ELL: the discarded N-terminal EAF-binding site, and a second subtraction the graph had not recorded — the fusion delocalises endogenous EAF1
also called MLL-ELL EAF1 · ELL N-terminal EAF2 site lost · EAF1 delocalisation
ELL normally works with two partner proteins, EAF1 and EAF2, docking them at two separate sites. The leukemia fusion keeps one docking site and loses the other, and on top of that it pulls the remaining partner away from where it normally sits in the nucleus.
The same thing, for a scientist
ELL (UniProt P55199, 621 aa) binds EAF1 and EAF2 at two distinct sites: an N-terminal interaction domain that binds both, and a C-terminal site (within/near the OCEL/occludin-homology domain, aa 507-617) that binds EAF1 but not EAF2. MLL-ELL disrupts the N-terminal site and retains the C-terminal one, so the fusion keeps an EAF1 contact and loses EAF2 binding entirely. Functionally the retained C-terminal EAF1-interaction domain is critical for immortalisation while the ELL elongation domain is dispensable — which also corrects this graph's framing of the retained 'elongation-stimulatory region' as the transforming element. A second, cellular-level subtraction is documented: MLL-ELL delocalises endogenous EAF1 out of its nuclear speckle pattern into diffuse nucleoplasm, a dominant effect on wild-type ELL's normal interactions.
What the intact protein does with its N-terminus
EAF1 was isolated as an ELL-interacting protein that co-immunoprecipitates with endogenous ELL and with ELL2, contains a serine/aspartate/glutamate-rich transcriptional activation domain homologous to the activation domains of AF4, LAF4 and AF5q31, and colocalises with ELL in a distinct nuclear speckled pattern 1. EAF2 is 58% identical to EAF1 and also colocalises with ELL in speckles 2.
The decisive architectural fact comes from the EAF2 paper: 'We identified a protein-protein interaction domain within the amino-terminus of ELL that binds to both EAF1 and EAF2. This amino-terminal interaction domain is disrupted in the formation of the MLL-ELL fusion protein. Thus, MLL-ELL retains an interaction domain for EAF1 but not for EAF2' 2.
So the intact protein has redundant, non-equivalent EAF docking: two sites, differing in partner specificity.
Is it genuinely discarded at the observed breakpoints?
Yes, and this is stated directly rather than inferred 2. This graph's breakpoint records for both the paediatric intron-9 and the therapy-related intron-11 architectures list an 'ELL extreme N-terminal segment' under domains_lost_3, described there as a Pol II/DSIF-contacting region. That description should be revised. The functionally characterised property of the discarded N-terminal region is that it is the dual EAF1/EAF2 docking site 2; the Pol II/DSIF framing is not what the primary ELL-fusion literature assigns to it.
Coordinates: UniProt P55199 annotates only one domain in ELL, the OCEL (occludin-homology) domain at 507-617. The N-terminal EAF-binding region has no UniProt feature, so this entry deliberately gives no residue range for it rather than inventing one — the boundary is defined operationally by the MLL-ELL junction in the primary paper.
Does the loss contribute to transformation? Partly — but the retained site matters more1 deeper
Luo et al. ran the structure-function analysis that this beat keeps asking for, in the deletion direction. Their findings 3:
- The elongation domain of ELL is dispensable for MLL-ELL immortalisation of myeloid progenitors.
- The EAF1 interaction domain of ELL is critical — MLL fused to the minimal EAF1-interaction domain alone still produced AML in transplanted mice, with longer latency than full MLL-ELL.
- A heterologous MLL-EAF1 fusion immortalised myeloid progenitors and induced AML with shorter latency than MLL-ELL.
Two things follow. First, an addition mechanism is firmly established: what MLL gains from ELL is recruitment of an AF4-family-like transactivation domain, and supplying that domain directly (MLL-EAF1) is, if anything, more potent. Second, this graph's domains_retained_3 framing — which lists 'ELL elongation-stimulatory region' as a retained module — names the one element the primary literature shows to be dispensable.
For the subtraction side the evidence is real but indirect. Loss of the N-terminal site removes EAF2 binding entirely 2, and no one has tested whether restoring it suppresses transformation. Given that MLL-EAF1 is more potent than MLL-ELL, the naive prediction is that adding back an EAF-binding site would not suppress anything — which is a genuine argument against calling this a deleted brake.
