{"gene":"NSD3","run_date":"2026-04-29T11:37:57","timeline":{"discoveries":[{"year":2011,"finding":"NSD3 interacts with the extraterminal (ET) domain of BRD4 (and BRD2/BRD3), and the BRD4/NSD3 complex regulates H3K36 methylation at BRD4 target genes; NSD3 is recruited to regulated genes in a BRD4-dependent manner and imparts pTEFb-independent transcriptional activation.","method":"Proteomic/mass spectrometry pulldown, co-immunoprecipitation, ChIP, siRNA knockdown with H3K36me measurement","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, ChIP, and functional depletion with defined histone modification readout; moderate-to-strong evidence from multiple orthogonal methods","pmids":["21555454"],"is_preprint":false},{"year":2015,"finding":"NSD3-short (a short isoform lacking the methyltransferase domain) acts as an adaptor protein linking BRD4 to the CHD8 chromatin remodeler via its PWWP chromatin-reader module and an acidic transactivation domain; the BRD4-NSD3-CHD8 complex co-localizes at super-enhancers in AML cells and is required for leukemia maintenance.","method":"Co-immunoprecipitation, ChIP-seq, CRISPR/shRNA knockdown with transcriptional and phenotypic readouts, genetic epistasis","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Co-IP, ChIP-seq, genetic targeting), replicated phenotypic and molecular readouts","pmids":["26626481"],"is_preprint":false},{"year":2016,"finding":"Crystal structure of the BRD4 ET domain bound to an NSD3-derived amphipathic peptide revealed that ET domain recognition occurs via a two-strand antiparallel β-sheet anchored on a hydrophobic cleft of a three-helix bundle; this structural mechanism is essential for AML maintenance.","method":"X-ray crystallography, structure-guided mutagenesis, functional validation in AML cells","journal":"Structure (London, England : 1993)","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with functional validation","pmids":["27291650"],"is_preprint":false},{"year":2012,"finding":"The PHD5-C5HCH module of NSD3 folds into a novel integrated PHD-PHD-like structural module that binds unmodified H3K4 and trimethylated H3K9 (H3K9me3) on the surface of PHD5; this differs from NSD2 (which prefers H3K9me0) and NSD1 (which does not bind H3 peptides), providing a mechanism for genomic targeting.","method":"X-ray crystallography of PHD5-C5HCH free and in complex with H3 peptides; binding assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — crystal structures with multiple peptide complexes and orthogonal binding assays","pmids":["23269674"],"is_preprint":false},{"year":2021,"finding":"NSD3 is the principal oncogenic driver in lung squamous cell carcinoma (LUSC) within the 8p11-12 amplicon; a cancer-associated variant NSD3(T1232A) shows increased catalytic activity for H3K36me2 in vitro and in vivo, and structural dynamic analyses revealed that T1232A relieves auto-inhibition and increases H3 substrate accessibility.","method":"In vitro methyltransferase assay, structural dynamic analysis, mouse LUSC model (KO and knock-in), patient-derived xenografts, ChIP-seq","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro catalytic assay, structural analysis, and multiple in vivo models with strong mechanistic follow-up","pmids":["33536620"],"is_preprint":false},{"year":2017,"finding":"NSD3 (WHSC1L1) directly methylates IRF3 at lysine 366 (K366me1) via its SET domain; NSD3 binds the IRF3 C-terminal region through its PWWP1 domain. K366 monomethylation promotes IRF3 dissociation from the phosphatase PP1cc, sustaining IRF3 phosphorylation and type I interferon production during antiviral innate immunity.","method":"Mass spectrometry identification of IRF3-associated proteins, co-immunoprecipitation, in vitro methylation assay, NSD3 knockout mice, site-directed mutagenesis","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro methylation, in vivo KO, and mechanistic dissection of PP1cc interaction with multiple orthogonal methods","pmids":["29101251"],"is_preprint":false},{"year":2017,"finding":"WHSC1L1 (NSD3) mono-methylates EGFR at lysine 721 (K721) in the tyrosine kinase domain, enhancing ERK cascade activation without EGF stimulation; nuclear EGFR K721 methylation also enhances interaction with PCNA, promoting DNA synthesis and cell cycle progression in head and neck squamous cell carcinoma.","method":"In vitro methylation assay, co-immunoprecipitation, functional siRNA knockdown, cell cycle analysis","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro methylation assay with site-specific mutagenesis and multiple downstream functional readouts","pmids":["28102297"],"is_preprint":false},{"year":2016,"finding":"WHSC1L1 (NSD3) and H3K36me2 are enriched in the gene bodies of CDC6 and CDK2; WHSC1L1 knockdown causes G0/G1 arrest that is rescued by wild-type WHSC1L1 but not by enzyme-inactive WHSC1L1, demonstrating that catalytic activity-dependent H3K36me2 drives G1-to-S phase transition in head and neck cancer cells.","method":"ChIP, siRNA knockdown, cell cycle analysis, rescue with catalytic mutant","journal":"Oncotarget","confidence":"High","confidence_rationale":"Tier 2 — ChIP with catalytic mutant rescue establishes enzymatic mechanism clearly","pmids":["27285764"],"is_preprint":false},{"year":2020,"finding":"The long isoform of NSD3 (but not the short isoform lacking the catalytic domain) cooperates with EZH2 and RNA polymerase II to stimulate H3K36me2/3-dependent transactivation of genes involved in NOTCH receptor cleavage, leading to nuclear accumulation of NICD and NICD-mediated E-cadherin repression in breast cancer.","method":"Co-immunoprecipitation, ChIP, isoform-specific knockdown/overexpression, in vivo mouse model","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 — isoform-specific functional dissection with co-IP, ChIP, and in vivo validation","pmids":["32967925"],"is_preprint":false},{"year":2019,"finding":"The PWWP1 domain of NSD3 binds the methyl-lysine site and is required for viability of AML cells; the fragment-derived chemical probe BI-9321 antagonizes this domain with sub-micromolar in vitro activity and cellular target engagement, downregulating Myc mRNA.","method":"Fragment-based drug discovery, structural characterization, cellular target engagement assay, mRNA expression","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1–2 — structure-guided probe development with cellular functional validation","pmids":["31285596"],"is_preprint":false},{"year":2014,"finding":"NSD3-NUT fusion oncoprotein is necessary and sufficient for blockade of differentiation and maintenance of proliferation in NUT midline carcinoma cells; NSD3-NUT binds BRD4, and NSD3 is also required for the blockade of differentiation in BRD4-NUT-expressing NMC cells.","method":"Patient-derived cell line, shRNA knockdown, overexpression, co-immunoprecipitation, BET bromodomain inhibitor treatment","journal":"Cancer discovery","confidence":"High","confidence_rationale":"Tier 2 — necessity and sufficiency experiments with Co-IP; replicated in multiple NMC cell line contexts","pmids":["24875858"],"is_preprint":false},{"year":2023,"finding":"NSD3 (long isoform) interacts with the cohesin loader complex kollerin (NIPBL/MAU2) and promotes chromatin recruitment of MAU2 and cohesin at mitotic exit; NSD3 associates with chromatin in early anaphase before cohesin loading and its methyltransferase activity is required for efficient sister chromatid cohesion.","method":"Co-immunoprecipitation, chromatin fractionation, live cell imaging, siRNA knockdown, catalytic mutant rescue","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 — Co-IP, fractionation, live imaging, and catalytic mutant rescue across multiple orthogonal approaches","pmids":["37288770"],"is_preprint":false},{"year":2014,"finding":"NSD3 is required for neural crest specification and migration in chick embryos; NSD3 loss impairs expression of neural plate border gene Msx1 and neural crest transcription factors Sox10, Snail2, Sox9, and FoxD3; H3K36me2 at the Sox10 locus specifically requires NSD3, and NSD3-related methyltransferase activity is independently required for neural crest migration.","method":"Morpholino knockdown in chick, dominant-negative expression, ChIP for H3K36me2, temporal rescue experiments","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — ChIP-validated H3K36me2 dependence, temporal loss-of-function, and dominant-negative approach with specific phenotypic readouts","pmids":["25318671"],"is_preprint":false},{"year":2024,"finding":"NSD3 deposits H3K36me2 peaks specifically at active promoters and enhancers (not broad intergenic domains), occupying a distinct genomic niche from NSD1/NSD2 which establish broad intergenic H3K36me2 domains; a hierarchy of K36 methyltransferase activity was established: NSD1 > NSD2 > NSD3 > ASH1L.","method":"Sequential CRISPR knockouts of multiple K36 methyltransferases, ChIP-seq, comparative H3K36me1/2/3 mapping in mouse mesenchymal stem cells","journal":"Genome biology","confidence":"High","confidence_rationale":"Tier 2 — systematic genetic perturbation with genome-wide ChIP-seq; strong mechanistic dissection across multiple enzymes","pmids":["39390582"],"is_preprint":false},{"year":2021,"finding":"A NSD3-targeting PROTAC (MS9715) linking BI-9321 (PWWP1 antagonist) to a VHL ligand induces specific NSD3 degradation and suppresses both NSD3- and cMyc-associated gene expression programs in hematological cancer cells; degradation is superior to PWWP1 domain blockade alone.","method":"PROTAC design, Western blot protein degradation, RNA-seq, CRISPR-Cas9 NSD3 KO comparison, cell viability","journal":"Cell chemical biology","confidence":"High","confidence_rationale":"Tier 2 — mechanistic PROTAC study with transcriptomic validation and comparison to CRISPR KO","pmids":["34469831"],"is_preprint":false},{"year":2010,"finding":"NSD3 (WHISTLE isoform) is recruited to the p450c17 promoter via interaction with SF-1 and represses steroidogenesis gene transcription during prepubertal stages; it interacts with HSP90α and the H3K9 demethylase JMJD1C, which subsequently replaces WHISTLE to activate target gene expression.","method":"TAP immunoaffinity purification of WHISTLE complexes, co-immunoprecipitation, ChIP","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 — TAP-purification and ChIP with functional context, but single lab","pmids":["20530532"],"is_preprint":false},{"year":2006,"finding":"The WHISTLE isoform of NSD3 induces apoptosis in an HMTase activity-dependent manner and represses transcription through HDAC1 recruitment; the N-terminus PWWP region is required for HMTase activity, and SET domain cysteine 297 is a critical catalytic