Oncofusion

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Proteinmoderate confidence 3 of 5: One strong study, or several smaller consistent ones.Q103-arginine-marks

PRMT7 - the enzyme whose class is still disputed, which represses a KMT2 enzyme by writing H4R3me2s, which is required for leukaemia stem cells in CML, and whose only H3R2 claim is the one this beat was dispatched to check

also called PRMT7 · protein arginine N-methyltransferase 7 · histone-arginine N-methyltransferase PRMT7 · [myelin basic protein]-arginine N-methyltransferase PRMT7 · KIAA1933

PRMT7 adds methyl tags to arginines, and it is the odd one out in its family - biochemists still disagree about whether it can add one tag or two. The tag it puts on histone H4 blocks a KMT2 enzyme from working, and losing PRMT7 kills leukaemia stem cells in another leukaemia without harming normal blood.

The same thing, for a scientist

PRMT7 (Q9NVM4, 692 aa, 16q22.1, HGNC:25557, ENSG00000132600) is the arginine methyltransferase whose product specificity has never been settled. UniProt records that it forms both monomethylarginine and symmetric dimethylarginine with a preference for MMA, annotates its catalytic reaction as the **monomethyl** one, and names **H4R3me2s** as the histone mark it specifically mediates - with no mention of H3R2 [E1]. A dedicated enzymology study found full-length human PRMT7 formed **only** monomethylarginine on every substrate tested, including recombinant human histones H2A/H2B/H3/H4, and concluded it is a **type III** enzyme [E2]. Against that, three cellular experiments report symmetric dimethyl phenotypes: **PRMT7, but not PRMT5, represses KMT2D target genes by raising H4R3me2s**, inhibiting KMT2D's own tandem PHD(4-6) and lowering KMT2D-catalysed H3K4me3 at many HOXA/HOXB genes [E3]; a **B-cell-specific Prmt7 knockout** shows PRMT7 recruits H4R3me1 **and symmetric H4R3me2** to the *Bcl6* promoter, with reduced mature marginal-zone B cells, increased follicular B cells and enhanced germinal-centre formation [E4]; and the mark's discovery paper named PRMT7 alongside PRMT5 as an H3R2me2s writer [E5]. Haematologically PRMT7 is not idle: **Prmt7 loss and a PRMT7 inhibitor impair CML leukaemia-stem-cell self-renewal in mouse and in primary human CML CD34+ cells without affecting normal haematopoiesis**, through glycine-metabolism reprogramming [E6], and PRMT7 is high in mature T-ALL where CRISPR deletion reduces colony formation and deregulates RUNX1 target genes [E7]. A **cell-active chemical probe exists** - SGC3027, a prodrug of the SAM-competitive SGC8158 [E8]. PRMT7 is **not** a DepMap dependency (mean gene effect -0.1513 across 1,258 screened lines) [E9]. **There is no KMT2A connection at all**: `PRMT7[tiab] AND KMT2A[tiab]` = 0, re-run 0; `AND MLL[tiab]` = 1, which is the H3R2me2s discovery paper [E10].

What it looks like
PRMT7692 aa
SAM-dependent MTase, PRMT-type 1SAM-dependent MTase, PRMT-type 1 · residues 14–345SAM-dependent MTase, PRMT-type 2SAM-dependent MTase, PRMT-type 2 · residues 358–6840200400600
loading AF-Q9NVM4-F1…
AlphaFold AF-Q9NVM4-F1 ↗
colourshape

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.

very high (90+)confident (70–90)low (50–70)very low (<50)
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.

Go deeper
Why this entry exists, and the premise it partly refutes

This beat's dispatch brief said: "gene-prmt7 does not exist and is reported to be a second H3R2me2s writer - verify that before asserting it." Verified, and the answer is half right in a way that matters.

claimverdict
gene-prmt7 does not existTRUE. Full id listing of 1,991 node ids on 2026-09-22: no gene-prmt7, and find data/graph/nodes -iname "*prmt*" returns PRMT1, PRMT3, PRMT5, PRMT6 and two analysis/mechanism entries only.
PRMT7 is a second H3R2me2s writerWEAKLY SUPPORTED AND CONTESTED. It rests on one clause in PMID 22231400's abstract 5. "H3R2me2s"[tiab] AND PRMT7[tiab] returns 2 records, one of which is that paper. UniProt does not name H3R2 in PRMT7's FUNCTION block at all 1. And a same-year enzymology study concluded PRMT7 cannot make any dimethylarginine 2.
(not in the brief) PRMT7's better-supported symmetric histone markH4R3me2s, which UniProt names specifically 1, which a KMT2D trans-tail study attributes to PRMT7 and explicitly not to PRMT5 3, and which a B-cell knockout localises to a promoter in vivo 4.

