PRMT5 - the type II arginine methyltransferase this graph has reached for sixteen times, whose mark on H3R2 RECRUITS WDR5 to chromatin
also called PRMT5 · protein arginine N-methyltransferase 5 · HRMT1L5 · JBP1 · SKB1 · IBP72 · 72 kDa ICln-binding protein
PRMT5 is an enzyme that adds a pair of methyl tags to arginine residues, on histones and on many other proteins. The tag it places on one spot of histone H3 pulls in WDR5, a part of the very machine this disease's fusion protein hijacks.
The same thing, for a scientist
**CORRECTION, cycle 56, before anything below is quoted:** this entry says H3R2me2s **ENHANCES** WDR5 binding, following PMID 22231400. PMID 32207970 supersedes that direction - H3R2me2a *prevents* the WDR5 interaction while me0, me1 and me2s are **equally permissive**, so me2s relieves a block rather than adding affinity. The RBBP7 exclusion is unaffected. See E3's counter-evidence; the therapeutic consequence is opposite - inhibit PRMT6, not activate PRMT5. PRMT5 (O14744, 637 aa, HGNC:10894) is the dominant type II protein arginine methyltransferase: it makes monomethyl-arginine and SYMMETRIC dimethyl-arginine, working as the methylosome with WDR77/MEP50 and CLNS1A [E1]. Sixteen entries in this graph already name it and none of them is about it. Three facts make it a chromatin entry and not only a splicing entry. First, PRMT5 symmetrically dimethylates histone H3 Arg-2, and H3R2me2s ENHANCES WDR5 binding while EXCLUDING RBBP7 - the mirror image of PRMT6's H3R2me2a, which impedes WDR5 recruitment and antagonises H3K4 trimethylation [E3]; WDR5 is a COMPASS/WRAD component this project has an entry, an interface and an adjudication node for. Second, in murine MLL-AF9 AML the PAF complex is a direct transcriptional activator of the Prmt5 locus, with CDC73 and LEO1 peaks over the PRMT5 TSS in human THP-1, and H4R3me2s falls when Cdc73 is excised [E2]. Third, PRMT5 symmetrically dimethylates HOXA9 itself at Arg-140, a NON-histone substrate that happens to be this disease's central effector transcription factor [E4]. The one human t(4;11)-relevant experiment exists and is positive: in a CRISPR/Cas9 cord-blood model of MLL-AF4 and MLL-AF9, PRMT5 and DOT1L inhibitors are synergistic [E5]. Against all of that, PRMT5 is near-pan-essential (DepMap mean -1.19 over 1,258 screens, 94.8% of lines depleted) [E6], it is ANTI-selective in this project's own KMT2A scan at rank 17,006 of 17,728, and the PRMT5-inhibitor trial that enrolled AML patients was terminated [E7].
This is a prediction, not a measurement. No one has seen this protein in this shape. The colours say how much the software trusts itself, and that is worth reading before anything else — the orange stretches are places the model is effectively saying this part has no fixed shape.
I have never read one of these pictures before
A protein is one long chain of amino acids that folds up. The ribbon traces that chain from one end to the other; it is not a wire, it is a simplification of where the backbone runs. Drag to rotate, scroll to zoom.
Domains are the stretches of chain that do a particular job, and they are what the coloured blocks above the picture mark out. Click one and the view flies to it. In this project the important question about any domain is usually whether the fusion still has it — the labels say lost where it does not.
Anything in yellow sticks is a bound small molecule, which is usually the drug.
The two-way switch on H3 arginine 2, and why it is the most important thing in this entry
Histone H3 Arg-2 can be dimethylated two ways, and the two products do opposite things to the complex this project is about.
| mark | writer | effect measured |
|---|---|---|
| H3R2me2a (asymmetric) | PRMT6 | repressive; mutually exclusive with H3K4me2/me3; impedes WDR5 recruitment |
| H3R2me2s (symmetric) | PRMT5 and PRMT7 | euchromatic; ENHANCES WDR5 binding; excludes RBBP7, a shared subunit of Sin3a, NuRD and PRC2 |
Both statements come from one paper that profiled H3-tail interactors by SILAC mass spectrometry and then solved the WDR5/H3R2me2s co-crystal 3. The functional reading its authors give is that H3R2me2s keeps genes poised in euchromatin for activation on cell-cycle withdrawal and differentiation.
Why this graph should care. WDR5 is a WRAD component; gene-wdr5, interface-wdr5-win-kmt2a-arg3765 and concept-wdr5-what-is-established-for-wild-type-kmt2a-and-what-for-the-fusion all exist here, and the standing question in that adjudication is what actually brings WRAD to a KMT2A fusion. An arginine mark that changes WDR5's affinity for the H3 tail is a WRAD-recruitment lever this graph has never considered, and its two writers - PRMT5 and PRMT6 - had no entries.
And the honest limit. 3 is a HeLa and NT2-differentiation study. Nobody has measured H3R2me2s or H3R2me2a at a KMT2A fusion target, in any fusion, in any lineage. H3R2[tiab] AND methyl*[tiab] returns 58 records and the intersection with KMT2A is empty 8.
The PAF-complex route, which is the only KMT2A-fusion experiment that names PRMT5
In murine MLL-AF9 AML (MA9-Cdc73fl-CreER cells; the full text contains no MLL-AF4 experiment), conditional excision of the PAFc subunit Cdc73 induces myeloid differentiation and reduces PRMT5-mediated H4R3me2s, placing that mark downstream of the PAF complex. Prmt5 is a direct PAFc target: re-analysis of PAFc ChIP-seq in the human MLL-AF9 line THP-1 shows CDC73 and LEO1 peaks over the PRMT5 transcription start site coincident with RNA Pol II, confirmed by ChIP-qPCR in mouse cells. The activating unit the authors name is PAFc plus MLL1 plus HOXA9 plus STAT5 2.
