Affinage

EAF1

ELL-associated factor 1 · UniProt Q96JC9

Length
268 aa
Mass
29.0 kDa
Annotated
2026-04-28
21 papers in source corpus 15 papers cited in narrative 18 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

EAF1 is a transcriptional regulator that operates at the interface of RNA Polymerase II elongation control, chromatin remodeling, and signal transduction. In mammals, EAF1 directly binds ELL via ELL's C-terminus, localizes with ELL to Cajal bodies in a transcription-dependent manner, and competes with the SEC scaffold AFF1 for ELL binding, thereby modulating the balance between elongation-competent SEC and a distinct ELL–EAF1 complex that mediates global transcriptional inhibition upon ATM-dependent genotoxic stress (PMID:11418481, PMID:32087315, PMID:36305813). EAF1 also engages MED26's N-terminal domain in the same groove occupied by TAF7, facilitating the switch from transcription initiation to elongation (PMID:28893534), and stabilizes ELL protein by competing with HDAC3 at ELL's N-terminus to reduce ELL ubiquitylation (PMID:36036574). In yeast, the ortholog Eaf1 serves as the essential scaffold of the NuA4 histone H4/H2A acetyltransferase complex, coupling histone acetylation to H2A.Z incorporation at promoters genome-wide, and its structural relationship to human p400 links yeast NuA4 to the mammalian TIP60 complex (PMID:18212047, PMID:25841019).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 2001 High

    Identifying EAF1 as a direct ELL-binding partner established EAF1 as a nuclear transcription elongation factor and revealed that the MLL-ELL leukemia fusion dominantly disrupts EAF1 subnuclear localization.

    Evidence Yeast two-hybrid screen, reciprocal co-IP from multiple cell lines, confocal microscopy of nuclear speckle patterns and MLL-ELL leukemia cells

    PMID:11418481

    Open questions at the time
    • Binding domain on EAF1 for ELL not mapped
    • Functional consequence of EAF1 binding on ELL elongation activity not tested
    • Mechanism by which MLL-ELL delocalizes EAF1 unknown
  2. 2002 High

    Domain mapping showed EAF1 and EAF2 bind distinct regions of ELL (C-terminus vs. N-terminus), explaining why MLL-ELL retains EAF1 but loses EAF2 interaction.

    Evidence Co-IP with ELL deletion constructs and yeast two-hybrid domain mapping

    PMID:12446457

    Open questions at the time
    • Structural basis of the EAF1–ELL C-terminus interaction not resolved
    • Whether EAF1 and EAF2 can simultaneously bind ELL not tested
  3. 2003 High

    Demonstrating that EAF1 and ELL co-reside in Cajal bodies in a transcription-dependent manner connected EAF1 to active transcription sites and suggested a functional link between Cajal body integrity and ELL-mediated elongation.

    Evidence Confocal co-localization with p80 coilin, treatment with actinomycin D/DRB/α-amanitin, analysis of MLL-ELL leukemia cells

    PMID:12686606

    Open questions at the time
    • Whether EAF1 has a direct structural role in Cajal body formation or is passively recruited unclear
    • Functional significance of Cajal body disruption in MLL-ELL leukemogenesis not mechanistically tested
  4. 2008 High

    Discovery that yeast Eaf1 is the essential scaffold for NuA4 assembly — and that it structurally corresponds to human p400 — revealed a conserved role for the EAF1 gene family in chromatin remodeling and linked NuA4-dependent histone H4 acetylation to H2A.Z incorporation.

    Evidence Genetic deletion (eaf1Δ collapses NuA4), complex fractionation, chimeric Eaf1-Swr1 reconstitution, genetic epistasis between NuA4 and SWR1, ChIP for Htz1 and acetylation

    PMID:18212047 PMID:18212056

    Open questions at the time
    • Structural details of Eaf1 scaffold interfaces within NuA4 not determined
    • Whether human EAF1 retains any scaffold function in the TIP60 complex not established
  5. 2009 Medium

    Zebrafish studies placed EAF1 upstream of noncanonical Wnt signaling, showing it maintains wnt11/wnt5 expression to control convergence and extension, thereby extending EAF1 function beyond transcription elongation to developmental signaling.

    Evidence Morpholino knockdown with mRNA rescue (wnt11, wnt5, rhoA), in situ hybridization, cell tracing

    PMID:19380582

    Open questions at the time
    • Mechanism by which EAF1 maintains wnt11/wnt5 transcription not defined
    • Morpholino off-target effects not fully excluded
  6. 2010 Medium

    ChIP evidence that EAF1/EAF2 directly bind the Wnt4 promoter to suppress its expression — while Wnt4 upregulates EAF1/2 — established a negative feedback loop connecting EAF1 transcriptional repression to Wnt pathway homeostasis.