residue.","method":"Point mutagenesis, deletion mapping, luciferase reporter assay, caspase-3 activation assay","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2/3 — active-site mutagenesis with functional readouts, single lab","pmids":["17239852"],"is_preprint":false},{"year":2025,"finding":"NSD3 interacts with and methylates NSD3 itself at lysine 477 (via EHMT2); this methylation stabilizes NSD3 protein levels in variant hESCs by protecting it from proteasomal degradation, driving oncogenic transformation.","method":"Co-immunoprecipitation, mass spectrometry, site-directed mutagenesis, protein stability assays, NSD3 knockdown rescue","journal":"Life science alliance","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP with MS identification and functional mutagenesis, single lab","pmids":["39741006"],"is_preprint":false},{"year":2018,"finding":"NSD3-short (NSD3S) directly interacts with MYC; a TR-FRET assay was developed to monitor this interaction and confirmed by an orthogonal protein-protein interaction assay, supporting a mechanism by which NSD3S regulates cell proliferation through MYC engagement.","method":"TR-FRET cell lysate assay, orthogonal Co-IP/pulldown confirmation","journal":"Assay and drug development technologies","confidence":"Medium","confidence_rationale":"Tier 3 — biochemical interaction assay with orthogonal confirmation, functional significance inferred","pmids":["29634317"],"is_preprint":false},{"year":2024,"finding":"NSD3 binds PPP1CB and p-STAT3, forming a trimeric complex that dephosphorylates p-STAT3 via PPP1CB phosphatase activity, leading to suppression of HK2 transcription and glycolysis inhibition in lung adenocarcinoma.","method":"Co-immunoprecipitation, siRNA knockdown, metabolic assays (glucose uptake, lactate), Western blot","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2/3 — Co-IP demonstrating trimeric complex with functional metabolic readouts, single lab","pmids":["39119928"],"is_preprint":false},{"year":2019,"finding":"ISO-induced cardiac hypertrophy decreases NSD3 expression, which reduces H3K27me2/3 on the ANF promoter and disrupts NSD3-BRD4 association; overexpression of NSD3 attenuates hypertrophy by promoting BRD4-association and H3K27 methylation to suppress ANF transcription.","method":"Co-immunoprecipitation, ChIP, overexpression and knockdown in cardiomyocytes, in vivo mouse model","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2/3 — Co-IP, ChIP, and in vivo model, single lab","pmids":["31254363"],"is_preprint":false},{"year":2025,"finding":"The short isoform NSD3S (lacking the methyltransferase domain) is stabilized by CUL3-ZBTB2 E3 ligase complex dysregulation; ATR kinase drives localization of NSD3S to stalled replication forks, where NSD3S antagonizes PTIP-dependent MRE11 nuclease recruitment to protect nascent DNA from degradation and confer PARP inhibitor resistance.","method":"Co-immunoprecipitation, proximity ligation, replication fork protection assay, NSD3-targeting PROTAC, xenograft and PDX mouse models","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1–2 — mechanistic dissection with fork protection assays, Co-IP, in vivo PDX models, and pharmacological validation","pmids":["40578344"],"is_preprint":false},{"year":2025,"finding":"NSD3 specifically enhances H3K27 di-methylation (not H3K36me) in osteosarcoma cells to inactivate the transcriptional repressor ARID3A, causing altered expression of RUNX2, MMP13, OCT4, and NANOG and a shift toward a primitive differentiation state.","method":"CRISPR-Cas9 and lentiviral gain/loss-of-function, ChIP, transcriptomic analysis, spontaneous metastasis mouse model","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP with gain/loss-of-function and in vivo model, single lab; unexpected substrate (H3K27me2) warrants independent replication","pmids":["40967468"],"is_preprint":false},{"year":2023,"finding":"WHSC1L1 (NSD3) epigenetically suppresses VMP1 transcription via H3K36me2-dependent recruitment of DNMT3A to the VMP1 promoter following HSV-1 infection; NSD3 upregulation impairs mitophagy and promotes neuroinflammation in microglia.","method":"ChIP, siRNA knockdown, VMP1 overexpression rescue, in vivo mouse HSV-1 infection model","journal":"Molecular immunology","confidence":"Medium","confidence_rationale":"Tier 2/3 — ChIP with DNMT3A recruitment mechanism and in vivo rescue, single lab","pmids":["37748280"],"is_preprint":false},{"year":2026,"finding":"NSD3 is recruited to β-globin gene promoters by G9a; NSD3 stabilizes Mediator complex binding at the promoter and facilitates SETD2-mediated H3K36me3 in the gene body to activate globin gene expression; G9a, NSD3, and SETD2 form a coactivator axis in differentiating erythroid cells.","method":"Co-immunoprecipitation, ChIP, siRNA knockdown of NSD3 and G9a, gene expression analysis in differentiating erythroid cells","journal":"Frontiers in cell and developmental biology","confidence":"Medium","confidence_rationale":"Tier 2/3 — Co-IP, ChIP, and functional knockdown in erythroid differentiation context, single lab","pmids":["41970952"],"is_preprint":false},{"year":2001,"finding":"NSD3 (WHSC1L1) encodes a protein with two PWWP domains, five PHD zinc finger motifs, a SAC domain, and a SET domain; two major isoforms arise from alternative splicing — a long isoform (1437 aa, full SET domain) and a short isoform (645 aa, PWWP domain only); the gene maps to 8p11.2 and is frequently amplified in breast cancer.","method":"cDNA cloning, genomic mapping, domain analysis, Northern blot, FISH","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 3 — foundational characterization study, gene structure and isoform identification","pmids":["11549311"],"is_preprint":false}],"current_model":"NSD3 is a histone H3K36 mono- and di-methyltransferase whose long isoform (NSD3L) deposits H3K36me2 preferentially at active promoters and enhancers to drive transcription, while its short catalytically-inactive isoform (NSD3S) acts as a chromatin adaptor linking BRD4 to the CHD8 remodeler and MYC via its PWWP1 reader domain; beyond histone substrates, NSD3 also directly methylates non-histone proteins including IRF3 (K366) and EGFR (K721), regulates sister chromatid cohesion by promoting cohesin loader (kollerin) recruitment, protects stalled replication forks from MRE11-mediated degradation, and its oncogenic gain-of-function variant T1232A relieves catalytic auto-inhibition to hyperstimulate H3K36me2 in lung squamous cell carcinoma."},"narrative":{"teleology":[{"year":2001,"claim":"Identification of NSD3 as a SET-domain gene at 8p11.2 with two major isoforms (long/catalytic and short/PWWP-only) established the molecular framework for understanding its dual enzymatic and adaptor functions.","evidence":"cDNA cloning, domain analysis, and FISH mapping in breast cancer amplicon","pmids":["11549311"],"confidence":"Medium","gaps":["No enzymatic activity demonstrated","Protein partners unknown","Single-lab characterization"]},{"year":2006,"claim":"Demonstration that the WHISTLE isoform possesses HMTase activity dependent on the SET domain C297 residue and PWWP region, and that this activity is required for transcriptional repression and apoptosis induction, established NSD3 as a functional methyltransferase.","evidence":"Point mutagenesis, luciferase reporter, caspase-3 assay","pmids":["17239852"],"confidence":"Medium","gaps":["Histone substrate specificity not defined","No structural basis for catalysis","Single-lab study"]},{"year":2011,"claim":"Discovery that NSD3 physically interacts with BRD4 via the ET domain and deposits H3K36me at BRD4-target genes revealed how NSD3 is genomically targeted and established the BRD4-NSD3 axis as a transcriptional activation mechanism independent of pTEFb.","evidence":"Mass spectrometry pulldown, reciprocal Co-IP, ChIP, siRNA knockdown in human cells","pmids":["21555454"],"confidence":"High","gaps":["Isoform-specific contributions to BRD4 complex not resolved","Genome-wide H3K36me targets not mapped","Mechanism of pTEFb-independent activation unclear"]},{"year":2012,"claim":"Structural determination of the PHD5-C5HCH module revealed a novel integrated reader that binds H3K4me0/H3K9me3, providing a chromatin-targeting mechanism distinct from NSD1 and NSD2.","evidence":"X-ray crystallography of PHD5-C5HCH with H3 peptide complexes and binding assays","pmids":["23269674"],"confidence":"High","gaps":["Genomic loci where PHD5-dependent targeting operates not identified","Functional consequence of H3K9me3 recognition on gene expression not tested"]},{"year":2014,"claim":"Two studies established NSD3's biological roles in differentiation: NSD3-NUT fusions block differentiation in NUT midline carcinoma through BRD4, and NSD3 is required for neural crest specification/migration via H3K36me2 at the Sox10 locus, demonstrating context-dependent developmental and oncogenic functions.","evidence":"shRNA/overexpression in NMC cells with BET inhibitor validation; morpholino and dominant-negative in chick embryos with ChIP","pmids":["24875858","25318671"],"confidence":"High","gaps":["Direct NSD3-NUT catalytic activity not assessed","Full target gene repertoire in neural crest unknown"]},{"year":2015,"claim":"Identification of NSD3-short as a non-catalytic adaptor bridging BRD4 to CHD8 at super-enhancers in AML cells resolved how the short isoform contributes to oncogenesis independently of methyltransferase activity.","evidence":"Co-IP, ChIP-seq, CRISPR/shRNA knockdown in AML cells with transcriptional and phenotypic readouts","pmids":["26626481"],"confidence":"High","gaps":["Whether NSD3S-CHD8 complex remodels nucleosomes directly not shown","Relative contribution of long vs. short isoform in AML unclear"]},{"year":2016,"claim":"Crystal structure of the BRD4 ET–NSD3 peptide interface and demonstration that NSD3 catalytic activity drives G1-to-S cell cycle progression through H3K36me2 at CDC6/CDK2 gene bodies defined both the structural basis of the BRD4 interaction and a direct proliferative mechanism.","evidence":"X-ray crystallography with structure-guided mutagenesis; ChIP with catalytic mutant rescue and cell cycle analysis in HNSCC cells","pmids":["27291650","27285764"],"confidence":"High","gaps":["Whether cell cycle role is BRD4-dependent not tested","Genome-wide targets beyond CDC6/CDK2 not mapped"]},{"year":2017,"claim":"Discovery that NSD3 methylates non-histone substrates IRF3 (K366) and EGFR (K721) expanded NSD3's substrate repertoire beyond histones, linking it to innate immune signaling and receptor tyrosine kinase pathways.","evidence":"In vitro methylation assays, Co-IP, NSD3 KO mice for IRF3; siRNA and cell cycle analysis for EGFR in