This graph already holds every protein in that list except PRMT5 and STAT5: gene-paf1, gene-cdc73, gene-ctr9, gene-leo1, gene-kmt2a, gene-hoxa9. gene-cdc73 carries this paper in one sentence; the mechanism lives here.
Bound the therapeutic claim honestly. Prmt5 knockdown or EPZ015666 caused a G1 arrest and reduced proliferation, and extended median survival by 4.5 days in the MLL-AF9 transplant and by 4.5 days in a Hoxa9/Meis1 model. All moribund mice still died of leukaemia. The human lines tested were U937, NB4 and MonoMac6 - not a t(4;11) line - and NB4, which has low MTAP, was the most sensitive 2, which is the MTA/MTAP mechanism this graph already holds as cell-state-mtap-deleted-mta-high.
A non-histone substrate that is this project's own effector: HOXA9 Arg-140
PRMT5 was pulled out as a TNF-alpha-dependent HOXA9 binding partner by mass spectrometry in endothelial cells, is recruited to the E-selectin promoter after HOXA9 binds it, and symmetrically dimethylates HOXA9 at Arg-140; that event is essential for E-selectin and VCAM-1 induction 4.
Put beside 2 this closes a loop neither paper notices, because one is an endothelial inflammation study and the other a leukaemia study: HOXA9, with PAFc, MLL1 and STAT5, drives PRMT5 transcription, and PRMT5 methylates HOXA9. That is a candidate feed-forward circuit sitting on the two genes this project cares most about downstream of the fusion. It is a synthesis, not a measurement - nobody has tested HOXA9 R140 methylation in any leukaemia cell - and it is recorded here as a hypothesis-grade observation with its own open question.
The sign is not settled. In cardiomyocytes PRMT5 methylates HoxA9 and represses HoxA9 expression, and PRMT5 loss is pro-hypertrophic - PRMT5 restrains HOXA9 there, the opposite direction from a pro-leukaemic reading. That result is carried as counter-evidence on 4 rather than buried in a caveat, because it inverts the therapeutic prediction.
Localization, cell type, and the one number that argues against all of this
Subcellular (UniProt O14744, fetched 2026-09-22): four location values, all experimental - Cytoplasm (ECO:0000269 PubMed:21081503, 21917714, 22269951), Nucleus (ECO:0000269 PubMed:18404153, 21081503, 21917714, 22269951), Chromosome (ECO:0000269 PubMed:16428440, 33376131) and Golgi apparatus (ECO:0000269 PubMed:20421892) 1. PRMT5 is a shuttling enzyme with a coded chromatin-bound pool, and that Chromosome value is what licenses reading it as a chromatin enzyme at all.
Subnuclear: NO COMPARTMENT ASSIGNED. UniProt records no nucleolar, speckle or body assignment. RIOK1 recruits nucleolin/NCL as a PRMT5 substrate, mutually exclusive with CLNS1A 1, so a nucleolar pool is implied by its substrate and has not been imaged as such in any source read here. Recorded as an absence, not inferred.
Cell type and state. DepMap: 1,258 screens, 94.8% of lines depleted, mean gene effect -1.1947, isEssential true; in lymphoid tissue specifically, n = 97 lines including 13 B-cell acute lymphoblastic leukaemia lines, mean -1.2246 6.
And the number that cuts against the whole entry: in this project's own genome-wide KMT2A-selectivity scan PRMT5 ranks 17,006 of 17,728 - the 95.9th percentile, deep in the anti-selective tail. Both arms need it hard (KMT2A-rearranged -1.2344, other leukaemia -1.3403) and the KMT2A-rearranged arm needs it slightly less. Its obligate partner WDR77/MEP50 has the same shape (rank 15,455; -1.5903 against -1.6503), so this is a coherent complex-level signal rather than one gene's noise. Rule 84 applies to the framing: half of any gene set is above the median by construction and this graph's base rate is 45.3% - but the 95.9th percentile is not the median, and the honest statement is PRMT5 is a strong dependency of leukaemia cells and is not a KMT2A-fusion-selective dependency.
Bounded absences, with the query translations
All run 2026-09-22 with querytranslation and warninglist read back; every zero run twice 8.
| query | records |
|---|---|
PRMT5[tiab] | 1,365 |
PRMT5[tiab] AND MLL[tiab] | 18 |
PRMT5[tiab] AND KMT2A[tiab] | 2 (40181550 review, 28945229) |
PRMT5[tiab] AND MLL-AF9[tiab] | 2 |
PRMT5[tiab] AND MLL-AF4[tiab] | 1 (31417187) |
PRMT5[tiab] AND leukemia[tiab] | 65 |
PRMT5[tiab] AND HOXA9[tiab] | 3 |
PRMT5[tiab] AND MEIS1[tiab] | 0 |
PRMT5[tiab] AND infant[tiab] | 0 |
PRMT5[tiab] AND "B-ALL"[tiab] | 0 |
PRMT5[tiab] AND MTAP[tiab] | 140 |
Registry row 124 fires hard here. AND KMT2A returns 2 and AND MLL returns 18, so a beat running only the modern symbol would have found a review plus the PAFc paper and missed everything else; and the single human MLL-AF4 experiment is reached by neither, because it is indexed under the hyphenated fusion name. Three different spellings were needed to reach three different papers.
