KMT2A is called an H3K4 methyltransferase, and it is required for the mark at under 5% of the promoters that carry it
also called MLL1 is a minority H3K4me3 writer · Mll1-null MEF H3K4me3 genome-wide
KMT2A's job description is writing a chemical tag on DNA packaging at switched-on genes. When you delete it and look genome-wide, more than 95% of the genes carrying that tag still have it. It only matters at a small, specific set of genes - which is why the gene can be a cancer driver without being a general-purpose switch.
The same thing, for a scientist
Genome-wide H3K4 methylation in Mll1-null versus wild-type mouse embryonic fibroblasts: Mll1 is required for H3K4 trimethylation of LESS THAN 5% of the promoters carrying that modification, and the affected genes - Hox genes among them - show a matching fall in RNA polymerase II recruitment and expression [E1]. In the same study MLL3/MLL4 and the Set1 complexes have little to no effect on H3K4 methylation of Hox loci [E1]. This is the epigenetics statement that has been missing from gene-kmt2a, and it does not say what the summary of that entry implies: KMT2A is not the enzyme that makes chromatin active, it is an enzyme that is load-bearing at a small address list. The second and larger question is whether its catalytic activity matters at all, and the literature is split: a SET-domain deletion leaves HSC maintenance and MLL-AF9 leukaemogenesis intact [E2], while a WDR5-interface inhibitor of the same activity selectively kills MLL cells (PMID 24389101). Both results are already in this graph, in subtraction-kmt2a-set-domain and mark-h4k16ac, and neither was in gene-kmt2a.
The measurement
Wang et al. compared genome-wide H3K4 methylation in Mll1+/+ and Mll1-/- mouse embryonic fibroblasts 1. Findings, in the authors' framing:
- Mll1 is required for H3K4 trimethylation of fewer than 5% of the promoters carrying the mark.
- Many of the affected genes are developmental regulators including Hox genes, and they show decreased Pol II recruitment and decreased expression together with the loss of methylation.
- Loss of MLL3/MLL4 and/or the Set1 complexes has little to no effect on H3K4 methylation of Hox loci or their expression in these cells.
That last point is what makes the <5% figure a specificity statement rather than a redundancy statement: the other COMPASS-like complexes are not silently covering for Mll1 at the loci that matter.
Why this belongs in the KMT2A entry and not only here
gene-kmt2a's expert summary opens 'KMT2A (Q03164, 3,969 aa, 38 exons) is a histone H3K4 methyltransferase'. That is true and, as a description of what the protein does in a cell, it is misleading by about twenty-fold. Before this cycle the entry carried no epigenetics field of any kind, so nothing in it bounded the claim.
The bound is not an argument that the enzyme is unimportant. It is the reason the Hox dependency is specific, and the reason a catalytically targeted therapy against KMT2A would be expected to have a narrow rather than a global effect. Whether catalysis matters at all is separately contested: a SET-domain deletion says no (E2), a WDR5-interface inhibitor says yes (see the section below).
The harder result sitting next to it
Mishra et al. showed that the SET domain, and thus the HMT activity of MLL1, is dispensable for maintaining HSCs and for supporting MLL-AF9-driven leukaemogenesis; on Mll1 deletion the mark that is selectively lost at MLL1 target genes is H4K16 acetylation, recruited MOF activity rather than intrinsic MLL1 methyltransferase activity is what maintains the HSC target genes, and SIRT1 inhibition is sufficient to prevent the loss 2.
This graph already holds that result in subtraction-kmt2a-set-domain, mark-h4k16ac and mechanism-set-loss-neomorph-not-haploinsufficiency, and PMID 24813891 is cited in 32 entries. It was in none of them the entry for the gene itself. Put together with E1, the honest one-line description of KMT2A's epigenetics is: a targeting module that recruits activity to a short address list, whose own catalytic output is required at under 5% of marked promoters and dispensable for the phenotypes measured.