The second subtraction: delocalisation of endogenous EAF1
This one is at the cellular level rather than the domain level, and the graph had not recorded it.
'Transfection of the MLL-ELL fusion gene delocalized EAF1 from its nuclear speckled distribution to a diffuse nucleoplasmic pattern. In leukemic cell lines derived from mice transplanted with MLL-ELL-transduced bone marrow, EAF1 speckles were not detected.' The authors' conclusion: MLL-ELL 'may have a dominant effect on the normal protein-protein interactions of ELL' 1.
That is subtraction by sequestration: the fusion does not delete EAF1, it removes EAF1 from where wild-type ELL needs it. It is the same shape as the MLL-AF6 mechanism (see subtraction-afdn-n-terminus), and it means the subtraction class has at least two distinct members: discarded-module subtraction and sequestration subtraction. Neither is visible to a scan of retained modules, but they fail differently and would be drugged differently.
What is missing is any demonstration that the delocalisation contributes to transformation. It is a documented cell-biological consequence, observed in fusion-driven leukemic lines, with no separation-of-function test behind it.
| partner | gene-ell |
|---|---|
| fusion | fusion-kmt2a-ell |
| discarded region | N-terminal ELL protein-protein interaction domain that binds both EAF1 and EAF2 |
| residue coordinates note | Deliberately omitted. UniProt P55199 annotates only the OCEL domain (507-617); the N-terminal EAF-binding region has no database feature and the primary paper defines it by deletion constructs, not coordinates. Per the graph's join rule, an invented boundary is worse than none — this region is therefore described but not drawn. |
| intact function of discarded region | Dual docking site for EAF1 and EAF2, the ELL-associated factors that carry AF4-family-like transcriptional activation domains and localise ELL to nuclear speckles |
| genuinely discarded at observed breakpoints | true |
| loss shown to contribute to transformation | false |
| second subtraction mechanism | sequestration — MLL-ELL delocalises endogenous EAF1 out of nuclear speckles into diffuse nucleoplasm, a dominant effect on wild-type ELL's interactions; documented but never causally tested |
| verdict | both |
| verdict rationale | Addition is established and is the dominant mechanism (retained C-terminal EAF1-interaction domain is critical; MLL-EAF1 alone transforms). Two subtraction components are documented as facts — loss of the N-terminal dual EAF site with complete loss of EAF2 binding, and delocalisation of endogenous EAF1 — but neither has been shown to contribute to transformation, and one published result predicts the opposite. |
| experiment to settle | Restore the ELL N-terminal dual EAF1/EAF2 interaction domain in cis to MLL-ELL and score myeloid progenitor immortalisation and transplant latency, with an EAF2-binding-dead point mutant as the discriminating control. Separately, an EAF1 speckle-targeting rescue (forced EAF1 speckle retention in MLL-ELL cells) tests the sequestration arm. |
| discarded residues note | Resolved 2026-09-18 from the Luo et al. 2001 full text (PMC87288): the MLL-ELL chimera contains ELL amino acids 46 to 621, and ELL exon 1 spans aa 1-45 and is excluded because the genomic breaks occur 3' of it. So the discarded N-terminal segment is aa 1-45. That is the extent of the deleted sequence; Simone et al. 2002 (PMID 12446457) do not give residue boundaries for the N-terminal EAF1/EAF2-interaction domain itself, so equating the two is an inference and the domain is still not drawn. |
retained modules
[ "OCEL / occludin-homology domain aa 507-617 (contains the C-terminal EAF1-interaction site, critical for immortalisation)", "ELL elongation-stimulatory region (retained but dispensable for transformation)" ]
graph corrections raised
[ "fusion-kmt2a-ell breakpoint records describe the lost N-terminal segment as a 'Pol II/DSIF-contacting region in the wild-type elongation complex'; the primary MLL-ELL literature characterises it as the dual EAF1/EAF2 interaction domain.", "The same records list the 'ELL elongation-stimulatory region' as a retained module without noting that Luo et al. showed it is dispensable for MLL-ELL leukemogenesis, while the OCEL-proximal EAF1 site is essential." ]
graph corrections resolved
[ "RESOLVED 2026-09-18. fusion-kmt2a-ell has been corrected: both breakpoint records now label the lost 3' segment 'ELL exon 1, residues 1-45 — the N-terminal EAF1/EAF2-interaction domain' instead of a Pol II/DSIF-contacting region, the retained elongation-stimulatory region is now annotated as dispensable for transformation (Luo 2001, PMID 11463848), the mechanism and druggability sections have been rewritten accordingly, and the node's status moved from 'disputed' back to 'verified'. Both corrections raised by this node were upheld.", "Note on the mislabel's likely origin: PDB 7OKX is a Pol II-DSIF-ELL2-EAF1 complex, but ELL2 is the paralogue, the deposited ELL2 construct is full-length (640 aa), and the ordered ELL-family element in that architecture is the C-terminal OCEL module, not residues 1-45. Nothing in that structure licenses calling ELL's N-terminus a Pol II/DSIF contact." ]
- If the therapeutically relevant element is an EAF1-recruiting transactivation domain rather than elongation activity, then elongation-directed drugs (CDK9 inhibitors, and by extension parts of the SEC-targeting rationale) are aimed at the dispensable half of this fusion.
