{"gene":"E2F3","run_date":"2026-04-28T17:46:03","timeline":{"discoveries":[{"year":1998,"finding":"E2F3 DNA-binding activity specifically reaccumulates at G1/S transitions in proliferating cells (unlike other E2Fs), and immunodepletion of E2F3 activity inhibits S phase induction. E2F3 regulates a cell-cycle-regulated subset of E2F target genes including Cdc6, cyclin E, and cdk2.","method":"Immunodepletion, E2F-specific binding assays, cell cycle synchronization, gene expression analysis","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — reciprocal functional depletion with defined S phase phenotype, replicated across multiple methods","pmids":["9679057"],"is_preprint":false},{"year":2000,"finding":"The E2F3 locus encodes two isoforms: E2F3a (growth-regulated, expressed in proliferating cells) and E2F3b (constitutively expressed, transcribed from an intronic promoter). E2F3b specifically associates with Rb in quiescent cells and represents the predominant E2F-Rb complex in quiescent cells, whereas E2F3a is tightly regulated by cell growth.","method":"Identification of novel mRNA/protein isoform, co-immunoprecipitation, cell cycle fractionation, promoter mapping","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 — isoform identified by unique mRNA/exon, Rb interaction confirmed by Co-IP, expression pattern validated across conditions","pmids":["10779352"],"is_preprint":false},{"year":2000,"finding":"The E2F3a promoter is negatively regulated by E2F binding sites in quiescent cells (similar to E2F1/E2F2) and positively regulated by Myc-binding E-box elements in response to growth stimulation. E2F3b promoter is constitutively active, more similar to E2F4/E2F5 regulation.","method":"Promoter deletion analysis, reporter assays, Myc co-transfection","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — promoter dissection with defined binding sites and functional reporter assays","pmids":["10779353"],"is_preprint":false},{"year":2003,"finding":"E2F3-specific interaction with the E-box factor TFE3 is mediated by the marked box domain of E2F3 (not E2F1 or E2F2). This interaction synergistically activates transcription of the p68 subunit of DNA polymerase alpha, and both TFE3 and E2F3 are bound to the p68 promoter in vivo.","method":"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), reporter assays, domain mapping/mutagenesis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 — binding partner identified with reciprocal Co-IP, domain mapping, ChIP confirmation in vivo, functional reporter assays","pmids":["12748276"],"is_preprint":false},{"year":2003,"finding":"Loss of E2F3 (but not E2F1, E2F2, E2F4, or E2F5) in mouse embryo fibroblasts results in unregulated cyclin E-dependent kinase activity, defects in nucleophosmin B association with centrosomes, premature centriole separation/duplication, centrosome amplification, mitotic spindle defects, and aneuploidy.","method":"E2f3 knockout MEFs, kinase assays, centrosome immunofluorescence, comparison with other E2F knockouts","journal":"Cancer cell","confidence":"High","confidence_rationale":"Tier 2 — specific genetic loss-of-function with multiple orthogonal phenotypic readouts; E2F3-specific effect confirmed by comparison to other family members","pmids":["12726860"],"is_preprint":false},{"year":2004,"finding":"E2F3 (predominantly E2F3b in quiescent cells) occupies and represses the Arf tumor suppressor promoter in wild-type MEFs. Loss of E2f3 derepresses Arf, triggering p53 activation and p21Cip1 expression. Arf mutation suppresses p53/p21 induction in E2f3-deficient cells and rescues their cell cycle re-entry defect. Activating E2Fs (E2F1 and E2F3a) are recruited to the Arf promoter in oncogenic conditions.","method":"ChIP, genetic epistasis (E2f3/Arf double mutants), MEF proliferation assays, western blot for p53/p21","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP identifies E2F3 at Arf promoter, genetic epistasis with Arf mutation rescues E2f3-null phenotype, multiple orthogonal methods","pmids":["15175242"],"is_preprint":false},{"year":2009,"finding":"E2F3a is induced by DNA damage through both transcriptional and posttranslational mechanisms. E2F3a is a substrate for checkpoint kinases (Chk kinases) and mutation of the Chk phosphorylation site eliminates DNA damage inducibility. E2F3 is required for DNA damage-induced apoptosis and for transcriptional induction of E2F1 and E2F2 in response to DNA damage.","method":"In vitro kinase assay, phosphorylation site mutagenesis, E2f3-deficient MEFs and mice, apoptosis assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro kinase assay with mutagenesis, validated in vivo with E2f3 KO, multiple methods","pmids":["19917728"],"is_preprint":false},{"year":2006,"finding":"E2F1, E2F2, and E2F3 are required for the negative regulation of the p53-p21CIP1 axis; loss of all three leads to elevated p21CIP1 and G1/S arrest. Inactivation of p21CIP1 restores G1/S entry in E2f1-3 triple-deficient cells, while p53 loss restores both G1/S and G2/M progression and enables oncogenic transformation.","method":"Genetic epistasis (E2f1/2/3 triple KO combined with p21 or p53 KO MEFs), cell cycle analysis, transformation assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — clear genetic epistasis with multiple double/triple mutant combinations","pmids":["17008321"],"is_preprint":false},{"year":2002,"finding":"E2F3 loss has the most pronounced effect on reducing ectopic proliferation of fiber cells in Rb-/- lenses; E2F1 is uniquely required for apoptosis in Rb-/- lenses and retinas; E2F3 loss almost completely eliminates ectopic DNA replication and apoptosis in Rb-/- CNS.","method":"Compound Rb/E2f mutant mice, in vivo BrdU incorporation, TUNEL apoptosis assay","journal":"Cell growth & differentiation","confidence":"High","confidence_rationale":"Tier 2 — in vivo genetic epistasis with tissue-specific phenotypic readouts across multiple E2F family members","pmids":["12065245"],"is_preprint":false},{"year":2002,"finding":"E2f3 loss causes premature death with congestive heart failure (not tumor formation); E2F1 and E2F3 play critical overlapping roles in development of multiple tissues; tumor suppression is a specific property of E2F1, not E2F3.","method":"E2f3 mutant mice, E2f1/E2f3 compound mutant mice, pathological and developmental analysis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — in vivo genetic analysis with defined phenotypic outcomes distinguishing E2F family members","pmids":["11909960"],"is_preprint":false},{"year":2007,"finding":"Neuronal migration is specifically mediated through E2F3 in a cell-cycle-independent manner; both E2F1 and E2F3 are required for neural precursor proliferation and cell cycle exit, but only E2F3 mediates the Rb requirement for neuronal migration.","method":"Rb/E2f1 and Rb/E2f3 compound null mice, BrdU labeling, cortical layering analysis, migration assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — in vivo genetic epistasis with distinct tissue phenotypes, multiple E2F comparisons","pmids":["17452454"],"is_preprint":false},{"year":2008,"finding":"E2F3a and E2f3b make overlapping but different contributions: E2f3a inactivation causes a low-penetrance proliferation defect in vitro; combined E2f3a/E2f1 mutation causes neonatal lethality and cartilage defects; E2f3b loss alone has no detected in vitro or in vivo defect.","method":"Isoform-specific E2f3a and E2f3b knockout mice, MEF proliferation assays, developmental phenotype analysis","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 — isoform-specific genetic knockouts with multiple in vitro and in vivo readouts","pmids":["18663357"],"is_preprint":false},{"year":2008,"finding":"E2F3 directly binds to the Aurora-A promoter and transcriptionally activates Aurora-A expression during G2/M. Knockdown of E2F3 decreases Aurora-A mRNA/protein and delays G2/M entry. A region 96 bp upstream of the Aurora-A transcription start site is critical for E2F3-mediated activation.","method":"ChIP, promoter deletion/mutation analysis, reporter assay, E2F3 knockdown, cell cycle analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP, promoter mutagenesis, and KD with defined cell cycle