Instrument controls through the identical code path: H3K79me2[tiab] = 224 (positive); TMEM103[tiab] = 0 with the term echoed back unparsed (genuine-zero control) 8.
| uniprot | O14744 |
|---|---|
| uniprot ID | ANM5_HUMAN |
| gene symbol | PRMT5 |
| length AA | 637 |
| hgnc ID | HGNC:10894 |
| ensembl gene ID | ENSG00000100462 |
| alphafold ID | AF-O14744-F1 |
| accession assertion | O14744 asserted explicitly, NOT inferred from a length readback. gene_exact:PRMT5 AND organism_id:9606 AND reviewed:true returns exactly ONE reviewed human record (2026-09-22). The length defence is unusable inside this family: PRMT1 is 371 aa and PRMT6 is 375 aa, four residues apart, and both are in this corpus. |
| PDB count rcsb | 94 |
| PDB note | An RCSB accession-index query on O14744 returns 94 entries (2026-09-22); the ten listed are the first ten by identifier and are not a curated selection. No structure of PRMT5 with a KMT2A fusion, or with any KMT2A fragment, exists. |
| enzyme class | Type II protein arginine methyltransferase: forms omega-N-monomethylarginine (MMA) and SYMMETRIC omega-N,omega-N-prime-dimethylarginine (sDMA). UniProt records a preference for MMA formation. |
| localization | SHUTTLING, WITH A CODED CHROMATIN POOL. UniProt O14744 fetched 2026-09-22 carries four location values, all ECO:0000269: Cytoplasm (PubMed:21081503, 21917714, 22269951), Nucleus (PubMed:18404153, 21081503, 21917714, 22269951), Chromosome (PubMed:16428440, 33376131) and Golgi apparatus (PubMed:20421892). The Chromosome value is what licenses reading PRMT5 as a chromatin enzyme rather than only a cytoplasmic methylosome, and it rests on two papers, one of them the MBD2 methylation study. |
| localization evidence code | ECO:0000269 on all four location values, with no ECO:0000250 by-similarity locations - unusually good for this corpus, where 10.7% of localization annotations are uncoded. |
| subnuclear localization | NO COMPARTMENT ASSIGNED, recorded as an absence rather than inferred. UniProt gives no nucleolar, speckle, PML-body or other subnuclear value. A nucleolar pool is IMPLIED by substrate selection - the PRMT5-WDR77-RIOK1 form methylates nucleolin/NCL - but no PRMT5 immunofluorescence assigning a subnuclear compartment was found in any source read for this entry. REOPENING CONDITION: a PRMT5 fractionation or immunofluorescence in a t(4;11) line, scored for nucleolus and for the chromatin-bound fraction, would settle both this field and whether the chromatin pool is large enough to carry the H3R2me2s argument at all. |
| localization shown for fusion | NO - nobody has looked in any fusion. No PRMT5 localisation experiment in any KMT2A-rearranged cell was found. The fusion-adjacent PRMT5 experiments are transcriptional (PAFc occupancy of the PRMT5 gene in THP-1) and pharmacological (EPZ015666 in MLL-AF9 mice, PRMT5 plus DOT1L inhibitor in a CRISPR MLL-AF4/AF9 cord-blood model); none of them reports where the protein is. |
| epigenetic readout | WRITER - and a writer of BOTH a histone and a non-histone mark, which is the point. Histone marks: H4R3me2s and H3R8me2s, both annotated BY SIMILARITY in UniProt and therefore weaker in human cells than the textbook implies, plus H3R2me2s, which IS experimentally established in human cells and is the mechanistically important one here, because H3R2me2s ENHANCES WDR5 binding to the H3 tail and EXCLUDES RBBP7 - exactly opposite to PRMT6's H3R2me2a (PMID 22231400). The non-histone substrates carry the better-evidenced half of the record: SNRPD1/SNRPD3 symmetric dimethylation required for snRNP core assembly, plus SUPT5H, MBD2, the PIWI proteins, EGFR and nucleolin - and this graph has already filed a non-histone activity as a real epigenetics answer for CPT1A, so this is an answer and not a failure. The KMT2A-fusion-relevant measured mark is H4R3me2s, which FALLS on conditional Cdc73 excision in murine MLL-AF9 cells (PMID 28945229). BOUNDED, queries and translations read back 2026-09-22: H3R2[tiab] AND methyl*[tiab] = 58, H3R2me2a[tiab] = 47, H4R3[tiab] AND methyl*[tiab] = 98, H4R3me2s[tiab] = 92, H3R8[tiab] AND methyl*[tiab] = 30; the intersection of any of these with KMT2A or with a named KMT2A fusion is EMPTY. NOTE ON THE QUERY FORM, because it qualifies a standing rule: for arginine marks the compact spelling is NOT a false zero - H4R3me2s[tiab] = 92 against H4R3[tiab] AND methyl*[tiab] = 98, and H3R2me2a[tiab] = 47 against H3R2[tiab] AND methyl*[tiab] = 58 - so residue-plus-wildcard holds in DIRECTION but not in MAGNITUDE here, unlike the H3K18ac case that produced the rule. |
| epigenetic mark named | H3R2me2s, the WDR5-recruiting symmetric arginine mark; H4R3me2s, the mark that falls downstream of the PAF complex in MLL-AF9; H3R8me2s. The antagonistic mark on the same residue, H3R2me2a, is written by PRMT6 - see gene-prmt6. |
| cell type | DepMap CRISPR over 1,258 screened lines, mean -1.1947, 94.8% depleted; lymphoid tissue n = 97 lines, mean -1.2246, including 13 B-cell acute lymphoblastic leukaemia lines and 56 mature B-cell neoplasm lines. Primary and engineered cells read for this entry are human umbilical-cord-blood CD34+ cells (the CRISPR MLL-AF4/AF9 model), murine MLL-AF9 leukaemic cells, and primary human endothelial cells (the HOXA9 methylation work). NO measurement in an infant t(4;11) patient sample and none in fetal liver or LMPP: PRMT5[tiab] AND infant[tiab] = 0. |