- Sequestration mechanisms are dose-dependent: a drug that reduces but does not eliminate fusion protein could relieve EAF1 sequestration while leaving enough fusion to drive transcription, giving a partial response that looks like resistance.
- Does restoring the ELL N-terminal EAF1/EAF2 interaction domain in cis to MLL-ELL suppress transformation, do nothing, or enhance it? The MLL-EAF1 potency result predicts enhancement, which would make this the first partner where the add-back is expected to fail — a useful negative control for the whole subtraction programme.
- Does EAF2 have a non-redundant function that MLL-ELL escapes by losing its binding site? EAF2 is a known prostate tumour suppressor, which makes 'loss of EAF2 engagement' a non-trivial hypothesis rather than a bookkeeping detail.
- Is endogenous EAF1 delocalisation required for MLL-ELL leukemogenesis, or a bystander readout of fusion overexpression? Forced EAF1 speckle retention would answer it.
- This graph lists the ELL elongation-stimulatory region among retained modules and has reasoned from it. How many other retained-module lists in this graph include elements the primary literature has shown to be dispensable?
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
EAF1 is an ELL-associated factor that co-immunoprecipitates with endogenous ELL and ELL2, carries a transcriptional activation domain homologous to those of AF4, LAF4 and AF5q31, and colocalises with ELL in nuclear speckles; transfection of MLL-ELL delocalises EAF1 from speckles to a diffuse nucleoplasmic pattern, and EAF1 speckles are undetectable in MLL-ELL-derived leukemic cell lines, suggesting MLL-ELL has a dominant effect on the normal protein-protein interactions of ELL.
EAF1, a novel ELL-associated factor that is delocalized by expression of the MLL-ELL fusion protein · Simone F, Polak PE, Kaberlein JJ, Luo RT, Levitan DA, Thirman MJ · Blood 2001What this evidence cannot show
Confocal localisation in transfected cells and in mouse-derived leukemic lines; no separation-of-function experiment ties the delocalisation to transformation. A 2001 study, pre-dating current speckle markers and live-cell imaging. Verified against PubMed on 2026-09-18.
Evidence that argues against this (1)
- The delocalisation is a fixed-cell fluorescence result, and that readout is now known to be fixation-sensitive in exactly this direction. Irgen-Gioro et al. compared images of the same cells before and after paraformaldehyde fixation and found that fixation can both enhance and diminish apparent droplet-like nuclear puncta, that for specific proteins puncta appear in fixed cells which show none when live, and that fixing in the presence of glycine reverses the direction of the artefact; their kinetic model attributes this to the balance between protein-protein interaction dynamics and the relative fixation rates of the proteins involved. Co-expressing a second protein changes interaction dynamics, so a speckle pattern that becomes 'diffuse nucleoplasmic' on MLL-ELL transfection is confounded by the assay. Live-cell imaging of endogenously tagged EAF1 in an MLL-ELL line would settle it and has not been done. Irgen-Gioro S et al. 2022
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
ELL contains a protein-protein interaction domain within its amino terminus that binds both EAF1 and EAF2; this N-terminal interaction domain is disrupted in the formation of the MLL-ELL fusion protein, so MLL-ELL retains an interaction domain for EAF1 but not for EAF2. EAF2 is 58% identical to EAF1, colocalises with ELL in nuclear speckles, contains a transcriptional activation domain, and a heterologous MLL-EAF2 fusion immortalises haematopoietic progenitors.