phenotype","pmids":["18776222"],"is_preprint":false},{"year":2008,"finding":"E2F3 is essential for normal cardiac development; E2f3-/- mice show impaired embryonic myocardium proliferation, hypoplastic ventricular walls, septal defects, ultrastructural cardiac muscle defects, and death from congestive heart failure.","method":"E2f3 knockout mice, cardiac histology, BrdU proliferation, echocardiography/ultrastructure","journal":"Cell cycle","confidence":"High","confidence_rationale":"Tier 2 — in vivo KO with defined developmental and functional cardiac phenotype","pmids":["19029823"],"is_preprint":false},{"year":2011,"finding":"The SNF2-like helicase HELLS physically interacts with E2F3A in vivo and is required for induction of E2F target genes and cell cycle re-entry. HELLS and E2F3A/B co-occupy gene promoters genome-wide. HELLS depletion severely perturbs E2F3-dependent transcription and growth.","method":"Mass spectrometry identification of E2F3B interactors, Co-IP, ChIP-seq, siRNA knockdown, gene expression analysis","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1-2 — MS-identified binding partner validated by Co-IP, genome-wide ChIP-seq, functional knockdown with defined transcriptional phenotype","pmids":["22157815"],"is_preprint":false},{"year":2012,"finding":"APC/C(Cdh1) ubiquitin ligase targets E2F3 for proteasome-dependent degradation during cell cycle exit. E2F3 interacts with Cdh1 but not Cdc20; enforced Cdh1 expression causes proteasome-dependent E2F3 degradation; Cdh1 silencing stabilizes E2F3 in differentiating neuroblastoma cells.","method":"Co-immunoprecipitation (E2F3 with Cdh1/Cdc20), proteasome inhibitor experiments, Cdh1 overexpression/siRNA knockdown, western blot","journal":"Cell cycle","confidence":"High","confidence_rationale":"Tier 1-2 — biochemical interaction plus gain- and loss-of-function of the E3 ligase component","pmids":["22580460"],"is_preprint":false},{"year":2012,"finding":"Human Pumilio homologs Pum1 and Pum2 repress E2F3 translation by binding to the E2F3 3' UTR and enhance the activity of multiple E2F3-targeting miRNAs. This Pumilio/miRNA-mediated regulation of E2F3 is abrogated in cancer cells by selective miRNA downregulation or 3' UTR shortening.","method":"3' UTR reporter assays, Pumilio binding site mapping, Drosophila genetic screen (suppressor of dE2F1-RNAi), miRNA/Pumilio co-regulation assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1-2 — binding site mapping, reporter assays, conserved mechanism validated in human cells with multiple orthogonal methods","pmids":["22345517"],"is_preprint":false},{"year":2013,"finding":"E2F3 drives postnatal Igf2 down-regulation and E2F3 overexpression causally restores Igf2 expression in late juvenile hepatocytes. E2F3 directly activates mouse Igf2 promoter P2 via E2F binding sites, as shown by reporter assays.","method":"ChIP (E2f3 binding to Igf2 promoter), reporter constructs with Igf2 promoter P2 E2F sites, E2f3 gain-of-function in hepatocytes","journal":"Proceedings of the National Academy of Sciences","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP and reporter assays in single study; causal relationship shown by E2f3 restoration","pmids":["23530192"],"is_preprint":false},{"year":2013,"finding":"E2F3 mRNA associates with hnRNP-A1 through a conserved binding site in its 3' UTR in BCR/ABL-transformed myeloid cells; BCR/ABL kinase- and hnRNP-A1-dependent upregulation of E2F3 is required for clonogenic activity and leukemogenic potential of BCR/ABL.","method":"Ribonomics/RIP (RNA immunoprecipitation), 3' UTR binding site analysis, E2F3 shRNA knockdown, BCR/ABL-transduced E2F3-/- bone marrow cells, in vivo leukemogenesis assay","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 — RIP validates mRNA-protein interaction, genetic rescue confirms E2F3 requirement in leukemogenesis","pmids":["17925491"],"is_preprint":false},{"year":2016,"finding":"ATR-CHK1 signaling stabilizes E2F3 by phosphorylation at S124 in response to MNNG-induced DNA damage. Phosphorylated E2F3 co-transactivates RRM2 (ribonucleotide reductase M2) by directly binding to its promoter together with NFY, which interacts with E2F3 and binds adjacently.","method":"ChIP, promoter reporter assays, phosphorylation site analysis, kinase inhibitor experiments, co-IP of E2F3/NFY","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP and Co-IP with phosphorylation site identified; single lab study","pmids":["26921499"],"is_preprint":false},{"year":2017,"finding":"Copy number gains in E2f3b (but not E2f3a) result in dosage-dependent spontaneous hepatocellular carcinoma in mice without involvement of other organs; germ-line loss of E2f3b protects mice against HCC. E2F3B drives a distinct transcriptional program in HCC identified by chromatin occupancy and transcriptome profiling.","method":"Gain- and loss-of-function alleles in mice, ChIP-seq, transcriptome profiling, spontaneous tumor analysis","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 — in vivo gain/loss-of-function with isoform specificity, genome-wide chromatin occupancy, replicated across multiple alleles","pmids":["28134624"],"is_preprint":false},{"year":2019,"finding":"E2F3 directly binds to the miR-125a promoter (ChIP assay), transcriptionally activating its expression. miR-125a in turn targets DKK3 mRNA 3' UTR, forming an E2F3/miR-125a/DKK3 regulatory axis that promotes gastric cancer metastasis.","method":"ChIP assay, dual-luciferase reporter assay, qRT-PCR","journal":"Cancer cell international","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP confirms E2F3 occupancy at miR-125a promoter; single lab study","pmids":["31423109"],"is_preprint":false},{"year":2019,"finding":"E2F3/TFDP1/Rb1 complex preferentially binds the common (non-risk) allele of rs2107595 in a regulatory element that interacts with the HDAC9 promoter. E2F3 gain- and loss-of-function demonstrates its key role in mediating allele-specific transcriptional regulation of HDAC9.","method":"Proteome-wide allele-specific binding assay, ChIP, chromosome conformation capture (4C), luciferase reporter assay, genome editing, gain- and loss-of-function in cell lines","journal":"Stroke","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods including genome editing, 4C, and proteomics in single rigorous study","pmids":["31500558"],"is_preprint":false},{"year":2021,"finding":"E2F3 silencing in breast cancer cells reduces tumor growth in vivo by reducing the percentage of cells undergoing mitosis (not S phase); E2F3 modulates expression of EMT-associated genes (Snail, E-cadherin, MMPs) and drives invasion and metastasis.","method":"shRNA-mediated E2F3 silencing, in vivo mammary fat pad xenograft assay, mitotic index analysis, Transwell invasion assays","journal":"Experimental biology and medicine","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo and in vitro loss-of-function with defined mitotic and EMT phenotypes; single lab","pmids":["34365840"],"is_preprint":false},{"year":2020,"finding":"lncRNA RBAT1 recruits HNRNPL protein to the E2F3 promoter, thereby activating E2F3 transcription in cis. Demonstrated by ChIRP (chromatin isolation by RNA purification) assays identifying RBAT1-interacting proteins.","method":"ChIRP, promoter reporter assay, HNRNPL-E2F3 promoter binding analysis, loss-of-function in vivo","journal":"Molecular cancer","confidence":"Medium","confidence_rationale":"Tier 2 — ChIRP identifies protein-RNA interaction at promoter; functional consequence confirmed in vivo; single lab","pmids":["32669100"],"is_preprint":false},{"year":2022,"finding":"rtcisE2F (a read-through circRNA) functions as a scaffold for m6A reader IGF2BP2 and E2F3/E2F6 mRNAs, promoting their association with IGF2BP2 (which inhibits mRNA decay) and inhibiting their association with YTHDF2 (which promotes mRNA decay), thereby stabilizing E2F3 mRNA and promoting liver TIC self-renewal via Wnt/β-catenin.","method":"RNA immunoprecipitation (RIP), m6A reader pulldown, mRNA stability assay, loss-of-function experiments in TICs and xenografts","journal":"Science China. Life sciences","confidence":"Medium","confidence_rationale":"Tier 2 — biochemical mechanism of m6A reader switching validated