    Evidence Chromatin immunoprecipitation, reporter assays, morpholino knockdown and mRNA rescue in zebrafish and mammalian cells

    PMID:20161747

    Open questions at the time
    • Cofactors mediating EAF1 repression at the Wnt4 promoter not identified
    • Whether EAF1 represses Wnt4 via ELL-dependent or ELL-independent mechanism unknown
  7. 2013 Medium

    Mapping of direct EAF1–β-catenin interaction (via β-catenin Armadillo repeats) and identification of a repressive complex with c-Jun, Tcf, and Axin explained how EAF1 inhibits canonical Wnt/β-catenin signaling.

    Evidence Co-IP with domain-mapping constructs, β-catenin reporter assays, engrailed-fused dominant-negative EAF1, morpholino/mRNA in zebrafish

    PMID:23364330

    Open questions at the time
    • Stoichiometry and structure of the EAF1–β-catenin–Tcf repressive complex not determined
    • Endogenous relevance in mammalian tissues not validated beyond reporter assays
  8. 2015 High

    Genome-wide ChIP-seq in yeast confirmed that Eaf1-dependent NuA4 controls H2A.Z incorporation at highly enriched promoters and directly interacts with the Bas1 activator to preset ADE gene chromatin for rapid derepression.

    Evidence ChIP-seq for Htz1, expression arrays, in vivo Co-IP of NuA4 with Bas1, eaf1Δ genetic analysis

    PMID:25841019

    Open questions at the time
    • Whether Eaf1 scaffolding specificity dictates which promoters are targeted for H2A.Z not resolved
    • Direct acetylation targets of NuA4 at ADE promoters not fully mapped
  9. 2017 High

    Solving the NMR structure of MED26-NTD bound to EAF1 residues 239–268 revealed that EAF1 and TAF7 compete for the same groove, providing a structural mechanism for the transcription initiation-to-elongation transition mediated by Mediator.

    Evidence NMR structure determination, chemical shift perturbation, alanine mutagenesis, Kd measurement (~10 µM)

    PMID:28893534

    Open questions at the time
    • In vivo validation that TAF7-to-EAF1 exchange on MED26 drives the elongation switch at endogenous genes not shown
    • Whether other elongation factors compete for the same MED26 groove unknown
  10. 2020 Medium

    Demonstrating that EAF1 competes with AFF1 for ELL binding — reducing SEC formation and Tat-dependent HIV-1 transcription — established EAF1 as a negative regulator of SEC assembly.

    Evidence Co-IP competition assays, ChIP on HIV-1 proviral DNA, siRNA knockdown, HIV-1 reporter assays

    PMID:32087315

    Open questions at the time
    • Genome-wide impact of EAF1-mediated SEC disruption on host gene expression not assessed
    • In vivo relevance to HIV latency not tested
  11. 2022 High

    Two studies resolved how EAF1 controls ELL stability and stress-dependent transcription: EAF1 competes with HDAC3 at ELL's N-terminus to protect ELL from ubiquitylation, and upon genotoxic stress ATM phosphorylation of ELL enhances ELL–EAF1 interaction to promote ELL self-association and global transcriptional inhibition independent of SEC.

    Evidence Competitive Co-IP, ubiquitylation/acetylation assays, ATM inhibitor treatment, nascent transcription assays, TRIM28 identification as EAF1 E3 ligase, domain interaction mapping

    PMID:36036574 PMID:36305813

    Open questions at the time
    • Phosphorylation sites on ELL that mediate enhanced EAF1 binding not fully mapped
    • Whether EAF1 self-association complex has functions beyond transcriptional repression unknown
    • Structural basis of the EAF1–HDAC3 competition at ELL N-terminus not determined

Open questions

Synthesis pass · forward-looking unresolved questions
  • Whether human EAF1 retains any chromatin-remodeling scaffold function analogous to yeast Eaf1 in NuA4/TIP60, and how its elongation-regulatory and Wnt-inhibitory roles are coordinated in vivo, remain unresolved.
  • No evidence that human EAF1 integrates into the TIP60 complex
  • Tissue-specific and developmental roles in mammals not systematically characterized
  • Full interactome of mammalian EAF1 beyond ELL/SEC/MED26/β-catenin not mapped

