{"gene":"EAF1","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2001,"finding":"Human EAF1 was identified as a direct binding partner of ELL via yeast two-hybrid screen and confirmed by co-immunoprecipitation of endogenous proteins from multiple cell lines. EAF1 also interacts with ELL2. EAF1 and ELL colocalize in a nuclear speckled (Cajal body) pattern, and expression of MLL-ELL fusion protein delocalizes EAF1 from this nuclear speckled distribution to a diffuse nucleoplasmic pattern.","method":"Yeast two-hybrid screen, co-immunoprecipitation of endogenous proteins, confocal microscopy, transfection of MLL-ELL fusion gene","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP of endogenous proteins confirmed in multiple cell lines, plus localization by confocal microscopy with functional consequence (delocalization by MLL-ELL)","pmids":["11418481"],"is_preprint":false},{"year":2003,"finding":"ELL and EAF1 are components of Cajal bodies (CBs) and colocalize with p80 coilin, though without direct physical interaction with coilin. Localization of ELL and EAF1 in CBs is dependent on active RNA Pol II transcription, as treatment with actinomycin D, DRB, or alpha-amanitin disperses them from CBs. In MLL-ELL leukemia cells, CBs are disrupted and EAF1 and p80 coilin are delocalized from CBs, with diminished nuclear expression of EAF1.","method":"Confocal microscopy, co-immunoprecipitation, transcription inhibitor treatment (actinomycin D, DRB, alpha-amanitin), nuclear/cytoplasmic fractionation","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Moderate — direct localization experiments with multiple pharmacological inhibitors and fractionation, single lab but orthogonal methods","pmids":["12686606"],"is_preprint":false},{"year":2002,"finding":"EAF1 binds to the carboxy-terminus of ELL, whereas EAF2 does not; both EAF1 and EAF2 bind an amino-terminal interaction domain of ELL that is disrupted in MLL-ELL fusion protein formation, so MLL-ELL retains an interaction domain for EAF1 but not EAF2. EAF1 contains a transcriptional activation domain in a serine/aspartate/glutamate-rich region homologous to MLL translocation partners.","method":"Co-immunoprecipitation, domain mapping with ELL truncation/fusion constructs, functional transcriptional activation assays","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with domain mapping in multiple cell lines, single lab","pmids":["12446457"],"is_preprint":false},{"year":2008,"finding":"Yeast Eaf1 serves as the central platform/scaffold for assembly of the NuA4 histone acetyltransferase complex. Deletion of EAF1 causes collapse of the entire NuA4 complex in vivo, while depletion of other subunits does not. Eaf1 is found exclusively associated with NuA4 (not other complexes) in vivo. Expression of a chimeric Eaf1-Swr1 protein recreates a single human TIP60-like complex in yeast, demonstrating structural and functional equivalence. NuA4 and SWR1 show strong genetic interactions and NuA4 affects H2AZ incorporation/acetylation in vivo.","method":"Genetic deletion/depletion, co-immunoprecipitation/complex purification, chimeric protein expression, genetic interaction analysis, in vivo histone acetylation assays, chromatin immunoprecipitation","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — two independent papers same year using reciprocal co-IP, complex purification, genetic epistasis, and functional rescue with chimeric construct","pmids":["18212047","18212056"],"is_preprint":false},{"year":2015,"finding":"Loss of yeast Eaf1 affects H2A.Z (Htz1) incorporation predominantly at promoters normally highly enriched in this histone variant. NuA4 (via Eaf1 scaffold) directly interacts with the Bas1 transcription factor activation domain, and NuA4-dependent acetylation presets ADE gene promoter nucleosomes (enriched in Htz1 and acetylated) for rapid derepression of purine biosynthesis genes.","method":"Chromatin immunoprecipitation (ChIP), expression arrays, genome-wide Htz1 mapping, co-immunoprecipitation of NuA4 with Bas1 activation domain","journal":"Eukaryotic cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and genome-wide mapping combined with co-IP, single lab","pmids":["25841019"],"is_preprint":false},{"year":2009,"finding":"Zebrafish eaf1 (and eaf2) act upstream of noncanonical Wnt signaling to mediate convergence and extension movements. Morpholino knockdown of eaf1 reduces expression of wnt11 and wnt5, and cell tracing experiments demonstrate cell migration defects. Rescue with wnt11/wnt5 mRNA (and more effectively with rhoA mRNA, a convergence point of both) restores normal morphogenesis. Ectopic expression of wnt11/wnt5 does not affect eaf1/eaf2 expression, placing eaf1 upstream.","method":"Morpholino knockdown, mRNA rescue injection, in situ hybridization, cell tracing with kaeda mRNA","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis established by morpholino + mRNA rescue, cell tracing, single lab","pmids":["19380582"],"is_preprint":false},{"year":2010,"finding":"EAF1 and EAF2 are transcriptionally upregulated by Wnt4 signaling, and in turn, EAF1 and EAF2 directly bind to the Wnt4 promoter to suppress its expression, forming an auto-regulatory negative feedback loop. This was demonstrated by chromatin immunoprecipitation in both zebrafish embryos and mammalian cells.","method":"Chromatin immunoprecipitation (ChIP), mRNA/morpholino gain- and loss-of-function in zebrafish, reporter assays in mammalian cells","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP demonstrating direct promoter binding combined with functional rescue, single lab, two species","pmids":["20161747"],"is_preprint":false},{"year":2013,"finding":"EAF1 and EAF2 negatively regulate canonical Wnt/β-catenin signaling. By immunoprecipitation, Eaf1 and Eaf2 bind to the Armadillo repeat region and C-terminus of β-catenin, as well as to c-Jun, Tcf, and Axin (components of the β-catenin transcription complex). The N-terminus of Eaf1 binds β-catenin and exhibits dominant-negative activity; the C-terminus harbors a suppression domain or recruits a repressor. Both termini must be intact for full suppressive activity.","method":"Immunoprecipitation, zebrafish morpholino/mRNA gain- and loss-of-function, β-catenin reporter assays in cultured cells, domain deletion analysis","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with multiple components plus functional reporter assays and domain mapping, single lab","pmids":["23364330"],"is_preprint":false},{"year":2014,"finding":"Zebrafish