HNSCC","pmids":["29101251","28102297"],"confidence":"High","gaps":["Full non-histone substrate repertoire unknown","Structural basis for non-histone substrate recognition not determined","In vivo relevance of EGFR K721me not demonstrated in animal models"]},{"year":2019,"claim":"Development of the PWWP1-domain chemical probe BI-9321 that downregulates MYC in AML provided pharmacological validation that the PWWP1 reader domain is essential for NSD3-dependent oncogenic transcription.","evidence":"Fragment-based drug discovery, structural characterization, cellular target engagement in AML cells","pmids":["31285596"],"confidence":"High","gaps":["Selectivity over NSD1/NSD2 PWWP domains not fully defined","In vivo anti-tumor efficacy not demonstrated"]},{"year":2021,"claim":"Identification of NSD3 T1232A as a gain-of-function driver in lung squamous cell carcinoma that relieves autoinhibition to increase H3K36me2, and development of NSD3-targeting PROTACs, defined NSD3 as a druggable oncogenic target with a precise structural mechanism of activation.","evidence":"In vitro methyltransferase assay, structural dynamic analysis, LUSC mouse models, PDX; PROTAC degradation with RNA-seq comparison to CRISPR KO","pmids":["33536620","34469831"],"confidence":"High","gaps":["Whether autoinhibition relief mechanism is generalizable to other NSD3 mutations not tested","Clinical applicability of NSD3 PROTACs not evaluated"]},{"year":2023,"claim":"Discovery that NSD3 interacts with the kollerin cohesin loader to promote sister chromatid cohesion at mitotic exit revealed a novel non-transcriptional, cell-division-coupled function for NSD3's catalytic activity.","evidence":"Co-IP, chromatin fractionation, live cell imaging, catalytic mutant rescue","pmids":["37288770"],"confidence":"High","gaps":["Histone mark deposited at cohesion sites not identified","Whether cohesion defects contribute to NSD3-driven aneuploidy/oncogenesis not established"]},{"year":2024,"claim":"Genome-wide dissection of H3K36me2 deposition showed NSD3 uniquely marks active promoters and enhancers rather than broad intergenic domains, establishing a distinct chromatin niche from NSD1/NSD2 and clarifying the non-redundant function of NSD3 in the NSD family.","evidence":"Sequential CRISPR knockouts of K36 methyltransferases with ChIP-seq in mouse mesenchymal stem cells","pmids":["39390582"],"confidence":"High","gaps":["Whether promoter-specific targeting depends on reader domains or interacting partners not resolved","Functional consequence of promoter-restricted H3K36me2 vs. intergenic domains not tested"]},{"year":2025,"claim":"Demonstration that NSD3S is recruited to stalled replication forks by ATR kinase to protect nascent DNA from MRE11-mediated degradation, conferring PARP inhibitor resistance, revealed a replication stress response function for the catalytically inactive isoform.","evidence":"Co-IP, proximity ligation, fork protection assay, NSD3-targeting PROTAC, xenograft and PDX models","pmids":["40578344"],"confidence":"High","gaps":["Phosphorylation site(s) on NSD3S mediating ATR-dependent recruitment not mapped","Whether NSD3S fork protection is PWWP1-dependent not tested"]},{"year":null,"claim":"Key unresolved questions include how NSD3's promoter/enhancer-specific H3K36me2 deposition is mechanistically directed, the full scope of non-histone substrates, the structural basis for autoinhibition and its relief, and whether the cohesion and replication fork protection functions of NSD3 are coordinated or independent.","evidence":"","pmids":[],"confidence":"Low","gaps":["No full-length NSD3 structure available","Relative contributions of long and short isoforms in specific cancer types remain unclear","Interplay between NSD3 reader domains and catalytic activity in genomic targeting not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,4,5,6,7,8,12,13,16]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[3,9]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,18,21]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[5,6]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1,7,8,11,13]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[3,11,13]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,4,7,8,12,13]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,1,7,8,15,24]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[7,11]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[4,10,14]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[5]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[21]}],"complexes":["BRD4-NSD3-CHD8","NSD3-kollerin (NIPBL/MAU2)"],"partners":["BRD4","CHD8","MYC","NIPBL","MAU2","IRF3","EGFR","G9A"],"other_free_text":[]},"mechanistic_narrative":"NSD3 is a histone lysine methyltransferase that deposits H3K36me1/me2 at active promoters and enhancers to regulate transcription, cell cycle progression, and developmental programs, while also functioning through a catalytically inactive short isoform (NSD3S) that serves as a chromatin adaptor bridging BRD4, CHD8, and MYC [PMID:39390582, PMID:26626481, PMID:21555454]. The long isoform catalyzes H3K36 methylation through its SET domain—regulated by an autoinhibitory loop relieved by the oncogenic T1232A variant—and also methylates non-histone substrates IRF3 (K366) and EGFR (K721) to modulate innate immune signaling and receptor tyrosine kinase activity, respectively [PMID:33536620, PMID:29101251, PMID:28102297]. NSD3 promotes sister chromatid cohesion by recruiting the kollerin cohesin-loader complex at mitotic exit, and the NSD3S isoform protects stalled replication forks from MRE11-mediated degradation downstream of ATR kinase, conferring PARP inhibitor resistance [PMID:37288770, PMID:40578344]. NSD3 is recurrently amplified or mutationally activated in breast cancer, lung squamous cell carcinoma, and acute myeloid leukemia, and NSD3-NUT fusions drive NUT midline carcinoma [PMID:33536620, PMID:24875858]."},"prefetch_data":{"uniprot":{"accession":"Q9BZ95","full_name":"Histone-lysine N-methyltransferase NSD3","aliases":["Nuclear SET domain-containing protein 3","Protein whistle","WHSC1-like 1 isoform 9 with methyltransferase activity to lysine","Wolf-Hirschhorn syndrome candidate 1-like protein 1","WHSC1-like protein 1"],"length_aa":1437,"mass_kda":161.6,"function":"Histone methyltransferase. Preferentially dimethylates 'Lys-4' and 'Lys-27' of histone H3 forming H3K4me2 and H3K27me2. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation, while 'Lys-27' is a mark for transcriptional repression","subcellular_location":"Nucleus; Chromosome","url":"https://www.uniprot.org/uniprotkb/Q9BZ95/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NSD3","classification":"Not Classified","n_dependent_lines":5,"n_total_lines":1208,"dependency_fraction":0.0041390728476821195},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CBX1","stoichiometry":0.2},{"gene":"DHX9","stoichiometry":0.2},{"gene":"HIST2H2BE","stoichiometry":0.2},{"gene":"LAMTOR2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/NSD3","total_profiled":1310},"omim":[{"mim_id":"607083","title":"NUCLEAR RECEPTOR-BINDING SET DOMAIN PROTEIN 3; NSD3","url":"https://www.omim.org/entry/607083"},{"mim_id":"603395","title":"SPERM-ASSOCIATED ANTIGEN 1; SPAG1","url":"https://www.omim.org/entry/603395"},{"mim_id":"601021","title":"NUCLEOPORIN, 98-KD; NUP98","url":"https://www.omim.org/entry/601021"},{"mim_id":"117550","title":"SOTOS SYNDROME; SOTOS","url":"https://www.omim.org/entry/117550"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Mitochondria","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NSD3"},"hgnc":{"alias_symbol":["FLJ20353","WHISTLE","KMT3F"],"prev_symbol":["WHSC1L1"]},"alphafold":{"accession":"Q9BZ95","domains":[{"cath_id":"2.30.30.140","chopping":"273-351_364-396","consensus_level":"high","plddt":86.3593,"start":273,"end":396},{"cath_id":"3.30.40","chopping":"705-750","consensus_level":"medium","plddt":82.1078,"start":705,"end":750},{"cath_id":"3.30.40.10","chopping":"855-870_920-956","consensus_level":"medium","plddt":72.0947,"start":855,"end":956},{"cath_id":"2.30.30.140","chopping":"958-1023_1036-1067","consensus_level":"medium","plddt":83.8032,"start":958,"end":1067},{"cath_id":"2.170.270.10","chopping":"1077-1289","consensus_level":"high","plddt":90.3759,"start":1077,"end":1289},{"cath_id":"3.30.40.10","chopping":"1334-1422","consensus_level":"medium","plddt":84.9344,"start":1334,"end":1422}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BZ95","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BZ95-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BZ95-F1-predicted_aligned_error_v6.png","plddt_mean":61.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NSD3","jax_strain_url":"https://www.jax.org/strain/search?query=NSD3"},"sequence":{"accession":"Q9BZ95","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BZ95.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BZ95/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BZ95"}},"corpus_meta":[{"pmid":"21555454","id":"PMC_21555454","title":"The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3.","date":"2011","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/21555454","citation_count":435,"is_preprint":false},{"pmid":"24875858","id":"PMC_24875858","title":"NSD3-NUT fusion oncoprotein in NUT midline carcinoma: implications for a novel oncogenic mechanism.","date":"2014","source":"Cancer discovery","url":"https://pubmed.ncbi.nlm.nih.gov/24875858","citation_count":210,"is_preprint":false},{"pmid":"30993345","id":"PMC_30993345","title":"WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/30993345","citation_count":178,"is_preprint":false},{"pmid":"11986249","id":"PMC_11986249","title":"NUP98 is fused to the NSD3 gene in acute myeloid leukemia associated with t(8;11)(p11.2;p15).","date":"2002","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/11986249","citation_count":152,"is_preprint":false},{"pmid":"11374904","id":"PMC_11374904","title":"NSD3, a new SET domain-containing gene, maps to 8p12 and is amplified in human breast cancer cell lines.","date":"2001","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/11374904","citation_count":138,"is_preprint":false},{"pmid":"26626481","id":"PMC_26626481","title":"NSD3-Short Is an Adaptor Protein that Couples BRD4 to the CHD8 Chromatin Remodeler.","date":"2015","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/26626481","citation_count":131,"is_preprint":false},{"pmid":"33536620","id":"PMC_33536620","title":"Elevated NSD3 histone methylation activity drives squamous cell lung