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0042393 histone binding 3 GO:0098772 molecular function regulator activity 3 GO:0140110 transcription regulator activity 3
Localization
GO:0005634 nucleus 3 GO:0005654 nucleoplasm 3
Pathway
R-HSA-74160 Gene expression (Transcription) 4 R-HSA-162582 Signal Transduction 3 R-HSA-4839726 Chromatin organization 3 R-HSA-73894 DNA Repair 1
Partners
AFF1CTNNB1ELLELL2HDAC3MED26TRIM28
Complex memberships
ELL-EAF1 complexNuA4 (yeast)Super Elongation Complex (SEC, transient/competitive)

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2001 Human EAF1 was identified as a direct binding partner of ELL via yeast two-hybrid screen, and the endogenous EAF1-ELL interaction was confirmed by co-immunoprecipitation from multiple cell lines. EAF1 and ELL colocalize in a nuclear speckled pattern by confocal microscopy. EAF1 contains a transcriptional activation domain in a serine/aspartate/glutamate-rich region homologous to MLL translocation partners. Yeast two-hybrid screen, co-immunoprecipitation, confocal microscopy Blood High 11418481
2001 Expression of the MLL-ELL fusion protein delocalized EAF1 from its nuclear speckled pattern to a diffuse nucleoplasmic pattern, and in MLL-ELL leukemia cells EAF1 speckles were absent, indicating MLL-ELL dominantly disrupts normal EAF1-ELL protein-protein interactions. Confocal microscopy, transfection of MLL-ELL fusion construct, nuclear/cytoplasmic fractionation Blood High 11418481
2002 EAF1 binds the carboxy-terminus of ELL, whereas EAF2 binds the amino-terminus of ELL; the MLL-ELL fusion protein retains the EAF1 interaction domain but disrupts the EAF2 interaction domain, revealing distinct binding sites for EAF1 and EAF2 on ELL. Co-immunoprecipitation with deletion constructs, yeast two-hybrid domain mapping Blood High 12446457
2003 ELL and EAF1 are components of Cajal bodies (CBs), co-localizing with the CB marker p80 coilin, and their localization in CBs is dependent on active RNA Polymerase II transcription (disrupted by actinomycin D, DRB, or alpha-amanitin treatment). ELL and EAF1 do not directly interact with p80 coilin. Confocal microscopy, co-localization with p80 coilin, RNA Pol II inhibitor treatment, nuclear/cytoplasmic fractionation Molecular biology of the cell High 12686606
2003 In MLL-ELL leukemia cells, Cajal bodies are disrupted and EAF1 and p80 coilin are delocalized from CBs, with diminished nuclear expression of EAF1, establishing a direct role of CB disruption in MLL-ELL leukemogenesis. Nuclear/cytoplasmic fractionation, confocal microscopy, murine MLL-ELL leukemia cell lines Molecular biology of the cell Medium 12686606
2008 Yeast Eaf1 serves as the central scaffold/platform subunit for assembly of the NuA4 histone H4/H2A acetyltransferase complex. Deletion of EAF1 causes collapse of the entire NuA4 complex, unlike deletion of other nonessential subunits. Eaf1 is found exclusively associated with NuA4 in vivo and coordinates assembly of functional subunit groups. In vivo co-immunoprecipitation, complex fractionation, genetic deletion analysis, genetic interaction mapping Molecular and cellular biology High 18212047 18212056
2008 Yeast Eaf1 structurally resembles human p400/Domino of the TIP60 complex; expression of a chimeric Eaf1-Swr1 protein in yeast recreates a single merged complex resembling the human TIP60 complex, demonstrating that the human TIP60 complex is a physical merger of yeast NuA4 and SWR1 complexes. Chimeric protein expression, complex purification, co-immunoprecipitation, genetic interaction analysis Molecular and cellular biology High 18212047
2008 NuA4 (via Eaf1) functionally links histone H4 acetylation to H2AZ (Htz1) incorporation into chromatin; NuA4 and SWR1 mutants show strong genetic interactions, NuA4 affects H2AZ incorporation/acetylation in vivo, and both complexes preset the PHO5 promoter for activation. Genetic epistasis, chromatin immunoprecipitation, in vivo acetylation assays Molecular and cellular biology High 18212047 18212056
2009 Zebrafish Eaf1 and Eaf2 act upstream of noncanonical Wnt signaling to mediate convergence and extension movements by maintaining expression of wnt11 and wnt5; wnt11/wnt5 mRNA rescued CE defects in eaf1/2 morphants, and rhoA mRNA (downstream of Wnt11/Wnt5) rescued more effectively. Morpholino knockdown, mRNA rescue, in situ hybridization, cell tracing (kaeda mRNA), genetic epistasis The Journal of biological chemistry Medium 19380582