| cell state | Cell-cycle state is the documented one: Prmt5 knockdown or inhibition causes a G1 ARREST in MLL-AF9 leukaemic cells, mirroring the arrest caused by Cdc73 excision (PMID 28945229), and H3R2me2s is described as keeping genes poised for activation on cell-cycle WITHDRAWAL and differentiation (PMID 22231400). Differentiation is the second: Cdc73 excision drives myeloid differentiation with loss of c-Kit and gain of Cd14. No quiescence, persister or niche state has been examined for PRMT5 in this disease. |
| shown for fusion | PARTIAL, and it should be named rather than graded. PHARMACOLOGY shown in human MLL-AF4 and MLL-AF9 CRISPR cord-blood cells (PMID 31417187) and in murine MLL-AF9 in vivo (PMID 28945229). TRANSCRIPTIONAL REGULATION of the PRMT5 gene shown in human THP-1 (MLL-AF9) and murine MLL-AF9. NO physical contact with KMT2A or any KMT2A fusion reported anywhere. NOTHING in an infant-derived t(4;11) line or patient sample. |
| absence class | literature-absence-bounded |
| superseded reading h3r2me2s and wdr5 | This entry's statement that H3R2me2s ENHANCES WDR5 binding follows PMID 22231400 and is superseded in direction by PMID 32207970, which finds me0/me1/me2s equally permissive and only me2a inhibitory - a binary OFF switch rather than a two-way dial. Kept rather than rewritten because the original is a faithful report of its source; see E3 counter-evidence. Flagged by Q103 (cycle 56), which reported it rather than editing another beat's file, and verified by the coordinator. |
| absence class note | MIGRATED 2026-09-23, mechanically and not by judgement: the class string itself begins 'literature'. The field previously held the whole verdict as free text and that string is preserved here verbatim because it says more than the token can: 'literature - bounded with counts, querytranslations and controls; see epigenetic_readout and the bounded-absence section.' |
PDB IDS
[ "4GQB", "4X60", "4X61", "4X63", "5C9Z", "5EMJ", "6CKC", "6UGH", "7BO7", "7KIB" ]
domains — the numbers behind the chart
[
{
"name": "SAM-dependent MTase, PRMT-type",
"start": 308,
"end": 615,
"pfam": null
},
{
"name": "TIM barrel",
"start": 13,
"end": 292,
"pfam": null
},
{
"name": "Beta barrel",
"start": 465,
"end": 637,
"pfam": null
},
{
"name": "Dimerization region",
"start": 488,
"end": 494,
"pfam": null
}
]complex membership
{
"methylosome": "PRMT5 + WDR77/MEP50 + CLNS1A (pICln)",
"alternative": "PRMT5 + WDR77 + RIOK1; RIOK1 and CLNS1A bind mutually exclusively and select different substrates - nucleolin/NCL versus the Sm proteins",
"note": "No PRMT5-containing complex has been reported to include KMT2A, a KMT2A fusion, menin or any WRAD subunit."
}depmap
{
"source": "DepMap CRISPR (Chronos) via Open Targets Platform GraphQL, fetched 2026-09-22",
"release": "NOT STATED BY THE API - unverified (rule 83)",
"is_essential": true,
"n_screens": 1258,
"mean_gene_effect": -1.1947,
"fraction_lines_depleted_below_minus_0_5": 0.948,
"lymphoid_tissue": {
"n_lines": 97,
"mean_gene_effect": -1.2246,
"b_all_lines": 13
}
}depmap kmt2a selectivity
{
"chronos_mean_kmt2a_rearranged": -1.2344,
"chronos_mean_other_leukaemia": -1.3403,
"difference": 0.106,
"pan_essentiality_all_lines": -1.1967,
"selectivity_rank": 17006,
"rank_denominator": 17728,
"percentile": 95.927,
"direction": "ANTI-SELECTIVE - the KMT2A-rearranged arm needs PRMT5 SLIGHTLY LESS than other leukaemia lines, while both arms need it hard.",
"partner_control": "WDR77/MEP50, PRMT5's obligate methylosome partner, has the same shape: rank 15,455, KMT2A-rearranged -1.5903 against other leukaemia -1.6503. A complex-level agreement, not one gene's noise.",
"null_statement": "Rule 84: rank above the median is the null, half of any gene set sits there by construction, and this graph's base rate is 45.3%. The 95.9th percentile is not the median, so the direction is informative - but the magnitude (0.106 Chronos units) is small against a pan-essentiality of -1.20.",
"provenance": "Joined 2026-09-22 from analyses/depmap-kmt2a-selective-scan-full (generated 2026-09-19T10:12:06Z), over 11 KMT2A-rearranged and 43 other leukaemia lines. NOT re-fetched and NOT independent of that scan; every caveat it carries applies, including that the KMT2A-rearranged arm is 11 lines drawn from nine individuals and that the scan records NO DepMap release (rule 83)."
}clinical
{
"reached_myeloid_patients": true,
"trials": [
"NCT03614728",
"NCT03886831"
],
"gsk3326595_mds_aml": "NCT03614728, phase I/II, GSK3326595 with and without 5-azacitidine, myelodysplastic syndrome and AML, TERMINATED, 30 actual participants, 2018-10-16 to 2022-01-11, sponsor GlaxoSmithKline, whyStopped 'Trial terminated due to internal review of clinical data in context of indication under investigation'",
"prt543": "NCT03886831, phase I, PRT543, COMPLETED, 232 actual participants, cohorts including relapsed/refractory AML and refractory chronic myelomonocytic leukaemia, sponsor Prelude Therapeutics",
"minimum_age_both": "18 years - so no PRMT5 inhibitor that has reached myeloid disease is enrollable by the infant population this project exists for. Rule 75's shape applies: the barrier is demographic and regulatory, not bibliographic.",
"second_generation": "MTA-cooperative inhibitors (MRTX1719, AMG 193) target MTAP-deleted tumours; this project's own analysis found the KMT2A-rearranged arm is NOT MTAP-deleted."