cancer.","date":"2021","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/33536620","citation_count":127,"is_preprint":false},{"pmid":"31285596","id":"PMC_31285596","title":"Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3.","date":"2019","source":"Nature chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/31285596","citation_count":75,"is_preprint":false},{"pmid":"20530532","id":"PMC_20530532","title":"Regulation of mouse steroidogenesis by WHISTLE and JMJD1C through histone methylation balance.","date":"2010","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/20530532","citation_count":67,"is_preprint":false},{"pmid":"17705804","id":"PMC_17705804","title":"Testicular cancer trends as 'whistle blowers' of testicular developmental problems in populations.","date":"2007","source":"International journal of andrology","url":"https://pubmed.ncbi.nlm.nih.gov/17705804","citation_count":66,"is_preprint":false},{"pmid":"32967925","id":"PMC_32967925","title":"NSD3-Induced Methylation of H3K36 Activates NOTCH Signaling to Drive Breast Tumor Initiation and Metastatic Progression.","date":"2020","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/32967925","citation_count":63,"is_preprint":false},{"pmid":"27291650","id":"PMC_27291650","title":"Structural Mechanism of Transcriptional Regulator NSD3 Recognition by the ET Domain of BRD4.","date":"2016","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/27291650","citation_count":63,"is_preprint":false},{"pmid":"23011637","id":"PMC_23011637","title":"The histone methyltransferase Wolf-Hirschhorn syndrome candidate 1-like 1 (WHSC1L1) is involved in human carcinogenesis.","date":"2012","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/23011637","citation_count":59,"is_preprint":false},{"pmid":"23269674","id":"PMC_23269674","title":"The methyltransferase NSD3 has chromatin-binding motifs, PHD5-C5HCH, that are distinct from other NSD (nuclear receptor SET domain) family members in their histone H3 recognition.","date":"2012","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23269674","citation_count":53,"is_preprint":false},{"pmid":"29101251","id":"PMC_29101251","title":"The methyltransferase NSD3 promotes antiviral innate immunity via direct lysine methylation of IRF3.","date":"2017","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/29101251","citation_count":51,"is_preprint":false},{"pmid":"22389394","id":"PMC_22389394","title":"No one can whistle a symphony alone - how different ubiquitin linkages cooperate to orchestrate NF-κB activity.","date":"2012","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/22389394","citation_count":51,"is_preprint":false},{"pmid":"11549311","id":"PMC_11549311","title":"WHSC1L1, on human chromosome 8p11.2, closely resembles WHSC1 and maps to a duplicated region shared with 4p16.3.","date":"2001","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/11549311","citation_count":50,"is_preprint":false},{"pmid":"34469831","id":"PMC_34469831","title":"A NSD3-targeted PROTAC suppresses NSD3 and cMyc oncogenic nodes in cancer cells.","date":"2021","source":"Cell chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/34469831","citation_count":47,"is_preprint":false},{"pmid":"19380029","id":"PMC_19380029","title":"NUP98-NSD3 fusion gene in radiation-associated myelodysplastic syndrome with t(8;11)(p11;p15) and expression pattern of NSD family genes.","date":"2009","source":"Cancer genetics and cytogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/19380029","citation_count":45,"is_preprint":false},{"pmid":"35532818","id":"PMC_35532818","title":"The role of NSD1, NSD2, and NSD3 histone methyltransferases in solid tumors.","date":"2022","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/35532818","citation_count":43,"is_preprint":false},{"pmid":"28102297","id":"PMC_28102297","title":"WHSC1L1-mediated EGFR mono-methylation enhances the cytoplasmic and nuclear oncogenic activity of EGFR in head and neck cancer.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28102297","citation_count":43,"is_preprint":false},{"pmid":"25466466","id":"PMC_25466466","title":"NSD3-NUT-expressing midline carcinoma of the lung: first characterization of primary cancer tissue.","date":"2014","source":"Pathology, research and practice","url":"https://pubmed.ncbi.nlm.nih.gov/25466466","citation_count":39,"is_preprint":false},{"pmid":"27285764","id":"PMC_27285764","title":"WHSC1L1 drives cell cycle progression through transcriptional regulation of CDC6 and CDK2 in squamous cell carcinoma of the head and neck.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27285764","citation_count":38,"is_preprint":false},{"pmid":"27005559","id":"PMC_27005559","title":"Amplification of WHSC1L1 regulates expression and estrogen-independent activation of ERα in SUM-44 breast cancer cells and is associated with ERα over-expression in breast cancer.","date":"2016","source":"Molecular oncology","url":"https://pubmed.ncbi.nlm.nih.gov/27005559","citation_count":38,"is_preprint":false},{"pmid":"24051013","id":"PMC_24051013","title":"PPAPDC1B and WHSC1L1 are common drivers of the 8p11-12 amplicon, not only in breast tumors but also in pancreatic adenocarcinomas and lung tumors.","date":"2013","source":"The American journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/24051013","citation_count":34,"is_preprint":false},{"pmid":"15483650","id":"PMC_15483650","title":"Evaluation of NSD2 and NSD3 in overgrowth syndromes.","date":"2005","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/15483650","citation_count":33,"is_preprint":false},{"pmid":"25685583","id":"PMC_25685583","title":"Cytological Features of a Variant NUT Midline Carcinoma of the Lung Harboring the NSD3-NUT Fusion Gene: A Case Report and Literature Review.","date":"2015","source":"Case reports in pathology","url":"https://pubmed.ncbi.nlm.nih.gov/25685583","citation_count":32,"is_preprint":false},{"pmid":"35717870","id":"PMC_35717870","title":"Discovery of a potent and selective proteolysis targeting chimera (PROTAC) degrader of NSD3 histone methyltransferase.","date":"2022","source":"European journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/35717870","citation_count":31,"is_preprint":false},{"pmid":"34997561","id":"PMC_34997561","title":"Thyroid Carcinoma with NSD3::NUTM1 Fusion: a Case with Thyrocyte Differentiation and Colloid Production.","date":"2022","source":"Endocrine pathology","url":"https://pubmed.ncbi.nlm.nih.gov/34997561","citation_count":27,"is_preprint":false},{"pmid":"28781807","id":"PMC_28781807","title":"Amplification of the NSD3-BRD4-CHD8 pathway in pelvic high-grade serous carcinomas of tubo-ovarian and endometrial origin.","date":"2017","source":"Molecular and clinical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/28781807","citation_count":25,"is_preprint":false},{"pmid":"30013365","id":"PMC_30013365","title":"The role of histone lysine methyltransferase NSD3 in cancer.","date":"2018","source":"OncoTargets and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/30013365","citation_count":24,"is_preprint":false},{"pmid":"28901481","id":"PMC_28901481","title":"Silencing of histone methyltransferase NSD3 reduces cell viability in osteosarcoma with induction of apoptosis.","date":"2017","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/28901481","citation_count":24,"is_preprint":false},{"pmid":"36040068","id":"PMC_36040068","title":"NUTM1 -rearranged Carcinoma of the Thyroid : A Distinct Subset of NUT Carcinoma Characterized by Frequent NSD3 - NUTM1 Fusions.","date":"2022","source":"The American journal of surgical pathology","url":"https://pubmed.ncbi.nlm.nih.gov/36040068","citation_count":24,"is_preprint":false},{"pmid":"25318671","id":"PMC_25318671","title":"Neural crest specification and migration independently require NSD3-related lysine methyltransferase activity.","date":"2014","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/25318671","citation_count":22,"is_preprint":false},{"pmid":"31190890","id":"PMC_31190890","title":"Downregulation of NSD3 (WHSC1L1) inhibits cell proliferation and migration via ERK1/2 deactivation and decreasing CAPG expression in colorectal cancer cells.","date":"2019","source":"OncoTargets and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/31190890","citation_count":19,"is_preprint":false},{"pmid":"28484924","id":"PMC_28484924","title":"Development of mammary hyperplasia, dysplasia, and invasive ductal carcinoma in transgenic mice expressing the 8p11 amplicon oncogene NSD3.","date":"2017","source":"Breast cancer research and treatment","url":"https://pubmed.ncbi.nlm.nih.gov/28484924","citation_count":18,"is_preprint":false},{"pmid":"29634317","id":"PMC_29634317","title":"Development of a Time-Resolved Fluorescence Resonance Energy Transfer Ultrahigh-Throughput Screening Assay for Targeting the NSD3 and MYC Interaction.","date":"2018","source":"Assay and drug development technologies","url":"https://pubmed.ncbi.nlm.nih.gov/29634317","citation_count":16,"is_preprint":false},{"pmid":"39390582","id":"PMC_39390582","title":"Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation.","date":"2024","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/39390582","citation_count":14,"is_preprint":false},{"pmid":"33891143","id":"PMC_33891143","title":"NSD3-NUTM1-rearranged carcinoma of the median neck/thyroid bed developing after recent thyroidectomy for sclerosing mucoepidermoid carcinoma with eosinophilia: report of an extraordinary case.","date":"2021","source":"Virchows Archiv : an international journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/33891143","citation_count":14,"is_preprint":false},{"pmid":"34440470","id":"PMC_34440470","title":"Structure, Activity and Function of the NSD3 Protein Lysine Methyltransferase.","date":"2021","source":"Life (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/34440470","citation_count":13,"is_preprint":false},{"pmid":"37182335","id":"PMC_37182335","title":"NSD3: Advances in cancer therapeutic potential and inhibitors research.","date":"2023","source":"European journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37182335","citation_count":13,"is_preprint":false},{"pmid":"17239852","id":"PMC_17239852","title":"The histone methyltransferase activity of WHISTLE is important for the induction of apoptosis and HDAC1-mediated transcriptional repression.","date":"2006","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/17239852","citation_count":13,"is_preprint":false},{"pmid":"39119928","id":"PMC_39119928","title":"Histones Methyltransferase NSD3 Inhibits Lung Adenocarcinoma Glycolysis Through Interacting with PPP1CB to Decrease STAT3 Signaling Pathway.","date":"2024","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/39119928","citation_count":12,"is_preprint":false},{"pmid":"36291782","id":"PMC_36291782","title":"Dissecting the Immunological Profiles in NSD3-Amplified LUSC through Integrative Multi-Scale Analyses.","date":"2022","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/36291782","citation_count":11,"is_preprint":false},{"pmid":"28903324","id":"PMC_28903324","title":"The PWWP domain of the human oncogene WHSC1L1/NSD3 induces a metabolic shift toward fermentation.