eaf1 suppresses foxo3b expression; microarray analysis identified foxo3b as a target gene suppressed by eaf1. Dominant-negative foxo3b partially rescues primitive hematopoietic defects in eaf1 morphants. Foxo3b inhibits transcriptional activity of gata1 and spi1 through protein-protein interaction, establishing the pathway: eaf1 → (suppresses) foxo3b → (inhibits) gata1/spi1.","method":"Morpholino knockdown, microarray analysis, mRNA rescue, dominant-negative construct, protein-protein interaction assay","journal":"Developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with dominant-negative rescue and microarray identification of downstream target, single lab","pmids":["24445282"],"is_preprint":false},{"year":2017,"finding":"The NMR solution structure of MED26 N-terminal domain (NTD) revealed a 4-helix bundle. EAF1 (residues 239-268) binds the same groove on MED26-NTD (formed by H3 and H4 helices) as TAF7. Both interactions occur with dissociation constants in the 10-μM range and involve a folding-upon-binding mechanism generating an EAF1 helix (N247-S260). Ala mutations of charged residues in the C-terminal disordered part of EAF1 peptide reduced binding affinity ~10-fold.","method":"NMR structure determination, NMR chemical shift perturbation mapping, NOE contacts, mutagenesis (Ala substitutions), binding affinity measurements","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structure with mutagenesis and quantitative binding measurements in one study; single lab but multiple orthogonal methods","pmids":["28893534"],"is_preprint":false},{"year":2017,"finding":"Eaf1 and Eaf2 inhibit TGF-β signaling in zebrafish and mammalian cells. Loss-of-function expands mesoderm and endoderm, while gain-of-function reduces them. Using TGF-β reporters and eaf1/2-engrailed fusion proteins (repressor domain fusions), Eaf1/2 suppress TGF-β transduction synergistically via both P53-dependent and P53-independent pathways. Eaf1/2 co-localize and interact with TGF-β transcriptional factors as repressors in the transcriptional complex.","method":"Morpholino/mRNA gain- and loss-of-function in zebrafish, TGF-β reporter assays, engrailed repressor domain fusions, co-localization/interaction experiments, P53 mutant analysis","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reporter assays with dominant repressor fusions and genetic tools across two species, single lab","pmids":["28887217"],"is_preprint":false},{"year":2020,"finding":"EAF1 and EAF2 interact with Super Elongation Complex (SEC) components in an ELL1/2-dependent manner and negatively regulate HIV-1 transcription. EAF1/2 compete with the scaffolding subunit AFF1 for binding to ELL, thereby reducing SEC formation and its occupancy on HIV-1 proviral DNA. Depletion of EAF1/2 increases SEC formation and Tat-dependent HIV-1 transactivation.","method":"Co-immunoprecipitation, ChIP on HIV-1 proviral DNA, knockdown of EAF1/2, HIV-1 transcription reporter assays","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP demonstrating competition with AFF1, ChIP showing SEC occupancy change upon EAF1/2 depletion, single lab","pmids":["32087315"],"is_preprint":false},{"year":2022,"finding":"EAF1 regulates ELL protein stability by competing with HDAC3 for binding at the N-terminus of ELL; reduced HDAC3 binding causes increased ELL acetylation, leading to reduced ubiquitylation-mediated ELL degradation. EAF1 and DBC1 form a negative feedback loop: increased DBC1 reduces EAF1 level via TRIM28-mediated ubiquitylation, while increased EAF1 reduces DBC1 level through transcriptional repression. During genotoxic stress, the EAF1-dependent pathway is preferentially used for ELL level maintenance over the DBC1-dependent pathway.","method":"Co-immunoprecipitation, knockdown experiments, ubiquitylation assays, acetylation assays, transcriptional reporter assays, genotoxic stress treatments","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — competitive binding demonstrated by co-IP, PTM changes (acetylation, ubiquitylation) measured, single lab with multiple orthogonal methods","pmids":["36036574"],"is_preprint":false},{"year":2022,"finding":"During genotoxic stress, ATM phosphorylates ELL, which enhances ELL's interaction with EAF1. This enhanced EAF1 association promotes ELL self-association, which reduces ELL interaction with other SEC components (including AFF1), leading to global transcriptional inhibition. EAF1 alone forms a complex with ELL distinct from SEC and LEC, and contrary to in vitro studies, EAF1 inhibits ELL-dependent RNA Pol II transcription in vivo.","method":"Co-immunoprecipitation, ATM kinase inhibition, genotoxic stress treatments, ELL phosphorylation assays, transcription run-on/nascent RNA assays, complex purification","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phosphorylation-dependent co-IP and functional transcription assays with ATM inhibitor controls, single lab","pmids":["36305813"],"is_preprint":false}],"current_model":"EAF1 is a multifunctional transcriptional regulator that (1) serves as the essential scaffold for NuA4/TIP60 histone acetyltransferase complex assembly (yeast/human), linking H4 acetylation to H2A.Z incorporation; (2) directly binds ELL via ELL's N-terminal domain to regulate ELL stability, self-association, and incorporation into the Super Elongation Complex (SEC) — enhancing ELL activity in basal conditions but inhibiting SEC formation and global transcription during genotoxic stress via ATM-phosphorylation-dependent enhanced EAF1-ELL interaction; (3) binds the MED26 N-terminal domain (competing with TAF7) to regulate the transcription initiation-to-elongation switch; (4) negatively regulates canonical Wnt/β-catenin signaling through direct interaction with β-catenin and the transcription complex, and suppresses TGF-β signaling as a transcriptional repressor; and (5) localizes to Cajal bodies in a transcription-dependent manner, with this localization disrupted by MLL-ELL fusion protein expression."