}reached for by
[ "gene-epb41l3 - EPB41L3/DAL-1 modulates PRMT5 substrate-specifically, inhibiting Sm-protein methylation while enhancing myelin-basic-protein methylation (PMID 15737618), and names the absence of a PRMT5 entry as its own reopening condition", "cell-state-mtap-deleted-mta-high - the MTA/PRMT5 synthetic-lethal state, 51 mentions, the single heaviest PRMT5 user in the corpus", "gene-mat2a and cell-state-sam-methionine-dependence - the SAM-supply axis", "mechanism-menin-prmt5-represses-glp1r-transcription - a menin-PRMT5 complex on a non-leukaemic promoter", "gene-cdc73 - carries PMID 28945229 in one sentence", "gene-prmt1 - whose bite_back already warns that PRMT1 and PRMT5 are conflated in the MLL literature" ]
- Essential-function toxicity: PRMT5 is required by 94.8% of 1,258 DepMap lines with a mean gene effect of -1.1947, and its obligate partner WDR77 is comparably essential. This is the regime in which the type I PRMT inhibitor GSK3368715 was terminated for lack of efficacy AND dose-limiting toxicity (gene-prmt1).
- The clinical experiment in myeloid disease has already been stopped once: NCT03614728, GSK3326595 in MDS and AML, was TERMINATED at 30 participants on sponsor review of clinical data in the indication.
- Age: every PRMT5-inhibitor trial that reached myeloid disease set a minimum age of 18 years, so the infant t(4;11) population is outside the eligibility of the entire clinical programme and nothing about tolerability in an infant is known.
- Direction risk on the central substrate: in cardiomyocytes PRMT5 REPRESSES HOXA9, so PRMT5 inhibition RAISES HoxA9. If any of that sign carries into a haematopoietic cell, a PRMT5 inhibitor would be raising the output of the transcription factor this disease runs on.
- Resistance and compensation: H3R2me2s is written by PRMT5 AND PRMT7, and H4R3 is methylated asymmetrically by PRMT1 and PRMT3 as well. A single-enzyme inhibitor can leave the residue modified by a paralogue - and because the asymmetric product has the OPPOSITE effect on WDR5, paralogue compensation here does not merely blunt the drug, it can invert the readout.
- Delivery and combination: the one positive fusion-relevant result is a PRMT5-plus-DOT1L-inhibitor synergy in an engineered cord-blood model. DOT1L inhibition alone already failed to deliver durable responses in the clinic (drug-pinometostat), so the combination inherits two agents with thin single-agent records rather than one strong one.
- Selectivity is the wrong way round: this project's own scan puts PRMT5 in the 95.9th percentile of the ANTI-selective tail for KMT2A-rearranged lines. Any therapeutic argument here has to rest on absolute dependency rather than fusion selectivity, and that argument applies equally to every other leukaemia.
- Is H3R2me2s present at KMT2A::AFF1 target loci, and does it track WDR5 occupancy there? Nobody has measured either arginine mark at a fusion target in any lineage, and the two writers - PRMT5 and PRMT6 - push WDR5 in opposite directions.
- Does PRMT5 inhibition displace WDR5 from chromatin in a t(4;11) line? If H3R2me2s recruits WDR5 to the H3 tail, a PRMT5 inhibitor is an indirect WRAD-recruitment inhibitor, which is a completely different rationale from the anti-proliferative one the trials were run on.
- Is HOXA9 Arg-140 symmetrically dimethylated in a KMT2A-rearranged blast, and does it matter? The residue and the enzyme are both known; the experiment has only ever been done in endothelial cells, and in cardiomyocytes the sign is reversed.
- Why is PRMT5 anti-selective in the KMT2A arm (rank 17,006 of 17,728) if the PAF complex - which KMT2A fusions bind directly - is its transcriptional activator? One possibility is that PRMT5 levels are already saturating for function in every leukaemia; another is that the PAFc route is a property of mouse MLL-AF9.
- Does the 4.5-day survival extension scale with anything? Both the knockdown arm and the inhibitor arm gave +4.5 days in mice that all still died of leukaemia. Before any combination is proposed it is worth knowing whether that is a ceiling set by the biology or by the dosing.
- Where is PRMT5 in a t(4;11) blast? Four coded compartments including Chromosome and Golgi, no subnuclear assignment, and a nucleolar pool implied only by its substrate. One fractionation would tell us whether the chromatin argument in this entry has a chromatin pool to run on.
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
PRMT5 (O14744, 637 aa) is a type II protein arginine methyltransferase forming monomethyl- and SYMMETRIC dimethyl-arginine, is a component of the methylosome with WDR77 and CLNS1A, methylates the Sm proteins SNRPD1 and SNRPD3 as a requirement for snRNP core assembly, and carries four experimentally coded subcellular locations - Cytoplasm, Nucleus, Chromosome and Golgi apparatus - with a SAM-dependent MTase PRMT-type domain at 308-615, a TIM barrel at 13-292 and a beta barrel at 465-637.
UniProtKB O14744 (ANM5_HUMAN), Protein arginine N-methyltransferase 5 - FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, SUBCELLULAR LOCATION and feature table, fetched 2026-09-22 · UniProt Consortium 2026What this evidence cannot show
A database record, not a measurement. The SUBUNIT block is a single 2,301-character paragraph carrying 27 evidence codes for dozens of sentences, so an individual interaction sentence inside it - for instance the bare sentence 'Interacts with HOXA9' - cannot be attributed to a specific paper from the record alone. Rule 91 therefore applies and the HOXA9 claim in this entry is cited to its own primary paper (E4), not to UniProt. The accession is asserted explicitly rather than confirmed by a length readback, because PRMT1 (371 aa) and PRMT6 (375 aa) sit four residues apart and this family defeats a length check.
Evidence that argues against this (1)
- UniProt's own FUNCTION text says PRMT5 has 'a preference for the formation of MMA' - monomethyl-arginine - over symmetric dimethyl-arginine, and it weights the histone activities lower than the non-histone ones: methylation of histone H2A/H4 Arg-3 and of H3 Arg-8 are both annotated BY SIMILARITY, while the Sm D1/D3 symmetric dimethylation carries three experimental citations. The database's own evidence weighting therefore makes PRMT5 better established as a spliceosome enzyme than as a histone enzyme in human cells, which is the opposite of the emphasis a chromatin-focused entry naturally takes. UniProt Consortium 2026
- E2moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
In murine MLL-AF9 AML the PAF complex is a direct transcriptional activator of the Prmt5 locus - CDC73 and LEO1 occupy the PRMT5 TSS with RNA Pol II in the human MLL-AF9 line THP-1, PRMT5-mediated H4R3me2s falls after conditional Cdc73 excision, and the activating unit named is PAFc plus MLL1 plus HOXA9 plus STAT5 - and Prmt5 knockdown or EPZ015666 caused a G1 arrest and extended median survival by 4.5 days.