with RIP and mRNA stability assays; single lab","pmids":["35266112"],"is_preprint":false},{"year":2022,"finding":"IGF2BP3 stabilizes E2F3 mRNA in endometrial carcinoma cells by interacting with LINC00958. Silencing LINC00958 partially rescues IGF2BP3-mediated promotion of E2F3 mRNA stability.","method":"RIP-seq, RNA pulldown, immunofluorescence-RNA FISH, RNA stability assay, rescue experiments","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 — RIP-seq and RNA stability assays validate mechanism; single lab","pmids":["35676262"],"is_preprint":false},{"year":2022,"finding":"Smad3 binds to the E2F3 promoter and inhibits its transcription, thereby suppressing β cell proliferation. Smad3 knockout upregulates E2F3, promoting G1/S progression in β cells; silencing E2F3 abrogates the proliferative effect of Smad3 KO.","method":"ChIP (Smad3 at E2F3 promoter), RNA-seq, Smad3 KO + E2F3 siRNA epistasis, in vivo islet transplant models","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP and genetic epistasis in vivo; single lab","pmids":["34987651"],"is_preprint":false},{"year":2021,"finding":"E2F3 induces MEX3A transcription; MEX3A in turn activates WNT pathway by suppressing KLF4, retaining cancer cells in undifferentiated/proliferative state. E2F3-MEX3A-KLF4 axis validated by luciferase reporter assays, RNA CLIP, and rescue experiments.","method":"CLIP assay, luciferase reporter assay, MEX3A knockout mice, APC-floxed mouse model, rescue experiments","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 — CLIP and in vivo genetic models validate axis; single lab","pmids":["36276637"],"is_preprint":false},{"year":2019,"finding":"E2F3 binds to the HDAC9 promoter (ChIP confirmed) and, together with Rb1, mediates allele-specific transcriptional repression at the rs2107595 locus. Loss of E2F3 reduces HDAC9 expression in a manner dependent on allelic context.","method":"ChIP, gain- and loss-of-function, circularized chromosome conformation capture, genome editing","journal":"Stroke","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods confirm E2F3/Rb1 complex function at HDAC9 regulatory element","pmids":["31500558"],"is_preprint":false}],"current_model":"E2F3 is a cell-cycle-regulated transcription factor that exists as two isoforms (E2F3a, growth-regulated; E2F3b, constitutively expressed) encoded from the same locus: E2F3b associates specifically with Rb in quiescent cells to repress Arf and other targets, while E2F3a is induced at G1/S by Myc and drives expression of DNA replication genes (Cdc6, cyclin E, cdk2), Aurora-A, and Igf2 through direct promoter binding; E2F3 is specifically required for centrosome duplication cycle fidelity, cardiac development, neuronal migration, and DNA damage-induced apoptosis (via Chk-kinase-dependent phosphorylation and stabilization); its protein stability is regulated by APC/C(Cdh1)-mediated proteasomal degradation at cell cycle exit and by m6A reader-dependent mRNA stabilization; E2F3 activity is modulated by physical interactions with TFE3 (via marked box domain), HELLS, and the Pumilio translational repressor complex, and Smad3 directly occupies the E2F3 promoter to repress its transcription."},"narrative":{"teleology":[{"year":1998,"claim":"Establishing that E2F3 is the E2F family member whose DNA-binding activity specifically reaccumulates at G1/S resolved which E2F drives the periodic activation of replication genes (Cdc6, cyclin E, cdk2) and showed that E2F3 immunodepletion blocks S-phase entry.","evidence":"Immunodepletion, E2F-specific binding assays, and cell cycle synchronization in mammalian cells","pmids":["9679057"],"confidence":"High","gaps":["Mechanism by which E2F3 is preferentially reactivated at G1/S versus other E2Fs was not defined","Full repertoire of direct E2F3 target genes unknown at this stage"]},{"year":2000,"claim":"Discovery that the E2F3 locus produces two functionally distinct isoforms—growth-regulated E2F3a and constitutive E2F3b—and that E2F3b forms the predominant Rb complex in quiescent cells established an isoform-based division of labor and explained how promoter architecture (Myc-responsive E-boxes for E2F3a, constitutive elements for E2F3b) generates differential regulation.","evidence":"Novel isoform cloning, co-immunoprecipitation with Rb, promoter dissection and reporter assays","pmids":["10779352","10779353"],"confidence":"High","gaps":["Whether E2F3a and E2F3b regulate distinct or overlapping target gene sets was not resolved","No genome-wide binding data at this point"]},{"year":2002,"claim":"In vivo genetic studies revealed that E2F3 loss causes congestive heart failure and impaired cardiac development, and that E2F3 (not E2F1) is the critical mediator of ectopic proliferation in Rb-null tissues, establishing non-redundant developmental roles among activating E2Fs.","evidence":"E2f3 knockout and Rb/E2f compound mutant mice with tissue-specific phenotypic analysis","pmids":["11909960","12065245"],"confidence":"High","gaps":["Molecular targets of E2F3 in cardiac development not identified","Whether E2F3's role in Rb-null proliferation is transcription-dependent was not formally tested"]},{"year":2003,"claim":"Two discoveries established unique E2F3 functions: (1) E2F3 interacts specifically with TFE3 through its marked box domain to co-activate p68 DNA polymerase alpha transcription, and (2) E2F3 loss uniquely disrupts centrosome duplication through deregulated cyclin E-dependent kinase activity, linking E2F3 to genomic stability.","evidence":"Co-IP/domain mapping/ChIP for TFE3 interaction; E2f3 KO MEFs with centrosome immunofluorescence and kinase assays","pmids":["12748276","12726860"],"confidence":"High","gaps":["Whether the centrosome defect is a direct transcriptional consequence of E2F3 target gene deregulation or indirect","Other E2F3-specific protein partners at this domain not surveyed"]},{"year":2004,"claim":"ChIP and genetic epistasis demonstrated that E2F3b directly occupies and represses the Arf promoter in quiescent cells, and that Arf mutation rescues E2f3-null proliferative defects, establishing the E2F3b–Arf–p53 axis as a key tumor-suppressive circuit.","evidence":"ChIP at Arf promoter, E2f3/Arf double-mutant MEFs, p53/p21 Western blots","pmids":["15175242"],"confidence":"High","gaps":["Whether E2F3b represses Arf through recruitment of a specific corepressor complex was not determined","Relevance to in vivo tumorigenesis not yet tested"]},{"year":2007,"claim":"E2F3 was found to mediate neuronal migration in a cell-cycle-independent manner downstream of Rb, distinguishing a non-canonical developmental function from its canonical role in proliferation.","evidence":"Rb/E2f3 compound null mice with cortical layering and migration analysis","pmids":["17452454"],"confidence":"High","gaps":["Target genes mediating the migration function are unknown","Whether E2F3's migration role requires its transactivation domain was not tested"]},{"year":2008,"claim":"Multiple studies expanded E2F3's transcriptional program: E2F3 directly binds and activates the Aurora-A promoter at G2/M; isoform-specific knockouts showed E2F3a (not E2F3b) contributes to proliferation with E2F1 redundancy; and E2F3 loss causes cardiac hypoplasia, confirming its essential role in cardiomyocyte proliferation.","evidence":"ChIP and promoter mutagenesis for Aurora-A; isoform-specific KO mice; cardiac histology and echocardiography in E2f3-null mice","pmids":["18776222","18663357","19029823"],"confidence":"High","gaps":["Full G2/M transcriptional program of E2F3 not mapped","Mechanism of E2F3's cardiac-specific essentiality versus other tissues unclear"]},{"year":2009,"claim":"The discovery that checkpoint kinases phosphorylate E2F3a to stabilize it after DNA damage, and that E2F3 is required for damage-induced apoptosis and E2F1/E2F2 induction, linked E2F3 to the DNA damage response pathway.","evidence":"In vitro kinase assay, phosphorylation site mutagenesis, E2f3-deficient MEFs and mice with apoptosis assays","pmids":["19917728"],"confidence":"High","gaps":["Whether Chk1 or Chk2 is the primary physiological kinase was not resolved","Downstream apoptotic effectors controlled by E2F3 in this context not