},"narrative":{"mechanistic_narrative":"EAF1 is a transcriptional regulator that integrates RNA polymerase II elongation control, chromatin modification, and developmental signaling [PMID:11418481, PMID:18212047, PMID:18212056, PMID:23364330]. Its founding role is as a direct binding partner of the elongation factor ELL: EAF1 binds both an N-terminal interaction domain and the carboxy-terminus of ELL, contributing a serine/aspartate/glutamate-rich transcriptional activation domain, and the two proteins colocalize in Cajal bodies in an RNA Pol II transcription-dependent manner that is disrupted by expression of the leukemogenic MLL-ELL fusion [PMID:11418481, PMID:12446457, PMID:12686606]. Through ELL, EAF1 controls Super Elongation Complex (SEC) assembly by competing with the scaffold AFF1 for ELL binding, and during genotoxic stress ATM-phosphorylated ELL exhibits enhanced EAF1 association that promotes ELL self-association, displaces other SEC subunits, and globally inhibits ELL-dependent Pol II transcription [PMID:32087315, PMID:36305813]. EAF1 additionally stabilizes ELL by competing with HDAC3 at the ELL N-terminus, increasing ELL acetylation and reducing its ubiquitylation-mediated degradation, and operates in a negative feedback loop with DBC1 [PMID:36036574]. EAF1 binds the MED26 N-terminal domain in the same groove used by TAF7 via a folding-upon-binding mechanism, positioning it at the initiation-to-elongation switch [PMID:28893534]. In yeast, Eaf1 is the central scaffold for assembly of the NuA4 histone acetyltransferase complex, whose loss collapses the complex, and it links H4 acetylation to H2A.Z incorporation at promoters and to transcription-factor-directed gene activation [PMID:18212047, PMID:18212056, PMID:25841019]. In vertebrate development, EAF1 acts as a transcriptional repressor of multiple signaling pathways: it negatively regulates canonical Wnt/β-catenin signaling by binding β-catenin and associated factors, suppresses TGF-β signaling, controls noncanonical Wnt-driven convergence-extension movements, and regulates primitive hematopoiesis via suppression of foxo3b [PMID:23364330, PMID:28887217, PMID:19380582, PMID:24445282].","teleology":[{"year":2001,"claim":"Establishing EAF1 as a physical partner of ELL defined its entry point into RNA Pol II elongation biology and linked it to MLL-ELL leukemia.","evidence":"Yeast two-hybrid screen plus reciprocal co-IP of endogenous proteins and confocal microscopy across multiple cell lines, with MLL-ELL delocalization","pmids":["11418481"],"confidence":"High","gaps":["Functional consequence of the EAF1-ELL interaction on transcription not yet defined","Mechanism by which MLL-ELL delocalizes EAF1 unresolved"]},{"year":2002,"claim":"Domain mapping showed EAF1 binds an N-terminal ELL interaction domain retained in MLL-ELL and contributes its own activation domain, clarifying which contacts survive the leukemic fusion.","evidence":"Co-IP with ELL truncation/fusion constructs and transcriptional activation assays","pmids":["12446457"],"confidence":"Medium","gaps":["In vivo significance of the activation domain not tested","Single lab"]},{"year":2003,"claim":"Demonstrating that EAF1/ELL localization to Cajal bodies depends on active transcription connected the partnership to ongoing Pol II activity and to nuclear architecture disrupted in leukemia.","evidence":"Confocal microscopy with transcription inhibitors and nuclear/cytoplasmic fractionation","pmids":["12686606"],"confidence":"High","gaps":["Functional role of Cajal body localization for EAF1 activity unknown","No direct coilin interaction identified"]},{"year":2008,"claim":"Identifying yeast Eaf1 as the obligate scaffold of NuA4 established a distinct chromatin-modifying function and a structural equivalence to human TIP60 complex assembly.","evidence":"Genetic deletion/depletion, complex purification, chimeric Eaf1-Swr1 rescue, genetic interaction, and in vivo histone acetylation assays","pmids":["18212047","18212056"],"confidence":"High","gaps":["Whether human EAF1 plays the equivalent scaffolding role not directly shown","Link between NuA4 scaffolding and ELL functions not integrated"]},{"year":2009,"claim":"Zebrafish epistasis placed eaf1 upstream of noncanonical Wnt signaling, extending its role to morphogenetic movements.","evidence":"Morpholino knockdown, wnt11/wnt5/rhoA mRNA rescue, in situ hybridization, and cell tracing","pmids":["19380582"],"confidence":"Medium","gaps":["Direct transcriptional targets at the wnt loci not defined","Morpholino-only loss-of-function"]},{"year":2010,"claim":"Discovery of an EAF1-Wnt4 autoregulatory feedback loop showed EAF1 directly represses promoters of its own upstream activator.","evidence":"ChIP for Wnt4 promoter binding plus gain/loss-of-function in zebrafish and reporter assays in mammalian cells","pmids":["20161747"],"confidence":"Medium","gaps":["DNA-binding specificity / mechanism of promoter recognition unknown","Single lab"]},{"year":2013,"claim":"Mapping EAF1 contacts on β-catenin and its transcription complex defined EAF1 as a direct negative regulator of canonical Wnt signaling with separable N- and C-terminal functions.","evidence":"Co-IP with β-catenin/c-Jun/Tcf/Axin, reporter assays, and domain deletion analysis","pmids":["23364330"],"confidence":"Medium","gaps":["Identity of the C-terminal repressor activity unclear","Direct vs complex-mediated binding not fully resolved"]},{"year":2014,"claim":"Identifying foxo3b as an EAF1-suppressed target linked EAF1 to primitive hematopoiesis through a defined transcriptional cascade.","evidence":"Morpholino knockdown, microarray, dominant-negative foxo3b rescue, and protein interaction assays","pmids":["24445282"],"confidence":"Medium","gaps":["Whether foxo3b suppression is direct or indirect not established","Conservation in mammals untested"]},{"year":2017,"claim":"The NMR structure of the MED26-NTD complex revealed that EAF1 binds the same groove as TAF7 via folding-upon-binding, positioning EAF1 at the Mediator-controlled initiation-to-elongation switch.","evidence":"NMR structure determination, chemical shift perturbation, mutagenesis, and quantitative binding affinity measurements","pmids":["28893534"],"confidence":"High","gaps":["Cellular consequence of EAF1/TAF7 competition for MED26 not measured","Affinity in the 10-μM range raises questions about in vivo occupancy"]},{"year":2017,"claim":"Demonstrating that Eaf1/2 repress TGF-β signaling broadened its repressor activity to a second developmental pathway acting through both p53-dependent and -independent routes.","evidence":"Zebrafish gain/loss-of-function, TGF-β reporters, engrailed repressor fusions, and p53 mutant analysis","pmids":["28887217"],"confidence":"Medium","gaps":["Direct TGF-β transcription factor target not pinned down","Mechanism of synergy with p53 unclear"]},{"year":2020,"claim":"Showing EAF1/2 compete with AFF1 for ELL to limit SEC formation provided a mechanism for negative regulation of