 interaction causes SMYD3 mislocalization within the nucleus (loss of chromatin association), reducing cell proliferation.","method":"Co-immunoprecipitation, domain deletion/mutagenesis, in vitro methyltransferase assay, subcellular localization assay (immunofluorescence/fractionation), cell proliferation assay","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP with domain mapping, enzymatic assay, and localization with functional consequence; single lab","pmids":["25738358"],"is_preprint":false},{"year":2010,"finding":"SMYD3 interacts with HTLV-1 Tax protein via the C-terminal 180 amino acids of SMYD3; SMYD3 dominates the subcellular localization of Tax, tethering it to the cytoplasm, which enhances Tax-mediated NF-κB activation; SMYD3 knockdown attenuates this NF-κB activation.","method":"Co-immunoprecipitation, in vitro pull-down, colocalization (confocal microscopy), reporter gene assay, shRNA knockdown","journal":"Cancer science","confidence":"Medium","confidence_rationale":"Tier 2–3 — reciprocal Co-IP, pull-down, localization with functional consequence; single lab","pmids":["21054678"],"is_preprint":false},{"year":2014,"finding":"SMYD3 interacts with HCV NS5A protein via the MYND domain of SMYD3 and domain III of NS5A; SMYD3 overexpression decreases intracellular and extracellular HCV titers without affecting viral RNA replication, indicating SMYD3 negatively affects virus particle production in an NS5A-dependent manner.","method":"Co-immunoprecipitation, colocalization, mutational analysis (domain mapping), viral titer assay","journal":"Virology","confidence":"Medium","confidence_rationale":"Tier 2–3 — Co-IP with domain mutagenesis and functional viral production readout; single lab","pmids":["25092459"],"is_preprint":false},{"year":2019,"finding":"SMYD3 interacts directly with p53 via its post-SET domain; SMYD3 promotes p53 translocation from nucleus to cytoplasm and ubiquitination (independent of MDM2), forming a complex with UBE2R2 (an E2 ubiquitin-conjugating enzyme); SMYD3 ubiquitinates p53 at lysines 381, 382, and 386.","method":"Co-immunoprecipitation, mass spectrometry identification of UBE2R2, domain mapping (post-SET), ubiquitination assay, site-directed mutagenesis of p53 K381/382/386","journal":"Carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 2–3 — Co-IP, domain mapping, and ubiquitination assay with site identification; single lab","pmids":["31002112"],"is_preprint":false},{"year":2020,"finding":"ATM phosphorylates SMYD3, enabling formation of a multiprotein complex of ATM, SMYD3, CHK2, and BRCA2 required for RAD51 loading at DNA double-strand break sites and completion of homologous recombination (HR); pharmacological SMYD3 inhibition sensitizes HR-proficient cancer cells to PARP inhibitors.","method":"Co-immunoprecipitation, use of ATM phosphorylation-deficient SMYD3 mutant variant, RAD51 focus formation assay, PARP inhibitor sensitivity assay","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP of multiprotein complex, functional mutagenesis, and pharmacological validation; single lab","pmids":["33205017"],"is_preprint":false},{"year":2022,"finding":"SMYD3 methylates RNF113A, and this methylation impairs RNF113A interaction with the phosphatase PP4, controlling RNF113A phosphorylation levels; this cross-talk (methylation-phosphorylation) promotes RNF113A E3 ligase activity essential for the alkylation damage response, conferring SCLC resistance to alkylating chemotherapy; SMYD3 inhibition restores SCLC sensitivity.","method":"In vitro methyltransferase assay, Co-immunoprecipitation, phosphorylation assays, RNF113A ubiquitin ligase activity assay, SMYD3 inhibitor treatment in SCLC cells","journal":"Cancer discovery","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro methyltransferase assay, mechanistic dissection of PTM cross-talk, and functional cellular/pharmacological validation; strong mechanistic data","pmids":["35819319"],"is_preprint":false},{"year":2023,"finding":"SMYD3 binds to and regulates transcription of UHRF1; UHRF1 (a reader of H3K9me3) recruits DNMT1 to silence immune-related gene promoters; SMYD3 additionally deposits H4K20me3 at intragenic regions of immune-related genes to maintain their repression; SMYD3 depletion upregulates type I interferon response genes and increases CD8+ T cell infiltration, sensitizing tumors to anti-PD-1 therapy.","method":"ChIP-seq, siRNA/shRNA knockdown, gene expression analysis, in vivo mouse tumor model with anti-PD-1 treatment, H4K20me3 ChIP","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP-seq, in vivo model, and mechanistic epistasis; single lab","pmids":["37463106"],"is_preprint":false},{"year":2023,"finding":"SMYD3 methylates MAP3K2 in prostate cancer cells, promoting epithelial-mesenchymal transition-associated behaviors by altering vimentin abundance; SMYD3-MAP3K2 signaling creates a positive feedback loop that sustains high SMYD3 levels; catalytic mutant SMYD3 fails to promote these phenotypes.","method":"In vitro methyltransferase assay, catalytic mutant SMYD3, mouse xenograft models, vimentin western blot, EMT assays","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro assay, catalytic mutant, in vivo xenograft; single lab","pmids":["37976356"],"is_preprint":false},{"year":2022,"finding":"SMYD3 binds to and stabilizes HIF1α (independent of its methyltransferase activity and independent of prolyl hydroxylase/VHL pathways), enhancing HIF1α transcriptional activity under hypoxia; SMYD3 promotes reactive oxygen species accumulation and hypoxia-induced apoptosis; smyd3-null zebrafish exhibit higher hypoxia tolerance.","method":"Co-immunoprecipitation, western blot stability assay, enzymatic-dead mutant, zebrafish knockout model, reporter assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP, catalytic mutant establishing non-enzymatic mechanism, in vivo zebrafish model; single lab","pmids":["36273580"],"is_preprint":false},{"year":2020,"finding":"SMYD3 binds to the promoter of PARP16 and increases H3K4me3 at this locus to activate PARP16 transcription; PARP16 in turn ADP-ribosylates PERK and IRE1α to promote unfolded protein response (UPR) and vascular smooth muscle cell proliferation; SMYD3-PARP16 axis mediates neointimal hyperplasia after vascular injury.","method":"ChIP-seq, ChIP-qPCR, Co-immunoprecipitation, SMYD3/PARP16 knockdown, ADP-ribosylation assay, mouse vascular injury model","journal":"Acta pharmaceutica Sinica. B","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP-seq, biochemical assay, in vivo model; single lab","pmids":["34094832"],"is_preprint":false},{"year":2023,"finding":"In Alzheimer's disease/tauopathy context, elevated Smyd3 upregulates Fbxo2 (an E3 ubiquitin ligase) via H3K4me3 at the Fbxo2 promoter; Fbxo2 promotes NR1 (NMDAR subunit) ubiquitination and degradation; pharmacological Smyd3 inhibition (BCI-121) rescues NMDAR function and cognitive deficits in P301S Tau mice.","method":"ChIP, western blot of H3K4me3, Smyd3 inhibitor treatment, Fbxo2 knockdown rescue, electrophysiology, behavioral assays in mouse model","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP, mechanistic epistasis (Fbxo2 KD rescue), in vivo mouse model; single lab","pmids":["36609445"],"is_preprint":false},{"year":2018,"finding":"SMYD3 interacts with ANKHD1 (identified by mass spectrometry of H3K4me3 pulldown); ANKHD1 binds H3K4me3 in SMYD3-overexpressing cells and is required for SMYD3-mediated SLUG gene activation (via H3K4me3, H3K9Ac, H3K14Ac); ANKHD1 knockdown attenuates SMYD3-dependent HCC migration and invasion.","method":"Mass spectrometry, Co-immunoprecipitation, ChIP, EMSA, luciferase reporter, siRNA knockdown","journal":"Journal of experimental & clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2–3 — MS identification, Co-IP, ChIP; single lab","pmids":["30646949"],"is_preprint":false},{"year":2020,"finding":"SMYD3 nuclear-cytoplasmic distribution is regulated by cell geometry (shape and aspect ratio) in myoblasts via acto-myosin cytoskeleton; elongated cell geometries reduce SMYD3 nuclear import; cytoskeletal acto-myosin drugs induce SMYD3 nuclear accumulation; SMYD3 redistribution correlates with changes in trimethylation (Kme3) but not dimethylation levels.","method":"Live-cell imaging, pharmacological cytoskeletal perturbation, subcellular fractionation, immunofluorescence in micropatterned cells","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2–3 — direct localization experiment with functional consequence (Kme3 levels); single lab","pmids":["33244033"],"is_preprint":false},{"year":2019,"finding":"SMYD3 is recruited by Ebola virus nucleoprotein (NP) to viral inclusion bodies; SMYD3 depletion suppresses EBOV mRNA production; SMYD3 promotes NP-VP30 interaction in a dose-dependent manner, thereby facilitating viral mRNA transcription.","method":"Co-immunoprecipitation, mass spectrometry (NP pulldown), minigenome replication system, siRNA knockdown with mRNA quantification","journal":"Emerging microbes & infections","confidence":"Medium","confidence_rationale":"Tier 2–3 — Co-IP, MS identification, functional KD; single lab","pmids":["31516086"],"is_preprint":false},{"year":2021,"finding":"SMYD3 directly binds to the Cdkn1a (p21) promoter and increases H3K4me3 levels there, elevating p21 expression and driving senescence-associated phenotypes in endothelial cells; Smyd3 knockout mice are protected from Angiotensin II-induced vascular senescence.","method":"ChIP, Smyd3 knockout mouse model, siRNA knockdown, SMYD3 overexpression, Smyd3 inhibitor treatment","journal":"Aging cell","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP, in vivo mouse model, and pharmacological confirmation; single lab","pmids":["32779886"],"is_preprint":false}],"current_model":"SMYD3 is a multifunctional SET-domain lysine methyltransferase that methylates multiple histone (H3K4, H4K5, H4K20, H2A.Z.1-K101) and non-histone substrates (MAP3K2-K260, VEGFR1-K831, AKT1-K14, HER2-K175, RNF113A) to regulate gene transcription, cytoplasmic kinase signaling (Ras/MEK/ERK via MAP3K2 methylation that blocks PP2A binding), DNA damage response (via ATM-dependent complex with BRCA2/CHK2 for homologous recombination), and protein stability (HIF1α, p53); its activity is enhanced by HSP90A interaction with its TPR-like C-terminal domain, and its nuclear-cytoplasmic distribution is regulated by cell geometry and cytoskeletal tension."