identified"]},{"year":2011,"claim":"Identification of the chromatin remodeler HELLS as a genome-wide E2F3 cofactor showed that E2F3-dependent transcription requires an SNF2-like helicase for chromatin access at target promoters.","evidence":"Mass spectrometry, co-IP, ChIP-seq, siRNA knockdown with transcriptome analysis","pmids":["22157815"],"confidence":"High","gaps":["Whether HELLS remodels nucleosomes at E2F3 targets or acts through a different mechanism is unclear","Whether HELLS is required at all E2F3 targets or a subset was not resolved"]},{"year":2012,"claim":"Two regulatory layers of E2F3 were elucidated: APC/C(Cdh1) targets E2F3 for proteasomal degradation at cell cycle exit, and Pumilio proteins repress E2F3 translation via its 3′ UTR cooperatively with miRNAs—mechanisms subverted in cancer by miRNA loss or UTR shortening.","evidence":"Co-IP of E2F3-Cdh1, proteasome inhibitors, Cdh1 gain/loss-of-function; 3′ UTR reporter assays, Pumilio binding site mapping, Drosophila genetic screen","pmids":["22580460","22345517"],"confidence":"High","gaps":["Specific degron motifs in E2F3 recognized by Cdh1 not mapped","Relative contribution of translational versus post-translational regulation to E2F3 dosage in vivo unknown"]},{"year":2017,"claim":"Dosage-dependent gain-of-function of E2F3b (but not E2F3a) was shown to drive spontaneous hepatocellular carcinoma, and E2F3b loss protected against HCC, establishing E2F3b as an isoform-specific oncogene with a distinct chromatin occupancy program in liver.","evidence":"Isoform-specific gain- and loss-of-function alleles in mice, ChIP-seq, transcriptome profiling, spontaneous tumor monitoring","pmids":["28134624"],"confidence":"High","gaps":["Critical E2F3b target genes driving HCC not fully delineated","Whether E2F3b's oncogenic role extends to human HCC not directly tested"]},{"year":2019,"claim":"E2F3, in complex with TFDP1 and Rb1, was shown to bind allele-specifically to a regulatory element controlling HDAC9 transcription, connecting E2F3 to non-coding variant-mediated gene regulation at a cerebrovascular disease locus.","evidence":"Proteome-wide allele-specific binding, ChIP, 4C chromosome conformation capture, genome editing, gain/loss-of-function","pmids":["31500558"],"confidence":"High","gaps":["Whether E2F3 binding at other disease-associated non-coding variants is widespread","Functional consequence of allele-specific HDAC9 regulation for vascular phenotypes not directly shown"]},{"year":2022,"claim":"Multiple studies established post-transcriptional regulation of E2F3 mRNA by m6A reader proteins: IGF2BP2 (scaffolded by circRNA rtcisE2F) and IGF2BP3 (scaffolded by LINC00958) stabilize E2F3 mRNA, while Smad3 was shown to directly repress E2F3 transcription at its promoter to control β-cell proliferation.","evidence":"RIP, m6A reader pulldown, mRNA stability assays, ChIP of Smad3 at E2F3 promoter, genetic epistasis in islet transplant models","pmids":["35266112","35676262","34987651"],"confidence":"Medium","gaps":["Whether m6A-dependent stabilization of E2F3 mRNA operates in normal (non-cancer) contexts is unknown","Relative contributions of transcriptional vs. post-transcriptional control to E2F3 levels in different tissues not quantified","Single-lab findings for each mechanism"]},{"year":null,"claim":"Key open questions include: what is the structural basis of E2F3 isoform-specific partner selection, what is the complete set of E2F3b oncogenic targets in hepatocellular carcinoma, and how does E2F3 mediate neuronal migration independently of cell cycle control.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of E2F3 with isoform-specific partners","Cell-cycle-independent mechanism in neuronal migration uncharacterized","Relative in vivo contributions of protein stability versus mRNA stability regulation to E2F3 dosage undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,3,5,12,22]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,3,5,12,14,17,20,21]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,3,5,12,14,22]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,1,4,7,12,15]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,3,5,12,14,17,20]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[6]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[6,19]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[9,10,13]}],"complexes":["E2F3/DP","E2F3b/Rb"],"partners":["RB1","TFDP1","TFE3","HELLS","CDH1","PUM1","PUM2","NFYA"],"other_free_text":[]},"mechanistic_narrative":"E2F3 is a cell-cycle-regulated transcription factor that functions as a central activator of S-phase gene expression, a repressor of tumor suppressor loci in quiescent cells, and a regulator of centrosome duplication, cardiac development, and neuronal migration. The E2F3 locus encodes two isoforms—growth-regulated E2F3a, whose promoter is induced by Myc at G1/S, and constitutively expressed E2F3b, which forms the predominant Rb-containing repressor complex on targets such as Arf in quiescent cells [PMID:10779352, PMID:15175242]. E2F3 directly activates transcription of replication and mitotic genes including Cdc6, cyclin E, cdk2, Aurora-A, and RRM2 through promoter binding, and cooperates with cofactors TFE3 (via its marked box domain), HELLS, and NFY at specific target promoters [PMID:9679057, PMID:12748276, PMID:22157815, PMID:18776222]. E2F3 protein stability is regulated by APC/C(Cdh1)-mediated proteasomal degradation at cell cycle exit and by checkpoint kinase phosphorylation in response to DNA damage, while its mRNA is subject to post-transcriptional control by Pumilio/miRNA-mediated translational repression and m6A reader-dependent stabilization [PMID:22580460, PMID:19917728, PMID:22345517, PMID:35266112]."},"prefetch_data":{"uniprot":{"accession":"O00716","full_name":"Transcription factor E2F3","aliases":[],"length_aa":465,"mass_kda":49.2,"function":"Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F3 binds specifically to RB1 in a cell-cycle dependent manner. Inhibits adipogenesis, probably through the repression of CEBPA binding to its target gene promoters (By similarity)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/O00716/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/E2F3","classification":"Not Classified","n_dependent_lines":355,"n_total_lines":1208,"dependency_fraction":0.29387417218543044},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/E2F3","total_profiled":1310},"omim":[{"mim_id":"621290","title":"E2F1-REGULATED INHIBITOR OF CELL DEATH, NONCODING; ERICD","url":"https://www.omim.org/entry/621290"},{"mim_id":"620719","title":"NEURODEVELOPMENTAL DISORDER WITH MOTOR ABNORMALITIES, SEIZURES, AND FACIAL DYSMORPHISM; NEDMSF","url":"https://www.omim.org/entry/620719"},{"mim_id":"612270","title":"CELL DIVISION CYCLE-ASSOCIATED PROTEIN 4; CDCA4","url":"https://www.omim.org/entry/612270"},{"mim_id":"612047","title":"E2F TRANSCRIPTION FACTOR 8; E2F8","url":"https://www.omim.org/entry/612047"},{"mim_id":"609486","title":"E2F-ASSOCIATED PHOSPHOPROTEIN; EAPP","url":"https://www.omim.org/entry/609486"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/E2F3"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"O00716","domains":[{"cath_id":"1.10.10.10","chopping":"183-242","consensus_level":"high","plddt":91.2078,"start":183,"end":242}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O00716","model_url":"https://alphafold.ebi.ac.uk/files/AF-O00716-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O00716-F1-predicted_aligned_error_v6.png","plddt_mean":59.47},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=E2F3","jax_strain_url":"https://www.jax.org/strain/search?query=E2F3"},"sequence":{"accession":"O00716","fasta_url":"https://rest.uniprot.org/uniprotkb/O00716.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O00716/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O00716"}},"corpus_meta":[{"pmid":"9679057","id":"PMC_9679057","title":"E2F3 activity is regulated during the cell 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biology","url":"https://pubmed.ncbi.nlm.nih.gov/32822848","citation_count":21,"is_preprint":false},{"pmid":"29230020","id":"PMC_29230020","title":"SNP co-association and network analyses identify E2F3, KDM5A and BACH2 as key regulators of the bovine milk fatty acid profile.