elongation, exemplified by suppression of HIV-1 transcription.","evidence":"Co-IP, ChIP on HIV-1 proviral DNA, EAF1/2 knockdown, and Tat-dependent transcription reporters","pmids":["32087315"],"confidence":"Medium","gaps":["Stoichiometry of AFF1/EAF1 competition on ELL not quantified","Generalizability beyond HIV-1 loci not shown"]},{"year":2022,"claim":"Two studies established that EAF1 controls ELL protein stability (via HDAC3 competition and acetylation) and mediates an ATM-phosphorylation-dependent switch that inhibits SEC and global transcription during genotoxic stress.","evidence":"Co-IP, ubiquitylation and acetylation assays, ATM inhibition, genotoxic stress, nascent RNA/run-on transcription assays, and complex purification","pmids":["36036574","36305813"],"confidence":"Medium","gaps":["Phosphorylation site(s) on ELL required for enhanced EAF1 binding not mapped","Reconciliation of in vitro ELL-activating vs in vivo ELL-inhibiting roles incomplete"]},{"year":null,"claim":"How EAF1's chromatin-scaffolding role (NuA4/TIP60) is mechanistically coordinated with its ELL/SEC elongation control and developmental repressor functions in the same cell remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No integrated model linking NuA4 scaffolding to elongation regulation","Human EAF1 NuA4/TIP60 scaffolding role not directly demonstrated in the corpus","Genome-wide map of EAF1 occupancy and target genes lacking"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[7,10,6]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[3,0,9]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[11,12,13]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[6]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,11,13]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[3,4]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[7,10,5]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[5,8,10]}],"complexes":["NuA4 histone acetyltransferase complex","Super Elongation Complex (SEC)"],"partners":["ELL","ELL2","MED26","CTNNB1","AFF1","HDAC3","DBC1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96JC9","full_name":"ELL-associated factor 1","aliases":[],"length_aa":268,"mass_kda":29.0,"function":"Acts as a transcriptional transactivator of ELL and ELL2 elongation activities","subcellular_location":"Nucleus speckle; Nucleus, Cajal body","url":"https://www.uniprot.org/uniprotkb/Q96JC9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/EAF1","classification":"Not Classified","n_dependent_lines":430,"n_total_lines":1208,"dependency_fraction":0.35596026490066224},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/EAF1","total_profiled":1310},"omim":[{"mim_id":"608315","title":"ELL-ASSOCIATED FACTOR 1; EAF1","url":"https://www.omim.org/entry/608315"},{"mim_id":"607659","title":"ELL-ASSOCIATED FACTOR 2; EAF2","url":"https://www.omim.org/entry/607659"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Nuclear bodies","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"bone marrow","ntpm":53.9}],"url":"https://www.proteinatlas.org/search/EAF1"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q96JC9","domains":[{"cath_id":"-","chopping":"15-109","consensus_level":"medium","plddt":93.4193,"start":15,"end":109}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JC9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JC9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JC9-F1-predicted_aligned_error_v6.png","plddt_mean":70.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=EAF1","jax_strain_url":"https://www.jax.org/strain/search?query=EAF1"},"sequence":{"accession":"Q96JC9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96JC9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96JC9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JC9"}},"corpus_meta":[{"pmid":"18212047","id":"PMC_18212047","title":"Eaf1 is the platform for NuA4 molecular assembly that evolutionarily links chromatin acetylation to ATP-dependent exchange of histone H2A variants.","date":"2008","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/18212047","citation_count":142,"is_preprint":false},{"pmid":"18212056","id":"PMC_18212056","title":"Functional dissection of the NuA4 histone acetyltransferase reveals its role as a genetic hub and that Eaf1 is essential for complex integrity.","date":"2008","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/18212056","citation_count":95,"is_preprint":false},{"pmid":"11418481","id":"PMC_11418481","title":"EAF1, a novel ELL-associated factor that is delocalized by expression of the MLL-ELL fusion protein.","date":"2001","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/11418481","citation_count":72,"is_preprint":false},{"pmid":"12446457","id":"PMC_12446457","title":"ELL-associated factor 2 (EAF2), a functional homolog of EAF1 with alternative ELL binding properties.","date":"2002","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/12446457","citation_count":72,"is_preprint":false},{"pmid":"23364330","id":"PMC_23364330","title":"Eaf1 and Eaf2 negatively regulate canonical Wnt/β-catenin signaling.","date":"2013","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/23364330","citation_count":50,"is_preprint":false},{"pmid":"19380582","id":"PMC_19380582","title":"Zebrafish eaf1 and eaf2/u19 mediate effective convergence and extension movements through the maintenance of wnt11 and wnt5 expression.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19380582","citation_count":44,"is_preprint":false},{"pmid":"12686606","id":"PMC_12686606","title":"ELL and EAF1 are Cajal body components that are disrupted in MLL-ELL leukemia.","date":"2003","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/12686606","citation_count":38,"is_preprint":false},{"pmid":"21880729","id":"PMC_21880729","title":"Regulation of fertility, survival, and cuticle collagen function by the Caenorhabditis elegans eaf-1 and ell-1 genes.