},"narrative":{"teleology":[{"year":2004,"claim":"The foundational question of SMYD3's enzymatic identity was resolved: it is an H3K4-specific methyltransferase whose activity is enhanced by HSP90A, and it associates with RNA Pol II via HELZ to transactivate target genes, establishing it as a transcription-coupled chromatin modifier.","evidence":"In vitro methyltransferase assay, Co-IP, promoter binding assay, and siRNA knockdown in cancer cell lines","pmids":["15235609"],"confidence":"High","gaps":["HSP90A stimulation mechanism not structurally resolved","direct versus indirect nature of RNA Pol II association unclear","full substrate specificity unknown"]},{"year":2007,"claim":"SMYD3 was shown to methylate the non-histone substrate VEGFR1 at K831, extending its activity beyond chromatin and suggesting it regulates receptor tyrosine kinase signaling; separately, N-terminal processing and HSP90α interaction were shown to modulate enzymatic output.","evidence":"In vitro methyltransferase assay with mass spectrometry site identification; N-terminal sequencing and mutagenesis with Co-IP","pmids":["18006819","17998933"],"confidence":"Medium","gaps":["VEGFR1 methylation not validated in vivo","physiological relevance of N-terminal cleavage unclear","structural basis for HSP90-mediated activation unknown"]},{"year":2009,"claim":"SMYD3 was established as a nuclear coactivator of estrogen receptor α, linking its H3K4 methyltransferase activity to hormone-regulated transcription programs.","evidence":"Co-IP of SMYD3–ERα, ChIP at ER target genes, siRNA knockdown with transcriptional readout","pmids":["19509295"],"confidence":"Medium","gaps":["whether SMYD3 methylates ERα directly not tested","contribution relative to other H3K4 methyltransferases at ER targets undetermined"]},{"year":2011,"claim":"The crystal structure of full-length SMYD3 revealed how the C-terminal TPR domain, SET domain, and post-SET domain cooperate to form the substrate binding cleft, and identified Tyr239 as catalytically essential; DNA binding through the MYND domain was shown to stimulate methyltransferase activity.","evidence":"2.8 Å X-ray crystallography, active-site mutagenesis, in vitro histone methyltransferase and DNA-binding assays","pmids":["21266482"],"confidence":"High","gaps":["no co-crystal with histone peptide substrate","how DNA binding allosterically activates catalysis not resolved"]},{"year":2012,"claim":"H4K5 was identified as an additional histone substrate, broadening SMYD3's chromatin-modifying repertoire beyond H3K4 and linking its enzymatic activity to cancer cell phenotypes.","evidence":"In vitro methyltransferase assay with mass spectrometry, siRNA knockdown with H4K5me detection","pmids":["22419068"],"confidence":"High","gaps":["genomic distribution of SMYD3-dependent H4K5me not mapped","whether H4K5me is functionally distinct from H3K4me at SMYD3 targets unknown"]},{"year":2013,"claim":"The mechanism of SMYD3-driven transcriptional elongation was elucidated: SMYD3 recruits BRD4 and the p-TEFb pause-release factor to gene regulatory regions, promoting Ser2-phosphorylated Pol II elongation, with in vivo relevance in glucocorticoid-induced muscle atrophy.","evidence":"Co-IP of SMYD3–BRD4, ChIP for elongation marks, shRNA knockdown, mouse dexamethasone-atrophy model","pmids":["23752591"],"confidence":"High","gaps":["whether SMYD3 methylates BRD4 directly not tested","precise recruitment order of SMYD3 versus BRD4 undetermined"]},{"year":2014,"claim":"A major cytoplasmic function was defined: SMYD3 methylates MAP3K2 at K260 to block PP2A binding, amplifying Ras-ERK signaling and driving Ras-dependent tumorigenesis — establishing SMYD3 as a bona fide oncogenic signaling regulator outside the nucleus.","evidence":"Protein array substrate screen, in vitro methyltransferase assay, Co-IP, KRAS-driven mouse pancreatic and lung cancer models, catalytic mutant and MEK inhibitor epistasis","pmids":["24847881"],"confidence":"High","gaps":["whether additional MAP kinase pathway kinases are SMYD3 substrates unknown","signals governing SMYD3 nuclear versus cytoplasmic partitioning not defined"]},{"year":2015,"claim":"The HSP90–TPR domain interaction was mapped as essential for SMYD3 chromatin association and basal enzymatic activity; separately, the transcriptional coactivator PC4 was identified as a co-dependent partner for SMYD3-mediated H3K4me3 at target genes.","evidence":"Domain deletion/mutagenesis with Co-IP and subcellular fractionation; Co-IP and ChIP for PC4–SMYD3 co-occupancy","pmids":["25738358","26350217"],"confidence":"Medium","gaps":["whether HSP90 acts as an allosteric activator or a folding chaperone for SMYD3 not distinguished","PC4 interaction not confirmed by independent group"]},{"year":2016,"claim":"Multiple advances converged: structural co-crystals with MAP3K2 and VEGFR1 peptides explained substrate preference determinants; H2A.Z.1-K101 methylation was discovered to stabilize H2A.Z.1 at promoters driving cell cycle progression; SMYD3 was found to read H3K4me3 and recruit Pol II genome-wide; and AKT1-K14 methylation was linked to AKT membrane localization.","evidence":"Co-crystallography with kinetic validation; in vitro methyltransferase assays; ChIP-seq and Smyd3-knockout mice in chemical carcinogenesis; subcellular fractionation of methylated AKT1","pmids":["26929412","27066749","27569210","26908355","27626683"],"confidence":"High","gaps":["physiological significance of AKT1-K14 methylation confirmed only in cell lines","relative contribution of SMYD3's histone versus non-histone activities to tumorigenesis not separated in vivo"]},{"year":2017,"claim":"SMYD3 was shown to trimethylate HER2-K175, promoting receptor homodimerization and autophosphorylation, adding another receptor tyrosine kinase to its non-histone substrate portfolio.","evidence":"In vitro methyltransferase assay, K175A mutagenesis reducing dimerization, siRNA knockdown in breast cancer cells","pmids":["28639750"],"confidence":"Medium","gaps":["HER2 methylation not validated in vivo","structural basis for how K175 methylation promotes dimerization unknown"]},{"year":2019,"claim":"Three new functional axes were defined: SMYD3 facilitates SMAD3 chromatin binding during TGFβ-driven EMT; promotes p53 cytoplasmic translocation and MDM2-independent ubiquitination via UBE2R2; and is recruited by Ebola virus NP to enhance viral mRNA transcription.","evidence":"Co-IP and ChIP for SMAD3 with SMYD3 inhibitor; Co-IP of SMYD3–p53–UBE2R2 with ubiquitination assay; MS-identified NP–SMYD3 interaction with minigenome system","pmids":["30544196","31002112","31516086"],"confidence":"Medium","gaps":["p53 ubiquitination mechanism (E3 ligase vs. scaffolding) not clarified","SMYD3-dependent SMAD3 chromatin binding mechanism unresolved","EBOV finding from single system without in vivo confirmation"]},{"year":2020,"claim":"ATM phosphorylation of SMYD3 was shown to nucleate a BRCA2–CHK2 complex essential for RAD51 loading and homologous recombination, placing SMYD3 in the DNA damage response and rationalizing PARP-inhibitor synergy; separately, SMYD3 nuclear-cytoplasmic shuttling was found to be regulated by cell geometry and actomyosin tension.","evidence":"Co-IP with ATM phospho-mutant SMYD3, RAD51 foci assay, PARP inhibitor sensitization; live-cell imaging of SMYD3 in micropatterned cells with cytoskeletal drugs","pmids":["33205017","33244033"],"confidence":"Medium","gaps":["ATM phosphorylation sites on SMYD3 not identified","whether SMYD3 methyltransferase activity is required for HR function not fully resolved","mechanotransduction pathway linking cytoskeleton to SMYD3 import unknown"]},{"year":2021,"claim":"SMYD3-mediated H3K4me3 at the Cdkn1a/p21 promoter was identified as a driver of endothelial senescence, with Smyd3-knockout mice protected from angiotensin II-induced vascular aging.","evidence":"ChIP, Smyd3-KO mouse with angiotensin II challenge, siRNA/overexpression, inhibitor treatment","pmids":["32779886"],"confidence":"Medium","gaps":["whether SMYD3's senescence role extends beyond endothelial cells not tested","downstream mediators beyond p21 not characterized"]},{"year":2022,"claim":"Two new non-enzymatic and enzymatic functions emerged: SMYD3 methylates RNF113A to regulate its E3 ligase activity in alkylation damage repair (conferring chemotherapy resistance in SCLC); and SMYD3 stabilizes HIF1α protein independently of its methyltransferase activity, promoting hypoxia responses.","evidence":"In vitro methyltransferase assay for RNF113A with PP4 binding and ubiquitin ligase assays, SMYD3 inhibitor in SCLC cells; Co-IP with catalytically dead SMYD3 mutant, zebrafish knockout for HIF1α stability","pmids":["35819319","36273580"],"confidence":"High","gaps":["RNF113A methylation site(s) not structurally characterized","mechanism of methylation-independent HIF1α stabilization not defined","whether HIF1α stabilization and RNF113A methylation occur in same cell types unknown"]},{"year":2023,"claim":"SMYD3's role in immune evasion was delineated: it deposits H4K20me3 at immune gene loci and transcriptionally activates UHRF1/DNMT1-mediated silencing, suppressing type I interferon signaling; SMYD3 depletion restores immune gene expression and sensitizes tumors to anti-PD-1 therapy. In parallel, SMYD3–MAP3K2 signaling was confirmed to sustain EMT in prostate cancer via a positive feedback loop, and SMYD3-dependent H3K4me3 at Fbxo2 was linked to NMDAR degradation in tauopathy models.","evidence":"ChIP-seq for H4K20me3 and SMYD3, in vivo anti-PD-1 mouse tumor model; catalytic mutant SMYD3 with xenografts; ChIP and electrophysiology in P301S tau mice","pmids":["37463106","37976356","36609445"],"confidence":"Medium","gaps":["direct versus indirect deposition of H4K20me3 by SMYD3 at immune loci not fully established","Fbxo2 mechanism requires independent replication","whether SMYD3–MAP3K2 feedback operates in non-prostate contexts unknown"]},{"year":null,"claim":"Key unresolved questions include: the signals and mechanisms controlling SMYD3 nuclear-cytoplasmic partitioning; the relative in vivo contributions of its histone versus non-histone methyltransferase activities to its oncogenic functions; whether the reported E3 ubiquitin ligase-like activity toward p53 reflects a direct catalytic role; and the structural basis for methylation-independent protein stabilization functions.","evidence":"","pmids":[],"confidence":"Low","gaps":["no reconstituted system separating nuclear from cytoplasmic SMYD3 functions in vivo","p53 ubiquitination mechanism unresolved","no structural basis for HIF1α stabilization"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,2,3,9,10,11,13,14,21,22,23]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,4]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,6,7,8,12,15,22,25,26,27,30]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[0,3,9,12]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,4,6,7,8,12,16,28]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,13,17,28]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[9,12,15]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,3,9,12,22]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,6,7,8,12,15,25,26,27,30]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,2,13,14,23]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[20,21]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[9]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[22]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[1,12,21,23]}],"complexes":["SMYD3–HSP90α complex","ATM–SMYD3–CHK2–BRCA2 complex"],"partners":["HSP90AA1","MAP3K2","BRD4","ESR1","SMAD3","SUB1","BRCA2","RNF113A"],"other_free_text":[]},"mechanistic_narrative":"SMYD3 is a SET-domain lysine methyltransferase that functions both as a chromatin modifier and a cytoplasmic signaling regulator, coupling histone methylation-dependent transcriptional control to post-translational modification of non-histone substrates in kinase and DNA-damage-response pathways. In the nucleus, SMYD3 catalyzes H3K4, H4K5, H4K20, and H2A.Z.1-K101 methylation at target gene promoters, cooperating with cofactors including ERα, BRD4, PC4/SUB1, and SMAD3 to activate transcription of cell-cycle, EMT, and immune-regulatory genes [PMID:15235609, PMID:22419068, PMID:27569210, PMID:23752591, PMID:26350217, PMID:30544196, PMID:37463106]. In the cytoplasm, SMYD3 methylates MAP3K2 at K260 to block PP2A binding and potentiate Ras-ERK signaling, methylates AKT1 at K14 to promote its membrane recruitment, trimethylates HER2-K175 to enhance homodimerization, and methylates RNF113A to regulate its E3 ligase activity in the alkylation damage response [PMID:24847881, PMID:27626683, PMID:28639750, PMID:35819319]. Its enzymatic activity is stimulated by HSP90α binding to a C-terminal TPR-like domain and by DNA binding, and ATM-dependent phosphorylation recruits SMYD3 into a BRCA2–CHK2 complex required for RAD51 loading during homologous recombination [PMID:15235609, PMID:25738358, PMID:21266482, PMID:33205017]."