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/29230020","citation_count":21,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":49600,"output_tokens":7098,"usd":0.127635},"stage2":{"model":"claude-opus-4-6","input_tokens":10779,"output_tokens":3765,"usd":0.22203},"total_usd":0.349665,"stage1_batch_id":"msgbatch_0118RScg3WGaGkaZRtWZbtce","stage2_batch_id":"msgbatch_01Cpfzvtbj42aqp5oYZ5Te2s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1998,\n      \"finding\": \"E2F3 DNA-binding activity specifically reaccumulates at G1/S transitions in proliferating cells (unlike other E2Fs), and immunodepletion of E2F3 activity inhibits S phase induction. E2F3 regulates a cell-cycle-regulated subset of E2F target genes including Cdc6, cyclin E, and cdk2.\",\n      \"method\": \"Immunodepletion, E2F-specific binding assays, cell cycle synchronization, gene expression analysis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal functional depletion with defined S phase phenotype, replicated across multiple methods\",\n      \"pmids\": [\"9679057\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"The E2F3 locus encodes two isoforms: E2F3a (growth-regulated, expressed in proliferating cells) and E2F3b (constitutively expressed, transcribed from an intronic promoter). E2F3b specifically associates with Rb in quiescent cells and represents the predominant E2F-Rb complex in quiescent cells, whereas E2F3a is tightly regulated by cell growth.\",\n      \"method\": \"Identification of novel mRNA/protein isoform, co-immunoprecipitation, cell cycle fractionation, promoter mapping\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — isoform identified by unique mRNA/exon, Rb interaction confirmed by Co-IP, expression pattern validated across conditions\",\n      \"pmids\": [\"10779352\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"The E2F3a promoter is negatively regulated by E2F binding sites in quiescent cells (similar to E2F1/E2F2) and positively regulated by Myc-binding E-box elements in response to growth stimulation. E2F3b promoter is constitutively active, more similar to E2F4/E2F5 regulation.\",\n      \"method\": \"Promoter deletion analysis, reporter assays, Myc co-transfection\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — promoter dissection with defined binding sites and functional reporter assays\",\n      \"pmids\": [\"10779353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"E2F3-specific interaction with the E-box factor TFE3 is mediated by the marked box domain of E2F3 (not E2F1 or E2F2). This interaction synergistically activates transcription of the p68 subunit of DNA polymerase alpha, and both TFE3 and E2F3 are bound to the p68 promoter in vivo.\",\n      \"method\": \"Co-immunoprecipitation, chromatin immunoprecipitation (ChIP), reporter assays, domain mapping/mutagenesis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — binding partner identified with reciprocal Co-IP, domain mapping, ChIP confirmation in vivo, functional reporter assays\",\n      \"pmids\": [\"12748276\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Loss of E2F3 (but not E2F1, E2F2, E2F4, or E2F5) in mouse embryo fibroblasts results in unregulated cyclin E-dependent kinase activity, defects in nucleophosmin B association with centrosomes, premature centriole separation/duplication, centrosome amplification, mitotic spindle defects, and aneuploidy.\",\n      \"method\": \"E2f3 knockout MEFs, kinase assays, centrosome immunofluorescence, comparison with other E2F knockouts\",\n      \"journal\": \"Cancer cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — specific genetic loss-of-function with multiple orthogonal phenotypic readouts; E2F3-specific effect confirmed by comparison to other family members\",\n      \"pmids\": [\"12726860\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"E2F3 (predominantly E2F3b in quiescent cells) occupies and represses the Arf tumor suppressor promoter in wild-type MEFs. Loss of E2f3 derepresses Arf, triggering p53 activation and p21Cip1 expression. Arf mutation suppresses p53/p21 induction in E2f3-deficient cells and rescues their cell cycle re-entry defect. Activating E2Fs (E2F1 and E2F3a) are recruited to the Arf promoter in oncogenic conditions.\",\n      \"method\": \"ChIP, genetic epistasis (E2f3/Arf double mutants), MEF proliferation assays, western blot for p53/p21\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP identifies E2F3 at Arf promoter, genetic epistasis with Arf mutation rescues E2f3-null phenotype, multiple orthogonal methods\",\n      \"pmids\": [\"15175242\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"E2F3a is induced by DNA damage through both transcriptional and posttranslational mechanisms. E2F3a is a substrate for checkpoint kinases (Chk kinases) and mutation of the Chk phosphorylation site eliminates DNA damage inducibility. E2F3 is required for DNA damage-induced apoptosis and for transcriptional induction of E2F1 and E2F2 in response to DNA damage.\",\n      \"method\": \"In vitro kinase assay, phosphorylation site mutagenesis, E2f3-deficient MEFs and mice, apoptosis assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro kinase assay with mutagenesis, validated in vivo with E2f3 KO, multiple methods\",\n      \"pmids\": [\"19917728\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"E2F1, E2F2, and E2F3 are required for the negative regulation of the p53-p21CIP1 axis; loss of all three leads to elevated p21CIP1 and G1/S arrest. Inactivation of p21CIP1 restores G1/S entry in E2f1-3 triple-deficient cells, while p53 loss restores both G1/S and G2/M progression and enables oncogenic transformation.\",\n      \"method\": \"Genetic epistasis (E2f1/2/3 triple KO combined with p21 or p53 KO MEFs), cell cycle analysis, transformation assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clear genetic epistasis with multiple double/triple mutant combinations\",\n      \"pmids\": [\"17008321\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"E2F3 loss has the most pronounced effect on reducing ectopic proliferation of fiber cells in Rb-/- lenses; E2F1 is uniquely required for apoptosis in Rb-/- lenses and retinas; E2F3 loss almost completely eliminates ectopic DNA replication and apoptosis in Rb-/- CNS.\",\n      \"method\": \"Compound Rb/E2f mutant mice, in vivo BrdU incorporation, TUNEL apoptosis assay\",\n      \"journal\": \"Cell growth & differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic epistasis with tissue-specific phenotypic readouts across multiple E2F family members\",\n      \"pmids\": [\"12065245\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"E2f3 loss causes premature death with congestive heart failure (not tumor formation); E2F1 and E2F3 play critical overlapping roles in development of multiple tissues; tumor suppression is a specific property of E2F1, not E2F3.\",\n      \"method\": \"E2f3 mutant mice, E2f1/E2f3 compound mutant mice, pathological and developmental analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic analysis with defined phenotypic outcomes distinguishing E2F family members\",\n      \"pmids\": [\"11909960\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Neuronal migration is specifically mediated through E2F3 in a cell-cycle-independent manner; both E2F1 and E2F3 are required for neural precursor proliferation and cell cycle exit, but only E2F3 mediates the Rb requirement for neuronal migration.\",\n      \"method\": \"Rb/E2f1 and Rb/E2f3 compound null mice, BrdU labeling, cortical layering analysis, migration assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic epistasis with distinct tissue phenotypes, multiple E2F comparisons\",\n      \"pmids\": [\"17452454\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"E2F3a and E2f3b make overlapping but different contributions: E2f3a inactivation causes a low-penetrance proliferation defect in vitro; combined E2f3a/E2f1 mutation causes neonatal lethality and cartilage defects; E2f3b loss alone has no detected in vitro or in vivo defect.