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21880729","citation_count":29,"is_preprint":false},{"pmid":"28887217","id":"PMC_28887217","title":"Transcriptional factors Eaf1/2 inhibit endoderm and mesoderm formation via suppressing TGF-β signaling.","date":"2017","source":"Biochimica et biophysica acta. Gene regulatory mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/28887217","citation_count":23,"is_preprint":false},{"pmid":"20161747","id":"PMC_20161747","title":"Negative feedback regulation of Wnt4 signaling by EAF1 and EAF2/U19.","date":"2010","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/20161747","citation_count":18,"is_preprint":false},{"pmid":"24445282","id":"PMC_24445282","title":"Zebrafish eaf1 suppresses foxo3b expression to modulate transcriptional activity of gata1 and spi1 in primitive hematopoiesis.","date":"2014","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/24445282","citation_count":16,"is_preprint":false},{"pmid":"28893534","id":"PMC_28893534","title":"Solution Structure of the N-Terminal Domain of Mediator Subunit MED26 and Molecular Characterization of Its Interaction with EAF1 and TAF7.","date":"2017","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/28893534","citation_count":12,"is_preprint":false},{"pmid":"25841019","id":"PMC_25841019","title":"Eaf1 Links the NuA4 Histone Acetyltransferase Complex to Htz1 Incorporation and Regulation of Purine Biosynthesis.","date":"2015","source":"Eukaryotic cell","url":"https://pubmed.ncbi.nlm.nih.gov/25841019","citation_count":11,"is_preprint":false},{"pmid":"36036574","id":"PMC_36036574","title":"Negative Feedback Loop Mechanism between EAF1/2 and DBC1 in Regulating ELL Stability and Functions.","date":"2022","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/36036574","citation_count":10,"is_preprint":false},{"pmid":"29910681","id":"PMC_29910681","title":"Eaf1 and Eaf2 mediate zebrafish dorsal-ventral axis patterning via suppressing Wnt/β-Catenin activity.","date":"2018","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/29910681","citation_count":9,"is_preprint":false},{"pmid":"32087315","id":"PMC_32087315","title":"ELL-associated factors EAF1/2 negatively regulate HIV-1 transcription through inhibition of Super Elongation Complex formation.","date":"2020","source":"Biochimica et biophysica acta. Gene regulatory mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/32087315","citation_count":9,"is_preprint":false},{"pmid":"36305813","id":"PMC_36305813","title":"ATM-mediated ELL phosphorylation enhances its self-association through increased EAF1 interaction and inhibits global transcription during genotoxic stress.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/36305813","citation_count":9,"is_preprint":false},{"pmid":"37002435","id":"PMC_37002435","title":"Zebrafish ELL-associated factors Eaf1/2 modulate erythropoiesis via regulating gata1a expression and WNT signaling to facilitate hypoxia tolerance.","date":"2023","source":"Cell regeneration (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/37002435","citation_count":6,"is_preprint":false},{"pmid":"34821091","id":"PMC_34821091","title":"[Effects of miR-155-3p on the degradation rate of EAF1 mRNA and malignant proliferation in HANK1 cells].","date":"2021","source":"Zhongguo ying yong sheng li xue za zhi = Zhongguo yingyong shenglixue zazhi = Chinese journal of applied physiology","url":"https://pubmed.ncbi.nlm.nih.gov/34821091","citation_count":0,"is_preprint":false},{"pmid":"41881247","id":"PMC_41881247","title":"PEAR1/EAF1 deficiency impairs aspirin responsiveness in atherosclerotic endothelium: A novel mechanism of atypical aspirin resistance.","date":"2026","source":"Microvascular research","url":"https://pubmed.ncbi.nlm.nih.gov/41881247","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12991,"output_tokens":4236,"usd":0.051257,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12188,"output_tokens":4228,"usd":0.08332,"stage2_stop_reason":"end_turn"},"total_usd":0.134577,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"Human EAF1 was identified as a direct binding partner of ELL via yeast two-hybrid screen and confirmed by co-immunoprecipitation of endogenous proteins from multiple cell lines. EAF1 also interacts with ELL2. EAF1 and ELL colocalize in a nuclear speckled (Cajal body) pattern, and expression of MLL-ELL fusion protein delocalizes EAF1 from this nuclear speckled distribution to a diffuse nucleoplasmic pattern.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation of endogenous proteins, confocal microscopy, transfection of MLL-ELL fusion gene\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP of endogenous proteins confirmed in multiple cell lines, plus localization by confocal microscopy with functional consequence (delocalization by MLL-ELL)\",\n      \"pmids\": [\"11418481\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"ELL and EAF1 are components of Cajal bodies (CBs) and colocalize with p80 coilin, though without direct physical interaction with coilin. Localization of ELL and EAF1 in CBs is dependent on active RNA Pol II transcription, as treatment with actinomycin D, DRB, or alpha-amanitin disperses them from CBs. In MLL-ELL leukemia cells, CBs are disrupted and EAF1 and p80 coilin are delocalized from CBs, with diminished nuclear expression of EAF1.\",\n      \"method\": \"Confocal microscopy, co-immunoprecipitation, transcription inhibitor treatment (actinomycin D, DRB, alpha-amanitin), nuclear/cytoplasmic fractionation\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiments with multiple pharmacological inhibitors and fractionation, single lab but orthogonal methods\",\n      \"pmids\": [\"12686606\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"EAF1 binds to the carboxy-terminus of ELL, whereas EAF2 does not; both EAF1 and EAF2 bind an amino-terminal interaction domain of ELL that is disrupted in MLL-ELL fusion protein formation, so MLL-ELL retains an interaction domain for EAF1 but not EAF2. EAF1 contains a transcriptional activation domain in a serine/aspartate/glutamate-rich region homologous to MLL translocation partners.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping with ELL truncation/fusion constructs, functional transcriptional activation assays\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with domain mapping in multiple cell lines, single lab\",\n      \"pmids\": [\"12446457\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Yeast Eaf1 serves as the central platform/scaffold for assembly of the NuA4 histone acetyltransferase complex. Deletion of EAF1 causes collapse of the entire NuA4 complex in vivo, while depletion of other subunits does not. Eaf1 is found exclusively associated with NuA4 (not other complexes) in vivo. Expression of a chimeric Eaf1-Swr1 protein recreates a single human TIP60-like complex in yeast, demonstrating structural and functional equivalence. NuA4 and SWR1 show strong genetic interactions and NuA4 affects H2AZ incorporation/acetylation in vivo.