And the result that pulls the other way, which this graph already holds. MM-401, which blocks the MLL1-WDR5 interaction and so MLL1's H3K4 methyltransferase activity specifically, blocks proliferation of MLL cells with cell-cycle arrest, apoptosis and myeloid differentiation, without general toxicity to normal marrow or non-MLL cells, and produces a transcriptome change resembling MLL1 deletion (PMID 24389101; recorded in subtraction-kmt2a-set-domain as the contradicting result). A SET deletion and an assembly blockade are not the same perturbation, and MM-401 removes WDR5-dependent assembly as well as catalysis - but 'the activity is dispensable' should never be stated in this graph without this sentence next to it.
| epigenetic readout | MLL1 WRITES H3K4me1/2/3 through its C-terminal SET domain, which every 5'-KMT2A direct fusion deletes. Two measurements bound what that writing is worth: (1) Mll1 is REQUIRED for H3K4me3 at UNDER 5% of promoters carrying the mark in Mll1-null MEFs, with the affected set enriched for Hox and other developmental regulators and showing matched losses of Pol II and expression, while MLL3/MLL4 and Set1 complexes do not cover for it at Hox loci [E1]; (2) the SET domain is DISPENSABLE for HSC maintenance and for MLL-AF9 leukaemogenesis, and the mark that actually falls at MLL1 targets on Mll1 deletion is H4K16ac, restored by SIRT1 inhibition, i.e. the functional output is recruited MOF activity not intrinsic methyltransferase activity [E2]. CONTESTED: pharmacological blockade of the same activity via the MLL1-WDR5 interface (MM-401) DOES selectively block MLL-cell proliferation with differentiation and apoptosis and no general marrow toxicity (PMID 24389101), so the genetic dispensability and the pharmacological requirement disagree, and the likeliest reconciliation is that the inhibitor removes complex assembly as well as catalysis. |
|---|---|
| writer of that mark | KMT2A SET domain (aa 3829-3945 per subtraction-kmt2a-set-domain), lost in every 5'-KMT2A direct fusion product |
| fraction of h3k4me3 promoters requiring mll1 | <5% |
| fraction system | Mll1-null mouse embryonic fibroblasts (PMID 19703992) |
| mark that actually falls on mll1 loss | H4K16ac, via recruited KAT8/MOF; SIRT1 inhibition prevents the loss (PMID 24813891) |
| shown for fusion | PARTIAL, and name which: the SET-dispensability arm was shown IN MLL-AF9 (mouse). The <5% promoter arm was shown in Mll1-null MEFs with no fusion. Neither was shown in KMT2A::AFF1 or in any B-lineage system. |
mark written
[ "H3K4me3", "H3K4me2", "H3K4me1" ]
existing graph entries that already held this
[ "subtraction-kmt2a-set-domain", "mark-h4k16ac", "mechanism-set-loss-neomorph-not-haploinsufficiency", "mechanism-kat8-h4k16ac-sets-the-hsc-quiescence-set-point" ]
- A therapeutic strategy aimed at KMT2A catalysis is aimed at the activity two independent results say is not the load-bearing one. Pinometostat's target is DOT1L for exactly this kind of reason, and a hypothetical MLL1 SET inhibitor would be expected to fail in the same way the SET deletion did.
- If SIRT1 inhibition restores H4K16ac at MLL1 targets, then a SIRT1 inhibitor given for any other indication could partially substitute for MLL1 function - an off-target drug interaction nobody screens for in this disease.
- What is the equivalent percentage in a haematopoietic cell? The <5% figure is from fibroblasts, and the one number this project would actually use - the fraction of H3K4me3 promoters requiring MLL1 in an HSPC - has never been measured.
- Does the fusion change the wild-type allele's address list? Every measurement here deletes Mll1 in a fusion-free cell. A degron on the wild-type allele in a KMT2A::AFF1 line, with H3K4me3 CUT&RUN, is the missing experiment and it is not in this graph's experiment set.
- If MOF recruitment rather than SET catalysis is MLL1's functional output, does the fusion still recruit MOF? subtraction-kmt2a-mof-contact records the MOF contact as LOST from the KMT2A half and not shown to matter to the fusion - which would mean the fusion loses the part that did the work, not the part with the enzyme name on it.
