DOT1L leaves chromatin before menin does when the fusion is degraded, and the ordering survives a change of instrument that destroys the magnitudes - ChIP-qPCR at selected loci, target-restricted read counts and genome-wide peak presence all rank DOT1L ahead of menin while disagreeing about every number
also called DOT1L before menin · ordering transfers across instruments · 68.7% versus 80.0% · sluggish menin
When the fusion protein is destroyed one of its partners comes off DNA quickly and another lingers, and three completely different ways of measuring this disagree wildly about how much comes off while all three agree on which one goes first. That kind of agreement is worth more than any of the individual numbers.
The same thing, for a scientist
**The ordering, from three instruments on the same degron system:** | instrument | DOT1L | menin | ordering | |---|---|---|---| | ChIP-qPCR at selected loci [E1] | ~50% lost at 15 min, near-complete at 30 min | "more sluggish", robust change only at 3 h | DOT1L first | | Target-restricted normalised read counts, 3 h [E1] | ~70% lost | >50% lost | DOT1L first | | Genome-wide peak presence, 3 h [E2] | 68.7% retained (loss/HA 0.33) | 80.0% retained (loss/HA 0.21) | DOT1L first | The authors state it plainly: *"DOT1L dissociates from chromatin faster than MENIN upon MLL::AF9 degradation"* [E1]. **The magnitudes are irreconcilable and the ordering is unanimous.** Near-complete DOT1L loss at 30 minutes by ChIP-qPCR versus 68.7% of peak calls retained at three hours genome-wide is a disagreement of a different order from measurement error; it is the denominator and the quantity differing (see `concept-q139-a-target-restricted-signal-measure-and-a-genome-wide-peak-measure-are-different-instruments`). **Yet the rank does not move.** **Why this matters beyond the two proteins.** This project's standing finding is that between KMT2A::MLLT3 and KMT2A::AFF1 lines **per-gene ordering transfers and magnitude does not**. That was established across *cell lines*. Here the same asymmetry appears across **instruments applied to one experiment** — which is a stronger and more general statement: it is not that the two leukaemias are similar, it is that **rank is the robust feature of an occupancy measurement and magnitude is the fragile one.** **The proposed mechanism, which is the authors' and is testable.** DOT1L is recruited directly by the AF9 portion of the fusion — *"the AF9 fusion partner directly binds and recruits DOT1L to chromatin"* [E1, E3] — so removing the fusion removes DOT1L's tether. Menin has an additional, fusion-independent anchorage through LEDGF/PSIP1 [E4], so it persists. **Direct tether versus redundant tether predicts exactly this ordering.**
What this predicts, and where it could break
Prediction 1. In a fusion whose 3' partner does not bind DOT1L — for example KMT2A::AFF1, where DOT1L recruitment runs through AFF1/AF4-family and SEC contacts rather than the AF9/ENL YEATS route — the DOT1L-before-menin ordering should weaken or invert. The ordering's mechanistic warrant is partner-specific even though this project's ordering-transfer rule is not.
Prediction 2. Removing LEDGF should convert menin from the sluggish component to the fast one. Nothing in any deposit tests this.
Where it breaks: if a KMT2A::AFF1 degron showed DOT1L leaving first just as fast, the direct-tether explanation would be wrong even though the ordering rule held — the ordering would then need a different cause, such as differing residence-time kinetics independent of which subunit does the recruiting.
- If menin is held by a redundant tether while DOT1L is held by a direct one, then a menin-directed drug is attacking the more buffered of the two contacts. That is an argument for DOT1L or combination pressure that this project's menin-interface focus would not naturally generate, and it comes from the authors' own proposed mechanism.
- A drug that displaces menin without removing the fusion leaves DOT1L's direct AF9 tether intact, so menin displacement alone need not disassemble the complex. The ladder in this beat shows precisely that - VTP-50469 alone leaves 51.7-76.9% of the fusion's own sites occupied.
- Does the DOT1L-before-menin ordering hold in a KMT2A::AFF1 degron? The mechanistic explanation is AF9-specific, so this is the experiment that separates a general rule from a partner-specific one - and no KMT2A::AFF1 degron line with paired ChIP exists publicly.
- Would depleting LEDGF/PSIP1 convert menin into the fast-dissociating component? A MEN1 ChIP 3 h after fusion degradation in PSIP1-knockdown versus control cells is a single, cheap, decisive experiment that nobody has run.
- Is 'ordering transfers, magnitude does not' a property of ChIP occupancy generally rather than of these leukaemias? This entry is the first instance of it holding across instruments on ONE experiment, which would generalise the rule considerably if it replicated elsewhere.
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
DOT1L dissociates from chromatin faster than MENIN upon MLL::AF9 degradation - ~50% DOT1L loss at 15 min and near-complete at 30 min by ChIP-qPCR, against MENIN loss that is 'more sluggish' with robust changes only after 3 hours - and the authors attribute the difference to AF9 directly recruiting DOT1L while menin has additional LEDGF anchorage.
MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape. · Olsen SN, Godfrey L, Healy JP, Choi YA, Kai Y, Hatton C, Perner F, Haarer EL, Nabet B, Yuan GC, Armstrong SA · Molecular Cell 2022What this evidence cannot show
The 15 and 30 minute kinetics come from ChIP-qPCR at a small number of selected MLL::AF9-bound loci in experimental triplicate, not genome-wide, and there is no ChIP-seq at those early timepoints. The LEDGF explanation is offered in the discussion as a possibility ('could explain'), not demonstrated in this paper. HCB1 is KMT2A::MLLT3; no KMT2A::AFF1 degron exists to test the partner-specificity prediction.
