'AF4 bodies' - a named subnuclear compartment that is non-nucleolar and coincident with no known nuclear structure, and the one place a KMT2A fusion has been shown to move a partner
also called AF4 body · AF4-AF9 subnuclear foci · Erfurth AF4 bodies
In 2004 a group found that the two commonest partners of the leukemia fusion, AF4 and AF9, meet each other in small nuclear spots they called 'AF4 bodies' - spots that did not line up with any nuclear structure they tested. When the MLL-AF4 fusion was present, AF9 moved.
The same thing, for a scientist
The two most frequent KMT2A partners, AFF1/AF4 and MLLT3/AF9, interact, and that interaction is restricted to discrete nuclear foci the authors named **AF4 bodies**. The bodies are explicitly **non-nucleolar** and, in the authors' words, 'not coincident with any known nuclear structures we have examined'. The AF4-AF9 interaction is maintained by the MLL-AF4 fusion protein, and expression of MLL-AF4 **can alter the subnuclear localization of AF9** [E1]. That last clause is the important one: it is one of very few published statements in which a KMT2A fusion changes where another protein sits, as opposed to a statement about where the fusion itself sits. The attribution status is the familiar one - the fusion was introduced into cells by expression, so the species carrying the readout is unambiguous, but the system is overexpression and the level is not physiological. This entry is written because the AF4 body is a *named compartment with a negative co-localisation result*, and this graph's compartment entries have been organised around structures the fusion was assumed to occupy (speckles, nucleolus, Pol II clusters, PML bodies, Polycomb bodies) without a source that tested the alternative that the relevant compartment is none of them.
What the negative co-localisation means for the speckle assumption
This graph's nuclear-speckle entry records that three of the four AFF-family proteins have been shown to live in speckles but not AFF1, the one actually fused in t(4;11), and that nobody has co-stained a real KMT2A fusion with a speckle marker. The AF4-body result is the closest thing to a direct test and it points the other way: the foci where AF4 and AF9 meet are reported as matching no known structure the authors examined 1.
Two cautions before that is used as a refutation. The abstract does not enumerate which structures were examined, so 'any known nuclear structures' cannot be assumed to include SC35/SRSF2 speckles. And the paper is from 2004, before several compartments now in routine use were well marked. The honest statement is that the only published attempt to place AF4-associated foci among named compartments failed to place them, and that this is a reason to hold the speckle assumption loosely rather than a reason to discard it.
The fusion moves the partner - a rarer claim than it looks
Almost every localisation statement about KMT2A fusions is of the form 'the fusion is here'. Two published statements are of the form 'the fusion moves something else':
- MLL-AF4 alters the subnuclear localisation of AF9 1 - within the nucleus, in an expression system.
- MLL-AF6-rearranged cells relocate endogenous AF6 from cytoplasm to nucleus, with consequent RAS activation, and silencing the fusion restores cytoplasmic AF6 and reduces RAS-GTP 2 - across compartments, in rearranged cells, with a functional readout and a rescue.
The second is much the stronger design, and it is the template the first is missing: a rearranged cell rather than a transfectant, an endogenous readout, and a knockdown that reverses the phenotype. Whether MLL-AF4 sequesters endogenous AF9 - or endogenous AFF1 - in a t(4;11) line is unmeasured, and the reagents exist.
Attribution status
Positive-but-overexpressed, the same class the fusion-attribution audit found for every surviving localisation claim. The fusion is introduced, so the signal is attributable to the fusion; the level is not physiological, so the compartment may be an artefact of concentration. The relevant general caution is that at physiological expression, low-complexity-domain interactions that control transcription form dynamic hubs without detectable phase separation, so a discrete focus in an overexpressing cell is weak evidence about the endogenous protein 3.
| compartment | AF4 bodies |
|---|---|
| named by | Erfurth et al. 2004 |
| non nucleolar | true |
| coincident with known structure | false |
| fusion effect | MLL-AF4 expression alters subnuclear localisation of AF9 |
| system | expression system (not an endogenous t(4;11) cell) |
| attribution | positive but overexpressed |
proteins
[ "gene-aff1", "gene-mllt3" ]
- If the fusion's functional compartment is a structure with no marker, no imaging-based pharmacodynamic assay can be built for it, and occupancy remains the only tractable readout.
- If MLL-AF4 sequesters endogenous AF9 into fusion-driven foci, an AF9-directed therapeutic would also deplete a wild-type pool already depleted by the fusion, widening the on-target toxicity window in the wrong direction.
- Which nuclear structures did the 2004 study actually test AF4 bodies against - were SC35 speckles among them?
- Do endogenous AFF1 and MLLT3 co-localise in foci in a t(4;11) line, and does knocking down the fusion disperse them?