So the right reason to write this entry is not the reason the brief gave. PRMT7 belongs in this graph because it is the enzyme that writes the mark which blocks a KMT2-family enzyme's own reader module, because it has a B-lineage in-vivo chromatin experiment, because it is a leukaemia-stem-cell dependency in CML with a tool compound, and because it has a cell-active chemical probe. The H3R2me2s attribution is the weakest thing about it.

The enzyme-class dispute, and why it is not a technicality here

PRMTs are classified by product: type I makes asymmetric dimethylarginine (PRMT1, 3, 4/CARM1, 6, 8), type II makes symmetric dimethylarginine (PRMT5, 9), type III makes monomethylarginine only. PRMT7 has been assigned to type II, to type I/II, and to type III, by different groups.

  • Type II, by the founding paper: PMID 15494416 is titled "PRMT7, a new protein arginine methyltransferase that synthesizes symmetric dimethylarginine" 11.
  • Type III, by dedicated re-examination: only omega-N-monomethylarginine, on peptides, GST-GAR, myelin basic protein and recombinant human histones H2A, H2B, H3 and H4, under all conditions tested, with PRMT1 and PRMT5 controls behaving correctly in the same experiments 2.
  • Both, by UniProt: "can both catalyze the formation of omega-N monomethylarginine (MMA) and symmetrical dimethylarginine (sDMA), with a preference for the formation of MMA" - while the annotated CATALYTIC ACTIVITY reaction in the same record is the monomethyl one 1.

Why it matters for this graph. Every mechanism attributed to PRMT7 in this beat runs through a symmetric dimethyl mark - H4R3me2s blocking KMT2D's PHD(4-6), H4R3me2s at the Bcl6 promoter, H3R2me2s as a permissive WDR5 state. If PRMT7 is type III in cells, none of those is a direct PRMT7 product, and the cellular phenotypes would have to be indirect: PRMT7 monomethylation priming another enzyme, or PRMT7 acting on a non-histone substrate that controls a symmetric writer. The B-cell ChIP-PCR result 4, which reports H4R3me1 and symmetric H4R3me2 at the same promoter in a PRMT7 conditional knockout, is the strongest cellular evidence and is consistent with either reading - a type III enzyme supplying me1 as the substrate for a type II enzyme would produce exactly that pattern.

A rule-91-shaped observation, worth recording. UniProt's only ECO:0000269 subcellular-location evidence for PRMT7 - Cytoplasm/cytosol and Nucleus - is PubMed:15494416, i.e. the founding paper whose central enzymological claim is the disputed one 111. The evidence code tells you a curator saw an experiment in that paper; it does not tell you the paper's headline conclusion has held. Both the localisation and the type II assignment come from the same 2005 source and they are not equally durable.

Localization, cell type, cell state and the epigenetic answer

Localization. Cytoplasm/cytosol and Nucleus, both ECO:0000269 from a single source, PubMed:15494416 1. So PRMT7 is a shuttling enzyme on the database's own account, and the nuclear pool is what licenses reading it as a chromatin enzyme. No subnuclear compartment is assigned anywhere - recorded as an absence, not inferred. The chromatin engagement that is actually demonstrated is recruitment to specific promoters: the H19 imprinted control region by CTCFL 1 and the Bcl6 promoter in B cells 4.

Cell type. The haematopoietic evidence is real and spans three lineages: B cells (conditional Prmt7 knockout: fewer mature marginal-zone B cells, more follicular B cells, enhanced germinal-centre formation, low IgG1 and IgA) 4; CML leukaemia stem cells (mouse model plus primary human CML CD34+ cells) 6; T-ALL, where PRMT7 mRNA is high particularly in mature subtypes 7. Non-haematopoietic: NT2/D1 embryonal carcinoma 3, and human cell lines for the probe work 8.