},"prefetch_data":{"uniprot":{"accession":"Q9H7B4","full_name":"Histone-lysine N-methyltransferase SMYD3","aliases":["SET and MYND domain-containing protein 3","Zinc finger MYND domain-containing protein 1"],"length_aa":428,"mass_kda":49.1,"function":"Histone methyltransferase. Specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation (PubMed:15235609, PubMed:22419068). Also methylates 'Lys-5' of histone H4 (PubMed:22419068). Plays an important role in transcriptional activation as a member of an RNA polymerase complex (PubMed:15235609). Binds DNA containing 5'-CCCTCC-3' or 5'-GAGGGG-3' sequences (PubMed:15235609)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9H7B4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SMYD3","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/SMYD3","total_profiled":1310},"omim":[{"mim_id":"609487","title":"MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 2; MAP3K2","url":"https://www.omim.org/entry/609487"},{"mim_id":"608783","title":"SET AND MYND DOMAIN-CONTAINING PROTEIN 3; SMYD3","url":"https://www.omim.org/entry/608783"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SMYD3"},"hgnc":{"alias_symbol":["KMT3E"],"prev_symbol":["ZNFN3A1","ZMYND1"]},"alphafold":{"accession":"Q9H7B4","domains":[{"cath_id":"2.170.270.10","chopping":"2-36_199-271","consensus_level":"medium","plddt":97.9144,"start":2,"end":271},{"cath_id":"1.10.220.160","chopping":"40-183","consensus_level":"high","plddt":97.1915,"start":40,"end":183},{"cath_id":"1.25.40.970","chopping":"277-354","consensus_level":"medium","plddt":96.6767,"start":277,"end":354},{"cath_id":"1.25.40.10","chopping":"363-428","consensus_level":"medium","plddt":97.527,"start":363,"end":428}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H7B4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H7B4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H7B4-F1-predicted_aligned_error_v6.png","plddt_mean":97.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SMYD3","jax_strain_url":"https://www.jax.org/strain/search?query=SMYD3"},"sequence":{"accession":"Q9H7B4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H7B4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H7B4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H7B4"}},"corpus_meta":[{"pmid":"15235609","id":"PMC_15235609","title":"SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells.","date":"2004","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/15235609","citation_count":594,"is_preprint":false},{"pmid":"24847881","id":"PMC_24847881","title":"SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer.","date":"2014","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/24847881","citation_count":318,"is_preprint":false},{"pmid":"16441421","id":"PMC_16441421","title":"Enhanced SMYD3 expression is essential for the growth of breast cancer cells.","date":"2006","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/16441421","citation_count":215,"is_preprint":false},{"pmid":"20725992","id":"PMC_20725992","title":"Mutated KRAS results in overexpression of DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase, in rectal carcinomas.","date":"2010","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/20725992","citation_count":172,"is_preprint":false},{"pmid":"22194464","id":"PMC_22194464","title":"SMYD3 promotes cancer invasion by epigenetic upregulation of the metalloproteinase MMP-9.","date":"2011","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/22194464","citation_count":149,"is_preprint":false},{"pmid":"22419068","id":"PMC_22419068","title":"Smyd3 regulates cancer cell phenotypes and catalyzes histone H4 lysine 5 methylation.","date":"2012","source":"Epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/22419068","citation_count":148,"is_preprint":false},{"pmid":"18006819","id":"PMC_18006819","title":"The lysine 831 of vascular endothelial growth factor receptor 1 is a novel target of methylation by SMYD3.","date":"2007","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/18006819","citation_count":143,"is_preprint":false},{"pmid":"26908355","id":"PMC_26908355","title":"Smyd3 Is a Transcriptional Potentiator of Multiple Cancer-Promoting Genes and Required for Liver and Colon Cancer Development.","date":"2016","source":"Cancer cell","url":"https://pubmed.ncbi.nlm.nih.gov/26908355","citation_count":120,"is_preprint":false},{"pmid":"25728514","id":"PMC_25728514","title":"A SMYD3 Small-Molecule Inhibitor Impairing Cancer Cell Growth.","date":"2015","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/25728514","citation_count":98,"is_preprint":false},{"pmid":"16155568","id":"PMC_16155568","title":"A variable number of tandem repeats polymorphism in an E2F-1 binding element in the 5' flanking region of SMYD3 is a risk factor for human cancers.","date":"2005","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/16155568","citation_count":97,"is_preprint":false},{"pmid":"17363582","id":"PMC_17363582","title":"The telomerase reverse transcriptase (hTERT) gene is a direct target of the histone methyltransferase SMYD3.","date":"2007","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/17363582","citation_count":93,"is_preprint":false},{"pmid":"22819820","id":"PMC_22819820","title":"Epigenetic regulation of miR-124 by hepatitis C virus core protein promotes migration and invasion of intrahepatic cholangiocarcinoma cells by targeting SMYD3.","date":"2012","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/22819820","citation_count":87,"is_preprint":false},{"pmid":"29253179","id":"PMC_29253179","title":"The interaction of lncRNA EZR-AS1 with SMYD3 maintains overexpression of EZR in ESCC cells.","date":"2018","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/29253179","citation_count":85,"is_preprint":false},{"pmid":"19509295","id":"PMC_19509295","title":"Requirement of histone methyltransferase SMYD3 for estrogen receptor-mediated transcription.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19509295","citation_count":80,"is_preprint":false},{"pmid":"30544196","id":"PMC_30544196","title":"SMYD3 promotes the epithelial-mesenchymal transition in breast cancer.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/30544196","citation_count":75,"is_preprint":false},{"pmid":"23752591","id":"PMC_23752591","title":"The methyltransferase SMYD3 mediates the recruitment of transcriptional cofactors at the myostatin and c-Met genes and regulates skeletal muscle atrophy.","date":"2013","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/23752591","citation_count":70,"is_preprint":false},{"pmid":"26350217","id":"PMC_26350217","title":"Cooperation between SMYD3 and PC4 drives a distinct transcriptional program in cancer cells.","date":"2015","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/26350217","citation_count":69,"is_preprint":false},{"pmid":"25980436","id":"PMC_25980436","title":"SMYD3 contributes to a more aggressive phenotype of prostate cancer and targets Cyclin D2 through H4K20me3.","date":"2015","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/25980436","citation_count":65,"is_preprint":false},{"pmid":"24174655","id":"PMC_24174655","title":"SMYD3 as an oncogenic driver in prostate cancer by stimulation of androgen receptor transcription.","date":"2013","source":"Journal of the National Cancer Institute","url":"https://pubmed.ncbi.nlm.nih.gov/24174655","citation_count":65,"is_preprint":false},{"pmid":"25669152","id":"PMC_25669152","title":"Epigenetic control of Foxp3 by SMYD3 H3K4 histone methyltransferase controls iTreg development and regulates pathogenic T-cell responses during pulmonary viral infection.","date":"2015","source":"Mucosal immunology","url":"https://pubmed.ncbi.nlm.nih.gov/25669152","citation_count":65,"is_preprint":false},{"pmid":"21887258","id":"PMC_21887258","title":"Smyd3 is required for the development of cardiac and skeletal muscle in zebrafish.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21887258","citation_count":61,"is_preprint":false},{"pmid":"31935919","id":"PMC_31935919","title":"SMYD3: An Oncogenic Driver Targeting Epigenetic Regulation and Signaling Pathways.","date":"2020","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/31935919","citation_count":59,"is_preprint":false},{"pmid":"21266482","id":"PMC_21266482","title":"Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding.","date":"2011","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/21266482","citation_count":58,"is_preprint":false},{"pmid":"33637115","id":"PMC_33637115","title":"SMYD3: a regulator of epigenetic and signaling pathways in cancer.","date":"2021","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/33637115","citation_count":56,"is_preprint":false},{"pmid":"30842588","id":"PMC_30842588","title":"Amplification of SMYD3 promotes tumorigenicity and intrahepatic metastasis of hepatocellular carcinoma via upregulation of CDK2 and MMP2.","date":"2019","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/30842588","citation_count":56,"is_preprint":false},{"pmid":"27554136","id":"PMC_27554136","title":"Smyd3-associated regulatory pathways in cancer.","date":"2016","source":"Seminars in cancer biology","url":"https://pubmed.ncbi.nlm.nih.gov/27554136","citation_count":56,"is_preprint":false},{"pmid":"17998933","id":"PMC_17998933","title":"Enhanced methyltransferase activity of SMYD3 by the cleavage of its N-terminal region in human cancer cells.","date":"2007","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/17998933","citation_count":53,"is_preprint":false},{"pmid":"19321255","id":"PMC_19321255","title":"Knockdown of SMYD3 by RNA interference down-regulates c-Met expression and inhibits cells migration and invasion induced by HGF.","date":"2009","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/19321255","citation_count":53,"is_preprint":false},{"pmid":"29746925","id":"PMC_29746925","title":"SMYD3 controls a Wnt-responsive epigenetic switch for ASCL2 activation and cancer stem cell maintenance.","date":"2018","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/29746925","citation_count":52,"is_preprint":false},{"pmid":"24189459","id":"PMC_24189459","title":"Histone methyltransferase SMYD3 promotes MRTF-A-mediated transactivation of MYL9 and migration of MCF-7 breast cancer cells.","date":"2013","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/24189459","citation_count":52,"is_preprint":false},{"pmid":"29856759","id":"PMC_29856759","title":"Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/29856759","citation_count":51,"is_preprint":false},{"pmid":"27569210","id":"PMC_27569210","title":"SMYD3-Mediated H2A.Z.1 Methylation Promotes Cell Cycle and Cancer Proliferation.","date":"2016","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/27569210","citation_count":49,"is_preprint":false},{"pmid":"26676636","id":"PMC_26676636","title":"Upregulated SMYD3 promotes bladder cancer progression by targeting BCLAF1 and activating autophagy.","date":"2015","source":"Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26676636","citation_count":49,"is_preprint":false},{"pmid":"27066749","id":"PMC_27066749","title":"Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets.","date":"2016","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/27066749","citation_count":49,"is_preprint":false},{"pmid":"18452649","id":"PMC_18452649","title":"Knockdown of SMYD3 by RNA interference inhibits cervical carcinoma cell growth and invasion in vitro.","date":"2008","source":"BMB reports","url":"https://pubmed.ncbi.nlm.nih.gov/18452649","citation_count":48,"is_preprint":false},{"pmid":"25738358","id":"PMC_25738358","title":"C-terminal domain of SMYD3 serves as a unique HSP90-regulated motif in oncogenesis.","date":"2015","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/25738358","citation_count":47,"is_preprint":false},{"pmid":"27626683","id":"PMC_27626683","title":"SMYD3-mediated lysine methylation in the PH domain is critical for activation of AKT1.