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/28903324","citation_count":11,"is_preprint":false},{"pmid":"34245870","id":"PMC_34245870","title":"WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction.","date":"2021","source":"Methods (San Diego, Calif.)","url":"https://pubmed.ncbi.nlm.nih.gov/34245870","citation_count":11,"is_preprint":false},{"pmid":"33835461","id":"PMC_33835461","title":"WHISTLE: A Functionally Annotated High-Accuracy Map of Human m6A Epitranscriptome.","date":"2021","source":"Methods in molecular biology (Clifton, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/33835461","citation_count":9,"is_preprint":false},{"pmid":"37072259","id":"PMC_37072259","title":"Identification of novel class inhibitors of NSD3 methyltransferase showing a unique, bivalent binding mode in the SET domain.","date":"2023","source":"Chemical biology & drug design","url":"https://pubmed.ncbi.nlm.nih.gov/37072259","citation_count":8,"is_preprint":false},{"pmid":"34357103","id":"PMC_34357103","title":"High WHSC1L1 Expression Reduces Survival Rates in Operated Breast Cancer Patients with Decreased CD8+ T Cells: Machine Learning Approach.","date":"2021","source":"Journal of personalized medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34357103","citation_count":8,"is_preprint":false},{"pmid":"31254363","id":"PMC_31254363","title":"Protective effect of histone methyltransferase NSD3 on ISO-induced cardiac hypertrophy.","date":"2019","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/31254363","citation_count":7,"is_preprint":false},{"pmid":"38256018","id":"PMC_38256018","title":"NSD3 in Cancer: Unraveling Methyltransferase-Dependent and Isoform-Specific Functions.","date":"2024","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38256018","citation_count":6,"is_preprint":false},{"pmid":"22131849","id":"PMC_22131849","title":"A case of autologous microfat grafting in lip reconstruction of a whistle deformity following cancer treatment.","date":"2010","source":"The Canadian journal of plastic surgery = Journal canadien de chirurgie plastique","url":"https://pubmed.ncbi.nlm.nih.gov/22131849","citation_count":6,"is_preprint":false},{"pmid":"37400043","id":"PMC_37400043","title":"Prospect of targeting lysine methyltransferase NSD3 for tumor therapy.","date":"2023","source":"Pharmacological research","url":"https://pubmed.ncbi.nlm.nih.gov/37400043","citation_count":5,"is_preprint":false},{"pmid":"35502835","id":"PMC_35502835","title":"Rhabdomyosarcoma With Epithelioid Features And NSD3::FOXO1 Fusion: Evidence For Reconsideration Of Previously Reported FOXO1::FGFR1 Fusion.","date":"2022","source":"International journal of surgical pathology","url":"https://pubmed.ncbi.nlm.nih.gov/35502835","citation_count":5,"is_preprint":false},{"pmid":"35880417","id":"PMC_35880417","title":"Possible Primary Thyroid Nuclear Protein in Testis Carcinomas with NSD3::NUTM1 Translocation Revealed by RNA Sequencing: A Report of Two Cases.","date":"2022","source":"Thyroid : official journal of the American Thyroid Association","url":"https://pubmed.ncbi.nlm.nih.gov/35880417","citation_count":5,"is_preprint":false},{"pmid":"37748280","id":"PMC_37748280","title":"WHSC1L1-mediated epigenetic downregulation of VMP1 participates in herpes simplex virus 1 infection-induced mitophagy impairment and neuroinflammation.","date":"2023","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/37748280","citation_count":4,"is_preprint":false},{"pmid":"37288770","id":"PMC_37288770","title":"The histone methyltransferase NSD3 contributes to sister chromatid cohesion and to cohesin loading at mitotic exit.","date":"2023","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/37288770","citation_count":4,"is_preprint":false},{"pmid":"37905045","id":"PMC_37905045","title":"Systematic perturbations of SETD2, NSD1, NSD2, NSD3 and ASH1L reveals their distinct contributions to H3K36 methylation.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37905045","citation_count":3,"is_preprint":false},{"pmid":"39628352","id":"PMC_39628352","title":"Targeted RNA sequencing in diagnostically challenging head and neck carcinomas identifies novel MON2::STAT6, NFATC2::NUTM2B, POC5::RAF1, and NSD3::NCOA2 gene fusions.","date":"2024","source":"Histopathology","url":"https://pubmed.ncbi.nlm.nih.gov/39628352","citation_count":3,"is_preprint":false},{"pmid":"31563542","id":"PMC_31563542","title":"High yield recombinant expression and purification of oncogenic NSD1, NSD2, and NSD3 with human influenza hemagglutinin tag.","date":"2019","source":"Protein expression and purification","url":"https://pubmed.ncbi.nlm.nih.gov/31563542","citation_count":3,"is_preprint":false},{"pmid":"39200173","id":"PMC_39200173","title":"NSD3::NUTM1 Fusion Sarcoma Mimicking Malignant Peripheral Nerve Sheath Tumor with Prolonged Survival.","date":"2024","source":"Biomedicines","url":"https://pubmed.ncbi.nlm.nih.gov/39200173","citation_count":3,"is_preprint":false},{"pmid":"40792216","id":"PMC_40792216","title":"Acquisition of FGFR1 and NSD3 Amplifications During the Transformation of EGFR-Mutated Lung Adenocarcinoma into Squamous Cell Carcinoma: A Case Report.","date":"2025","source":"JTO clinical and research reports","url":"https://pubmed.ncbi.nlm.nih.gov/40792216","citation_count":2,"is_preprint":false},{"pmid":"40036479","id":"PMC_40036479","title":"NSD3::FGFR1 : A Novel Gene Fusion First to Be Described in Merkel Cell Carcinoma.","date":"2025","source":"The American Journal of dermatopathology","url":"https://pubmed.ncbi.nlm.nih.gov/40036479","citation_count":2,"is_preprint":false},{"pmid":"33579784","id":"PMC_33579784","title":"Histone Methyltransferase NSD3 Is a Lung Squamous Cell Carcinoma Driver.","date":"2021","source":"Cancer discovery","url":"https://pubmed.ncbi.nlm.nih.gov/33579784","citation_count":2,"is_preprint":false},{"pmid":"25036702","id":"PMC_25036702","title":"Wetting the whistle: neurotropic factor improves salivary function.","date":"2014","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/25036702","citation_count":2,"is_preprint":false},{"pmid":"40967468","id":"PMC_40967468","title":"The histone lysine methyltransferase NSD3 drives osteosarcomagenesis by inactivating ARID3A.","date":"2025","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/40967468","citation_count":1,"is_preprint":false},{"pmid":"40578344","id":"PMC_40578344","title":"Isoform-specific function of NSD3 in DNA replication stress confers resistance to PARP inhibitors in prostate cancer.","date":"2025","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/40578344","citation_count":1,"is_preprint":false},{"pmid":"35303440","id":"PMC_35303440","title":"Degradation of NSD3: What to Myc of it all?","date":"2022","source":"Cell chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/35303440","citation_count":1,"is_preprint":false},{"pmid":"40532307","id":"PMC_40532307","title":"H3K36 histone methyltransferase NSD3 functions as a multifaceted regulator of late erythropoiesis.","date":"2025","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/40532307","citation_count":1,"is_preprint":false},{"pmid":"40143436","id":"PMC_40143436","title":"NSD3: A Promising Target for Cancer Therapy.","date":"2025","source":"Cell biochemistry and function","url":"https://pubmed.ncbi.nlm.nih.gov/40143436","citation_count":1,"is_preprint":false},{"pmid":"38516186","id":"PMC_38516186","title":"Structural insights into the C-terminus of the histone-lysine N-methyltransferase NSD3 by small-angle X-ray scattering.","date":"2024","source":"Frontiers in molecular biosciences","url":"https://pubmed.ncbi.nlm.nih.gov/38516186","citation_count":1,"is_preprint":false},{"pmid":"39741006","id":"PMC_39741006","title":"NSD3 protein methylation and stabilization transforms human ES cells into variant state.","date":"2024","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/39741006","citation_count":0,"is_preprint":false},{"pmid":"41970952","id":"PMC_41970952","title":"Histone methyltransferase G9a crosstalks with H3K36 histone methyltransferases NSD3 and SETD2 to mediate gene activation.","date":"2026","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/41970952","citation_count":0,"is_preprint":false},{"pmid":"41360235","id":"PMC_41360235","title":"Histone methyltransferase NSD3 orchestrates early erythropoiesis by regulating erythroid progenitor cell differentiation and survival.","date":"2025","source":"Biochimica et biophysica acta. Molecular cell research","url":"https://pubmed.ncbi.nlm.nih.gov/41360235","citation_count":0,"is_preprint":false},{"pmid":"41727024","id":"PMC_41727024","title":"NSD3 stabilizes nuclear compartmentalization and promotes megabase-scale chromatin interactions.","date":"2026","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41727024","citation_count":0,"is_preprint":false},{"pmid":"41820229","id":"PMC_41820229","title":"Fluorogenic Ligand Enables Identification of NSD3-Overexpressed Tumors by Targeting the PWWP1 Domain of NSD3.","date":"2026","source":"Analytical chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41820229","citation_count":0,"is_preprint":false},{"pmid":"40990092","id":"PMC_40990092","title":"NSD3::NUTM1 fusion evidenced on RNA sequencing in poorly differentiated thyroid cancer: a report of two cases.","date":"2025","source":"European thyroid journal","url":"https://pubmed.ncbi.nlm.nih.gov/40990092","citation_count":0,"is_preprint":false},{"pmid":"39285723","id":"PMC_39285723","title":"Thyroid Carcinoma With NSD3::NUTM1 Fusion and Secondary TERT Promoter Mutation: A Case Report and Literature Review.","date":"2024","source":"International journal of surgical pathology","url":"https://pubmed.ncbi.nlm.nih.gov/39285723","citation_count":0,"is_preprint":false},{"pmid":"30236198","id":"PMC_30236198","title":"[NSD3 suppresses LPS-triggered TNF-α production via promoting the dimethylation of histone H3K36 in macrophages].","date":"2018","source":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/30236198","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.11.11.687848","title":"Loop Plasticity Drives Paralog-Specific Recognition in BET ET