Lost from the KMT2A half: the FYRN-FYRC clamp (2018-2074 / 3666-3747) that holds wild-type KMT2A together
also called FYRN FYRC interaction · N320 C180 heterodimer · MLL self-association clamp
After normal KMT2A is cut in two, a pair of matching clips on the two halves snap them back together. Without its partner, the clip on the front half is not inert - it is the very thing the cell grabs to destroy the orphaned piece. The leukemic protein is cut off long before either clip and has neither, which is part of why it survives.
The same thing, for a scientist
FYRN (UniProt Q03164, aa 2018-2074) on the N320 fragment binds FYRC (aa 3666-3747) and the SET domain on C180 [E1, E2]; structurally the two are halves of a single alpha+beta fold with a ~1,600-residue insertion between them, so an unpartnered FYRN is half a beta-sheet rather than a domain [E5]. **Corrected cycle 31 on three points.** (i) **Scope.** Both halves are C-terminal to the breakpoint cluster region, so **der(11) KMT2A::partner** contains neither - but the reciprocal **der(4) AFF1::KMT2A** product contains both, and there the FYRN/FYRC heterodimer is the activating step that protects the oncoprotein from SIAH1/2 ubiquitinylation and is a proposed decoy target [E4]. (ii) **The fate of an unpartnered FYRN is known, and it is not inertness.** Free MLL(N) is destroyed by a mechanism that targets the FYRN domain; FYRN is a degron [E3]. The fusion escapes it by not having FYRN at all. (iii) **Direction.** This entry was built on the reading that cleavage plus reassociation 'confers stability'. At the level of the whole protein the opposite is now reported: uncleaved MLL1 is the longer-lived, more chromatin-bound species [E6]. The clamp is better described as a determinant of which fragment survives than as the source of MLL1's stability.
CORRECTION (cycle 31): the fusion has no FYRN, and FYRN is a degron
Three corrections, all in the body because each changes what a reader takes away.
1. There is no orphaned FYRN in the fusion. FYRN and FYRC are split by the taspase1 cleavage at 2666/2718, not by the translocation breakpoint. The breakpoint cluster region ends around residue 1400-1445, so FYRN at 2018-2074 sits roughly 600 residues beyond it and der(11) fusions lose both halves. (The cycle-31 dispatch to this beat asserted the opposite - that the fusion keeps FYRN - and that premise is wrong; it is recorded in the ledger's corrections_owed.) The genuinely orphaned fragment is the wild-type MLL(N) produced by cleavage when its C180 partner is unavailable.
2. That orphan's fate is known: FYRN is a degron. Yokoyama et al. built the MLL(C)-null mouse and showed that MLL(N) stability depends on intramolecular contacts through PHD1, PHD4 and FYRN, and that free MLL(N) is destroyed by a mechanism that targets the FYRN domain, while free MLL(C) is exported and degraded by the proteasome 3. An unpartnered half-fold is not nothing; it is a destruction signal - which is what 5 would lead you to expect, since FYRN alone is half a beta-sheet with its partner strands missing.
The consequence for this beat is the interesting one. The fusion's KMT2A half is, topologically, exactly a free MLL(N) - an N-terminal fragment with no C-terminal partner - except that it stops short of the degron. Losing FYRN is therefore not a neutral subtraction; it is how the fusion avoids the pathway that disposes of unpartnered MLL N-termini. Together with the missing taspase1 sites and the missing PHD2 E3 ligase, that is three independent degradation determinants absent from one protein.
3. 'Confers stability' needs a direction. The founding claim 1 is that disrupting the N320-C180 interaction decreases N320 levels, which is true and unchallenged. But this entry's summary generalised it into cleavage-plus-reassociation being what makes MLL1 stable. Zhao et al. report the opposite at the level of the whole protein: uncleaved MLL1 is longer-lived and more chromatin-bound than the cleaved product 6. Both can hold - if you cleave, N320 needs C180 to survive; if you never cleave, you are better off - but the entry must not be read as saying that cleavage is a stabilising event.
Why this is a separate loss from the cleavage sites
Taspase1 cleavage and FYRN-FYRC reassociation are sequential but mechanistically distinct. A protein could in principle be uncleavable yet still fold with FYRN against FYRC; a protein could be cleaved and then fail to reassociate. Hsieh et al. built exactly that second mutant and found the consequence: markedly decreased N320 and diffuse C180 1.
The leukemic fusion loses both, but it loses them for different reasons and with different predicted consequences:
- losing the cleavage sites means the fusion is never processed (a missing regulatory event);
- losing the FYRN-FYRC clamp means the fusion has no intramolecular determinant of its own stability or subnuclear placement (a missing structural constraint).