\",\n      \"method\": \"Genetic deletion/depletion, co-immunoprecipitation/complex purification, chimeric protein expression, genetic interaction analysis, in vivo histone acetylation assays, chromatin immunoprecipitation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — two independent papers same year using reciprocal co-IP, complex purification, genetic epistasis, and functional rescue with chimeric construct\",\n      \"pmids\": [\"18212047\", \"18212056\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Loss of yeast Eaf1 affects H2A.Z (Htz1) incorporation predominantly at promoters normally highly enriched in this histone variant. NuA4 (via Eaf1 scaffold) directly interacts with the Bas1 transcription factor activation domain, and NuA4-dependent acetylation presets ADE gene promoter nucleosomes (enriched in Htz1 and acetylated) for rapid derepression of purine biosynthesis genes.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), expression arrays, genome-wide Htz1 mapping, co-immunoprecipitation of NuA4 with Bas1 activation domain\",\n      \"journal\": \"Eukaryotic cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and genome-wide mapping combined with co-IP, single lab\",\n      \"pmids\": [\"25841019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Zebrafish eaf1 (and eaf2) act upstream of noncanonical Wnt signaling to mediate convergence and extension movements. Morpholino knockdown of eaf1 reduces expression of wnt11 and wnt5, and cell tracing experiments demonstrate cell migration defects. Rescue with wnt11/wnt5 mRNA (and more effectively with rhoA mRNA, a convergence point of both) restores normal morphogenesis. Ectopic expression of wnt11/wnt5 does not affect eaf1/eaf2 expression, placing eaf1 upstream.\",\n      \"method\": \"Morpholino knockdown, mRNA rescue injection, in situ hybridization, cell tracing with kaeda mRNA\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis established by morpholino + mRNA rescue, cell tracing, single lab\",\n      \"pmids\": [\"19380582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"EAF1 and EAF2 are transcriptionally upregulated by Wnt4 signaling, and in turn, EAF1 and EAF2 directly bind to the Wnt4 promoter to suppress its expression, forming an auto-regulatory negative feedback loop. This was demonstrated by chromatin immunoprecipitation in both zebrafish embryos and mammalian cells.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), mRNA/morpholino gain- and loss-of-function in zebrafish, reporter assays in mammalian cells\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP demonstrating direct promoter binding combined with functional rescue, single lab, two species\",\n      \"pmids\": [\"20161747\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"EAF1 and EAF2 negatively regulate canonical Wnt/β-catenin signaling. By immunoprecipitation, Eaf1 and Eaf2 bind to the Armadillo repeat region and C-terminus of β-catenin, as well as to c-Jun, Tcf, and Axin (components of the β-catenin transcription complex). The N-terminus of Eaf1 binds β-catenin and exhibits dominant-negative activity; the C-terminus harbors a suppression domain or recruits a repressor. Both termini must be intact for full suppressive activity.\",\n      \"method\": \"Immunoprecipitation, zebrafish morpholino/mRNA gain- and loss-of-function, β-catenin reporter assays in cultured cells, domain deletion analysis\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with multiple components plus functional reporter assays and domain mapping, single lab\",\n      \"pmids\": [\"23364330\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Zebrafish eaf1 suppresses foxo3b expression; microarray analysis identified foxo3b as a target gene suppressed by eaf1. Dominant-negative foxo3b partially rescues primitive hematopoietic defects in eaf1 morphants. Foxo3b inhibits transcriptional activity of gata1 and spi1 through protein-protein interaction, establishing the pathway: eaf1 → (suppresses) foxo3b → (inhibits) gata1/spi1.\",\n      \"method\": \"Morpholino knockdown, microarray analysis, mRNA rescue, dominant-negative construct, protein-protein interaction assay\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with dominant-negative rescue and microarray identification of downstream target, single lab\",\n      \"pmids\": [\"24445282\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The NMR solution structure of MED26 N-terminal domain (NTD) revealed a 4-helix bundle. EAF1 (residues 239-268) binds the same groove on MED26-NTD (formed by H3 and H4 helices) as TAF7. Both interactions occur with dissociation constants in the 10-μM range and involve a folding-upon-binding mechanism generating an EAF1 helix (N247-S260). Ala mutations of charged residues in the C-terminal disordered part of EAF1 peptide reduced binding affinity ~10-fold.\",\n      \"method\": \"NMR structure determination, NMR chemical shift perturbation mapping, NOE contacts, mutagenesis (Ala substitutions), binding affinity measurements\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure with mutagenesis and quantitative binding measurements in one study; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"28893534\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Eaf1 and Eaf2 inhibit TGF-β signaling in zebrafish and mammalian cells. Loss-of-function expands mesoderm and endoderm, while gain-of-function reduces them. Using TGF-β reporters and eaf1/2-engrailed fusion proteins (repressor domain fusions), Eaf1/2 suppress TGF-β transduction synergistically via both P53-dependent and P53-independent pathways. Eaf1/2 co-localize and interact with TGF-β transcriptional factors as repressors in the transcriptional complex.\",\n      \"method\": \"Morpholino/mRNA gain- and loss-of-function in zebrafish, TGF-β reporter assays, engrailed repressor domain fusions, co-localization/interaction experiments, P53 mutant analysis\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reporter assays with dominant repressor fusions and genetic tools across two species, single lab\",\n      \"pmids\": [\"28887217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"EAF1 and EAF2 interact with Super Elongation Complex (SEC) components in an ELL1/2-dependent manner and negatively regulate HIV-1 transcription. EAF1/2 compete with the scaffolding subunit AFF1 for binding to ELL, thereby reducing SEC formation and its occupancy on HIV-1 proviral DNA. Depletion of EAF1/2 increases SEC formation and Tat-dependent HIV-1 transactivation.