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27626683","citation_count":45,"is_preprint":false},{"pmid":"26980013","id":"PMC_26980013","title":"SMYD3 stimulates EZR and LOXL2 transcription to enhance proliferation, migration, and invasion in esophageal squamous cell carcinoma.","date":"2016","source":"Human pathology","url":"https://pubmed.ncbi.nlm.nih.gov/26980013","citation_count":42,"is_preprint":false},{"pmid":"20957523","id":"PMC_20957523","title":"Effects of SMYD3 over-expression on cell cycle acceleration and cell proliferation in MDA-MB-231 human breast cancer cells.","date":"2010","source":"Medical oncology (Northwood, London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/20957523","citation_count":42,"is_preprint":false},{"pmid":"31417652","id":"PMC_31417652","title":"Overexpression of SMYD3 in Ovarian Cancer is Associated with Ovarian Cancer Proliferation and Apoptosis via Methylating H3K4 and H4K20.","date":"2019","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/31417652","citation_count":40,"is_preprint":false},{"pmid":"32779886","id":"PMC_32779886","title":"Histone methyltransferase Smyd3 is a new regulator for vascular senescence.","date":"2020","source":"Aging cell","url":"https://pubmed.ncbi.nlm.nih.gov/32779886","citation_count":39,"is_preprint":false},{"pmid":"28957646","id":"PMC_28957646","title":"A High-Throughput Dose-Response Cellular Thermal Shift Assay for Rapid Screening of Drug Target Engagement in Living Cells, Exemplified Using SMYD3 and IDO1.","date":"2017","source":"SLAS discovery : advancing life sciences R & D","url":"https://pubmed.ncbi.nlm.nih.gov/28957646","citation_count":37,"is_preprint":false},{"pmid":"31503345","id":"PMC_31503345","title":"SMYD3 promotes implant metastasis of ovarian cancer via H3K4 trimethylation of integrin promoters.","date":"2019","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/31503345","citation_count":37,"is_preprint":false},{"pmid":"17963297","id":"PMC_17963297","title":"Silencing SMYD3 in hepatoma demethylates RIZI promoter induces apoptosis and inhibits cell proliferation and migration.","date":"2007","source":"World journal of gastroenterology","url":"https://pubmed.ncbi.nlm.nih.gov/17963297","citation_count":37,"is_preprint":false},{"pmid":"30646949","id":"PMC_30646949","title":"ANKHD1 is required for SMYD3 to promote tumor metastasis in hepatocellular carcinoma.","date":"2019","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/30646949","citation_count":35,"is_preprint":false},{"pmid":"33542221","id":"PMC_33542221","title":"LncRNA LTSCCAT promotes tongue squamous cell carcinoma metastasis via targeting the miR-103a-2-5p/SMYD3/TWIST1 axis.","date":"2021","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/33542221","citation_count":34,"is_preprint":false},{"pmid":"26929412","id":"PMC_26929412","title":"Structural Basis for Substrate Preference of SMYD3, a SET Domain-containing Protein Lysine Methyltransferase.","date":"2016","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26929412","citation_count":34,"is_preprint":false},{"pmid":"30998113","id":"PMC_30998113","title":"Small-molecule inhibitors of lysine methyltransferases SMYD2 and SMYD3: current trends.","date":"2019","source":"Future medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30998113","citation_count":33,"is_preprint":false},{"pmid":"19082926","id":"PMC_19082926","title":"Hepatitis B virus X protein upregulates expression of SMYD3 and C-MYC in HepG2 cells.","date":"2008","source":"Medical oncology (Northwood, London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/19082926","citation_count":32,"is_preprint":false},{"pmid":"25382779","id":"PMC_25382779","title":"Lysine methylation in cancer: SMYD3-MAP3K2 teaches us new lessons in the Ras-ERK pathway.","date":"2014","source":"BioEssays : news and reviews in molecular, cellular and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/25382779","citation_count":31,"is_preprint":false},{"pmid":"28639750","id":"PMC_28639750","title":"Protein lysine methyltransferase SMYD3 is involved in tumorigenesis through regulation of HER2 homodimerization.","date":"2017","source":"Cancer medicine","url":"https://pubmed.ncbi.nlm.nih.gov/28639750","citation_count":31,"is_preprint":false},{"pmid":"20039369","id":"PMC_20039369","title":"Novobiocin decreases SMYD3 expression and inhibits the migration of MDA-MB-231 human breast cancer cells.","date":"2010","source":"IUBMB life","url":"https://pubmed.ncbi.nlm.nih.gov/20039369","citation_count":29,"is_preprint":false},{"pmid":"25471787","id":"PMC_25471787","title":"Overexpression of SMYD3 was associated with increased STAT3 activation in gastric cancer.","date":"2014","source":"Medical oncology (Northwood, London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/25471787","citation_count":29,"is_preprint":false},{"pmid":"21450690","id":"PMC_21450690","title":"Hepatitis C virus core upregulates the methylation status of the RASSF1A promoter through regulation of SMYD3 in hilar cholangiocarcinoma cells.","date":"2011","source":"Acta biochimica et biophysica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/21450690","citation_count":29,"is_preprint":false},{"pmid":"31968646","id":"PMC_31968646","title":"Chitooligosaccharides Modulate Glucose-Lipid Metabolism by Suppressing SMYD3 Pathways and Regulating Gut Microflora.","date":"2020","source":"Marine drugs","url":"https://pubmed.ncbi.nlm.nih.gov/31968646","citation_count":28,"is_preprint":false},{"pmid":"29302370","id":"PMC_29302370","title":"ATM Signaling Pathway Is Implicated in the SMYD3-mediated Proliferation and Migration of Gastric Cancer Cells.","date":"2017","source":"Journal of gastric cancer","url":"https://pubmed.ncbi.nlm.nih.gov/29302370","citation_count":27,"is_preprint":false},{"pmid":"34094832","id":"PMC_34094832","title":"SMYD3-PARP16 axis accelerates unfolded protein response and mediates neointima formation.","date":"2020","source":"Acta pharmaceutica Sinica. B","url":"https://pubmed.ncbi.nlm.nih.gov/34094832","citation_count":26,"is_preprint":false},{"pmid":"32291411","id":"PMC_32291411","title":"VHL-HIF-2α axis-induced SMYD3 upregulation drives renal cell carcinoma progression via direct trans-activation of EGFR.","date":"2020","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/32291411","citation_count":26,"is_preprint":false},{"pmid":"35819319","id":"PMC_35819319","title":"SMYD3 Impedes Small Cell Lung Cancer Sensitivity to Alkylation Damage through RNF113A Methylation-Phosphorylation Cross-talk.","date":"2022","source":"Cancer discovery","url":"https://pubmed.ncbi.nlm.nih.gov/35819319","citation_count":25,"is_preprint":false},{"pmid":"37463106","id":"PMC_37463106","title":"SMYD3 represses tumor-intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37463106","citation_count":25,"is_preprint":false},{"pmid":"36609445","id":"PMC_36609445","title":"Inhibition of histone methyltransferase Smyd3 rescues NMDAR and cognitive deficits in a tauopathy mouse model.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/36609445","citation_count":25,"is_preprint":false},{"pmid":"26790435","id":"PMC_26790435","title":"Residual expression of SMYD2 and SMYD3 is associated with the acquisition of complex karyotype in chronic lymphocytic leukemia.","date":"2016","source":"Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26790435","citation_count":25,"is_preprint":false},{"pmid":"19472189","id":"PMC_19472189","title":"Effects of SMYD3 overexpression on transformation, serum dependence, and apoptosis sensitivity in NIH3T3 cells.","date":"2009","source":"IUBMB life","url":"https://pubmed.ncbi.nlm.nih.gov/19472189","citation_count":25,"is_preprint":false},{"pmid":"31441002","id":"PMC_31441002","title":"Overexpression of the SMYD3 Promotes Proliferation, Migration, and Invasion of Pancreatic Cancer.","date":"2019","source":"Digestive diseases and sciences","url":"https://pubmed.ncbi.nlm.nih.gov/31441002","citation_count":24,"is_preprint":false},{"pmid":"29029425","id":"PMC_29029425","title":"MiR-346 suppresses cell proliferation through SMYD3 dependent approach in hepatocellular carcinoma.