Hsieh et al. make the second point explicitly as a prediction: fusions that cannot complex with C180 have their stability conferred instead by the fusion partner 1. That prediction is the reason partner identity might set fusion abundance - a link the graph's partner beat has not drawn.
Withdrawn, cycle 31. This section said fusions 'lose both' the cleavage sites and the clamp. True for der(11); false for the reciprocal der(4) AFF1::KMT2A, which keeps both and uses the clamp as its activating step 4. The graph's hyp-reciprocal-product-as-enforceable-remainder is the entry that should carry that forward.
The subnuclear consequence nobody has followed up
The 2003 result is not only about stability. Disrupting the N320-C180 interaction redistributes C180 to a diffuse nuclear pattern 1 - i.e. the clamp is what places the complex in its subnuclear compartment. The graph has an entire localisation beat (mechanism-kmt2a-subnuclear-localization, localization-nuclear-matrix-mitotic-scaffold-kmt2a) built largely on the retained N-terminal SNL signals.
The unasked question: if wild-type KMT2A's placement depends on a C-terminal clamp the fusion does not have, then the fusion's subnuclear distribution is determined by a different set of signals from the wild-type protein's, even though both share the same N-terminus. Any claim that fusion and wild-type KMT2A occupy the same compartment because they share the SNL region is therefore under-determined.
| module | FYRN-FYRC reassociation clamp |
|---|---|
| uniprot | Q03164 |
| fate in fusion | lost from der(11) KMT2A::partner; RETAINED by the reciprocal der(4) AFF1::KMT2A product, where the FYRN/FYRC heterodimer is the activating step and a proposed decoy target (PMID 21233834) |
| consequence type | loss of a degron and of an intramolecular stability/localisation determinant |
| wild type function | FYRN on N320 binds FYRC and SET on C180; the heterodimer stabilises N320 and directs subnuclear placement |
| authors prediction for fusions | fusion stability is conferred by the partner instead (Hsieh et al. 2003, stated as a prediction) |
| demonstrated functional consequence of loss to the fusion | FYRN is the domain targeted by the mechanism that destroys free MLL(N) (PMID 21670200); the fusion, which stops short of FYRN, escapes that route. Demonstrated on wild-type fragments, not on a fusion. |
| loss class | demonstrated degradation determinant (upgraded from 'lost, with an explicit 23-year-old untested prediction attached') |
| structure note | FYRN and FYRC are halves of one alpha+beta fold (TBRG1 structure, PMID 20506279); in MLL they are separated by ~1,600 residues, so an unpartnered FYRN is half a beta-sheet, not a domain. |
sub features
[
{
"name": "FYRN",
"start": 2018,
"end": 2074,
"source": "UniProt Q03164"
},
{
"name": "FYRC",
"start": 3666,
"end": 3747,
"source": "UniProt Q03164"
}
]also mediating holocomplex
[ "PHD1 (1431-1482)", "PHD4 (1931-1978)" ]
- If partner identity sets fusion abundance, then any therapy whose effect depends on reducing fusion levels will have partner-dependent potency, undermining the partner-agnostic premise of the menin-inhibitor strategy.
- A degrader exploiting an exposed N-terminal degron would act on sequence shared with wild-type KMT2A, which is under extreme loss-of-function constraint; the exposure, not the sequence, would have to supply the selectivity, and exposure is a much weaker discriminator than a distinct binding site.
- Re-installing FYRN into the fusion as a destabilising add-back is attractive precisely because it predicts a loss of protein rather than a gain of regulation - but that makes it hard to interpret: any insertion that lowers fusion abundance will lower replating, which is the same confound that makes the PHD3 add-back result hard to trust.
- A FYRC decoy that destroys AF4-MLL would also engage wild-type MLL's own FYRN, and the wild-type allele is genetically required for MLL-AF9 leukemogenesis (PMID 20159607). The therapeutic window for that strategy is not obviously open.
- Does fusion protein half-life vary by partner, as Hsieh et al. predicted in 2003? Still unmeasured, and now more pointed: three degradation determinants are missing, so partner-supplied determinants are the only ones left.
- Is the fusion's KMT2A half degradable through a FYRN-independent route that the free-MLL(N) work would have missed? If the FYRN degron is the only disposal pathway for an unpartnered MLL N-terminus, then re-installing FYRN in cis into the fusion should destabilise it - a four-kilobase-free, purely destabilising add-back that nobody has tried and that would be a cleaner test of the whole abundance hypothesis than any occupancy experiment.
- In t(4;11) patients who express the reciprocal AFF1::KMT2A, does the FYRC decoy strategy have any selectivity over wild-type MLL, which uses the same interface? The decoy cannot tell the two apart, and that is the obvious objection to PMID 21233834's proposal.