Cell state. Two documented states. Self-renewal: PRMT7 loss impairs LSC self-renewal in CML, and the mechanism is metabolic - reduced glycine decarboxylase expression, glycine metabolism reprogrammed to generate methylglyoxal, which is detrimental to LSCs 6. Proteostasis/stress: PRMT7 inhibition or knockout drastically reduces arginine monomethylation of HSP70-family stress-associated proteins and decreases tolerance for heat shock and proteasome inhibitors 8. Neither state has been examined in a KMT2A-rearranged cell.

Epigenetics. WRITER, of a repressive symmetric arginine mark, with a measured antagonism against a KMT2-family methyltransferase: H4R3me2s inhibits the tandem PHD(4-6) of KMT2D, PRMT7 but not PRMT5 raises it at KMT2D targets, and PRMT7 knockdown increases KMT2D-catalysed H3K4me3 at genes including many HOXA and HOXB 3. In B cells the same enzyme recruits H4R3me1 and symmetric H4R3me2 to the Bcl6 promoter and negatively regulates Bcl6 4. The H3R2me2s attribution 5 is the weak one. And the substrate set that is best evidenced is non-histone: symmetric dimethylation of SNRPD1 and SNRPD3 required for snRNP core assembly 1, and monomethylation of HSP70 at R469 8.

The KMT2A-fusion connection, which is empty, and the one thing that is not

Bounded 2026-09-22, translation read back, zeros re-run:

querynrecords
PRMT7[tiab]172-
PRMT7[tiab] AND KMT2A[tiab]0 (re-run 0)-
PRMT7[tiab] AND MLL[tiab]122231400 - the H3R2me2s discovery paper, where "MLL" appears only as the name of a WDR5-containing coactivator complex
PRMT7[tiab] AND menin[tiab]132859041 - a GLI/hedgehog arginine-methylation review, not a menin study
PRMT7[tiab] AND leukemia[tiab]9including 35508169 (CML LSC), 35565298 (T-ALL/RUNX1), 26179907 (B-cell/Bcl6), 23249737 (KMT2D trans-tail, which enters only via the legacy name "mixed-lineage leukemia 4")
PRMT7[tiab] AND "H3R2me2s"[tiab]222231400, 33980975
PRMT7[tiab] AND H3R2[tiab]322231400, 33980975, 37541527
PRMT7[tiab] AND SGC3027[tiab]5the probe literature
operand control KMT2A[tiab]1652

So there is no PRMT7-KMT2A literature whatsoever - the single MLL hit is a complex name, and the single menin hit is a review about a different pathway. The nearest real thing is the KMT2D result 3, which is a KMT2-family enzyme, in the right direction, on the right genes (HOXA/HOXB), with PRMT7 as the antagonist - and it is in embryonal carcinoma stem cells, not leukaemia.

And the second-nearest is a recurring coincidence worth flagging rather than over-reading. PRMT6 deregulates RUNX1 target genes through H3R2me2a (gene-prmt6, PMID 22777353); PRMT7 deregulates RUNX1 target genes in T-ALL 7. Two different arginine methyltransferases, two different marks, the same haematopoietic transcription factor, in two independent papers. gene-runx1 exists in this graph. That is a pattern with two points and no mechanism linking them, and it is recorded as an open question, not a finding.