\",\n      \"method\": \"Isoform-specific E2f3a and E2f3b knockout mice, MEF proliferation assays, developmental phenotype analysis\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — isoform-specific genetic knockouts with multiple in vitro and in vivo readouts\",\n      \"pmids\": [\"18663357\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"E2F3 directly binds to the Aurora-A promoter and transcriptionally activates Aurora-A expression during G2/M. Knockdown of E2F3 decreases Aurora-A mRNA/protein and delays G2/M entry. A region 96 bp upstream of the Aurora-A transcription start site is critical for E2F3-mediated activation.\",\n      \"method\": \"ChIP, promoter deletion/mutation analysis, reporter assay, E2F3 knockdown, cell cycle analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP, promoter mutagenesis, and KD with defined cell cycle phenotype\",\n      \"pmids\": [\"18776222\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"E2F3 is essential for normal cardiac development; E2f3-/- mice show impaired embryonic myocardium proliferation, hypoplastic ventricular walls, septal defects, ultrastructural cardiac muscle defects, and death from congestive heart failure.\",\n      \"method\": \"E2f3 knockout mice, cardiac histology, BrdU proliferation, echocardiography/ultrastructure\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo KO with defined developmental and functional cardiac phenotype\",\n      \"pmids\": [\"19029823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The SNF2-like helicase HELLS physically interacts with E2F3A in vivo and is required for induction of E2F target genes and cell cycle re-entry. HELLS and E2F3A/B co-occupy gene promoters genome-wide. HELLS depletion severely perturbs E2F3-dependent transcription and growth.\",\n      \"method\": \"Mass spectrometry identification of E2F3B interactors, Co-IP, ChIP-seq, siRNA knockdown, gene expression analysis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — MS-identified binding partner validated by Co-IP, genome-wide ChIP-seq, functional knockdown with defined transcriptional phenotype\",\n      \"pmids\": [\"22157815\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"APC/C(Cdh1) ubiquitin ligase targets E2F3 for proteasome-dependent degradation during cell cycle exit. E2F3 interacts with Cdh1 but not Cdc20; enforced Cdh1 expression causes proteasome-dependent E2F3 degradation; Cdh1 silencing stabilizes E2F3 in differentiating neuroblastoma cells.\",\n      \"method\": \"Co-immunoprecipitation (E2F3 with Cdh1/Cdc20), proteasome inhibitor experiments, Cdh1 overexpression/siRNA knockdown, western blot\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — biochemical interaction plus gain- and loss-of-function of the E3 ligase component\",\n      \"pmids\": [\"22580460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Human Pumilio homologs Pum1 and Pum2 repress E2F3 translation by binding to the E2F3 3' UTR and enhance the activity of multiple E2F3-targeting miRNAs. This Pumilio/miRNA-mediated regulation of E2F3 is abrogated in cancer cells by selective miRNA downregulation or 3' UTR shortening.\",\n      \"method\": \"3' UTR reporter assays, Pumilio binding site mapping, Drosophila genetic screen (suppressor of dE2F1-RNAi), miRNA/Pumilio co-regulation assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — binding site mapping, reporter assays, conserved mechanism validated in human cells with multiple orthogonal methods\",\n      \"pmids\": [\"22345517\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"E2F3 drives postnatal Igf2 down-regulation and E2F3 overexpression causally restores Igf2 expression in late juvenile hepatocytes. E2F3 directly activates mouse Igf2 promoter P2 via E2F binding sites, as shown by reporter assays.\",\n      \"method\": \"ChIP (E2f3 binding to Igf2 promoter), reporter constructs with Igf2 promoter P2 E2F sites, E2f3 gain-of-function in hepatocytes\",\n      \"journal\": \"Proceedings of the National Academy of Sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and reporter assays in single study; causal relationship shown by E2f3 restoration\",\n      \"pmids\": [\"23530192\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"E2F3 mRNA associates with hnRNP-A1 through a conserved binding site in its 3' UTR in BCR/ABL-transformed myeloid cells; BCR/ABL kinase- and hnRNP-A1-dependent upregulation of E2F3 is required for clonogenic activity and leukemogenic potential of BCR/ABL.\",\n      \"method\": \"Ribonomics/RIP (RNA immunoprecipitation), 3' UTR binding site analysis, E2F3 shRNA knockdown, BCR/ABL-transduced E2F3-/- bone marrow cells, in vivo leukemogenesis assay\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — RIP validates mRNA-protein interaction, genetic rescue confirms E2F3 requirement in leukemogenesis\",\n      \"pmids\": [\"17925491\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"ATR-CHK1 signaling stabilizes E2F3 by phosphorylation at S124 in response to MNNG-induced DNA damage. Phosphorylated E2F3 co-transactivates RRM2 (ribonucleotide reductase M2) by directly binding to its promoter together with NFY, which interacts with E2F3 and binds adjacently.\",\n      \"method\": \"ChIP, promoter reporter assays, phosphorylation site analysis, kinase inhibitor experiments, co-IP of E2F3/NFY\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and Co-IP with phosphorylation site identified; single lab study\",\n      \"pmids\": [\"26921499\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Copy number gains in E2f3b (but not E2f3a) result in dosage-dependent spontaneous hepatocellular carcinoma in mice without involvement of other organs; germ-line loss of E2f3b protects mice against HCC. E2F3B drives a distinct transcriptional program in HCC identified by chromatin occupancy and transcriptome profiling.\",\n      \"method\": \"Gain- and loss-of-function alleles in mice, ChIP-seq, transcriptome profiling, spontaneous tumor analysis\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo gain/loss-of-function with isoform specificity, genome-wide chromatin occupancy, replicated across multiple alleles\",\n      \"pmids\": [\"28134624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"E2F3 directly binds to the miR-125a promoter (ChIP assay), transcriptionally activating its expression. miR-125a in turn targets DKK3 mRNA 3' UTR, forming an E2F3/miR-125a/DKK3 regulatory axis that promotes gastric cancer metastasis.\",\n      \"method\": \"ChIP assay, dual-luciferase reporter assay, qRT-PCR\",\n      \"journal\": \"Cancer cell international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP confirms E2F3 occupancy at miR-125a promoter; single lab study\",\n      \"pmids\": [\"31423109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"E2F3/TFDP1/Rb1 complex preferentially binds the common (non-risk) allele of rs2107595 in a regulatory element that interacts with the HDAC9 promoter. E2F3 gain- and loss-of-function demonstrates its key role in mediating allele-specific transcriptional regulation of HDAC9.\",\n      \"method\": \"Proteome-wide allele-specific binding assay, ChIP, chromosome conformation capture (4C), luciferase reporter assay, genome editing, gain- and loss-of-function in cell lines\",\n      \"journal\": \"Stroke\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods including genome editing, 4C, and proteomics in single rigorous study\",\n      \"pmids\": [\"31500558\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"E2F3 silencing in breast cancer cells reduces tumor growth in vivo by reducing the percentage of cells undergoing mitosis (not S phase); E2F3 modulates expression of EMT-associated genes (Snail, E-cadherin, MMPs) and drives invasion and metastasis.\",\n      \"method\": \"shRNA-mediated E2F3 silencing, in vivo mammary fat pad xenograft assay, mitotic index analysis, Transwell invasion assays\",\n      \"journal\": \"Experimental biology and medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo and in vitro loss-of-function with defined mitotic and EMT phenotypes; single lab\",\n      \"pmids\": [\"34365840\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"lncRNA RBAT1 recruits HNRNPL protein to the E2F3 promoter, thereby activating E2F3 transcription in cis. Demonstrated by ChIRP (chromatin isolation by RNA purification) assays identifying RBAT1-interacting proteins.