- Is the AF4 body the same structure later described as SEC condensates, or a distinct one?
- E1moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
AF4 and AF9, the two commonest MLL fusion partners, interact, and the interaction is restricted to discrete nuclear foci named 'AF4 bodies' that are non-nucleolar and not coincident with any known nuclear structures the authors examined; the interaction is maintained by the MLL-AF4 fusion protein and expression of MLL-AF4 can alter the subnuclear localization of AF9.
MLL fusion partners AF4 and AF9 interact at subnuclear foci · Erfurth F, et al. · Leukemia 2004What this evidence cannot show
Abstract only - the Europe PMC core record returns no pmcid, so routes 2-4 of the unreadable test were not reachable and the cell system, tags and the list of nuclear structures examined are all unstated in the abstract. 'Expression of the MLL-AF4 fusion' indicates a transfection or transduction rather than an endogenous t(4;11) cell.
Evidence that argues against this (1)
- A 1998 study of AF4 in real t(4;11) cells reported that both t(4;11) and non-t(4;11) leukaemic cells show a similar punctate nuclear pattern, i.e. no detectable fusion-driven redistribution at endogenous level - although that experiment could not have detected one. Li Q et al. 1998
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
MLL-AF6-rearranged cells relocate endogenous AF6 from the cytoplasm to the nucleus with consequent RAS activation, and silencing the fusion restores cytoplasmic AF6 and significantly reduces RAS-GTP levels.
MLL-AF6 fusion oncogene sequesters AF6 into the nucleus to trigger RAS activation in myeloid leukemia · Manara E, et al. · Blood 2014What this evidence cannot show
A different fusion (t(6;11), AFDN partner) and a cytoplasm-to-nucleus move rather than a subnuclear one, so it is a design template rather than direct evidence about AF4 bodies. The readout on the endogenous partner is attributable because wild-type AF6's compartment change is the measurement, not the fusion's position.
Evidence that argues against this (1)
- The same logic has not been shown for septin fusions despite their cytoplasmic partners, so partner sequestration is not established as a general property of KMT2A fusions with cytoplasmic partners. Ono R et al. 2005
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
At physiological expression, low-complexity-domain interactions that control transcription form dynamic hubs without detectable phase separation, so a discrete punctate structure in an overexpressing cell is weak evidence about the endogenous protein.
Imaging dynamic and selective low-complexity domain interactions that control gene transcription · Chong S, et al. · Science (New York, N.Y.) 2018What this evidence cannot show
A general result about transcription-factor low-complexity domains, not about AF4 or AF9 specifically, and it constrains interpretation rather than refuting the observation.
Evidence that argues against this (1)
- Clustered binding to spatially clustered sites - the rival model to phase separation - would also produce discrete foci, and would be a substantive mechanism rather than an artefact, so 'not phase separation' is not 'not real'. Muzzopappa F et al. 2022
AF4 bodies are AFF1 only named subnuclear compartment and match no known structure
- ← related toMLLT3 / AF9 — a famous fusion partner that is not a dependency, and a hub domain that is
AF9 is the other half of the AF4 body, and MLL-AF4 moves it
- ← related toAFF3 (LAF4) — the AFF-family scaffold of SEC-L3, and a KMT2A fusion partner in its own right
Family contrast: AFF2/AFF3/AFF4 are speckle proteins while AFF1's only named compartment is AF4 bodies, explicitly not coincident with any known structure - three laboratories' worth of assay difference, never controlled (Q89 2026-09-21)
The one NAMED body SPT6 has ever been placed in is the Drosophila HISTONE LOCUS BODY, by RNAi and proteomics with hierarchical recruitment (PMID 21576393) - and it may be the occupancy result seen through another instrument, because the HLB forms at the histone gene cluster being transcribed. No mammalian body assignment exists for SPT6 in any organism (Q95 2026-09-22)
AF4 bodies are defined by AF4 and are the only named compartment attributed to it
- related to →MLLT3 / AF9 — a famous fusion partner that is not a dependency, and a hub domain that is
AF9 is the partner whose subnuclear position MLL-AF4 expression alters
the only attempt to place AF4-associated foci among named compartments placed them nowhere, which weakens the speckle assumption
- related to →The nucleolus — the one compartment with direct published images of a KMT2A fusion inside it
AF4 bodies are explicitly non-nucleolar, which is a constraint on the nucleolar entry
- analogous to →KMT2A::AFDN (MLL-AF6), t(6;11)(q27;q23)
the MLL-AF6 partner-sequestration experiment is the design template AF4 bodies lack
a discrete focus in an overexpressing cell is graded by the same standards as a condensate claim