Facts and figures
gene symbolPRMT7
uniprotQ9NVM4
uniprot IDANM7_HUMAN
length AA692
hgnc IDHGNC:25557
ensembl gene IDENSG00000132600
cytoband16q22.1
alphafold IDAF-Q9NVM4-F1
PDB count rcsb0
PDB noteZERO structures. RCSB Search API accession-index query on Q9NVM4 returned HTTP 204 (no content) on 2026-09-22, and UniProt Q9NVM4 carries no PDB cross-reference. There is no experimental structure of human PRMT7, and therefore no structure of PRMT7 with a nucleosome, with a histone tail, or with any KMT2-family component. Structures exist for non-human PRMT7 orthologues under different accessions and are not asserted here.
domain architecture noteTWO tandem PRMT-type methyltransferase domains, which is the structural feature that makes PRMT7 the odd member of the family - PRMT1 (371 aa), PRMT6 (375 aa) and PRMT3 (531 aa) each carry one. Only the N-terminal module is catalytically competent in the published literature; the C-terminal one is degenerate and its role is a live question. Boundaries are UniProt feature-table values read back 2026-09-22.
accession assertionQ9NVM4 asserted explicitly and fetched live, NOT inferred from a length readback. IDENTIFIER SAFETY: at 692 aa PRMT7 is well separated from PRMT1 (371), PRMT6 (375), PRMT5 (637) and PRMT3 (531), so unlike the PRMT1/PRMT6 pair (four residues apart) a length check CAN discriminate it. HGNC returns exactly one UniProt id for the symbol.
enzyme classDISPUTED, and the dispute is load-bearing. Type II (symmetric dimethyl) by the 2005 founding paper (PMID 15494416); TYPE III (monomethyl only) by a dedicated 2012 product-specificity study across peptides, GST-GAR, myelin basic protein and recombinant human histones H2A/H2B/H3/H4 (PMID 22241471); BOTH by UniProt, which says it forms MMA and sDMA with a preference for MMA while annotating the monomethyl reaction as its catalytic activity. Every symmetric-dimethyl mechanism attributed to PRMT7 inherits this dispute, and a type III enzyme feeding monomethyl substrate to a type II one would reproduce the cellular observations.
localizationSHUTTLING, ON A SINGLE SOURCE. UniProt Q9NVM4 fetched 2026-09-22 carries exactly two subcellular-location values - Cytoplasm/cytosol and Nucleus - and BOTH are ECO:0000269:PubMed:15494416, i.e. one 2005 paper, which is the founding characterisation whose central enzymological claim (symmetric dimethylarginine synthesis) was later contradicted. RULE 91 APPLIES: the evidence code means a curator saw an experiment in that paper; this beat did NOT read its abstract to confirm the paper contains a localisation experiment, and records that gap rather than papering over it. The nuclear pool is what licenses reading PRMT7 as a chromatin enzyme at all, and the demonstrated chromatin engagements are promoter-specific: the H19 imprinted control region via CTCFL, and the Bcl6 promoter in B cells (PMID 26179907).
subnuclear localizationNO COMPARTMENT ASSIGNED - recorded as an absence, not inferred. UniProt gives no nucleolar, speckle, PML-body or other subnuclear value for PRMT7. A nuclear-speckle or spliceosomal association is IMPLIED by substrate selection, since PRMT7's best-evidenced substrates are the Sm proteins SNRPD1 and SNRPD3 whose symmetric dimethylation is required for snRNP core particle assembly, but NO PRMT7 immunofluorescence or fractionation assigning a subnuclear compartment was found in any source read for this entry. REOPENING CONDITION: a PRMT7 immunofluorescence or biochemical fractionation in a t(4;11) line, scored for nucleolus, speckles and the chromatin-bound fraction, would settle this field and would also decide whether the chromatin pool is large enough to carry the H4R3me2s argument.
localization shown for fusionNO - nobody has looked in any fusion. No PRMT7 localisation experiment in any KMT2A-rearranged cell exists; PRMT7[tiab] AND KMT2A[tiab] = 0 and AND MLL[tiab] = 1 (a complex name, not an experiment).
localization evidence codeECO:0000269 for both values, but from a SINGLE publication (PubMed:15494416). No ECO:0000250 or ECO:0000305 values. Coverage is nominally experimental and actually single-sourced.
cell typeHaematopoietic evidence across three lineages, which is unusual for this family. B CELLS: murine B-cell-specific Prmt7 knockout - decreased mature marginal-zone B cells, increased follicular B cells, promoted germinal-centre formation after immunisation, low IgG1 and IgA, deregulated Bcl6/Prdm1/Irf4; plus the B-lymphoma lines Raji and A20 (PMID 26179907). CML LEUKAEMIA STEM CELLS: mouse CML model and primary human CML CD34+ cells (PMID 35508169). T-ALL: high PRMT7 mRNA across haematological malignancies with the highest levels in mature T-ALL subtypes; CRISPR deletion reduces colony formation (PMID 35565298). NON-HAEMATOPOIETIC: NT2/D1 embryonal carcinoma differentiation (PMID 23249737). DepMap: 1,258 screened lines, lymphoid tissue n = 97. NO measurement in fetal liver HSC, LMPP, pro-B, or any KMT2A-rearranged line or patient sample.