\",\n      \"method\": \"ChIRP, promoter reporter assay, HNRNPL-E2F3 promoter binding analysis, loss-of-function in vivo\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIRP identifies protein-RNA interaction at promoter; functional consequence confirmed in vivo; single lab\",\n      \"pmids\": [\"32669100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"rtcisE2F (a read-through circRNA) functions as a scaffold for m6A reader IGF2BP2 and E2F3/E2F6 mRNAs, promoting their association with IGF2BP2 (which inhibits mRNA decay) and inhibiting their association with YTHDF2 (which promotes mRNA decay), thereby stabilizing E2F3 mRNA and promoting liver TIC self-renewal via Wnt/β-catenin.\",\n      \"method\": \"RNA immunoprecipitation (RIP), m6A reader pulldown, mRNA stability assay, loss-of-function experiments in TICs and xenografts\",\n      \"journal\": \"Science China. Life sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — biochemical mechanism of m6A reader switching validated with RIP and mRNA stability assays; single lab\",\n      \"pmids\": [\"35266112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"IGF2BP3 stabilizes E2F3 mRNA in endometrial carcinoma cells by interacting with LINC00958. Silencing LINC00958 partially rescues IGF2BP3-mediated promotion of E2F3 mRNA stability.\",\n      \"method\": \"RIP-seq, RNA pulldown, immunofluorescence-RNA FISH, RNA stability assay, rescue experiments\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — RIP-seq and RNA stability assays validate mechanism; single lab\",\n      \"pmids\": [\"35676262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Smad3 binds to the E2F3 promoter and inhibits its transcription, thereby suppressing β cell proliferation. Smad3 knockout upregulates E2F3, promoting G1/S progression in β cells; silencing E2F3 abrogates the proliferative effect of Smad3 KO.\",\n      \"method\": \"ChIP (Smad3 at E2F3 promoter), RNA-seq, Smad3 KO + E2F3 siRNA epistasis, in vivo islet transplant models\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and genetic epistasis in vivo; single lab\",\n      \"pmids\": [\"34987651\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"E2F3 induces MEX3A transcription; MEX3A in turn activates WNT pathway by suppressing KLF4, retaining cancer cells in undifferentiated/proliferative state. E2F3-MEX3A-KLF4 axis validated by luciferase reporter assays, RNA CLIP, and rescue experiments.\",\n      \"method\": \"CLIP assay, luciferase reporter assay, MEX3A knockout mice, APC-floxed mouse model, rescue experiments\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — CLIP and in vivo genetic models validate axis; single lab\",\n      \"pmids\": [\"36276637\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"E2F3 binds to the HDAC9 promoter (ChIP confirmed) and, together with Rb1, mediates allele-specific transcriptional repression at the rs2107595 locus. Loss of E2F3 reduces HDAC9 expression in a manner dependent on allelic context.\",\n      \"method\": \"ChIP, gain- and loss-of-function, circularized chromosome conformation capture, genome editing\",\n      \"journal\": \"Stroke\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods confirm E2F3/Rb1 complex function at HDAC9 regulatory element\",\n      \"pmids\": [\"31500558\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"E2F3 is a cell-cycle-regulated transcription factor that exists as two isoforms (E2F3a, growth-regulated; E2F3b, constitutively expressed) encoded from the same locus: E2F3b associates specifically with Rb in quiescent cells to repress Arf and other targets, while E2F3a is induced at G1/S by Myc and drives expression of DNA replication genes (Cdc6, cyclin E, cdk2), Aurora-A, and Igf2 through direct promoter binding; E2F3 is specifically required for centrosome duplication cycle fidelity, cardiac development, neuronal migration, and DNA damage-induced apoptosis (via Chk-kinase-dependent phosphorylation and stabilization); its protein stability is regulated by APC/C(Cdh1)-mediated proteasomal degradation at cell cycle exit and by m6A reader-dependent mRNA stabilization; E2F3 activity is modulated by physical interactions with TFE3 (via marked box domain), HELLS, and the Pumilio translational repressor complex, and Smad3 directly occupies the E2F3 promoter to repress its transcription.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"E2F3 is a cell-cycle-regulated transcription factor that functions as a central activator of S-phase gene expression, a repressor of tumor suppressor loci in quiescent cells, and a regulator of centrosome duplication, cardiac development, and neuronal migration. The E2F3 locus encodes two isoforms—growth-regulated E2F3a, whose promoter is induced by Myc at G1/S, and constitutively expressed E2F3b, which forms the predominant Rb-containing repressor complex on targets such as Arf in quiescent cells [PMID:10779352, PMID:15175242]. E2F3 directly activates transcription of replication and mitotic genes including Cdc6, cyclin E, cdk2, Aurora-A, and RRM2 through promoter binding, and cooperates with cofactors TFE3 (via its marked box domain), HELLS, and NFY at specific target promoters [PMID:9679057, PMID:12748276, PMID:22157815, PMID:18776222]. E2F3 protein stability is regulated by APC/C(Cdh1)-mediated proteasomal degradation at cell cycle exit and by checkpoint kinase phosphorylation in response to DNA damage, while its mRNA is subject to post-transcriptional control by Pumilio/miRNA-mediated translational repression and m6A reader-dependent stabilization [PMID:22580460, PMID:19917728, PMID:22345517, PMID:35266112].\",\n  \"teleology\": [\n    {\n      \"year\": 1998,\n      \"claim\": \"Establishing that E2F3 is the E2F family member whose DNA-binding activity specifically reaccumulates at G1/S resolved which E2F drives the periodic activation of replication genes (Cdc6, cyclin E, cdk2) and showed that E2F3 immunodepletion blocks S-phase entry.\",\n      \"evidence\": \"Immunodepletion, E2F-specific binding assays, and cell cycle synchronization in mammalian cells\",\n      \"pmids\": [\"9679057\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which E2F3 is preferentially reactivated at G1/S versus other E2Fs was not defined\", \"Full repertoire of direct E2F3 target genes unknown at this stage\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Discovery that the E2F3 locus produces two functionally distinct isoforms—growth-regulated E2F3a and constitutive E2F3b—and that E2F3b forms the predominant Rb complex in quiescent cells established an isoform-based division of labor and explained how promoter architecture (Myc-responsive E-boxes for E2F3a, constitutive elements for E2F3b) generates differential regulation.\",\n      \"evidence\": \"Novel isoform cloning, co-immunoprecipitation with Rb, promoter dissection and reporter assays\",\n      \"pmids\": [\"10779352\", \"10779353\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether E2F3a and E2F3b regulate distinct or overlapping target gene sets was not resolved\", \"No genome-wide binding data at this point\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"In vivo genetic studies revealed that E2F3 loss causes congestive heart failure and impaired cardiac development, and that E2F3 (not E2F1) is the critical mediator of ectopic proliferation in Rb-null tissues, establishing non-redundant developmental roles among activating E2Fs.\",\n      \"evidence\": \"E2f3 knockout and Rb/E2f compound mutant mice with tissue-specific phenotypic analysis\",\n      \"pmids\": [\"11909960\", \"12065245\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular targets of E2F3 in cardiac development not identified\", \"Whether E2F3's role in Rb-null proliferation is transcription-dependent was not formally tested\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Two discoveries established unique E2F3 functions: (1) E2F3 interacts specifically with TFE3 through its marked box domain to co-activate p68 DNA polymerase alpha transcription, and (2) E2F3 loss uniquely disrupts centrosome duplication through deregulated cyclin E-dependent kinase activity, linking E2F3 to genomic stability.