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/29029425","citation_count":24,"is_preprint":false},{"pmid":"24993551","id":"PMC_24993551","title":"Effect of the downregulation of SMYD3 expression by RNAi on RIZ1 expression and proliferation of esophageal squamous cell carcinoma.","date":"2014","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/24993551","citation_count":24,"is_preprint":false},{"pmid":"31223458","id":"PMC_31223458","title":"Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3.","date":"2019","source":"ACS medicinal chemistry letters","url":"https://pubmed.ncbi.nlm.nih.gov/31223458","citation_count":23,"is_preprint":false},{"pmid":"21054678","id":"PMC_21054678","title":"SMYD3 interacts with HTLV-1 Tax and regulates subcellular localization of Tax.","date":"2010","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/21054678","citation_count":22,"is_preprint":false},{"pmid":"31516086","id":"PMC_31516086","title":"Host factor SMYD3 is recruited by Ebola virus nucleoprotein to facilitate viral mRNA transcription.","date":"2019","source":"Emerging microbes & infections","url":"https://pubmed.ncbi.nlm.nih.gov/31516086","citation_count":22,"is_preprint":false},{"pmid":"34301921","id":"PMC_34301921","title":"SMYD3 promotes hepatocellular carcinoma progression by methylating S1PR1 promoters.","date":"2021","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/34301921","citation_count":22,"is_preprint":false},{"pmid":"25918436","id":"PMC_25918436","title":"Histone methyltransferase Smyd3 regulates early embryonic lineage commitment in mice.","date":"2015","source":"Reproduction (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/25918436","citation_count":21,"is_preprint":false},{"pmid":"31002112","id":"PMC_31002112","title":"SMYD3 promotes epithelial ovarian cancer metastasis by downregulating p53 protein stability and promoting p53 ubiquitination.","date":"2019","source":"Carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/31002112","citation_count":21,"is_preprint":false},{"pmid":"34154424","id":"PMC_34154424","title":"Discovery of the SMYD3 Inhibitor BAY-6035 Using Thermal Shift Assay (TSA)-Based High-Throughput Screening.","date":"2021","source":"SLAS discovery : advancing life sciences R & D","url":"https://pubmed.ncbi.nlm.nih.gov/34154424","citation_count":21,"is_preprint":false},{"pmid":"18294291","id":"PMC_18294291","title":"Association of the variable number of tandem repeats polymorphism in the promoter region of the SMYD3 gene with risk of esophageal squamous cell carcinoma in relation to tobacco smoking.","date":"2008","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/18294291","citation_count":21,"is_preprint":false},{"pmid":"31754141","id":"PMC_31754141","title":"The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/31754141","citation_count":21,"is_preprint":false},{"pmid":"33205017","id":"PMC_33205017","title":"Targeting SMYD3 to Sensitize Homologous Recombination-Proficient Tumors to PARP-Mediated Synthetic Lethality.","date":"2020","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/33205017","citation_count":20,"is_preprint":false},{"pmid":"37237385","id":"PMC_37237385","title":"Histone lysine methyltransferase SMYD3 promotes oral squamous cell carcinoma tumorigenesis via H3K4me3-mediated HMGA2 transcription.","date":"2023","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/37237385","citation_count":19,"is_preprint":false},{"pmid":"25092459","id":"PMC_25092459","title":"The lysine methyltransferase SMYD3 interacts with hepatitis C virus NS5A and is a negative regulator of viral particle production.","date":"2014","source":"Virology","url":"https://pubmed.ncbi.nlm.nih.gov/25092459","citation_count":18,"is_preprint":false},{"pmid":"33144524","id":"PMC_33144524","title":"Smyd3-PARP16 axis accelerates unfolded protein response and vascular aging.","date":"2020","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/33144524","citation_count":17,"is_preprint":false},{"pmid":"33244033","id":"PMC_33244033","title":"Cell geometry and the cytoskeleton impact the nucleo-cytoplasmic localisation of the SMYD3 methyltransferase.","date":"2020","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33244033","citation_count":17,"is_preprint":false},{"pmid":"37386026","id":"PMC_37386026","title":"SMYD3 drives the proliferation in gastric cancer cells via reducing EMP1 expression in an H4K20me3-dependent manner.","date":"2023","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/37386026","citation_count":17,"is_preprint":false},{"pmid":"34621667","id":"PMC_34621667","title":"A SMYD3/ITGB6/TGFβ1 Positive Feedback Loop Promotes the Invasion and Adhesion of Ovarian Cancer Spheroids.","date":"2021","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34621667","citation_count":17,"is_preprint":false},{"pmid":"36330911","id":"PMC_36330911","title":"The SMYD3-MTHFD1L-formate metabolic regulatory axis mediates mitophagy to inhibit M1 polarization in macrophages.","date":"2022","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/36330911","citation_count":17,"is_preprint":false},{"pmid":"25563599","id":"PMC_25563599","title":"Histone methyltransferase SMYD3 regulates the expression of transcriptional factors during bovine oocyte maturation and early embryonic development.","date":"2015","source":"Cytotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/25563599","citation_count":16,"is_preprint":false},{"pmid":"36116234","id":"PMC_36116234","title":"Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3.","date":"2022","source":"European journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/36116234","citation_count":16,"is_preprint":false},{"pmid":"29969917","id":"PMC_29969917","title":"SMYD3 promoter hypomethylation is associated with the risk of colorectal cancer.","date":"2018","source":"Future oncology (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/29969917","citation_count":15,"is_preprint":false},{"pmid":"30263847","id":"PMC_30263847","title":"SMYD3-associated pathway is involved in the anti-tumor effects of sulforaphane on gastric carcinoma cells.","date":"2018","source":"Food science and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/30263847","citation_count":15,"is_preprint":false},{"pmid":"37192621","id":"PMC_37192621","title":"Mechanical pressure-induced dedifferentiation of myofibroblasts inhibits scarring via SMYD3/ITGBL1 signaling.","date":"2023","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/37192621","citation_count":14,"is_preprint":false},{"pmid":"34560329","id":"PMC_34560329","title":"Elevated placental histone H3K4 methylation via upregulated histone methyltransferases SETD1A and SMYD3 in preeclampsia and its possible involvement in hypoxia-induced pathophysiological process.","date":"2021","source":"Placenta","url":"https://pubmed.ncbi.nlm.nih.gov/34560329","citation_count":14,"is_preprint":false},{"pmid":"38091832","id":"PMC_38091832","title":"SMYD3 activates the TCA cycle to promote M1-M2 conversion in macrophages.","date":"2023","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/38091832","citation_count":14,"is_preprint":false},{"pmid":"37534166","id":"PMC_37534166","title":"SMYD3 induces sorafenib resistance by activating SMAD2/3-mediated epithelial-mesenchymal transition in hepatocellular carcinoma.","date":"2023","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/37534166","citation_count":14,"is_preprint":false},{"pmid":"35495117","id":"PMC_35495117","title":"Identifying novel SMYD3 interactors on the trail of cancer hallmarks.","date":"2022","source":"Computational and structural biotechnology journal","url":"https://pubmed.ncbi.nlm.nih.gov/35495117","citation_count":13,"is_preprint":false},{"pmid":"37976356","id":"PMC_37976356","title":"The SMYD3-MAP3K2 signaling axis promotes tumor aggressiveness and metastasis in prostate cancer.","date":"2023","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/37976356","citation_count":13,"is_preprint":false},{"pmid":"39159723","id":"PMC_39159723","title":"Matrix stiffness-dependent PD-L2 deficiency improves SMYD3/xCT-mediated ferroptosis and the efficacy of anti-PD-1 in HCC.","date":"2024","source":"Journal of advanced research","url":"https://pubmed.ncbi.nlm.nih.gov/39159723","citation_count":13,"is_preprint":false},{"pmid":"34510321","id":"PMC_34510321","title":"Novel insights into SMYD2 and SMYD3 inhibitors: from potential anti-tumoural therapy to a variety of new applications.","date":"2021","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/34510321","citation_count":13,"is_preprint":false},{"pmid":"31218443","id":"PMC_31218443","title":"STAT3-induced SMYD3 transcription enhances chronic lymphocytic leukemia cell growth in vitro and in vivo.","date":"2019","source":"Inflammation research : official journal of the European Histamine Research Society ... [et al.]","url":"https://pubmed.ncbi.nlm.nih.gov/31218443","citation_count":13,"is_preprint":false},{"pmid":"33827259","id":"PMC_33827259","title":"H3K4 Methyltransferase Smyd3 Mediates Vascular Smooth Muscle Cell Proliferation, Migration, and Neointima Formation.","date":"2021","source":"Arteriosclerosis, thrombosis, and vascular biology","url":"https://pubmed.ncbi.nlm.nih.gov/33827259","citation_count":13,"is_preprint":false},{"pmid":"28019723","id":"PMC_28019723","title":"Therapeutical potential of deregulated lysine methyltransferase SMYD3 as a safe target for novel anticancer agents.","date":"2016","source":"Expert opinion on therapeutic targets","url":"https://pubmed.ncbi.nlm.nih.gov/28019723","citation_count":12,"is_preprint":false},{"pmid":"33400854","id":"PMC_33400854","title":"Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase.","date":"2021","source":"Chembiochem : a European journal of chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/33400854","citation_count":12,"is_preprint":false},{"pmid":"36273580","id":"PMC_36273580","title":"Methyltransferase SMYD3 impairs hypoxia tolerance by augmenting hypoxia signaling independent of its enzymatic activity.","date":"2022","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/36273580","citation_count":12,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":48543,"output_tokens":7436,"usd":0.128584},"stage2":{"model":"claude-opus-4-6","input_tokens":11194,"output_tokens":4670,"usd":0.25908},"total_usd":0.387664,"stage1_batch_id":"msgbatch_011rkcQdVV1RaFq9XhcG6df6","stage2_batch_id":"msgbatch_01RzgrJafdF4EWHhj5mNi6dh","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"SMYD3 SET domain possesses histone H3-lysine 4 (H3K4)-specific methyltransferase activity, which is enhanced by heat-shock protein HSP90A; SMYD3 forms a complex with RNA polymerase II through interaction with the RNA helicase HELZ and binds to a 5'-CCCTCC-3' promoter motif to transactivate downstream genes.\",\n      \"method\": \"In vitro methyltransferase assay, Co-immunoprecipitation, promoter binding assay, siRNA knockdown with proliferation readout\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — original discovery with in vitro enzymatic assay, Co-IP of complex, and functional KD; highly cited foundational paper\",\n      \"pmids\": [\"15235609\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SMYD3 methylates MAP3K2 (MEKK2) at lysine 260, potentiating Ras/Raf/MEK/ERK signaling; methylation of MAP3K2 blocks binding of the PP2A phosphatase complex (a negative regulator of the MAP kinase pathway), thereby increasing ERK activation and promoting Ras-driven pancreatic and lung carcinomas.\",\n      \"method\": \"Protein array substrate identification, in vitro methyltransferase assay, Co-IP, mouse cancer models (KRAS-driven pancreatic and lung adenocarcinoma), catalytic mutant SMYD3, MEK inhibitor synergy\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods (array, in vitro assay, mouse models, mechanistic epistasis), replicated and highly cited\",\n      \"pmids\": [\"24847881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"SMYD3 methylates vascular endothelial growth factor receptor 1 (VEGFR1) at lysine 831 in its kinase domain, and this methylation enhances VEGFR1 kinase activity in cells.\",\n      \"method\": \"In vitro methyltransferase assay, mass spectrometry identification of methylated residue, cell-based kinase activity assay\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro assay with site identification and cellular functional readout, single lab\",\n      \"pmids\": [\"18006819\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"SMYD3 catalyzes mono- and di-methylation of histone H4 at lysine 5 (H4K5me), a mark detectable in diverse cell types whose formation is attenuated by SMYD3 depletion; SMYD3-driven cancer cell phenotypes require its enzymatic activity.