Domains","date":"2025-11-12","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.11.687848","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.10.29.685249","title":"Inhibitory-stabilization is sufficient for history-dependent computation in a randomly connected attractor network","date":"2025-10-30","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.29.685249","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.04.12.648498","title":"Nightingales imitate the duration of whistle syllables","date":"2025-04-13","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.12.648498","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.05.16.654575","title":"Mechanisms and control of a novel vocalization: The singing mouse song is a whistle that depends on air sac inflation","date":"2025-05-22","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.16.654575","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.04.21.647658","title":"First evidence for widespread sharing of stereotyped non-signature whistle types by wild dolphins","date":"2025-04-22","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.21.647658","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.07.11.664350","title":"RACLET: the Ramp Above Critical Level Endurance Test to evaluate critical velocity in running","date":"2025-07-15","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.11.664350","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.10.15.618471","title":"Whistle variability and social acoustic interactions in bottlenose dolphins","date":"2024-10-16","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.15.618471","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.03.07.642090","title":"Shared PRAME Epitopes are T-Cell Targets in NUT Carcinoma","date":"2025-03-12","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.07.642090","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.02.14.638254","title":"Zebra finches produce intralaryngeal laminar flow whistles during panting","date":"2025-02-14","source":"bioRxiv","url":"https://doi.org/10.1101/2025.02.14.638254","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.01.13.632779","title":"Courtship vocalizations in male ducks: spectral composition and resonance of the syringeal bulla","date":"2025-01-14","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.13.632779","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.08.10.607446","title":"H3K36 Methylation - a Guardian of Epigenome Integrity","date":"2024-08-10","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.10.607446","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.05.14.594143","title":"Pulsed sounds caused by internal oxygen transport during photosynthesis in the seagrass<i>Halophila ovalis</i>","date":"2024-05-14","source":"bioRxiv","url":"https://doi.org/10.1101/2024.05.14.594143","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":42144,"output_tokens":6035,"usd":0.108479},"stage2":{"model":"claude-opus-4-6","input_tokens":9656,"output_tokens":3533,"usd":0.204907},"total_usd":0.313386,"stage1_batch_id":"msgbatch_012ZiiCUBfB62NCTQd4Bk1Jo","stage2_batch_id":"msgbatch_01Xuqq9aUHoQouS7UVGZNStZ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"NSD3 interacts with the extraterminal (ET) domain of BRD4 (and BRD2/BRD3), and the BRD4/NSD3 complex regulates H3K36 methylation at BRD4 target genes; NSD3 is recruited to regulated genes in a BRD4-dependent manner and imparts pTEFb-independent transcriptional activation.\",\n      \"method\": \"Proteomic/mass spectrometry pulldown, co-immunoprecipitation, ChIP, siRNA knockdown with H3K36me measurement\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, ChIP, and functional depletion with defined histone modification readout; moderate-to-strong evidence from multiple orthogonal methods\",\n      \"pmids\": [\"21555454\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"NSD3-short (a short isoform lacking the methyltransferase domain) acts as an adaptor protein linking BRD4 to the CHD8 chromatin remodeler via its PWWP chromatin-reader module and an acidic transactivation domain; the BRD4-NSD3-CHD8 complex co-localizes at super-enhancers in AML cells and is required for leukemia maintenance.\",\n      \"method\": \"Co-immunoprecipitation, ChIP-seq, CRISPR/shRNA knockdown with transcriptional and phenotypic readouts, genetic epistasis\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Co-IP, ChIP-seq, genetic targeting), replicated phenotypic and molecular readouts\",\n      \"pmids\": [\"26626481\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Crystal structure of the BRD4 ET domain bound to an NSD3-derived amphipathic peptide revealed that ET domain recognition occurs via a two-strand antiparallel β-sheet anchored on a hydrophobic cleft of a three-helix bundle; this structural mechanism is essential for AML maintenance.\",\n      \"method\": \"X-ray crystallography, structure-guided mutagenesis, functional validation in AML cells\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with functional validation\",\n      \"pmids\": [\"27291650\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The PHD5-C5HCH module of NSD3 folds into a novel integrated PHD-PHD-like structural module that binds unmodified H3K4 and trimethylated H3K9 (H3K9me3) on the surface of PHD5; this differs from NSD2 (which prefers H3K9me0) and NSD1 (which does not bind H3 peptides), providing a mechanism for genomic targeting.\",\n      \"method\": \"X-ray crystallography of PHD5-C5HCH free and in complex with H3 peptides; binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structures with multiple peptide complexes and orthogonal binding assays\",\n      \"pmids\": [\"23269674\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NSD3 is the principal oncogenic driver in lung squamous cell carcinoma (LUSC) within the 8p11-12 amplicon; a cancer-associated variant NSD3(T1232A) shows increased catalytic activity for H3K36me2 in vitro and in vivo, and structural dynamic analyses revealed that T1232A relieves auto-inhibition and increases H3 substrate accessibility.\",\n      \"method\": \"In vitro methyltransferase assay, structural dynamic analysis, mouse LUSC model (KO and knock-in), patient-derived xenografts, ChIP-seq\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro catalytic assay, structural analysis, and multiple in vivo models with strong mechanistic follow-up\",\n      \"pmids\": [\"33536620\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"NSD3 (WHSC1L1) directly methylates IRF3 at lysine 366 (K366me1) via its SET domain; NSD3 binds the IRF3 C-terminal region through its PWWP1 domain. K366 monomethylation promotes IRF3 dissociation from the phosphatase PP1cc, sustaining IRF3 phosphorylation and type I interferon production during antiviral innate immunity.\",\n      \"method\": \"Mass spectrometry identification of IRF3-associated proteins, co-immunoprecipitation, in vitro methylation assay, NSD3 knockout mice, site-directed mutagenesis\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro methylation, in vivo KO, and mechanistic dissection of PP1cc interaction with multiple orthogonal methods\",\n      \"pmids\": [\"29101251\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"WHSC1L1 (NSD3) mono-methylates EGFR at lysine 721 (K721) in the tyrosine kinase domain, enhancing ERK cascade activation without EGF stimulation; nuclear EGFR K721 methylation also enhances interaction with PCNA, promoting DNA synthesis and cell cycle progression in head and neck squamous cell carcinoma.\",\n      \"method\": \"In vitro methylation assay, co-immunoprecipitation, functional siRNA knockdown, cell cycle analysis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro methylation assay with site-specific mutagenesis and multiple downstream functional readouts\",\n      \"pmids\": [\"28102297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"WHSC1L1 (NSD3) and H3K36me2 are enriched in the gene bodies of CDC6 and CDK2; WHSC1L1 knockdown causes G0/G1 arrest that is rescued by wild-type WHSC1L1 but not by enzyme-inactive WHSC1L1, demonstrating that catalytic activity-dependent H3K36me2 drives G1-to-S phase transition in head and neck cancer cells.\",\n      \"method\": \"ChIP, siRNA knockdown, cell cycle analysis, rescue with catalytic mutant\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP with catalytic mutant rescue establishes enzymatic mechanism clearly\",\n      \"pmids\": [\"27285764\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The long isoform of NSD3 (but not the short isoform lacking the catalytic domain) cooperates with EZH2 and RNA polymerase II to stimulate H3K36me2/3-dependent transactivation of genes involved in NOTCH receptor cleavage, leading to nuclear accumulation of NICD and NICD-mediated E-cadherin repression in breast cancer.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, isoform-specific knockdown/overexpression, in vivo mouse model\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — isoform-specific functional dissection with co-IP, ChIP, and in vivo validation\",\n      \"pmids\": [\"32967925\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The PWWP1 domain of NSD3 binds the methyl-lysine site and is required for viability of AML cells; the fragment-derived chemical probe BI-9321 antagonizes this domain with sub-micromolar in vitro activity and cellular target engagement, downregulating Myc mRNA.\",\n      \"method\": \"Fragment-based drug discovery, structural characterization, cellular target engagement assay, mRNA expression\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — structure-guided probe development with cellular functional validation\",\n      \"pmids\": [\"31285596\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NSD3-NUT fusion oncoprotein is necessary and sufficient for blockade of differentiation and maintenance of proliferation in NUT midline carcinoma cells; NSD3-NUT binds BRD4, and NSD3 is also required for the blockade of differentiation in BRD4-NUT-expressing NMC cells.\",\n      \"method\": \"Patient-derived cell line, shRNA knockdown, overexpression, co-immunoprecipitation, BET bromodomain inhibitor treatment\",\n      \"journal\": \"Cancer discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — necessity and sufficiency experiments with Co-IP; replicated in multiple NMC cell line contexts\",\n      \"pmids\": [\"24875858\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NSD3 (long isoform) interacts with the cohesin loader complex kollerin (NIPBL/MAU2) and promotes chromatin recruitment of MAU2 and cohesin at mitotic exit; NSD3 associates with chromatin in early anaphase before cohesin loading and its methyltransferase activity is required for efficient sister chromatid cohesion.