- Wild-type KMT2A's subnuclear placement depends on this C-terminal clamp. Does the fusion therefore occupy a different compartment despite sharing the SNL region, and has any imaging study controlled for that?
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
The FYRN domain of MLL N320 directly interacts with the FYRC and SET domains of C180; disrupting the interaction between N320 and C180 leads to a marked decrease in N320 levels and redistribution of C180 to a diffuse nuclear pattern, supporting a model in which dynamic post-cleavage association confers stability on N320 and correct nuclear sublocalisation on the complex; and MLL fusion proteins of leukemia, which lose the ability to complex with C180, are predicted to have their stability conferred instead by the fusion partners.
Proteolytic cleavage of MLL generates a complex of N- and C-terminal fragments that confers protein stability and subnuclear localization · Hsieh JJ-D, Ernst P, Erdjument-Bromage H, Tempst P, Korsmeyer SJ · Molecular and Cellular Biology 23(1):186-194 2003What this evidence cannot show
ABSTRACT ONLY. Transfected cell lines with mutant constructs and immunofluorescence; 'subnuclear compartment' is defined by microscopy in that system and is not mapped onto any modern compartment ontology. The statement about fusion proteins is the authors' explicit prediction, not a measurement on a fusion protein, and is cited as such.
Evidence that argues against this (1)
- Zhao et al. report that taspase1 cleavage primes MLL1 for degradation and that uncleaved MLL1 is the MORE stable species with higher chromatin occupancy, which inverts the 'cleavage confers stability' reading of this model at the level of the whole protein. Zhao Z et al. 2019
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
UniProt Q03164 places the FYR N-terminal domain at residues 2018-2074 and the FYR C-terminal domain at 3666-3747, both C-terminal to the KMT2A breakpoint cluster region.
UniProtKB entry Q03164 (KMT2A_HUMAN) - domain feature table, retrieved via the UniProt REST API · UniProt Consortium · UniProtKB 2026What this evidence cannot show
Accession verified by reading back the primary gene name (KMT2A) and length (3,969 aa). These ranges match the values already stored in gene-kmt2a (FYRN 2018-2072 vs 2018-2074; FYRC 3666-3747 exactly), so no correction is owed here - the 2-residue FYRN difference is within normal curatorial tolerance.
Evidence that argues against this (1)
- Both boundaries come from one annotation source and the FYR region is exactly where sources disagree, because FYRN and FYRC are scored as separate features by profile methods while the structural work argues they are one module. Quoting 2018-2074 and 3666-3747 as two domains embeds the annotation's answer to the question this entry is about. Protein Science 2010
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
The stability of MLL(N) depends on its intramolecular interaction with MLL(C), mediated through PHD1, PHD4 and the FYRN domain of MLL(N); free MLL(N) is destroyed by a mechanism that targets the FYRN domain, whereas free MLL(C) is exported to the cytoplasm and degraded by the proteasome; a mouse line lacking MLL(C) shows that the holocomplex, not the separated subunits, carries MLL's developmental functions; and PHD1, encoded by an alternatively spliced exon occasionally deleted in T-cell leukemia, is required for holocomplex formation, making its absence a loss-of-function allele.
Proteolytically cleaved MLL subunits are susceptible to distinct degradation pathways · Yokoyama A, Ficara F, Murphy MJ, Meisel C, Naresh A, Kitabayashi I, Cleary ML · Journal of Cell Science 124(Pt 13):2208-2219 2011What this evidence cannot show
ABSTRACT ONLY. A genetically engineered MLL(C)-null mouse plus construct biochemistry in cell lines; the FYRN-directed degradation is inferred from fragment stability and the responsible ubiquitin machinery is not identified. This is the source that answers the beat's 'what happens to an unpartnered FYRN' question - and answers it about wild-type MLL(N), not about the fusion, which has no FYRN at all.
Evidence that argues against this (1)
- The degradation route described is a property of the intact wild-type protein being cleaved and its halves separated. In a fusion there is no MLL(C), so 'free MLL(N) is destroyed' describes a fate that the fusion's N-terminal portion, fused to a partner, does not obviously share - and this entry needs that step to hold. Journal of Cell Science 2011
- E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
The reciprocal AFF1::KMT2A (AF4-MLL) product of t(4;11) contains both FYRN and FYRC: it is activated by taspase1-mediated hydrolysis into AF4-MLL-N and MLL-C, which heterodimerise through the FYRN and FYRC interaction domains; that heterodimer induces a high-molecular-weight complex protected against SIAH1/2-mediated polyubiquitinylation; and expressing FYRC or smaller portions of it blocks heterodimerisation, blocks complex formation and destroys the AF4-MLL oncoprotein, which the authors propose as a decoy-inhibitor strategy.