The PAF complex regulation of Prmt5 facilitates the progression and maintenance of MLL fusion leukemia. · Serio J, Ropa J, Chen W, Mysliwski M, Saha N, Chen L, Wang J, Miao H, Cierpicki T, Grembecka J, Muntean AG · Oncogene 2018What this evidence cannot show
The system is murine MLL-AF9 (MA9-Cdc73fl-CreER) plus a Hoxa9/Meis1 overexpression model. Full text read from Europe PMC (PMC5785415) on 2026-09-22: the string MLL-AF4 appears ZERO times. The human cells are THP-1 (a public ChIP-seq re-analysis, not a new experiment), U937, NB4 and MonoMac6 - none of them a t(4;11) line. The in vivo effect is small and non-curative: median survival +4.5 days by knockdown and +4.5 days by EPZ015666, with every moribund animal still dying of leukaemia. And the result is about the PRMT5 GENE being a PAFc target, not about PRMT5 protein being in a fusion complex - no PRMT5-KMT2A physical contact is reported anywhere.
Evidence that argues against this (1)
- This project's own genome-wide DepMap scan places PRMT5 at rank 17,006 of 17,728 for KMT2A-rearranged selectivity - the 95.9th percentile of the anti-selective tail, with KMT2A-rearranged lines at -1.2344 against -1.3403 in other leukaemia lines. If PRMT5 sat downstream of an MLL-fusion-specific transcriptional unit, the KMT2A-rearranged arm should need it MORE, not marginally less. WDR77/MEP50, PRMT5's obligate methylosome partner, shows the same direction (rank 15,455, -1.5903 against -1.6503), so the signal is complex-level and consistent. The compatible reading is that PRMT5 is a general leukaemia dependency the PAFc happens to supply, not a fusion-created one. Broad Institute DepMap via Open Targets Platform 2026
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Histone H3 Arg-2 is symmetrically dimethylated by PRMT5 and PRMT7 to give H3R2me2s, a euchromatic mark that ENHANCES binding of WDR5 - a shared component of the MLL, SET1A, SET1B and ATAC coactivator complexes - and EXCLUDES binding of RBBP7, a central subunit of the Sin3a, NuRD and PRC2 corepressor complexes; this is the opposite of PRMT6's asymmetric H3R2me2a, which impedes WDR5 recruitment to chromatin and antagonises H3K4 trimethylation.
Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance. · Migliori V, Muller J, Phalke S, Low D, Bezzi M, Mok WC, Sahu SK, Gunaratne J, Capasso P, Bassi C, Cecatiello V, De Marco A, Blackstock W, Kuznetsov V, Amati B, Mapelli M, Guccione E · Nature Structural and Molecular Biology 2012What this evidence cannot show
Human cells, but the systems are HeLa and NT2 differentiation - not haematopoietic, and not any fusion. The WDR5 affinity result is an H3-tail peptide and SILAC-MS interactor result plus a peptide co-crystal; it is not a demonstration that H3R2me2s recruits an intact MLL/COMPASS complex to a gene, and certainly not in a KMT2A-fusion cell. PRMT7 is a second writer of the same mark and has no entry in this graph, so the mark must not be attributed to PRMT5 alone.
Evidence that argues against this (2)
- The whole idea that H3R2 arginine marks matter by gating WDR5 depends on WDR5's H3-tail binding being functionally load-bearing for KMT2A, and the structurally defined KMT2A-WDR5 contact is not a histone-tail contact at all: it is the WIN motif, a short arginine-containing peptide from the SET-domain region of the KMT2 protein inserting into WDR5's central channel. If WDR5 recruitment to a KMT2A fusion runs through a WIN motif that most fusions have LOST along with the SET domain, then an H3R2 mark modulating WDR5's histone-tail affinity may be irrelevant to the chimera even where it matters for wild-type COMPASS. This graph's own `concept-wdr5-what-is-established-for-wild-type-kmt2a-and-what-for-the-fusion` exists precisely to keep those two cases apart. Dharmarajan V et al. 2012
- SUPERSEDED IN DIRECTION, and the superseding paper names this one. PMID 32207970 (Lorton BM, et al., 'A Binary Arginine Methylation Switch on Histone H3 Arginine 2 Regulates Its Interaction with WDR5', Biochemistry, doi 10.1021/acs.biochem.0c00035) states in its own abstract that previous studies suggested H3R2me2s specified a high-affinity interaction with WDR5, and then, using quantitative binding analysis with high-resolution crystal structures of WDR5 bound to unmodified, me1 and me2s arginine, reports a BINARY switch: H3R2me2a PREVENTS the WDR5 interaction while H3R2me0, me1 and me2s are EQUALLY PERMISSIVE. So H3R2me2s does not enhance WDR5 binding over unmodified chromatin; it relieves a block that me2a imposes. The claim above is an accurate report of PMID 22231400 and should be read as the superseded model. Verified by efetch 2026-09-22. THE CONSEQUENCE IS THERAPEUTIC AND OPPOSITE: a graded switch says ACTIVATE PRMT5 to gain WDR5 recruitment, while a binary switch says the only available move is to INHIBIT PRMT6 and relieve the block, because no intervention can push binding above the unmodified baseline. The RBBP7 exclusion in this evidence item is NOT affected by that paper and stands as written.