cell stateTWO documented states, neither examined in this disease. (1) SELF-RENEWAL: Prmt7 loss or pharmacologic inhibition impairs leukaemia-stem-cell self-renewal in CML while sparing normal haematopoiesis, via reduced glycine decarboxylase and glycine reprogramming to methylglyoxal (PMID 35508169). (2) PROTEOSTASIS / STRESS RESPONSE: PRMT7 inhibition or knockout drastically lowers arginine monomethylation of HSP70-family stress proteins and decreases tolerance for heat shock and proteasome inhibition (PMID 32409666). (3) DIFFERENTIATION, as an antagonist: PRMT7 antagonises KMT2D-mediated differentiation by raising H4R3me2s, and PRMT7 knockdown raises KMT2D-catalysed H3K4me3 (PMID 23249737). No quiescence, persister or niche state has been examined for PRMT7 in KMT2A-rearranged leukaemia.
epigenetic mark namedH4R3me2s - the mark UniProt names specifically for PRMT7, the one that inhibits KMT2D's tandem PHD(4-6), and the one recruited with H4R3me1 to the Bcl6 promoter in B cells. H4R3me1 - the monomethyl state, consistent with the type III reading. H3R2me2s - WEAK, one clause in PMID 22231400, not carried by UniProt, no independent replication found. H2A R3 and myelin basic protein - in vitro, with UniProt itself calling the in vivo relevance unclear.
epigenetic readoutWRITER of a REPRESSIVE mark, and the only enzyme in this beat with a measured antagonism against a KMT2-family methyltransferase: PRMT7 but not PRMT5 raises H4R3me2s at KMT2D target genes, inhibiting KMT2D's own PHD(4-6) module and lowering KMT2D-catalysed H3K4me3 at genes including many HOXA and HOXB, with PRMT7 knockdown reversing it (PMID 23249737). In B cells PRMT7 recruits H4R3me1 and symmetric H4R3me2 to the Bcl6 promoter and negatively regulates Bcl6 (PMID 26179907). BUT the best-evidenced substrates are NON-HISTONE: SNRPD1/SNRPD3 symmetric dimethylation required for snRNP core assembly (UniProt), and HSP70 R469 monomethylation, which is the validated cellular pharmacodynamic of the chemical probe (PMID 32409666). And the one leukaemia proteomic result measured arginine MONOmethylation changes, not symmetric dimethylation (PMID 35565298). So the honest readout is: writer of a repressive histone arginine mark on paper, monomethyl-transferase in the assays that actually engage the enzyme in cells.
disease germlineSBIDDS - short stature, brachydactyly, impaired intellectual development and seizures; autosomal recessive, caused by PRMT7 loss of function (UniProt Q9NVM4 DISEASE block, read back 2026-09-22). A germline loss-of-function syndrome with developmental delay and skeletal abnormalities - i.e. PRMT7 is required for normal human development, which is the essential-function toxicity axis for any inhibitor.
shown for fusionNO - nobody has looked in any fusion. PRMT7[tiab] AND KMT2A[tiab] = 0 (re-run 0); AND MLL[tiab] = 1, and that record uses 'MLL' as the name of a WDR5-containing coactivator complex rather than reporting an experiment on a KMT2A protein. The nearest relevant result is against KMT2D in NT2/D1 embryonal carcinoma (PMID 23249737). No physical contact between PRMT7 and KMT2A or any KMT2A fusion is reported anywhere.
absence classliterature-absence-bounded
absence class noteMIGRATED 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, warninglists, re-runs and an operand control; the clinical absence is UNBOUNDED and labelled as such because no trial registry was queried'
PDB IDS
[]
domains
[
  {
    "name": "SAM-dependent MTase, PRMT-type 1",
    "start": 14,
    "end": 345,
    "pfam": null
  },
  {
    "name": "SAM-dependent MTase, PRMT-type 2",
    "start": 358,
    "end": 684,
    "pfam": null
  }
]
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": false,
  "n_screens": 1258,
  "mean_gene_effect": -0.1513,
  "fraction_lines_depleted_below_minus_0_5": 0.0167,
  "lymphoid_tissue": {
    "n_lines": 97,
    "mean_gene_effect": -0.1039
  },
  "interpretation": "NOT A DEPENDENCY in cell-line screens. No KMT2A-selectivity join was performed, because both arms would sit within 0.16 Chronos units of zero and any selectivity rank would be a ranking of noise - the same reasoning gene-prmt6 records for its rank 4,735. IMPORTANT: this does NOT contradict the CML result, because a proliferation screen cannot see a stem-cell self-renewal requirement."
}
chemical probes
{
  "sgc3027": "Cell-permeable PRODRUG converted in cells to SGC8158, a potent SAM-competitive PRMT7 inhibitor; potent, selective and cell-active chemical probe (PMID 32409666). PRMT7[tiab] AND SGC3027[tiab] = 5 records, 2026-09-22.",
  "validated_pharmacodynamic": "Arginine MONOmethylation of HSP70-family proteins - NOT any histone mark. So the available probe's published target-engagement readout says nothing about H4R3me2s, and any experiment using it to test a chromatin hypothesis must add its own chromatin measurement.",
  "clinical": "NONE FOUND. No PRMT7-selective agent is known to this beat to have entered a clinical trial, and NO trial-registry search for PRMT7 was run - so this is an unbounded absence and is labelled as one. A separate small-molecule PRMT7 inhibitor was developed and tested in the CML study (PMID 35508169) without a named compound in the abstract.",
  "direction_warning": "PRMT7 inhibition SENSITISES cells to proteasome inhibitors and heat shock (PMID 32409666) - an on-target liability in any combination, and a confound for any proteostasis-stressing regimen."