2010 EAF1 and EAF2 suppress Wnt4 expression by directly binding to the Wnt4 promoter (shown by chromatin immunoprecipitation), and Wnt4 in turn upregulates EAF1/2, forming an auto-regulatory negative feedback loop conserved between zebrafish and mammals. Chromatin immunoprecipitation, reporter assays, morpholino knockdown and mRNA rescue in zebrafish, mammalian cell assays PloS one Medium 20161747
2013 Zebrafish/mammalian EAF1 and EAF2 inhibit canonical Wnt/β-catenin signaling by binding to the Armadillo repeat region and C-terminus of β-catenin, as well as to c-Jun, Tcf, and Axin, forming a novel repressive complex. The N-terminus of EAF1 binds β-catenin and exhibits dominant-negative activity. Immunoprecipitation, domain-mapping with N- and C-terminal constructs, β-catenin reporter assays, morpholino/mRNA gain- and loss-of-function in zebrafish, engrailed fusion dominant-negative assays Development (Cambridge, England) Medium 23364330
2014 Zebrafish eaf1 suppresses foxo3b expression; Foxo3b inhibits transcriptional activity of gata1 and spi1 through protein-protein interaction. A regulatory pathway eaf1-foxo3b-gata1/spi1 controls primitive hematopoiesis. Morpholino knockdown, microarray, mRNA rescue, dominant-negative Foxo3b, protein-protein interaction assays Developmental biology Medium 24445282
2015 Yeast Eaf1 (NuA4 scaffold) regulates genome-wide H2A.Z (Htz1) incorporation, particularly at promoters normally highly enriched in Htz1. NuA4 directly interacts with the Bas1 transcription factor activation domain, and NuA4-dependent acetylation presets ADE gene promoter chromatin (with Htz1 enrichment) for rapid derepression. ChIP-seq/ChIP, expression arrays, in vivo Co-IP of NuA4 with Bas1, genetic deletion (eaf1Δ) Eukaryotic cell High 25841019
2017 The NMR structure of the MED26 N-terminal domain (4-helix bundle) was solved; EAF1 (residues 239-268) and TAF7 (205-235) both bind the same groove formed by H3 and H4 helices of MED26-NTD with Kd ~10 µM, via a folding-upon-binding mechanism. This competitive binding mediates the switch from transcription initiation (TAF7-MED26) to elongation (EAF1-MED26) phases. NMR structure determination, NMR chemical shift perturbation mapping, mutagenesis (Ala mutations of charged residues), dissociation constant measurement, NOE contacts Journal of molecular biology High 28893534
2017 EAF1 and EAF2 suppress TGF-β signaling in zebrafish and mammalian cells; they co-localize and interact with TGF-β transcriptional factors in the transcriptional complex as repressors. EAF1/2 suppress both p53-dependent and non-p53-dependent TGF-β signaling, shown using engrailed-fused EAF1/2 and a P53M214K mutant. TGF-β reporter assays, EAF-engrailed fusion proteins, loss/gain-of-function in zebrafish, gene expression profiling in mammalian cells, co-localization/interaction assays Biochimica et biophysica acta. Gene regulatory mechanisms Medium 28887217
2020 Human EAF1 and EAF2 interact with Super Elongation Complex (SEC) components in an ELL1/2-dependent manner and compete with the scaffolding subunit AFF1 for binding to ELL, thereby reducing SEC formation and inhibiting Tat-activated HIV-1 transcription. EAF1/2 depletion increases SEC formation and occupancy on HIV-1 proviral DNA. Co-immunoprecipitation, ChIP on HIV-1 proviral DNA, siRNA knockdown, HIV-1 reporter assays Biochimica et biophysica acta. Gene regulatory mechanisms Medium 32087315
2022 Human EAF1 regulates ELL protein stability by competing with HDAC3 for binding at the N-terminus of ELL; reduced HDAC3-ELL interaction caused by EAF1 leads to increased ELL acetylation and reduced ubiquitylation-mediated degradation. A negative feedback loop exists between DBC1 and EAF1/2: increased DBC1 reduces EAF1/2 levels through TRIM28-mediated ubiquitylation, while increased EAF1/2 reduces DBC1 through transcriptional repression. Co-immunoprecipitation (competitive binding), ubiquitylation assays, acetylation assays, siRNA knockdown, TRIM28 identification as E3 ubiquitin ligase for EAF1/2 Molecular and cellular biology Medium 36036574
2022 ATM-mediated phosphorylation of ELL upon genotoxic stress enhances ELL's interaction with EAF1; EAF1 in turn enhances ELL self-association (via ELL's intrinsic self-association property), reducing ELL's interaction with other SEC components (AFF1, etc.) and causing global transcriptional inhibition. ELL forms a distinct complex with EAF1 alone, separate from SEC and LEC. Co-immunoprecipitation, ELL phosphorylation assays, ATM inhibitor, genotoxic stress treatment, RNA Pol II ChIP/nascent transcription assays, domain interaction mapping Nucleic acids research High 36305813