\",\n      \"method\": \"In vitro methyltransferase assay, mass spectrometry, siRNA knockdown with H4K5me detection, cell phenotype assays\",\n      \"journal\": \"Epigenetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro enzymatic assay with MS confirmation and functional link to enzymatic activity\",\n      \"pmids\": [\"22419068\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Crystal structure of full-length human SMYD3 in complex with S-adenosyl-L-homocysteine at 2.8 Å resolution revealed a C-terminal tetratricopeptide repeat (TPR) domain that together with the SET and post-SET domains forms the substrate binding pocket; Tyr239 hydroxyl group is critical for enzymatic activity; DNA binding stimulates SMYD3 histone methyltransferase activity, possibly mediated via the MYND domain.\",\n      \"method\": \"X-ray crystallography, mutagenesis of active site residues, in vitro histone methyltransferase assay, DNA binding biochemical assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with mutagenesis and biochemical validation\",\n      \"pmids\": [\"21266482\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Cleavage of the N-terminal 34 amino acids of SMYD3 in cancer cells produces a form with higher histone methyltransferase activity; substitution of conserved glycines 15 and 17 also enhances activity; the N-terminal region mediates association with HSP90α, whose binding modulates enzymatic activity.\",\n      \"method\": \"Protein biochemistry, N-terminal sequencing, site-directed mutagenesis, in vitro methyltransferase assay, Co-immunoprecipitation with HSP90α\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mutagenesis and in vitro assay with Co-IP; single lab\",\n      \"pmids\": [\"17998933\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"SMYD3 functions as a coactivator of estrogen receptor alpha (ERα) by directly interacting with the ERα ligand-binding domain; upon estrogen induction, SMYD3 is recruited to ER target gene promoters and is responsible for accumulation of H3K4me2/3, which is required for ER-regulated gene transcription.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), siRNA knockdown with gene expression readout, domain mapping\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, ChIP, and functional KD; single lab\",\n      \"pmids\": [\"19509295\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"SMYD3 recruits the bromodomain protein BRD4 to myostatin and c-Met gene regulatory regions through protein-protein interaction; this promotes engagement of the pause-release factor p-TEFb and elongation of Ser2-phosphorylated RNA Pol II, driving transcription; reducing SMYD3 decreases myostatin and c-Met transcription and protects against glucocorticoid-induced myotube atrophy in vivo.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, siRNA/shRNA knockdown, mouse model of dexamethasone-induced atrophy\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, ChIP, in vivo mouse model with clean phenotype; multiple orthogonal methods\",\n      \"pmids\": [\"23752591\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SMYD3 interacts with PC4 (human positive coactivator 4) and cooperates with it to drive expression of proliferation- and invasion-linked genes; PC4 depletion abolishes SMYD3-mediated H3K4me3 and target gene expression; SMYD3 and PC4 recruit each other to target genes in a mutually dependent manner.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, siRNA knockdown, artificial tethering with catalytic mutant\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, ChIP, and functional depletion; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"26350217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SMYD3 methylates histone H2A.Z.1 at lysine 101 (H2A.Z.1K101me2), stabilizing H2A.Z.1 by preventing binding of the removal chaperone ANP32E and facilitating interaction with histone H3; SMYD3/H2A.Z.1K101me2 co-localizes at the cyclin A1 promoter, activates cyclin A1 expression, and promotes G1-S cell cycle progression and tumor formation.\",\n      \"method\": \"In vitro methyltransferase assay, Co-immunoprecipitation, ChIP, mutagenesis of K101, microarray, mouse tumor model\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro assay, mutagenesis, ChIP, and in vivo mouse model; multiple orthogonal methods\",\n      \"pmids\": [\"27569210\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Co-crystal structures of SMYD3 with VEGFR1 and MAP3K2 peptides revealed that MAP3K2 is a robust substrate due to a phenylalanine at the -2 position fitting a shallow hydrophobic pocket; VEGFR1 is a weaker substrate because the acceptor lysine is buried in the folded kinase domain, requiring drastic conformational rearrangement.\",\n      \"method\": \"X-ray co-crystallography, in vitro kinetic/biochemical assays, mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — co-crystal structures with biochemical validation of substrate preference determinants\",\n      \"pmids\": [\"26929412\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Co-crystal structure of SMYD3 with a MEKK2-peptide substrate and a SAM-competitive inhibitor (GSK2807, Ki = 14 nM) showed the inhibitor bridges the SAM-binding pocket and the substrate lysine tunnel; SMYD3 follows a partially processive methylation mechanism.\",\n      \"method\": \"X-ray crystallography (co-crystal with peptide substrate and inhibitor), kinetic characterization, biochemical inhibitor assays\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution co-crystal structure with kinetic mechanistic characterization\",\n      \"pmids\": [\"27066749\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SMYD3 interacts with H3K4me3-modified histone tails, facilitating its recruitment to core promoter regions of active genes; Smyd3 binding correlates with increased RNA polymerase II density and is required for chemically induced liver and colon cancer formation in mice.\",\n      \"method\": \"ChIP-seq, Smyd3 knockout mouse model with chemical carcinogenesis, Co-immunoprecipitation with H3K4me3\",\n      \"journal\": \"Cancer cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo knockout mouse model with carcinogenesis phenotype, genome-wide ChIP-seq; multiple orthogonal methods\",\n      \"pmids\": [\"26908355\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SMYD3 methylates AKT1 at lysine 14 in its PH domain; this methylation is required for AKT1 plasma membrane accumulation and for phosphorylation at threonine 308; K14-substituted AKT1 shows reduced membrane localization and lower growth-promoting activity.\",\n      \"method\": \"In vitro methyltransferase assay, Co-immunoprecipitation, site-directed mutagenesis, subcellular fractionation/imaging, SMYD3 KD and inhibitor treatment\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro assay with mutagenesis, cellular localization, and functional readout; single lab\",\n      \"pmids\": [\"27626683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SMYD3 trimethylates HER2 at lysine 175; this methylation promotes HER2 homodimerization; K175A substitution reduces homodimer formation and autophosphorylation; SMYD3 knockdown attenuates HER2 autophosphorylation in breast cancer cells.\",\n      \"method\": \"In vitro methyltransferase assay, Co-immunoprecipitation, site-directed mutagenesis, siRNA knockdown with phosphorylation readout\",\n      \"journal\": \"Cancer medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro assay, mutagenesis, Co-IP, and cellular functional readout; single lab\",\n      \"pmids\": [\"28639750\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SMYD3 directly interacts with SMAD3 and is required for SMAD3 association to chromatin at EMT gene regulatory regions in TGFβ-induced epithelial-mesenchymal transition; SMYD3 is dispensable for SMAD2/3 phosphorylation and nuclear translocation but is essential for SMAD3 chromatin binding.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, SMYD3 knockdown and pharmacological inhibition (BCI121), zebrafish xenograft invasion model\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, ChIP, KD with clean mechanistic dissection; single lab\",\n      \"pmids\": [\"30544196\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The C-terminal TPR-like domain of SMYD3 mediates physical interaction with HSP90; this interaction is essential for basal SMYD3 histone methyltransferase activity; loss of SMYD3-HSP90 interaction causes SMYD3 mislocalization within the nucleus (loss of chromatin association), reducing cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation, domain deletion/mutagenesis, in vitro methyltransferase assay, subcellular localization assay (immunofluorescence/fractionation), cell proliferation assay\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP with domain mapping, enzymatic assay, and localization with functional consequence; single lab\",\n      \"pmids\": [\"25738358\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"SMYD3 interacts with HTLV-1 Tax protein via the C-terminal 180 amino acids of SMYD3; SMYD3 dominates the subcellular localization of Tax, tethering it to the cytoplasm, which enhances Tax-mediated NF-κB activation; SMYD3 knockdown attenuates this NF-κB activation.\",\n      \"method\": \"Co-immunoprecipitation, in vitro pull-down, colocalization (confocal microscopy), reporter gene assay, shRNA knockdown\",\n      \"journal\": \"Cancer science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — reciprocal Co-IP, pull-down, localization with functional consequence; single lab\",\n      \"pmids\": [\"21054678\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SMYD3 interacts with HCV NS5A protein via the MYND domain of SMYD3 and domain III of NS5A; SMYD3 overexpression decreases intracellular and extracellular HCV titers without affecting viral RNA replication, indicating SMYD3 negatively affects virus particle production in an NS5A-dependent manner.\",\n      \"method\": \"Co-immunoprecipitation, colocalization, mutational analysis (domain mapping), viral titer assay\",\n      \"journal\": \"Virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — Co-IP with domain mutagenesis and functional viral production readout; single lab\",\n      \"pmids\": [\"25092459\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SMYD3 interacts directly with p53 via its post-SET domain; SMYD3 promotes p53 translocation from nucleus to cytoplasm and ubiquitination (independent of MDM2), forming a complex with UBE2R2 (an E2 ubiquitin-conjugating enzyme); SMYD3 ubiquitinates p53 at lysines 381, 382, and 386.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry identification of UBE2R2, domain mapping (post-SET), ubiquitination assay, site-directed mutagenesis of p53 K381/382/386\",\n      \"journal\": \"Carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — Co-IP, domain mapping, and ubiquitination assay with site identification; single lab\",\n      \"pmids\": [\"31002112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ATM phosphorylates SMYD3, enabling formation of a multiprotein complex of ATM, SMYD3, CHK2, and BRCA2 required for RAD51 loading at DNA double-strand break sites and completion of homologous recombination (HR); pharmacological SMYD3 inhibition sensitizes HR-proficient cancer cells to PARP inhibitors.