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
In a genome-wide comparison of Mll1+/+ and Mll1-/- mouse embryonic fibroblasts, Mll1 is required for the H3K4 trimethylation of less than 5% of the promoters carrying this modification; many affected genes are developmental regulators including Hox genes and show decreased RNA polymerase II recruitment and expression, while loss of MLL3/MLL4 and/or the Set1 complexes has little to no effect on H3K4 methylation of Hox loci or their expression in these cells.
Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II. · Wang P, Lin C, Smith ER, Guo H, Sanderson BW, Wu M, Gogol M, Alexander T, Seidel C, Wiedemann LM, Ge K, Krumlauf R, Shilatifard A · Mol Cell Biol 2009What this evidence cannot show
Mouse embryonic fibroblasts, NOT a haematopoietic cell and not a fusion-bearing cell. The 5% figure is a promoter-level call on a 2009 ChIP-chip/ChIP-seq-era platform and its denominator (promoters scored as carrying H3K4me3 in wild-type MEFs) is not quoted in the abstract; abstract read, full text not opened. A cell type in which Hox genes are not the dominant Mll1 dependency could give a different percentage.
Evidence that argues against this (1)
- A promoter-level requirement in fibroblasts is a poor guide to a leukaemic cell. In MLL-rearranged cells a specific inhibitor of MLL1's H3K4 methyltransferase activity blocks proliferation and induces differentiation with a transcriptome change resembling MLL1 deletion - which is hard to reconcile with an activity required at fewer than one promoter in twenty, unless the relevant promoters are exactly the ones that matter in that cell. Cao F et al. 2014
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
The SET domain, and thus the histone methyltransferase activity of MLL1, is dispensable for maintaining haematopoietic stem cells and for supporting leukaemogenesis driven by the MLL-AF9 fusion oncoprotein; on Mll1 deletion H4K16 acetylation is selectively depleted at MLL1 target genes together with reduced transcription, recruited MOF activity rather than intrinsic MLL1 HMT activity is central to maintaining HSC target genes, and inhibition of SIRT1 is sufficient to prevent the loss of H4K16 acetylation and the reduction in MLL1 target gene expression.
The histone methyltransferase activity of MLL1 is dispensable for hematopoiesis and leukemogenesis. · Mishra BP, Zaffuto KM, Artinger EL, Org T, Mikkola HKA, Cheng C, Djabali M, Ernst P · Cell Reports 2014What this evidence cannot show
Mouse; abstract read, full text not opened. Cited in 32 entries of this corpus already, so the conclusion is not new to the graph - it was new to gene-kmt2a. 'Dispensable' is a statement about a SET-domain deletion allele in the assays performed (HSC maintenance, MLL-AF9 leukaemogenesis); it is not a claim that the enzyme is inert, and a SET deletion can perturb folding as well as catalysis.
Evidence that argues against this (1)
- The opposite result from a pharmacological rather than a genetic experiment. MM-401 blocks the MLL1-WDR5 interaction and thus MLL1 H3K4 methyltransferase activity specifically, and inhibiting it blocks proliferation of MLL cells with cell-cycle arrest, apoptosis and myeloid differentiation, without general toxicity to normal bone marrow or non-MLL cells; the transcriptome change resembles MLL1 deletion. A SET DELETION and an ASSEMBLY BLOCKADE are not the same perturbation - MM-401 also removes WDR5-dependent complex assembly - but the graph should not state 'the activity is dispensable' without this beside it. Cao F et al. 2014
- ← regulatesKMT2A / MLL1 — the gene that breaks
KMT2A's own H3K4me3 requirement is under 5% of marked promoters (PMID 19703992)
the mark whose requirement is being bounded
the mark that actually falls at MLL1 targets on Mll1 deletion (PMID 24813891)
the catalytic module the fusion loses, and the dispensability result
Hox genes are the enriched class among the MLL1-requiring promoters
same paper, same system, the two halves of the asymmetry
the restricted MLL1 H3K4me3 requirement, of which the circadian promoters are one named subset