\",\n      \"evidence\": \"Co-IP/domain mapping/ChIP for TFE3 interaction; E2f3 KO MEFs with centrosome immunofluorescence and kinase assays\",\n      \"pmids\": [\"12748276\", \"12726860\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the centrosome defect is a direct transcriptional consequence of E2F3 target gene deregulation or indirect\", \"Other E2F3-specific protein partners at this domain not surveyed\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"ChIP and genetic epistasis demonstrated that E2F3b directly occupies and represses the Arf promoter in quiescent cells, and that Arf mutation rescues E2f3-null proliferative defects, establishing the E2F3b–Arf–p53 axis as a key tumor-suppressive circuit.\",\n      \"evidence\": \"ChIP at Arf promoter, E2f3/Arf double-mutant MEFs, p53/p21 Western blots\",\n      \"pmids\": [\"15175242\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether E2F3b represses Arf through recruitment of a specific corepressor complex was not determined\", \"Relevance to in vivo tumorigenesis not yet tested\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"E2F3 was found to mediate neuronal migration in a cell-cycle-independent manner downstream of Rb, distinguishing a non-canonical developmental function from its canonical role in proliferation.\",\n      \"evidence\": \"Rb/E2f3 compound null mice with cortical layering and migration analysis\",\n      \"pmids\": [\"17452454\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Target genes mediating the migration function are unknown\", \"Whether E2F3's migration role requires its transactivation domain was not tested\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Multiple studies expanded E2F3's transcriptional program: E2F3 directly binds and activates the Aurora-A promoter at G2/M; isoform-specific knockouts showed E2F3a (not E2F3b) contributes to proliferation with E2F1 redundancy; and E2F3 loss causes cardiac hypoplasia, confirming its essential role in cardiomyocyte proliferation.\",\n      \"evidence\": \"ChIP and promoter mutagenesis for Aurora-A; isoform-specific KO mice; cardiac histology and echocardiography in E2f3-null mice\",\n      \"pmids\": [\"18776222\", \"18663357\", \"19029823\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full G2/M transcriptional program of E2F3 not mapped\", \"Mechanism of E2F3's cardiac-specific essentiality versus other tissues unclear\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"The discovery that checkpoint kinases phosphorylate E2F3a to stabilize it after DNA damage, and that E2F3 is required for damage-induced apoptosis and E2F1/E2F2 induction, linked E2F3 to the DNA damage response pathway.\",\n      \"evidence\": \"In vitro kinase assay, phosphorylation site mutagenesis, E2f3-deficient MEFs and mice with apoptosis assays\",\n      \"pmids\": [\"19917728\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Chk1 or Chk2 is the primary physiological kinase was not resolved\", \"Downstream apoptotic effectors controlled by E2F3 in this context not identified\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identification of the chromatin remodeler HELLS as a genome-wide E2F3 cofactor showed that E2F3-dependent transcription requires an SNF2-like helicase for chromatin access at target promoters.\",\n      \"evidence\": \"Mass spectrometry, co-IP, ChIP-seq, siRNA knockdown with transcriptome analysis\",\n      \"pmids\": [\"22157815\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether HELLS remodels nucleosomes at E2F3 targets or acts through a different mechanism is unclear\", \"Whether HELLS is required at all E2F3 targets or a subset was not resolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Two regulatory layers of E2F3 were elucidated: APC/C(Cdh1) targets E2F3 for proteasomal degradation at cell cycle exit, and Pumilio proteins repress E2F3 translation via its 3′ UTR cooperatively with miRNAs—mechanisms subverted in cancer by miRNA loss or UTR shortening.\",\n      \"evidence\": \"Co-IP of E2F3-Cdh1, proteasome inhibitors, Cdh1 gain/loss-of-function; 3′ UTR reporter assays, Pumilio binding site mapping, Drosophila genetic screen\",\n      \"pmids\": [\"22580460\", \"22345517\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific degron motifs in E2F3 recognized by Cdh1 not mapped\", \"Relative contribution of translational versus post-translational regulation to E2F3 dosage in vivo unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Dosage-dependent gain-of-function of E2F3b (but not E2F3a) was shown to drive spontaneous hepatocellular carcinoma, and E2F3b loss protected against HCC, establishing E2F3b as an isoform-specific oncogene with a distinct chromatin occupancy program in liver.\",\n      \"evidence\": \"Isoform-specific gain- and loss-of-function alleles in mice, ChIP-seq, transcriptome profiling, spontaneous tumor monitoring\",\n      \"pmids\": [\"28134624\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Critical E2F3b target genes driving HCC not fully delineated\", \"Whether E2F3b's oncogenic role extends to human HCC not directly tested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"E2F3, in complex with TFDP1 and Rb1, was shown to bind allele-specifically to a regulatory element controlling HDAC9 transcription, connecting E2F3 to non-coding variant-mediated gene regulation at a cerebrovascular disease locus.\",\n      \"evidence\": \"Proteome-wide allele-specific binding, ChIP, 4C chromosome conformation capture, genome editing, gain/loss-of-function\",\n      \"pmids\": [\"31500558\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether E2F3 binding at other disease-associated non-coding variants is widespread\", \"Functional consequence of allele-specific HDAC9 regulation for vascular phenotypes not directly shown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Multiple studies established post-transcriptional regulation of E2F3 mRNA by m6A reader proteins: IGF2BP2 (scaffolded by circRNA rtcisE2F) and IGF2BP3 (scaffolded by LINC00958) stabilize E2F3 mRNA, while Smad3 was shown to directly repress E2F3 transcription at its promoter to control β-cell proliferation.\",\n      \"evidence\": \"RIP, m6A reader pulldown, mRNA stability assays, ChIP of Smad3 at E2F3 promoter, genetic epistasis in islet transplant models\",\n      \"pmids\": [\"35266112\", \"35676262\", \"34987651\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether m6A-dependent stabilization of E2F3 mRNA operates in normal (non-cancer) contexts is unknown\", \"Relative contributions of transcriptional vs. post-transcriptional control to E2F3 levels in different tissues not quantified\", \"Single-lab findings for each mechanism\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include: what is the structural basis of E2F3 isoform-specific partner selection, what is the complete set of E2F3b oncogenic targets in hepatocellular carcinoma, and how does E2F3 mediate neuronal migration independently of cell cycle control.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of E2F3 with isoform-specific partners\", \"Cell-cycle-independent mechanism in neuronal migration uncharacterized\", \"Relative in vivo contributions of protein stability versus mRNA stability regulation to E2F3 dosage undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 3, 5, 12, 22]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 3, 5, 12, 14, 17, 20, 21]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 3, 5, 12, 14, 22]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 1, 4, 7, 12, 15]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 3, 5, 12, 14, 17, 20]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [6, 19]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [9, 10, 13]}\n    ],\n    \"complexes\": [\n      \"E2F3/DP\",\n      \"E2F3b/Rb\"\n    ],\n    \"partners\": [\n      \"RB1\",\n      \"TFDP1\",\n      \"TFE3\",\n      \"HELLS\",\n      \"CDH1\",\n      \"PUM1\",\n      \"PUM2\",\n      \"NFYA\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}