The heterodimerization domains of MLL-FYRN and FYRC--are potential target structures in t(4;11) leukemia · Pless B, Oehm C, Knauer S, Stauber RH, Dingermann T, Marschalek R · Leukemia 25(4):663-670 2011What this evidence cannot show
ABSTRACT ONLY. Bacterial two-hybrid mapping and a mammalian biosensor assay in HeLa cells; construct-level destruction, not a leukemia model. The premise that AF4-MLL is oncogenic rests on the same group's own transplantation work. Cited to correct this entry's scope: the clamp is lost from der(11), not from t(4;11).
Evidence that argues against this (1)
- This is the strongest evidence in the entry and it applies to a minority situation. The AF4-MLL reciprocal requires an intact der(4) AND expression of the reciprocal transcript, which is present in roughly half of such patients. A heterodimerisation target that exists in a fraction of t(4;11) is a narrower proposition than the entry's framing. Leukemia 2011
- E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
FYRN and FYRC are two halves of one fold, not two domains: the crystal structure of the TBRG1 FYR region shows FYRN and FYRC each forming part of a single novel alpha+beta module, and in trithorax and MLL, where the motifs are separated by hundreds of residues, the FYR domain is expected to contain a large insertion between two strands of the same beta-sheet.
The structure of the FYR domain of transforming growth factor beta regulator 1 · Garcia-Alai MM, Allen MD, Joerger AC, Bycroft M · Protein Science 19(7):1432-1438 2010What this evidence cannot show
ABSTRACT ONLY, and solved on TBRG1 rather than MLL; the MLL statement is the authors' explicit homology-based extrapolation. Cited for one structural point only.
Evidence that argues against this (1)
- A TBRG1 structure. The single-fold conclusion is an inference to KMT2A, and the MLL arrangement's large inter-strand insertion is a documented difference between them. Treating 'one fold' as established for KMT2A is the entry's load-bearing assumption and it rests on a different protein. Protein Science 2010
- E6strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Taspase1 cleavage of MLL1 primes it for proteasomal degradation: taspase1 loss leaves MLL1 uncleaved, longer-lived under cycloheximide chase and markedly increased in chromatin occupancy, with localisation and MLL/COMPASS assembly unchanged.
Regulation of MLL/COMPASS stability through its proteolytic cleavage by taspase1 as a possible approach for clinical therapy of leukemia · Zhao Z, Wang L, Volk AG, Birch NW, Stoltz KL, Bartom ET, Marshall SA, Rendleman EJ, Nestler CM, Shilati J, Schiltz GE, Crispino JD, Shilatifard A · Genes & Development 33(1-2):61-74 2019What this evidence cannot show
FULL TEXT read via PMC6317322. Cited here as the direct counterweight to this entry's founding claim that post-cleavage association 'confers stability'. The two results are about different species - Hsieh measures N320 stability given cleavage, Zhao measures total MLL1 stability given no cleavage - but the entry's summary previously read as though cleavage plus reassociation made MLL1 a stable protein, and on Zhao's data the uncleaved precursor is the more stable species.
Evidence that argues against this (1)
- Cycloheximide chase plus chromatin abundance shows taspase1 loss stabilises MLL1; it does not isolate cleavage as the cause, because taspase1 has substrates besides MLL and its knockout perturbs more than one axis. The pharmacological arm compounds this - CKII has a very large substrate set, so CX-4945 is not a clean probe of the licensing phosphorylation. Genes & Development 2019
- supports →Hypothesis: what the KMT2A half loses is control of its own abundance, not control of its activity
[supported_by] FYRN is the degron on a free MLL N-terminal fragment
the FYRN/FYRC clamp is retained by der(4) AFF1::KMT2A, where it is the activating step and a decoy target
[regulated_by] the clamp acts only after taspase1 cleavage, which the fusion never undergoes
- ← depends onLost from the KMT2A half: both taspase1 cleavage sites (D2666 and D2718) - the fusion is never processed
cleavage is the step that creates the two fragments the clamp then rejoins
- part of →KMT2A / MLL1 — the gene that breaks
FYRN 2018-2074 and FYRC 3666-3747; both lost
- related to →Where KMT2A and its fusions sit inside the nucleus — SNL1/SNL2, nuclear speckles and the condensate question
wild-type placement depends on a C-terminal clamp the fusion lacks, so shared SNL sequence does not imply shared compartment
FYRN binds FYRC and the SET domain; the clamp and the catalytic domain are lost as one piece
- ← related toLost from the KMT2A half: PHD2 (aa 1479-1533), an E3 ubiquitin ligase that limits KMT2A's own activity
two independent stability determinants lost together; the fusion retains neither
rows: FYRN 2018-2074 and FYRC 3666-3747