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2008 Eaf1 is the platform for NuA4 molecular assembly that evolutionarily links chromatin acetylation to ATP-dependent exchange of histone H2A variants. Molecular and cellular biology 141 18212047
2008 Functional dissection of the NuA4 histone acetyltransferase reveals its role as a genetic hub and that Eaf1 is essential for complex integrity. Molecular and cellular biology 95 18212056
2002 ELL-associated factor 2 (EAF2), a functional homolog of EAF1 with alternative ELL binding properties. Blood 72 12446457
2001 EAF1, a novel ELL-associated factor that is delocalized by expression of the MLL-ELL fusion protein. Blood 72 11418481
2013 Eaf1 and Eaf2 negatively regulate canonical Wnt/β-catenin signaling. Development (Cambridge, England) 50 23364330
2009 Zebrafish eaf1 and eaf2/u19 mediate effective convergence and extension movements through the maintenance of wnt11 and wnt5 expression. The Journal of biological chemistry 44 19380582
2003 ELL and EAF1 are Cajal body components that are disrupted in MLL-ELL leukemia. Molecular biology of the cell 38 12686606
2011 Regulation of fertility, survival, and cuticle collagen function by the Caenorhabditis elegans eaf-1 and ell-1 genes. The Journal of biological chemistry 29 21880729
2017 Transcriptional factors Eaf1/2 inhibit endoderm and mesoderm formation via suppressing TGF-β signaling. Biochimica et biophysica acta. Gene regulatory mechanisms 22 28887217
1999 EAF1 regulates vegetative-phase change and flowering time in Arabidopsis. Plant physiology 20 10398702
2010 Negative feedback regulation of Wnt4 signaling by EAF1 and EAF2/U19. PloS one 18 20161747
2014 Zebrafish eaf1 suppresses foxo3b expression to modulate transcriptional activity of gata1 and spi1 in primitive hematopoiesis. Developmental biology 16 24445282
2017 Solution Structure of the N-Terminal Domain of Mediator Subunit MED26 and Molecular Characterization of Its Interaction with EAF1 and TAF7. Journal of molecular biology 12 28893534
2015 Eaf1 Links the NuA4 Histone Acetyltransferase Complex to Htz1 Incorporation and Regulation of Purine Biosynthesis. Eukaryotic cell 11 25841019
2022 Negative Feedback Loop Mechanism between EAF1/2 and DBC1 in Regulating ELL Stability and Functions. Molecular and cellular biology 9 36036574
2022 ATM-mediated ELL phosphorylation enhances its self-association through increased EAF1 interaction and inhibits global transcription during genotoxic stress. Nucleic acids research 9 36305813
2020 ELL-associated factors EAF1/2 negatively regulate HIV-1 transcription through inhibition of Super Elongation Complex formation. Biochimica et biophysica acta. Gene regulatory mechanisms 9 32087315
2018 Eaf1 and Eaf2 mediate zebrafish dorsal-ventral axis patterning via suppressing Wnt/β-Catenin activity. International journal of biological sciences 8 29910681
2023 Zebrafish ELL-associated factors Eaf1/2 modulate erythropoiesis via regulating gata1a expression and WNT signaling to facilitate hypoxia tolerance. Cell regeneration (London, England) 5 37002435
2026 PEAR1/EAF1 deficiency impairs aspirin responsiveness in atherosclerotic endothelium: A novel mechanism of atypical aspirin resistance. Microvascular research 0 41881247
2021 [Effects of miR-155-3p on the degradation rate of EAF1 mRNA and malignant proliferation in HANK1 cells]. Zhongguo ying yong sheng li xue za zhi = Zhongguo yingyong shenglixue zazhi = Chinese journal of applied physiology 0 34821091