}
reached for by
[
  "mark-h4r3me2s - PRMT7 is the writer UniProt names for this mark and the one that raises it at KMT2D targets where PRMT5 explicitly does not",
  "mark-h3r2me2s - PRMT7's contested attribution as a second writer, which is the premise this beat's dispatch brief asked to be verified and which verified only weakly",
  "gene-prmt5 - names PRMT5 and PRMT7 together as H3R2me2s writers, sourced to PMID 22231400; this entry supplies the counter-evidence (PMID 22241471) and UniProt's divergent assignment"
]
How this could bite us back
  • PRMT7 loss of function causes a germline human developmental syndrome - SBIDDS, with short stature, brachydactyly, impaired intellectual development and seizures. That is the essential-function toxicity axis for any PRMT7 inhibitor, and it is a developmental phenotype, which is the worst possible class for a drug intended for infants. This project's index disease is infant leukaemia.
  • The probe's own paper shows PRMT7 inhibition DECREASES tolerance for proteostasis perturbation, including heat shock and proteasome inhibitors (PMID 32409666). Any combination with a proteasome inhibitor, or any regimen imposing proteotoxic stress, carries an on-target sensitisation that is not selective for leukaemic cells.
  • The CML result is a self-renewal phenotype with a claimed sparing of normal haematopoiesis, and it is metabolic rather than epigenetic - glycine decarboxylase and methylglyoxal (PMID 35508169). So the most encouraging PRMT7 result in leukaemia does NOT run through the histone mark this beat cares about, and an inhibitor developed on the metabolic rationale would not be expected to have a chromatin pharmacodynamic. Attributing efficacy to H4R3me2s would misdirect the biomarker.
  • If PRMT7's mark represses a KMT2-family enzyme, then inhibiting PRMT7 RELEASES that enzyme - and in a HOXA-driven leukaemia releasing a KMT2-family H3K4 methyltransferase at HOXA/HOXB is plausibly pro-leukaemic. PRMT7 knockdown increases KMT2D-catalysed H3K4me3 at exactly those genes (PMID 23249737). The direction of benefit is not established and could be inverted.
  • PRMT7 is not a DepMap dependency (mean -0.1513 over 1,258 lines, 1.67% depleted), so no cell-line screen will support prioritising it and any in vitro proliferation experiment is likely to read as a negative. The assays that show a phenotype are primary-cell self-renewal and in vivo, which are the expensive ones - a real programme cost, not a scientific objection.
Still open
  1. Is PRMT7 type II or type III IN CELLS? Every symmetric-dimethyl mechanism attributed to it depends on the answer, and the discriminating experiment is a stable-isotope methyl-labelling and isomer-resolving mass-spectrometry read of H4R3 states in a PRMT7 knockout versus a PRMT5 knockout in the same cell. A type III result would not kill the mechanisms - it would place PRMT7 one step upstream of them, supplying monomethyl substrate.
  2. Does PRMT7 loss relieve a KMT2-family blockade in a KMT2A-rearranged cell? The KMT2D result (PMID 23249737) is the right direction on the right genes (HOXA/HOXB) in the wrong cell. A PRMT7 knockout or SGC3027 exposure in SEM or MV4;11, read out as H3K4me3 at HOXA9/MEIS1 plus H4R3 states by mass spectrometry, is one experiment and has never been done - PRMT7[tiab] AND KMT2A[tiab] = 0.
  3. Why do PRMT6 and PRMT7 both land on RUNX1 target genes through different marks in different lineages? PRMT6/H3R2me2a deregulates RUNX1 targets (PMID 22777353, carried in gene-prmt6 and gene-runx1); PRMT7 deregulates RUNX1 targets in T-ALL (PMID 35565298). Two points and no connecting mechanism, but RUNX1 has an entry here and the coincidence is in the haematopoietic compartment this project cares about.
  4. Does the degenerate C-terminal PRMT domain do anything? PRMT7 is the only family member in this graph with two tandem methyltransferase modules, there is no structure of the human protein at all, and the function of the second module is unresolved - which also means no structure-guided argument about PRMT7's substrate selection can be made here.
Every source behind this entry (11)
  1. E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    UniProt Q9NVM4 (ANM7_HUMAN, primary gene PRMT7, synonym KIAA1933, 692 aa, two SAM-dependent MTase PRMT-type domains at 14-345 and 358-684) records that PRMT7 can both catalyze the formation of omega-N monomethylarginine and symmetrical dimethylarginine with a preference for MMA, that it specifically mediates symmetrical dimethylation of the small nuclear ribonucleoproteins SNRPD1 and SNRPD3 as required for snRNP core particle assembly, that it specifically mediates the symmetric dimethylation of histone H4 'Arg-3' to form H4R3me2s, and that it is recruited by CTCFL at the H19 imprinted control region where it methylates histone H4 to form H4R3me2s; the annotated CATALYTIC ACTIVITY reaction is the monomethyl one; subcellular location is Cytoplasm/cytosol and Nucleus, both ECO:0000269:PubMed:15494416; loss-of-function causes SBIDDS (short stature, brachydactyly, impaired intellectual development and seizures), autosomal recessive; H3R2 is not named anywhere in the FUNCTION block.