ELL-associated factor 2 (EAF2), a functional homolog of EAF1 with alternative ELL binding properties · Simone F, Luo RT, Polak PE, Kaberlein JJ, Thirman MJ · Blood 2002What this evidence cannot show
Biochemical mapping with deletion constructs; no residue coordinates are carried into this entry because UniProt P55199 annotates no N-terminal feature and inventing one would break the domain-map join. Verified against PubMed on 2026-09-18.
Evidence that argues against this (1)
- That MLL-ELL 'retains an interaction domain for EAF1 but not for EAF2' is an inference from where one mapped fusion junction falls relative to deletion-mapped binding regions, and neither term of that comparison has patient-level support. Meyer et al. determined ELL among 94 molecularly characterised MLL partner genes across 2,345 patients and found 135 distinct rearrangements with an age- and lineage-dependent breakpoint shift; whether the ELL-side breakpoint is constant enough across t(11;19)(q23;p13.1) patients for 'the N-terminal site is disrupted' to be a property of the disease rather than of one construct has not been checked. The binding regions themselves carry no residue coordinates in UniProt, so the claim cannot currently be tested against a breakpoint at all. Meyer C et al. 2018
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
In myeloid progenitor immortalisation and transplant assays, the elongation domain of ELL is dispensable for MLL-ELL leukemogenesis whereas the EAF1-interaction domain is critical; MLL fused to the minimal EAF1-interaction domain of ELL causes AML with longer latency than full MLL-ELL, and a heterologous MLL-EAF1 fusion immortalises myeloid progenitors and causes AML with shorter latency than MLL-ELL.
The elongation domain of ELL is dispensable but its ELL-associated factor 1 interaction domain is essential for MLL-ELL-induced leukemogenesis · Luo RT, Lavau C, Du C, Simone F, Polak PE, Kawamata S, Thirman MJ · Molecular and Cellular Biology 2001What this evidence cannot show
Retroviral transduction of murine myeloid progenitors plus transplant; latency differences are the readout and cohort sizes in 2001-era transplant work were small. The 'EAF1 interaction domain' referred to here is the C-terminal, ELL-retained site, distinct from the N-terminal dual site discussed in E2 — the two papers are from the same group and use the same nomenclature for different sites, which is an easy error to make. Verified against PubMed on 2026-09-18.
Evidence that argues against this (1)
- That MLL-EAF1 is more potent than MLL-ELL argues the fusion's problem is too much EAF-type transactivation, not too little EAF binding. On that reading, restoring the lost N-terminal EAF site would not suppress transformation and might enhance it — a direct prediction against classifying the N-terminal loss as a deleted brake. Luo RT et al. 2001
sites lie in the retained OCEL EAF1 module
mechanism class of this fusion: both — addition dominant, two documented but untested subtraction components
N-terminal dual EAF1/EAF2 docking site disrupted by the fusion
refines the EAF module picture: two docking sites, only one retained
- refutes →Step 3 — The hijack: the fusion drags the super elongation complex to paused RNA polymerase II
Luo et al. show the ELL elongation domain is dispensable for MLL-ELL leukemogenesis while the EAF1-interaction domain is essential
- related to →Nuclear speckles — the compartment everyone assumes KMT2A::AFF1 uses, on evidence that skips AFF1 itself
MLL-ELL delocalises endogenous EAF1 out of nuclear speckles — sequestration subtraction
both are sequestration subtraction — the fusion relocates an endogenous protein rather than deleting a domain
per-partner entry feeding the synthesis
Luo 2001 (PMID 11463848) + Simone 2002 (PMID 12446457): the lost ELL segment is exon 1 / the N-terminal EAF1-EAF2 interaction domain, not a Pol II-DSIF contact; the retained elongation domain is dispensable for transformation