\",\n      \"method\": \"Co-immunoprecipitation, ChIP on HIV-1 proviral DNA, knockdown of EAF1/2, HIV-1 transcription reporter assays\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP demonstrating competition with AFF1, ChIP showing SEC occupancy change upon EAF1/2 depletion, single lab\",\n      \"pmids\": [\"32087315\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"EAF1 regulates ELL protein stability by competing with HDAC3 for binding at the N-terminus of ELL; reduced HDAC3 binding causes increased ELL acetylation, leading to reduced ubiquitylation-mediated ELL degradation. EAF1 and DBC1 form a negative feedback loop: increased DBC1 reduces EAF1 level via TRIM28-mediated ubiquitylation, while increased EAF1 reduces DBC1 level through transcriptional repression. During genotoxic stress, the EAF1-dependent pathway is preferentially used for ELL level maintenance over the DBC1-dependent pathway.\",\n      \"method\": \"Co-immunoprecipitation, knockdown experiments, ubiquitylation assays, acetylation assays, transcriptional reporter assays, genotoxic stress treatments\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — competitive binding demonstrated by co-IP, PTM changes (acetylation, ubiquitylation) measured, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"36036574\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"During genotoxic stress, ATM phosphorylates ELL, which enhances ELL's interaction with EAF1. This enhanced EAF1 association promotes ELL self-association, which reduces ELL interaction with other SEC components (including AFF1), leading to global transcriptional inhibition. EAF1 alone forms a complex with ELL distinct from SEC and LEC, and contrary to in vitro studies, EAF1 inhibits ELL-dependent RNA Pol II transcription in vivo.\",\n      \"method\": \"Co-immunoprecipitation, ATM kinase inhibition, genotoxic stress treatments, ELL phosphorylation assays, transcription run-on/nascent RNA assays, complex purification\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phosphorylation-dependent co-IP and functional transcription assays with ATM inhibitor controls, single lab\",\n      \"pmids\": [\"36305813\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"EAF1 is a multifunctional transcriptional regulator that (1) serves as the essential scaffold for NuA4/TIP60 histone acetyltransferase complex assembly (yeast/human), linking H4 acetylation to H2A.Z incorporation; (2) directly binds ELL via ELL's N-terminal domain to regulate ELL stability, self-association, and incorporation into the Super Elongation Complex (SEC) — enhancing ELL activity in basal conditions but inhibiting SEC formation and global transcription during genotoxic stress via ATM-phosphorylation-dependent enhanced EAF1-ELL interaction; (3) binds the MED26 N-terminal domain (competing with TAF7) to regulate the transcription initiation-to-elongation switch; (4) negatively regulates canonical Wnt/β-catenin signaling through direct interaction with β-catenin and the transcription complex, and suppresses TGF-β signaling as a transcriptional repressor; and (5) localizes to Cajal bodies in a transcription-dependent manner, with this localization disrupted by MLL-ELL fusion protein expression.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"EAF1 is a transcriptional regulator that integrates RNA polymerase II elongation control, chromatin modification, and developmental signaling [#0, #3, #7]. Its founding role is as a direct binding partner of the elongation factor ELL: EAF1 binds both an N-terminal interaction domain and the carboxy-terminus of ELL, contributing a serine/aspartate/glutamate-rich transcriptional activation domain, and the two proteins colocalize in Cajal bodies in an RNA Pol II transcription-dependent manner that is disrupted by expression of the leukemogenic MLL-ELL fusion [#0, #2, #1]. Through ELL, EAF1 controls Super Elongation Complex (SEC) assembly by competing with the scaffold AFF1 for ELL binding, and during genotoxic stress ATM-phosphorylated ELL exhibits enhanced EAF1 association that promotes ELL self-association, displaces other SEC subunits, and globally inhibits ELL-dependent Pol II transcription [#11, #13]. EAF1 additionally stabilizes ELL by competing with HDAC3 at the ELL N-terminus, increasing ELL acetylation and reducing its ubiquitylation-mediated degradation, and operates in a negative feedback loop with DBC1 [#12]. EAF1 binds the MED26 N-terminal domain in the same groove used by TAF7 via a folding-upon-binding mechanism, positioning it at the initiation-to-elongation switch [#9]. In yeast, Eaf1 is the central scaffold for assembly of the NuA4 histone acetyltransferase complex, whose loss collapses the complex, and it links H4 acetylation to H2A.Z incorporation at promoters and to transcription-factor-directed gene activation [#3, #4]. In vertebrate development, EAF1 acts as a transcriptional repressor of multiple signaling pathways: it negatively regulates canonical Wnt/\\u03b2-catenin signaling by binding \\u03b2-catenin and associated factors, suppresses TGF-\\u03b2 signaling, controls noncanonical Wnt-driven convergence-extension movements, and regulates primitive hematopoiesis via suppression of foxo3b [#7, #10, #5, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Establishing EAF1 as a physical partner of ELL defined its entry point into RNA Pol II elongation biology and linked it to MLL-ELL leukemia.\",\n      \"evidence\": \"Yeast two-hybrid screen plus reciprocal co-IP of endogenous proteins and confocal microscopy across multiple cell lines, with MLL-ELL delocalization\",\n      \"pmids\": [\"11418481\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of the EAF1-ELL interaction on transcription not yet defined\", \"Mechanism by which MLL-ELL delocalizes EAF1 unresolved\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Domain mapping showed EAF1 binds an N-terminal ELL interaction domain retained in MLL-ELL and contributes its own activation domain, clarifying which contacts survive the leukemic fusion.\",\n      \"evidence\": \"Co-IP with ELL truncation/fusion constructs and transcriptional activation assays\",\n      \"pmids\": [\"12446457\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo significance of the activation domain not tested\", \"Single lab\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Demonstrating that EAF1/ELL localization to Cajal bodies depends on active transcription connected the partnership to ongoing Pol II activity and to nuclear architecture disrupted in leukemia.