    What this evidence cannot show

    A curated annotation, not a measurement; accession fetched live rather than recalled. The record is internally tense: it asserts sDMA capability while annotating a monomethyl-only reaction. Several histone statements are hedged ('possibly leading to recruit DNA methyltransferases') or flagged as unclear in vivo ('also able to mediate the arginine methylation of histone H2A and myelin basic protein in vitro; the relevance of such results is however unclear in vivo'). RULE-91 NOTE: the ONLY experimental citation behind both subcellular-location values is PubMed:15494416, the 2005 founding paper whose central enzymological conclusion - that PRMT7 synthesises symmetric dimethylarginine - is the disputed one.

    Evidence that argues against this (1)
    • The type II assignment the database carries is contradicted by a dedicated product-specificity study which found only monomethylarginine under every condition tested, including on recombinant human histones. So the curated 'can form sDMA' is itself an unresolved claim, and any mechanism built on PRMT7 as a direct symmetric-dimethyl writer inherits that dispute. Zurita-Lopez CI et al. 2012
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Full-length human PRMT7 expressed as a GST fusion with robust activity produced only omega-N-monomethylarginine on a variety of arginine-containing synthetic peptides and protein substrates including GST-GAR (the fibrillarin N-terminal domain), myelin basic protein and recombinant human histones H2A, H2B, H3 and H4, regardless of incubation time, reaction volume or substrate concentration, while control mammalian GST-PRMT1 and Myc-PRMT5 dimethylated their peptides to the expected asymmetric and symmetric products - so PRMT7 is a type III human methyltransferase capable of forming only monomethylarginine under the conditions tested.