\",\n      \"method\": \"Co-immunoprecipitation, chromatin fractionation, live cell imaging, siRNA knockdown, catalytic mutant rescue\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, fractionation, live imaging, and catalytic mutant rescue across multiple orthogonal approaches\",\n      \"pmids\": [\"37288770\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NSD3 is required for neural crest specification and migration in chick embryos; NSD3 loss impairs expression of neural plate border gene Msx1 and neural crest transcription factors Sox10, Snail2, Sox9, and FoxD3; H3K36me2 at the Sox10 locus specifically requires NSD3, and NSD3-related methyltransferase activity is independently required for neural crest migration.\",\n      \"method\": \"Morpholino knockdown in chick, dominant-negative expression, ChIP for H3K36me2, temporal rescue experiments\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP-validated H3K36me2 dependence, temporal loss-of-function, and dominant-negative approach with specific phenotypic readouts\",\n      \"pmids\": [\"25318671\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NSD3 deposits H3K36me2 peaks specifically at active promoters and enhancers (not broad intergenic domains), occupying a distinct genomic niche from NSD1/NSD2 which establish broad intergenic H3K36me2 domains; a hierarchy of K36 methyltransferase activity was established: NSD1 > NSD2 > NSD3 > ASH1L.\",\n      \"method\": \"Sequential CRISPR knockouts of multiple K36 methyltransferases, ChIP-seq, comparative H3K36me1/2/3 mapping in mouse mesenchymal stem cells\",\n      \"journal\": \"Genome biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — systematic genetic perturbation with genome-wide ChIP-seq; strong mechanistic dissection across multiple enzymes\",\n      \"pmids\": [\"39390582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"A NSD3-targeting PROTAC (MS9715) linking BI-9321 (PWWP1 antagonist) to a VHL ligand induces specific NSD3 degradation and suppresses both NSD3- and cMyc-associated gene expression programs in hematological cancer cells; degradation is superior to PWWP1 domain blockade alone.\",\n      \"method\": \"PROTAC design, Western blot protein degradation, RNA-seq, CRISPR-Cas9 NSD3 KO comparison, cell viability\",\n      \"journal\": \"Cell chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — mechanistic PROTAC study with transcriptomic validation and comparison to CRISPR KO\",\n      \"pmids\": [\"34469831\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"NSD3 (WHISTLE isoform) is recruited to the p450c17 promoter via interaction with SF-1 and represses steroidogenesis gene transcription during prepubertal stages; it interacts with HSP90α and the H3K9 demethylase JMJD1C, which subsequently replaces WHISTLE to activate target gene expression.\",\n      \"method\": \"TAP immunoaffinity purification of WHISTLE complexes, co-immunoprecipitation, ChIP\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — TAP-purification and ChIP with functional context, but single lab\",\n      \"pmids\": [\"20530532\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"The WHISTLE isoform of NSD3 induces apoptosis in an HMTase activity-dependent manner and represses transcription through HDAC1 recruitment; the N-terminus PWWP region is required for HMTase activity, and SET domain cysteine 297 is a critical catalytic residue.\",\n      \"method\": \"Point mutagenesis, deletion mapping, luciferase reporter assay, caspase-3 activation assay\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — active-site mutagenesis with functional readouts, single lab\",\n      \"pmids\": [\"17239852\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NSD3 interacts with and methylates NSD3 itself at lysine 477 (via EHMT2); this methylation stabilizes NSD3 protein levels in variant hESCs by protecting it from proteasomal degradation, driving oncogenic transformation.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, site-directed mutagenesis, protein stability assays, NSD3 knockdown rescue\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP with MS identification and functional mutagenesis, single lab\",\n      \"pmids\": [\"39741006\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"NSD3-short (NSD3S) directly interacts with MYC; a TR-FRET assay was developed to monitor this interaction and confirmed by an orthogonal protein-protein interaction assay, supporting a mechanism by which NSD3S regulates cell proliferation through MYC engagement.\",\n      \"method\": \"TR-FRET cell lysate assay, orthogonal Co-IP/pulldown confirmation\",\n      \"journal\": \"Assay and drug development technologies\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — biochemical interaction assay with orthogonal confirmation, functional significance inferred\",\n      \"pmids\": [\"29634317\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NSD3 binds PPP1CB and p-STAT3, forming a trimeric complex that dephosphorylates p-STAT3 via PPP1CB phosphatase activity, leading to suppression of HK2 transcription and glycolysis inhibition in lung adenocarcinoma.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, metabolic assays (glucose uptake, lactate), Western blot\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — Co-IP demonstrating trimeric complex with functional metabolic readouts, single lab\",\n      \"pmids\": [\"39119928\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ISO-induced cardiac hypertrophy decreases NSD3 expression, which reduces H3K27me2/3 on the ANF promoter and disrupts NSD3-BRD4 association; overexpression of NSD3 attenuates hypertrophy by promoting BRD4-association and H3K27 methylation to suppress ANF transcription.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, overexpression and knockdown in cardiomyocytes, in vivo mouse model\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — Co-IP, ChIP, and in vivo model, single lab\",\n      \"pmids\": [\"31254363\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The short isoform NSD3S (lacking the methyltransferase domain) is stabilized by CUL3-ZBTB2 E3 ligase complex dysregulation; ATR kinase drives localization of NSD3S to stalled replication forks, where NSD3S antagonizes PTIP-dependent MRE11 nuclease recruitment to protect nascent DNA from degradation and confer PARP inhibitor resistance.\",\n      \"method\": \"Co-immunoprecipitation, proximity ligation, replication fork protection assay, NSD3-targeting PROTAC, xenograft and PDX mouse models\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — mechanistic dissection with fork protection assays, Co-IP, in vivo PDX models, and pharmacological validation\",\n      \"pmids\": [\"40578344\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NSD3 specifically enhances H3K27 di-methylation (not H3K36me) in osteosarcoma cells to inactivate the transcriptional repressor ARID3A, causing altered expression of RUNX2, MMP13, OCT4, and NANOG and a shift toward a primitive differentiation state.\",\n      \"method\": \"CRISPR-Cas9 and lentiviral gain/loss-of-function, ChIP, transcriptomic analysis, spontaneous metastasis mouse model\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP with gain/loss-of-function and in vivo model, single lab; unexpected substrate (H3K27me2) warrants independent replication\",\n      \"pmids\": [\"40967468\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"WHSC1L1 (NSD3) epigenetically suppresses VMP1 transcription via H3K36me2-dependent recruitment of DNMT3A to the VMP1 promoter following HSV-1 infection; NSD3 upregulation impairs mitophagy and promotes neuroinflammation in microglia.\",\n      \"method\": \"ChIP, siRNA knockdown, VMP1 overexpression rescue, in vivo mouse HSV-1 infection model\",\n      \"journal\": \"Molecular immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — ChIP with DNMT3A recruitment mechanism and in vivo rescue, single lab\",\n      \"pmids\": [\"37748280\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"NSD3 is recruited to β-globin gene promoters by G9a; NSD3 stabilizes Mediator complex binding at the promoter and facilitates SETD2-mediated H3K36me3 in the gene body to activate globin gene expression; G9a, NSD3, and SETD2 form a coactivator axis in differentiating erythroid cells.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, siRNA knockdown of NSD3 and G9a, gene expression analysis in differentiating erythroid cells\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — Co-IP, ChIP, and functional knockdown in erythroid differentiation context, single lab\",\n      \"pmids\": [\"41970952\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"NSD3 (WHSC1L1) encodes a protein with two PWWP domains, five PHD zinc finger motifs, a SAC domain, and a SET domain; two major isoforms arise from alternative splicing — a long isoform (1437 aa, full SET domain) and a short isoform (645 aa, PWWP domain only); the gene maps to 8p11.2 and is frequently amplified in breast cancer.\",\n      \"method\": \"cDNA cloning, genomic mapping, domain analysis, Northern blot, FISH\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — foundational characterization study, gene structure and isoform identification\",\n      \"pmids\": [\"11549311\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NSD3 is a histone H3K36 mono- and di-methyltransferase whose long isoform (NSD3L) deposits H3K36me2 preferentially at active promoters and enhancers to drive transcription, while its short catalytically-inactive isoform (NSD3S) acts as a chromatin adaptor linking BRD4 to the CHD8 remodeler and MYC via its PWWP1 reader domain; beyond histone substrates, NSD3 also directly methylates non-histone proteins including IRF3 (K366) and EGFR (K721), regulates sister chromatid cohesion by promoting cohesin loader (kollerin) recruitment, protects stalled replication forks from MRE11-mediated degradation, and its oncogenic gain-of-function variant T1232A relieves catalytic auto-inhibition to hyperstimulate H3K36me2 in lung squamous cell carcinoma.