Evidence that argues against this (1)
- If DOT1L's apparent speed is an antibody or epitope property rather than a residence property, the ordering would be an artefact shared by all three instruments, since all three use the same DOT1L antibody in the same cells. Instrument agreement does not protect against a reagent-level common cause. NCBI Gene Expression Omnibus 2022
- E2moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
Genome-wide, DOT1L retains 68.7% and menin 80.0% of their strongest peak calls 3 h after fusion degradation, ranking DOT1L as the more displaced of the two.
GSE173599, samples GSM5271647/GSM5271649 (DOT1L 3 h) and GSM5271682/GSM5271684 (MEN1 3 h) · Olsen SN, Armstrong SA, et al. · NCBI Gene Expression Omnibus 2022What this evidence cannot show
n = 1 per arm. The two pairs are in DIFFERENT sequencing batches (1909x2 for DOT1L, 1912x2 for MEN1), so the 11-point gap between 68.7% and 80.0% crosses a batch boundary and is not resolvable against batch effect - the only measured technical floor in this deposit is 4.6 points and that was within a single channel. The ordering is supported mainly by its agreement with the authors' two within-batch instruments, not by this gap on its own.
Evidence that argues against this (1)
- An 11-point difference across two sequencing batches, with n = 1 each and no spike-in, would not be reportable as a difference at all if the authors' ChIP-qPCR did not independently give the same rank. On its own this comparison is underpowered. Oncofusion knowledge graph 2026
- E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
DOT1 forms a stable complex with AF9 directly - in the absence of other factors it binds AF9 and does not interact with AF9-AF4-P-TEFb complexes - and DOT1L has three AF9 binding sites whose graded disruption grades H3K79 methylation and transformation, making AF9 the direct tether that removing the fusion would remove.
Function of leukemogenic mixed lineage leukemia 1 (MLL) fusion proteins through distinct partner protein complexes. · Biswas D, Milne TA, Basrur V, Kim J, Elenitoba-Johnson KS, Allis CD, Roeder RG · Proceedings of the National Academy of Sciences USA 2011What this evidence cannot show
CITED HERE BECAUSE OLSEN ET AL. CITE IT FOR THIS POINT, and it is paired in their sentence with Kuntimaddi et al. 2015 (PMID 25921540, Cell Rep 11:808-820), which maps three DOT1L-AF9 binding sites by NMR and shows graded recruitment grading H3K79me2/me3. I have read both abstracts and the citing sentence in Olsen et al., not the full papers. They establish the AF9-DOT1L architecture biochemically and structurally; neither measures the kinetics of DOT1L release after acute fusion removal, which is an inference. IDENTIFIER PROVENANCE: I first wrote PMID 21606356 here from recall. That is a mouse tracheal chemosensory-cell paper about breathing regulation and has nothing to do with this subject. It was caught by verification before the entry was finished, and the correct identifier was taken from the reference list of the citing paper itself and then confirmed against PubMed.
Evidence that argues against this (1)
- DOT1L also associates with chromatin independently of MLL fusions in normal cells, so a direct AF9 tether is not the only thing holding it there, and the fact that 68.7% of DOT1L peak calls survive fusion removal genome-wide is consistent with most DOT1L residence being fusion-independent. NCBI Gene Expression Omnibus 2022
- E4established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
Menin physically links MLL proteins to LEDGF on chromatin, providing an anchorage that does not require the fusion.
Menin critically links MLL proteins with LEDGF on cancer-associated target genes. · Yokoyama A, Cleary ML · Cancer Cell 2008What this evidence cannot show
Abstract-level reading plus the citing sentence in Olsen et al. The paper shows menin adapting MLL to LEDGF; it does not show that this anchorage persists in the absence of an MLL fusion, which is the step the mechanism here needs and which no experiment has tested.
Evidence that argues against this (1)
- This graph carries an entry titled mechanism-ledgf-dispensable-for-fusion-chromatin-retention. If LEDGF is dispensable for retaining the fusion, whether it is required for retaining menin after the fusion is gone is a separate and untested question, but the two entries pull in opposite directions and should be adjudicated. Oncofusion knowledge graph 2026
The peak-presence half of the three-instrument comparison: DOT1L 68.7% retained against menin 80.0%, the same rank the authors' ChIP-qPCR and target-restricted read counts give.
DOT1L's chromatin tether at fusion sites is the direct AF9 contact, which is destroyed with the fusion - the mechanistic reason it leaves before menin, whose second anchorage is not.
AF9/MLLT3 binds DOT1L directly through three mapped binding sites whose graded disruption grades H3K79 methylation and transformation (PMID 21896721, PMID 25921540) - the architecture that predicts DOT1L leaving first when the fusion is degraded.
Supplies the mechanism for menin's persistence: a redundant tether, against DOT1L's single direct one. The ordering is unanimous across three instruments while every magnitude disagrees.
The two-anchor model predicts the ordering: DOT1L's single direct AF9 tether is destroyed with the fusion, menin's second tether is not, so DOT1L leaves first.
- ← supportsThe order in which the complex leaves fusion-occupied promoters, all fifteen channels on one scale
third instrument agreeing: DOT1L 0.401 before MENIN 0.503 on the authors' own per-gene signal table