- E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
PRMT5 symmetrically dimethylates the homeobox transcription factor HOXA9 at Arg-140: PRMT5 was identified as a TNF-alpha-dependent HOXA9 binding partner by mass spectrometry in endothelial cells, is recruited to the E-selectin promoter following transient HOXA9 binding, and that methylation event is essential for E-selectin and VCAM-1 induction.
HOXA9 methylation by PRMT5 is essential for endothelial cell expression of leukocyte adhesion molecules. · Bandyopadhyay S, Harris DP, Adams GN, Lause GE, McHugh A, Tillmaand EG, Money A, Willard B, Fox PL, DiCorleto PE · Molecular and Cellular Biology 2012What this evidence cannot show
Human endothelial cells under TNF-alpha: an inflammation system with no haematopoietic or leukaemic arm at all, and readouts (E-selectin, VCAM-1) that are not a HOX program. Transfer to KMT2A-fusion leukaemia is an inference from shared substrate identity and nothing more - HOXA9 R140 methylation has never been measured in any leukaemia cell, and `PRMT5[tiab] AND HOXA9[tiab]` returns only 3 records in total.
Evidence that argues against this (1)
- The direction of the PRMT5-HOXA9 relationship reverses in another tissue. In cardiomyocytes PRMT5 symmetrically dimethylates HoxA9 AND REPRESSES HoxA9 expression, so that silencing or inhibiting PRMT5 RAISES HoxA9 and worsens hypertrophy, while PRMT5 overexpression suppresses it. Read that way PRMT5 is a restraint on HOXA9 rather than a co-activator of it, which predicts that PRMT5 inhibition would INCREASE HOXA9 output - the opposite of what a PRMT5-inhibitor strategy in a HOXA9-driven leukaemia assumes. Cai S et al. 2020
- E5moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
In a CRISPR/Cas9 umbilical-cord-blood model of 100% pure MLL-AF4- or MLL-AF9-rearranged human cells, PRMT5 and DOT1L inhibitors each reduced proliferation dose-dependently, impaired the cell cycle, increased differentiation and apoptosis, downregulated target genes and sensitised to chemotherapy - and the combination of the two was SYNERGISTIC.
Inhibition of DOT1L and PRMT5 promote synergistic anti-tumor activity in a human MLL leukemia model induced by CRISPR/Cas9. · Secker KA, Keppeler H, Duerr-Stoerzer S, Schmid H, Schneidawind D, Hentrich T, Schulze-Hentrich JM, Mankel B, Fend F, Schneidawind C · Oncogene 2019What this evidence cannot show
This is the ONLY record returned by `PRMT5[tiab] AND MLL-AF4[tiab]` (= 1, 2026-09-22), and the abstract does not separate the MLL-AF4 arm from the MLL-AF9 arm for the PRMT5 result, so 'shown in MLL-AF4' cannot be asserted at arm level from the abstract; the full text was not read for this entry, so this evidence item is abstract-level only. The model is engineered cord-blood CD34+ material, not infant patient cells, and the synergy is a culture proliferation readout with no in vivo or patient arm.
Evidence that argues against this (1)
- A synergy result between two epigenetic inhibitors in an engineered line is the weakest form of evidence for a combination, because both single agents are anti-proliferative in almost any dividing cell and PRMT5 is required by 94.8% of DepMap lines. The clinical experiment closest to this has been run and stopped: NCT03614728, a phase I/II of the PRMT5 inhibitor GSK3326595 in myelodysplastic syndrome and acute myeloid leukaemia, was TERMINATED after 30 actual participants, the sponsor's stated reason being an internal review of clinical data in the context of the indication under investigation. Synergy in a cord-blood model did not survive contact with myeloid patients. ClinicalTrials.gov 2022
- E6strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
PRMT5 is flagged essential in DepMap CRISPR (Chronos) with a mean gene effect of -1.1947 across 1,258 screened cell lines and 94.8% of lines depleted below -0.5; in lymphoid tissue specifically the mean is -1.2246 over 97 lines, of which 13 are B-cell acute lymphoblastic leukaemia lines.
DepMap CRISPR (Chronos) gene effect served through the Open Targets Platform GraphQL API, field depMapEssentiality, fetched 2026-09-22 with approvedSymbol read back as PRMT5 · Broad Institute DepMap via Open Targets Platform 2026What this evidence cannot show
Rule 83: the Open Targets GraphQL response does NOT state the DepMap release, so the release is unverified and only the fetch date is on record; the screen count of 1,258 is PRMT5's own and must not be read as a corpus-wide denominator. The approvedSymbol was read back to confirm the Ensembl id resolved correctly - a sibling lookup in the same call resolved ENSG00000116157 to GPX7 rather than the intended WDR77, which is exactly what the readback is for, and no WDR77 figure is quoted from that call. The lymphoid-tissue bucket is a tissue label, not a KMT2A-status label; no line in it is identified as t(4;11) by this query.
Evidence that argues against this (1)
- A near-pan-essential gene is a poor oncology target on its own terms, and this graph has already made that argument once for a PRMT: PRMT1 is depleted in 98.7% of lines and the first-in-human type I PRMT inhibitor was terminated for lack of efficacy AND dose-limiting toxicity. PRMT5 at 94.8% is in the same regime and its methylosome partner WDR77 is comparably essential, so a therapeutic window has to come from something other than differential expression - in practice from MTAP deletion, and this project's own analysis found the KMT2A-rearranged arm is NOT MTAP-deleted. Zhu Y et al. 2019
- E7established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.trial_registry
Two PRMT5-inhibitor trials reached myeloid patients: NCT03614728 (GSK3326595 with and without 5-azacitidine, phase I/II, myelodysplastic syndrome and AML) was TERMINATED with 30 actual participants for an internal review of clinical data in the context of the indication; NCT03886831 (PRT543, phase I) COMPLETED with 232 actual participants across cohorts that included relapsed/refractory AML and refractory chronic myelomonocytic leukaemia. Both set a minimum age of 18 years.