\",\n      \"evidence\": \"Confocal microscopy with transcription inhibitors and nuclear/cytoplasmic fractionation\",\n      \"pmids\": [\"12686606\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional role of Cajal body localization for EAF1 activity unknown\", \"No direct coilin interaction identified\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Identifying yeast Eaf1 as the obligate scaffold of NuA4 established a distinct chromatin-modifying function and a structural equivalence to human TIP60 complex assembly.\",\n      \"evidence\": \"Genetic deletion/depletion, complex purification, chimeric Eaf1-Swr1 rescue, genetic interaction, and in vivo histone acetylation assays\",\n      \"pmids\": [\"18212047\", \"18212056\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether human EAF1 plays the equivalent scaffolding role not directly shown\", \"Link between NuA4 scaffolding and ELL functions not integrated\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Zebrafish epistasis placed eaf1 upstream of noncanonical Wnt signaling, extending its role to morphogenetic movements.\",\n      \"evidence\": \"Morpholino knockdown, wnt11/wnt5/rhoA mRNA rescue, in situ hybridization, and cell tracing\",\n      \"pmids\": [\"19380582\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct transcriptional targets at the wnt loci not defined\", \"Morpholino-only loss-of-function\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Discovery of an EAF1-Wnt4 autoregulatory feedback loop showed EAF1 directly represses promoters of its own upstream activator.\",\n      \"evidence\": \"ChIP for Wnt4 promoter binding plus gain/loss-of-function in zebrafish and reporter assays in mammalian cells\",\n      \"pmids\": [\"20161747\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"DNA-binding specificity / mechanism of promoter recognition unknown\", \"Single lab\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Mapping EAF1 contacts on \\u03b2-catenin and its transcription complex defined EAF1 as a direct negative regulator of canonical Wnt signaling with separable N- and C-terminal functions.\",\n      \"evidence\": \"Co-IP with \\u03b2-catenin/c-Jun/Tcf/Axin, reporter assays, and domain deletion analysis\",\n      \"pmids\": [\"23364330\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of the C-terminal repressor activity unclear\", \"Direct vs complex-mediated binding not fully resolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identifying foxo3b as an EAF1-suppressed target linked EAF1 to primitive hematopoiesis through a defined transcriptional cascade.\",\n      \"evidence\": \"Morpholino knockdown, microarray, dominant-negative foxo3b rescue, and protein interaction assays\",\n      \"pmids\": [\"24445282\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether foxo3b suppression is direct or indirect not established\", \"Conservation in mammals untested\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"The NMR structure of the MED26-NTD complex revealed that EAF1 binds the same groove as TAF7 via folding-upon-binding, positioning EAF1 at the Mediator-controlled initiation-to-elongation switch.\",\n      \"evidence\": \"NMR structure determination, chemical shift perturbation, mutagenesis, and quantitative binding affinity measurements\",\n      \"pmids\": [\"28893534\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular consequence of EAF1/TAF7 competition for MED26 not measured\", \"Affinity in the 10-\\u03bcM range raises questions about in vivo occupancy\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrating that Eaf1/2 repress TGF-\\u03b2 signaling broadened its repressor activity to a second developmental pathway acting through both p53-dependent and -independent routes.\",\n      \"evidence\": \"Zebrafish gain/loss-of-function, TGF-\\u03b2 reporters, engrailed repressor fusions, and p53 mutant analysis\",\n      \"pmids\": [\"28887217\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct TGF-\\u03b2 transcription factor target not pinned down\", \"Mechanism of synergy with p53 unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showing EAF1/2 compete with AFF1 for ELL to limit SEC formation provided a mechanism for negative regulation of elongation, exemplified by suppression of HIV-1 transcription.\",\n      \"evidence\": \"Co-IP, ChIP on HIV-1 proviral DNA, EAF1/2 knockdown, and Tat-dependent transcription reporters\",\n      \"pmids\": [\"32087315\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Stoichiometry of AFF1/EAF1 competition on ELL not quantified\", \"Generalizability beyond HIV-1 loci not shown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Two studies established that EAF1 controls ELL protein stability (via HDAC3 competition and acetylation) and mediates an ATM-phosphorylation-dependent switch that inhibits SEC and global transcription during genotoxic stress.\",\n      \"evidence\": \"Co-IP, ubiquitylation and acetylation assays, ATM inhibition, genotoxic stress, nascent RNA/run-on transcription assays, and complex purification\",\n      \"pmids\": [\"36036574\", \"36305813\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phosphorylation site(s) on ELL required for enhanced EAF1 binding not mapped\", \"Reconciliation of in vitro ELL-activating vs in vivo ELL-inhibiting roles incomplete\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How EAF1's chromatin-scaffolding role (NuA4/TIP60) is mechanistically coordinated with its ELL/SEC elongation control and developmental repressor functions in the same cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No integrated model linking NuA4 scaffolding to elongation regulation\", \"Human EAF1 NuA4/TIP60 scaffolding role not directly demonstrated in the corpus\", \"Genome-wide map of EAF1 occupancy and target genes lacking\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [7, 10, 6]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3, 0, 9]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [11, 12, 13]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 11, 13]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [7, 10, 5]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [5, 8, 10]}\n    ],\n    \"complexes\": [\"NuA4 histone acetyltransferase complex\", \"Super Elongation Complex (SEC)\"],\n    \"partners\": [\"ELL\", \"ELL2\", \"MED26\", \"CTNNB1\", \"AFF1\", \"HDAC3\", \"DBC1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}