\",\n      \"method\": \"Co-immunoprecipitation, use of ATM phosphorylation-deficient SMYD3 mutant variant, RAD51 focus formation assay, PARP inhibitor sensitivity assay\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP of multiprotein complex, functional mutagenesis, and pharmacological validation; single lab\",\n      \"pmids\": [\"33205017\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SMYD3 methylates RNF113A, and this methylation impairs RNF113A interaction with the phosphatase PP4, controlling RNF113A phosphorylation levels; this cross-talk (methylation-phosphorylation) promotes RNF113A E3 ligase activity essential for the alkylation damage response, conferring SCLC resistance to alkylating chemotherapy; SMYD3 inhibition restores SCLC sensitivity.\",\n      \"method\": \"In vitro methyltransferase assay, Co-immunoprecipitation, phosphorylation assays, RNF113A ubiquitin ligase activity assay, SMYD3 inhibitor treatment in SCLC cells\",\n      \"journal\": \"Cancer discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro methyltransferase assay, mechanistic dissection of PTM cross-talk, and functional cellular/pharmacological validation; strong mechanistic data\",\n      \"pmids\": [\"35819319\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SMYD3 binds to and regulates transcription of UHRF1; UHRF1 (a reader of H3K9me3) recruits DNMT1 to silence immune-related gene promoters; SMYD3 additionally deposits H4K20me3 at intragenic regions of immune-related genes to maintain their repression; SMYD3 depletion upregulates type I interferon response genes and increases CD8+ T cell infiltration, sensitizing tumors to anti-PD-1 therapy.\",\n      \"method\": \"ChIP-seq, siRNA/shRNA knockdown, gene expression analysis, in vivo mouse tumor model with anti-PD-1 treatment, H4K20me3 ChIP\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP-seq, in vivo model, and mechanistic epistasis; single lab\",\n      \"pmids\": [\"37463106\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SMYD3 methylates MAP3K2 in prostate cancer cells, promoting epithelial-mesenchymal transition-associated behaviors by altering vimentin abundance; SMYD3-MAP3K2 signaling creates a positive feedback loop that sustains high SMYD3 levels; catalytic mutant SMYD3 fails to promote these phenotypes.\",\n      \"method\": \"In vitro methyltransferase assay, catalytic mutant SMYD3, mouse xenograft models, vimentin western blot, EMT assays\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro assay, catalytic mutant, in vivo xenograft; single lab\",\n      \"pmids\": [\"37976356\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SMYD3 binds to and stabilizes HIF1α (independent of its methyltransferase activity and independent of prolyl hydroxylase/VHL pathways), enhancing HIF1α transcriptional activity under hypoxia; SMYD3 promotes reactive oxygen species accumulation and hypoxia-induced apoptosis; smyd3-null zebrafish exhibit higher hypoxia tolerance.\",\n      \"method\": \"Co-immunoprecipitation, western blot stability assay, enzymatic-dead mutant, zebrafish knockout model, reporter assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, catalytic mutant establishing non-enzymatic mechanism, in vivo zebrafish model; single lab\",\n      \"pmids\": [\"36273580\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"SMYD3 binds to the promoter of PARP16 and increases H3K4me3 at this locus to activate PARP16 transcription; PARP16 in turn ADP-ribosylates PERK and IRE1α to promote unfolded protein response (UPR) and vascular smooth muscle cell proliferation; SMYD3-PARP16 axis mediates neointimal hyperplasia after vascular injury.\",\n      \"method\": \"ChIP-seq, ChIP-qPCR, Co-immunoprecipitation, SMYD3/PARP16 knockdown, ADP-ribosylation assay, mouse vascular injury model\",\n      \"journal\": \"Acta pharmaceutica Sinica. B\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP-seq, biochemical assay, in vivo model; single lab\",\n      \"pmids\": [\"34094832\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In Alzheimer's disease/tauopathy context, elevated Smyd3 upregulates Fbxo2 (an E3 ubiquitin ligase) via H3K4me3 at the Fbxo2 promoter; Fbxo2 promotes NR1 (NMDAR subunit) ubiquitination and degradation; pharmacological Smyd3 inhibition (BCI-121) rescues NMDAR function and cognitive deficits in P301S Tau mice.\",\n      \"method\": \"ChIP, western blot of H3K4me3, Smyd3 inhibitor treatment, Fbxo2 knockdown rescue, electrophysiology, behavioral assays in mouse model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP, mechanistic epistasis (Fbxo2 KD rescue), in vivo mouse model; single lab\",\n      \"pmids\": [\"36609445\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"SMYD3 interacts with ANKHD1 (identified by mass spectrometry of H3K4me3 pulldown); ANKHD1 binds H3K4me3 in SMYD3-overexpressing cells and is required for SMYD3-mediated SLUG gene activation (via H3K4me3, H3K9Ac, H3K14Ac); ANKHD1 knockdown attenuates SMYD3-dependent HCC migration and invasion.\",\n      \"method\": \"Mass spectrometry, Co-immunoprecipitation, ChIP, EMSA, luciferase reporter, siRNA knockdown\",\n      \"journal\": \"Journal of experimental & clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — MS identification, Co-IP, ChIP; single lab\",\n      \"pmids\": [\"30646949\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"SMYD3 nuclear-cytoplasmic distribution is regulated by cell geometry (shape and aspect ratio) in myoblasts via acto-myosin cytoskeleton; elongated cell geometries reduce SMYD3 nuclear import; cytoskeletal acto-myosin drugs induce SMYD3 nuclear accumulation; SMYD3 redistribution correlates with changes in trimethylation (Kme3) but not dimethylation levels.\",\n      \"method\": \"Live-cell imaging, pharmacological cytoskeletal perturbation, subcellular fractionation, immunofluorescence in micropatterned cells\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — direct localization experiment with functional consequence (Kme3 levels); single lab\",\n      \"pmids\": [\"33244033\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SMYD3 is recruited by Ebola virus nucleoprotein (NP) to viral inclusion bodies; SMYD3 depletion suppresses EBOV mRNA production; SMYD3 promotes NP-VP30 interaction in a dose-dependent manner, thereby facilitating viral mRNA transcription.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry (NP pulldown), minigenome replication system, siRNA knockdown with mRNA quantification\",\n      \"journal\": \"Emerging microbes & infections\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — Co-IP, MS identification, functional KD; single lab\",\n      \"pmids\": [\"31516086\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SMYD3 directly binds to the Cdkn1a (p21) promoter and increases H3K4me3 levels there, elevating p21 expression and driving senescence-associated phenotypes in endothelial cells; Smyd3 knockout mice are protected from Angiotensin II-induced vascular senescence.\",\n      \"method\": \"ChIP, Smyd3 knockout mouse model, siRNA knockdown, SMYD3 overexpression, Smyd3 inhibitor treatment\",\n      \"journal\": \"Aging cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP, in vivo mouse model, and pharmacological confirmation; single lab\",\n      \"pmids\": [\"32779886\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SMYD3 is a multifunctional SET-domain lysine methyltransferase that methylates multiple histone (H3K4, H4K5, H4K20, H2A.Z.1-K101) and non-histone substrates (MAP3K2-K260, VEGFR1-K831, AKT1-K14, HER2-K175, RNF113A) to regulate gene transcription, cytoplasmic kinase signaling (Ras/MEK/ERK via MAP3K2 methylation that blocks PP2A binding), DNA damage response (via ATM-dependent complex with BRCA2/CHK2 for homologous recombination), and protein stability (HIF1α, p53); its activity is enhanced by HSP90A interaction with its TPR-like C-terminal domain, and its nuclear-cytoplasmic distribution is regulated by cell geometry and cytoskeletal tension.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SMYD3 is a SET-domain lysine methyltransferase that functions both as a chromatin modifier and a cytoplasmic signaling regulator, coupling histone methylation-dependent transcriptional control to post-translational modification of non-histone substrates in kinase and DNA-damage-response pathways. In the nucleus, SMYD3 catalyzes H3K4, H4K5, H4K20, and H2A.Z.1-K101 methylation at target gene promoters, cooperating with cofactors including ERα, BRD4, PC4/SUB1, and SMAD3 to activate transcription of cell-cycle, EMT, and immune-regulatory genes [PMID:15235609, PMID:22419068, PMID:27569210, PMID:23752591, PMID:26350217, PMID:30544196, PMID:37463106]. In the cytoplasm, SMYD3 methylates MAP3K2 at K260 to block PP2A binding and potentiate Ras-ERK signaling, methylates AKT1 at K14 to promote its membrane recruitment, trimethylates HER2-K175 to enhance homodimerization, and methylates RNF113A to regulate its E3 ligase activity in the alkylation damage response [PMID:24847881, PMID:27626683, PMID:28639750, PMID:35819319]. Its enzymatic activity is stimulated by HSP90α binding to a C-terminal TPR-like domain and by DNA binding, and ATM-dependent phosphorylation recruits SMYD3 into a BRCA2–CHK2 complex required for RAD51 loading during homologous recombination [PMID:15235609, PMID:25738358, PMID:21266482, PMID:33205017].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"The foundational question of SMYD3's enzymatic identity was resolved: it is an H3K4-specific methyltransferase whose activity is enhanced by HSP90A, and it associates with RNA Pol II via HELZ to transactivate target genes, establishing it as a transcription-coupled chromatin modifier.\",\n      \"evidence\": \"In vitro methyltransferase assay, Co-IP, promoter binding assay, and siRNA knockdown in cancer cell lines\",\n      \"pmids\": [\"15235609\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"HSP90A stimulation mechanism not structurally resolved\", \"direct versus indirect nature of RNA Pol II association unclear\", \"full substrate specificity unknown\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"SMYD3 was shown to methylate the non-histone substrate VEGFR1 at K831, extending its activity beyond chromatin and suggesting it regulates receptor tyrosine kinase signaling; separately, N-terminal processing and HSP90α interaction were shown to modulate enzymatic output.\",\n      \"evidence\": \"In vitro methyltransferase assay with mass spectrometry site identification; N-terminal sequencing and mutagenesis with Co-IP\",\n      \"pmids\": [\"18006819\", \"17998933\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"VEGFR1 methylation not validated in vivo\", \"physiological relevance of N-terminal cleavage unclear\", \"structural basis for HSP90-mediated activation unknown\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"SMYD3 was established as a nuclear coactivator of estrogen receptor α, linking its H3K4 methyltransferase activity to hormone-regulated transcription programs.