ClinicalTrials.gov API v2 records for NCT03614728 and NCT03886831 - overallStatus, whyStopped, phases, enrollmentInfo, conditions and minimumAge, fetched 2026-09-22 · ClinicalTrials.gov 2026What this evidence cannot show
A registry record states status and the sponsor's stated reason for stopping; it does not report efficacy, and 'terminated due to internal review of clinical data in context of indication under investigation' is not a statement that the drug failed. Neither trial enrolled a KMT2A-rearranged cohort as such, and neither could enrol an infant - the minimum age is 18 years in both - so the population this project exists for is outside the eligibility of every PRMT5 inhibitor that has reached myeloid disease. Registry-only: no publication was read for either trial.
Evidence that argues against this (1)
- Reading the whole PRMT5 clinical picture off two myeloid trials understates the class, and the understatement runs in an unusual direction: the MTA-cooperative second generation (MRTX1719, AMG 193) is built for MTAP-deleted tumours and is where the class's activity now sits, which makes the myeloid programme's fate weak evidence about PRMT5 inhibition in general and strong evidence that undifferentiated PRMT5 inhibition in myeloid disease is hard. Measured 2026-09-22 with translations read back: MRTX1719[tiab] = 15, AMG 193[tiab] = 5, GSK3326595[tiab] = 38, JNJ-64619178[tiab] = 15, onametostat[tiab] = 3; none of these is in a KMT2A-rearranged indication. NCBI PubMed 2026
- E8strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
PRMT5's KMT2A-fusion literature is reachable only through three different names for the same disease - PRMT5[tiab] AND MLL[tiab] = 18, AND KMT2A[tiab] = 2, AND MLL-AF9[tiab] = 2, AND MLL-AF4[tiab] = 1 - while AND MEIS1[tiab] = 0, AND infant[tiab] = 0 and AND B-ALL[tiab] = 0.
NCBI E-utilities esearch, db=pubmed, counts with querytranslation and warninglist read back, run 2026-09-22; every load-bearing zero run twice · NCBI PubMed 2026What this evidence cannot show
A PubMed count bounds titles and abstracts only; rule 80 applies and these zeros say nothing about supporting figures. Three of these zeros were first returned with an EMPTY querytranslation - the transient instrument failure of registry row 123 - and were confirmed as genuine only on re-run; the values recorded here are the re-run values, each of which returned a fully parsed translation together with warninglist.outputmessages = ['No items found.']. Every count uses one tag per term (rule 94), never the grouped form.
Evidence that argues against this (1)
- These counts understate PRMT5's reach into this disease in a way no name list fixes, because the relevant datum can be full-text only. The same PAFc paper that is this entry's anchor also reports that PRMT5, PRMT1 AND PRMT3 are all significantly downregulated after loss of either CDC73 or PAF1 - and that PRMT3 result is invisible to every PRMT3 query, since PRMT3[tiab] AND MLL[tiab] returns 1 record and it is a fluorescence assay-development paper, while PRMT3[tiab] AND CDC73[tiab] and PRMT3[tiab] AND PAFc[tiab] both return 0 with fully parsed translations. A counted zero over abstracts can sit directly on top of a positive result in the body of a paper the same beat has already read. Serio J et al. 2018
- regulates →WDR5 — the partner that is not a partner: it binds the half of KMT2A the fusion throws away
H3R2me2s ENHANCES WDR5 binding to the H3 tail; H3R2me2a impedes it
H3R2me2s EXCLUDES RBBP7 from the H3 tail (Sin3a/NuRD/PRC2 subunit)
PRMT5 transcription is directly activated by the PAF complex in MLL-AF9 AML
PAF1 knockdown in THP-1 downregulates PRMT5
LEO1 and CDC73 peaks over the PRMT5 TSS in THP-1
TNF-dependent HOXA9 partner; symmetrically dimethylates HOXA9 Arg-140
- related to →KMT2A / MLL1 — the gene that breaks
MLL1 is named in the PAFc/HOXA9/STAT5 unit activating PRMT5; no physical contact reported
- related to →KMT2A::AFF1 (MLL-AF4), t(4;11)(q21;q23)
PRMT5 + DOT1L inhibitor synergy in a CRISPR MLL-AF4 cord-blood model; the only MLL-AF4 record
PRMT5 and DOT1L inhibitors are synergistic in MLL-AF4/AF9 cord-blood cells
- related to →Pinometostat (EPZ-5676) — the DOT1L inhibitor, and the most instructive failure in this field
the DOT1L arm of the only fusion-relevant PRMT5 combination
the MTA/PRMT5 synthetic-lethal state; NB4 (low MTAP) was the most inhibitor-sensitive line
PRMT5 is a SAM-consuming methyltransferase
MAT2A supplies the SAM PRMT5 consumes; the MTAP/MAT2A/PRMT5 axis
DAL-1/4.1B modulates PRMT5 substrate-specifically (inhibits Sm, enhances MBP)
the menin-PRMT5 complex this graph already holds
paralogue and a documented conflation hazard in the MLL literature
an arginine mark that gates WDR5 is a WRAD-recruitment lever that adjudication does not consider
the competing WDR5 route: a WIN-motif protein interface rather than a histone-tail interface
both PRMT5 and EHMT2 methylate non-histone substrates including p53
- related to →Plain-English: chromatin and epigenetics — the sticky notes on the DNA, and which ones matter here
arginine methylation as a chromatin mark class
opposite dimethyl states of the SAME residue H3R2, with opposite effects on WDR5
H3R2me2s excludes RBBP7, a subunit of the corepressor ING2 carries
opposite dimethyl states of the SAME residue H4R3 - me2a activating against me2s repressive
type II writer of the symmetric state on H3 Arg-2; established
writer at the beta-globin locus in primary human erythroid progenitors, and the writer whose abundance sets the mark in murine MLL-AF9
the two symmetric-dimethyl candidates, experimentally SEPARATED: PRMT7 and not PRMT5 raises H4R3me2s at KMT2D targets, while PRMT5 is the writer at globin and in MLL-AF9