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"NSD3 is a histone lysine methyltransferase that deposits H3K36me1/me2 at active promoters and enhancers to regulate transcription, cell cycle progression, and developmental programs, while also functioning through a catalytically inactive short isoform (NSD3S) that serves as a chromatin adaptor bridging BRD4, CHD8, and MYC [PMID:39390582, PMID:26626481, PMID:21555454]. The long isoform catalyzes H3K36 methylation through its SET domain—regulated by an autoinhibitory loop relieved by the oncogenic T1232A variant—and also methylates non-histone substrates IRF3 (K366) and EGFR (K721) to modulate innate immune signaling and receptor tyrosine kinase activity, respectively [PMID:33536620, PMID:29101251, PMID:28102297]. NSD3 promotes sister chromatid cohesion by recruiting the kollerin cohesin-loader complex at mitotic exit, and the NSD3S isoform protects stalled replication forks from MRE11-mediated degradation downstream of ATR kinase, conferring PARP inhibitor resistance [PMID:37288770, PMID:40578344]. NSD3 is recurrently amplified or mutationally activated in breast cancer, lung squamous cell carcinoma, and acute myeloid leukemia, and NSD3-NUT fusions drive NUT midline carcinoma [PMID:33536620, PMID:24875858].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Identification of NSD3 as a SET-domain gene at 8p11.2 with two major isoforms (long/catalytic and short/PWWP-only) established the molecular framework for understanding its dual enzymatic and adaptor functions.\",\n      \"evidence\": \"cDNA cloning, domain analysis, and FISH mapping in breast cancer amplicon\",\n      \"pmids\": [\"11549311\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No enzymatic activity demonstrated\", \"Protein partners unknown\", \"Single-lab characterization\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Demonstration that the WHISTLE isoform possesses HMTase activity dependent on the SET domain C297 residue and PWWP region, and that this activity is required for transcriptional repression and apoptosis induction, established NSD3 as a functional methyltransferase.\",\n      \"evidence\": \"Point mutagenesis, luciferase reporter, caspase-3 assay\",\n      \"pmids\": [\"17239852\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Histone substrate specificity not defined\", \"No structural basis for catalysis\", \"Single-lab study\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Discovery that NSD3 physically interacts with BRD4 via the ET domain and deposits H3K36me at BRD4-target genes revealed how NSD3 is genomically targeted and established the BRD4-NSD3 axis as a transcriptional activation mechanism independent of pTEFb.\",\n      \"evidence\": \"Mass spectrometry pulldown, reciprocal Co-IP, ChIP, siRNA knockdown in human cells\",\n      \"pmids\": [\"21555454\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Isoform-specific contributions to BRD4 complex not resolved\", \"Genome-wide H3K36me targets not mapped\", \"Mechanism of pTEFb-independent activation unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Structural determination of the PHD5-C5HCH module revealed a novel integrated reader that binds H3K4me0/H3K9me3, providing a chromatin-targeting mechanism distinct from NSD1 and NSD2.\",\n      \"evidence\": \"X-ray crystallography of PHD5-C5HCH with H3 peptide complexes and binding assays\",\n      \"pmids\": [\"23269674\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genomic loci where PHD5-dependent targeting operates not identified\", \"Functional consequence of H3K9me3 recognition on gene expression not tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Two studies established NSD3's biological roles in differentiation: NSD3-NUT fusions block differentiation in NUT midline carcinoma through BRD4, and NSD3 is required for neural crest specification/migration via H3K36me2 at the Sox10 locus, demonstrating context-dependent developmental and oncogenic functions.\",\n      \"evidence\": \"shRNA/overexpression in NMC cells with BET inhibitor validation; morpholino and dominant-negative in chick embryos with ChIP\",\n      \"pmids\": [\"24875858\", \"25318671\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct NSD3-NUT catalytic activity not assessed\", \"Full target gene repertoire in neural crest unknown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identification of NSD3-short as a non-catalytic adaptor bridging BRD4 to CHD8 at super-enhancers in AML cells resolved how the short isoform contributes to oncogenesis independently of methyltransferase activity.\",\n      \"evidence\": \"Co-IP, ChIP-seq, CRISPR/shRNA knockdown in AML cells with transcriptional and phenotypic readouts\",\n      \"pmids\": [\"26626481\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether NSD3S-CHD8 complex remodels nucleosomes directly not shown\", \"Relative contribution of long vs. short isoform in AML unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Crystal structure of the BRD4 ET–NSD3 peptide interface and demonstration that NSD3 catalytic activity drives G1-to-S cell cycle progression through H3K36me2 at CDC6/CDK2 gene bodies defined both the structural basis of the BRD4 interaction and a direct proliferative mechanism.\",\n      \"evidence\": \"X-ray crystallography with structure-guided mutagenesis; ChIP with catalytic mutant rescue and cell cycle analysis in HNSCC cells\",\n      \"pmids\": [\"27291650\", \"27285764\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether cell cycle role is BRD4-dependent not tested\", \"Genome-wide targets beyond CDC6/CDK2 not mapped\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Discovery that NSD3 methylates non-histone substrates IRF3 (K366) and EGFR (K721) expanded NSD3's substrate repertoire beyond histones, linking it to innate immune signaling and receptor tyrosine kinase pathways.\",\n      \"evidence\": \"In vitro methylation assays, Co-IP, NSD3 KO mice for IRF3; siRNA and cell cycle analysis for EGFR in HNSCC\",\n      \"pmids\": [\"29101251\", \"28102297\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full non-histone substrate repertoire unknown\", \"Structural basis for non-histone substrate recognition not determined\", \"In vivo relevance of EGFR K721me not demonstrated in animal models\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Development of the PWWP1-domain chemical probe BI-9321 that downregulates MYC in AML provided pharmacological validation that the PWWP1 reader domain is essential for NSD3-dependent oncogenic transcription.\",\n      \"evidence\": \"Fragment-based drug discovery, structural characterization, cellular target engagement in AML cells\",\n      \"pmids\": [\"31285596\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Selectivity over NSD1/NSD2 PWWP domains not fully defined\", \"In vivo anti-tumor efficacy not demonstrated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identification of NSD3 T1232A as a gain-of-function driver in lung squamous cell carcinoma that relieves autoinhibition to increase H3K36me2, and development of NSD3-targeting PROTACs, defined NSD3 as a druggable oncogenic target with a precise structural mechanism of activation.\",\n      \"evidence\": \"In vitro methyltransferase assay, structural dynamic analysis, LUSC mouse models, PDX; PROTAC degradation with RNA-seq comparison to CRISPR KO\",\n      \"pmids\": [\"33536620\", \"34469831\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether autoinhibition relief mechanism is generalizable to other NSD3 mutations not tested\", \"Clinical applicability of NSD3 PROTACs not evaluated\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Discovery that NSD3 interacts with the kollerin cohesin loader to promote sister chromatid cohesion at mitotic exit revealed a novel non-transcriptional, cell-division-coupled function for NSD3's catalytic activity.\",\n      \"evidence\": \"Co-IP, chromatin fractionation, live cell imaging, catalytic mutant rescue\",\n      \"pmids\": [\"37288770\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Histone mark deposited at cohesion sites not identified\", \"Whether cohesion defects contribute to NSD3-driven aneuploidy/oncogenesis not established\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Genome-wide dissection of H3K36me2 deposition showed NSD3 uniquely marks active promoters and enhancers rather than broad intergenic domains, establishing a distinct chromatin niche from NSD1/NSD2 and clarifying the non-redundant function of NSD3 in the NSD family.\",\n      \"evidence\": \"Sequential CRISPR knockouts of K36 methyltransferases with ChIP-seq in mouse mesenchymal stem cells\",\n      \"pmids\": [\"39390582\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether promoter-specific targeting depends on reader domains or interacting partners not resolved\", \"Functional consequence of promoter-restricted H3K36me2 vs. intergenic domains not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstration that NSD3S is recruited to stalled replication forks by ATR kinase to protect nascent DNA from MRE11-mediated degradation, conferring PARP inhibitor resistance, revealed a replication stress response function for the catalytically inactive isoform.\",\n      \"evidence\": \"Co-IP, proximity ligation, fork protection assay, NSD3-targeting PROTAC, xenograft and PDX models\",\n      \"pmids\": [\"40578344\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Phosphorylation site(s) on NSD3S mediating ATR-dependent recruitment not mapped\", \"Whether NSD3S fork protection is PWWP1-dependent not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include how NSD3's promoter/enhancer-specific H3K36me2 deposition is mechanistically directed, the full scope of non-histone substrates, the structural basis for autoinhibition and its relief, and whether the cohesion and replication fork protection functions of NSD3 are coordinated or independent.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No full-length NSD3 structure available\", \"Relative contributions of long and short isoforms in specific cancer types remain unclear\", \"Interplay between NSD3 reader domains and catalytic activity in genomic targeting not defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 4, 5, 6, 7, 8, 12, 13, 16]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [3, 9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 18, 21]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [5, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1, 7, 8, 11, 13]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [3, 11, 13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 4, 7, 8, 12, 13]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 1, 7, 8, 15, 24]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [7, 11]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [4, 10, 14]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [21]}\n    ],\n    \"complexes\": [\n      \"BRD4-NSD3-CHD8\",\n      \"NSD3-kollerin (NIPBL/MAU2)\"\n    ],\n    \"partners\": [\n      \"BRD4\",\n      \"CHD8\",\n      \"MYC\",\n      \"NIPBL\",\n      \"MAU2\",\n      \"IRF3\",\n      \"EGFR\",\n      \"G9a\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}