\",\n      \"evidence\": \"Co-IP of SMYD3–ERα, ChIP at ER target genes, siRNA knockdown with transcriptional readout\",\n      \"pmids\": [\"19509295\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"whether SMYD3 methylates ERα directly not tested\", \"contribution relative to other H3K4 methyltransferases at ER targets undetermined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"The crystal structure of full-length SMYD3 revealed how the C-terminal TPR domain, SET domain, and post-SET domain cooperate to form the substrate binding cleft, and identified Tyr239 as catalytically essential; DNA binding through the MYND domain was shown to stimulate methyltransferase activity.\",\n      \"evidence\": \"2.8 Å X-ray crystallography, active-site mutagenesis, in vitro histone methyltransferase and DNA-binding assays\",\n      \"pmids\": [\"21266482\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"no co-crystal with histone peptide substrate\", \"how DNA binding allosterically activates catalysis not resolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"H4K5 was identified as an additional histone substrate, broadening SMYD3's chromatin-modifying repertoire beyond H3K4 and linking its enzymatic activity to cancer cell phenotypes.\",\n      \"evidence\": \"In vitro methyltransferase assay with mass spectrometry, siRNA knockdown with H4K5me detection\",\n      \"pmids\": [\"22419068\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"genomic distribution of SMYD3-dependent H4K5me not mapped\", \"whether H4K5me is functionally distinct from H3K4me at SMYD3 targets unknown\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"The mechanism of SMYD3-driven transcriptional elongation was elucidated: SMYD3 recruits BRD4 and the p-TEFb pause-release factor to gene regulatory regions, promoting Ser2-phosphorylated Pol II elongation, with in vivo relevance in glucocorticoid-induced muscle atrophy.\",\n      \"evidence\": \"Co-IP of SMYD3–BRD4, ChIP for elongation marks, shRNA knockdown, mouse dexamethasone-atrophy model\",\n      \"pmids\": [\"23752591\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"whether SMYD3 methylates BRD4 directly not tested\", \"precise recruitment order of SMYD3 versus BRD4 undetermined\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"A major cytoplasmic function was defined: SMYD3 methylates MAP3K2 at K260 to block PP2A binding, amplifying Ras-ERK signaling and driving Ras-dependent tumorigenesis — establishing SMYD3 as a bona fide oncogenic signaling regulator outside the nucleus.\",\n      \"evidence\": \"Protein array substrate screen, in vitro methyltransferase assay, Co-IP, KRAS-driven mouse pancreatic and lung cancer models, catalytic mutant and MEK inhibitor epistasis\",\n      \"pmids\": [\"24847881\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"whether additional MAP kinase pathway kinases are SMYD3 substrates unknown\", \"signals governing SMYD3 nuclear versus cytoplasmic partitioning not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"The HSP90–TPR domain interaction was mapped as essential for SMYD3 chromatin association and basal enzymatic activity; separately, the transcriptional coactivator PC4 was identified as a co-dependent partner for SMYD3-mediated H3K4me3 at target genes.\",\n      \"evidence\": \"Domain deletion/mutagenesis with Co-IP and subcellular fractionation; Co-IP and ChIP for PC4–SMYD3 co-occupancy\",\n      \"pmids\": [\"25738358\", \"26350217\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"whether HSP90 acts as an allosteric activator or a folding chaperone for SMYD3 not distinguished\", \"PC4 interaction not confirmed by independent group\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Multiple advances converged: structural co-crystals with MAP3K2 and VEGFR1 peptides explained substrate preference determinants; H2A.Z.1-K101 methylation was discovered to stabilize H2A.Z.1 at promoters driving cell cycle progression; SMYD3 was found to read H3K4me3 and recruit Pol II genome-wide; and AKT1-K14 methylation was linked to AKT membrane localization.\",\n      \"evidence\": \"Co-crystallography with kinetic validation; in vitro methyltransferase assays; ChIP-seq and Smyd3-knockout mice in chemical carcinogenesis; subcellular fractionation of methylated AKT1\",\n      \"pmids\": [\"26929412\", \"27066749\", \"27569210\", \"26908355\", \"27626683\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"physiological significance of AKT1-K14 methylation confirmed only in cell lines\", \"relative contribution of SMYD3's histone versus non-histone activities to tumorigenesis not separated in vivo\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"SMYD3 was shown to trimethylate HER2-K175, promoting receptor homodimerization and autophosphorylation, adding another receptor tyrosine kinase to its non-histone substrate portfolio.\",\n      \"evidence\": \"In vitro methyltransferase assay, K175A mutagenesis reducing dimerization, siRNA knockdown in breast cancer cells\",\n      \"pmids\": [\"28639750\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"HER2 methylation not validated in vivo\", \"structural basis for how K175 methylation promotes dimerization unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Three new functional axes were defined: SMYD3 facilitates SMAD3 chromatin binding during TGFβ-driven EMT; promotes p53 cytoplasmic translocation and MDM2-independent ubiquitination via UBE2R2; and is recruited by Ebola virus NP to enhance viral mRNA transcription.\",\n      \"evidence\": \"Co-IP and ChIP for SMAD3 with SMYD3 inhibitor; Co-IP of SMYD3–p53–UBE2R2 with ubiquitination assay; MS-identified NP–SMYD3 interaction with minigenome system\",\n      \"pmids\": [\"30544196\", \"31002112\", \"31516086\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"p53 ubiquitination mechanism (E3 ligase vs. scaffolding) not clarified\", \"SMYD3-dependent SMAD3 chromatin binding mechanism unresolved\", \"EBOV finding from single system without in vivo confirmation\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"ATM phosphorylation of SMYD3 was shown to nucleate a BRCA2–CHK2 complex essential for RAD51 loading and homologous recombination, placing SMYD3 in the DNA damage response and rationalizing PARP-inhibitor synergy; separately, SMYD3 nuclear-cytoplasmic shuttling was found to be regulated by cell geometry and actomyosin tension.\",\n      \"evidence\": \"Co-IP with ATM phospho-mutant SMYD3, RAD51 foci assay, PARP inhibitor sensitization; live-cell imaging of SMYD3 in micropatterned cells with cytoskeletal drugs\",\n      \"pmids\": [\"33205017\", \"33244033\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"ATM phosphorylation sites on SMYD3 not identified\", \"whether SMYD3 methyltransferase activity is required for HR function not fully resolved\", \"mechanotransduction pathway linking cytoskeleton to SMYD3 import unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"SMYD3-mediated H3K4me3 at the Cdkn1a/p21 promoter was identified as a driver of endothelial senescence, with Smyd3-knockout mice protected from angiotensin II-induced vascular aging.\",\n      \"evidence\": \"ChIP, Smyd3-KO mouse with angiotensin II challenge, siRNA/overexpression, inhibitor treatment\",\n      \"pmids\": [\"32779886\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"whether SMYD3's senescence role extends beyond endothelial cells not tested\", \"downstream mediators beyond p21 not characterized\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Two new non-enzymatic and enzymatic functions emerged: SMYD3 methylates RNF113A to regulate its E3 ligase activity in alkylation damage repair (conferring chemotherapy resistance in SCLC); and SMYD3 stabilizes HIF1α protein independently of its methyltransferase activity, promoting hypoxia responses.\",\n      \"evidence\": \"In vitro methyltransferase assay for RNF113A with PP4 binding and ubiquitin ligase assays, SMYD3 inhibitor in SCLC cells; Co-IP with catalytically dead SMYD3 mutant, zebrafish knockout for HIF1α stability\",\n      \"pmids\": [\"35819319\", \"36273580\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"RNF113A methylation site(s) not structurally characterized\", \"mechanism of methylation-independent HIF1α stabilization not defined\", \"whether HIF1α stabilization and RNF113A methylation occur in same cell types unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"SMYD3's role in immune evasion was delineated: it deposits H4K20me3 at immune gene loci and transcriptionally activates UHRF1/DNMT1-mediated silencing, suppressing type I interferon signaling; SMYD3 depletion restores immune gene expression and sensitizes tumors to anti-PD-1 therapy. In parallel, SMYD3–MAP3K2 signaling was confirmed to sustain EMT in prostate cancer via a positive feedback loop, and SMYD3-dependent H3K4me3 at Fbxo2 was linked to NMDAR degradation in tauopathy models.\",\n      \"evidence\": \"ChIP-seq for H4K20me3 and SMYD3, in vivo anti-PD-1 mouse tumor model; catalytic mutant SMYD3 with xenografts; ChIP and electrophysiology in P301S tau mice\",\n      \"pmids\": [\"37463106\", \"37976356\", \"36609445\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"direct versus indirect deposition of H4K20me3 by SMYD3 at immune loci not fully established\", \"Fbxo2 mechanism requires independent replication\", \"whether SMYD3–MAP3K2 feedback operates in non-prostate contexts unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: the signals and mechanisms controlling SMYD3 nuclear-cytoplasmic partitioning; the relative in vivo contributions of its histone versus non-histone methyltransferase activities to its oncogenic functions; whether the reported E3 ubiquitin ligase-like activity toward p53 reflects a direct catalytic role; and the structural basis for methylation-independent protein stabilization functions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"no reconstituted system separating nuclear from cytoplasmic SMYD3 functions in vivo\", \"p53 ubiquitination mechanism unresolved\", \"no structural basis for HIF1α stabilization\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 2, 3, 9, 10, 11, 13, 14, 21, 22, 23]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 6, 7, 8, 12, 15, 22, 25, 26, 27, 30]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [0, 3, 9, 12]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 4, 6, 7, 8, 12, 16, 28]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 13, 17, 28]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [9, 12, 15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 3, 9, 12, 22]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 6, 7, 8, 12, 15, 25, 26, 27, 30]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 2, 13, 14, 23]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [20, 21]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [22]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [1, 12, 21, 23]}\n    ],\n    \"complexes\": [\n      \"SMYD3–HSP90α complex\",\n      \"ATM–SMYD3–CHK2–BRCA2 complex\"\n    ],\n    \"partners\": [\n      \"HSP90AA1\",\n      \"MAP3K2\",\n      \"BRD4\",\n      \"ESR1\",\n      \"SMAD3\",\n      \"SUB1\",\n      \"BRCA2\",\n      \"RNF113A\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}