    What this evidence cannot show

    Abstract read from the eutils record 2026-09-22; full text not read. In vitro, with a bacterially expressed GST fusion; the authors note a previous study characterised bacterially and mammalian-expressed PRMT7 fusions as type II/type I and qualify their own conclusion with 'under the conditions tested'. An in vitro negative on recombinant histone components does not exclude symmetric dimethylation of a nucleosomal substrate in a cell with cofactors, partners or allosteric regulation present.

    Evidence that argues against this (1)
    • Two independent cellular experiments report symmetric dimethyl phenotypes for PRMT7: a knockdown that raises H4R3me2s at KMT2D targets where PRMT5 does not, and a B-cell conditional knockout in which PRMT7 recruits both H4R3me1 and symmetric H4R3me2 to the Bcl6 promoter. Either PRMT7 makes sDMA in cells under conditions not reproduced in vitro, or it primes another enzyme by supplying monomethylarginine - and a type III enzyme feeding a type II one would produce exactly the observed pattern. Ying Z et al. 2015
  3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    The binding strength of the tandem plant homeodomain PHD(4-6) of MLL4 - the enzyme the paper also calls MLL2 and ALR, i.e. KMT2D - is inhibited by H4R3 symmetric dimethylation, and PHD(4-6) is required for MLL4's nucleosomal methyltransferase activity; PRMT7, but not PRMT5, represses MLL4 target genes by upregulating H4R3me2s levels and antagonises MLL4-mediated differentiation; PRMT7 knockdown increases MLL4-catalysed H3K4me3 levels; and during differentiation, decreased H4R3me2s levels are associated with increased H3K4me3 levels at a cohort of genes including many HOXA and HOXB genes.

    What this evidence cannot show

    Abstract read from the eutils record 2026-09-22; full text not read; no residue numbers asserted for PHD(4-6) because none were fetched from a sequence. NOMENCLATURE: the paper's 'MLL4' is KMT2D, settled by the aliases MLL2 and ALR and by the Kabuki-syndrome attribution in its own abstract, and NOT KMT2B, whose MLL4 alias travels with WBP7. System is NT2/D1 embryonal carcinoma differentiation - not haematopoietic, not leukaemic, and the enzyme is KMT2D not KMT2A. The PRMT7 arm is a knockdown, so an indirect route through PRMT7's non-histone substrates is not excluded.

    Evidence that argues against this (1)
    • If PRMT7 is a type III monomethyl-only enzyme as a dedicated product-specificity study concluded, PRMT7 cannot be the direct writer of the H4R3me2s this mechanism depends on, and the knockdown phenotype would be indirect - most plausibly through loss of the monomethyl substrate a type II enzyme needs. The mechanism could hold with PRMT7 one step removed from the mark. Zurita-Lopez CI et al. 2012
  4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    In mice with a B-cell-specific knockout of PRMT7, loss of PRMT7 led to decreased mature marginal-zone B cells, increased follicular B cells and promoted germinal-centre formation after immunisation, with low secreted IgG1 and IgA and abnormal expression of the germinal-centre genes Bcl6, Prdm1 and Irf4; overexpression of PRMT7 in the B-lymphoma-derived Raji and A20 lines validated that PRMT7 negatively regulates Bcl6 expression, and chromatin immunoprecipitation-PCR showed PRMT7 recruits H4R3me1 and symmetric H4R3me2 to the Bcl6 promoter.

    What this evidence cannot show

    Abstract read from the eutils record 2026-09-22; full text not read. Murine B-lineage in vivo plus two B-lymphoma cell lines - genuinely B-lineage, which is rare for this enzyme, but mature B-cell and germinal-centre biology, NOT a pro-B or fetal-liver progenitor and NOT a KMT2A-rearranged cell. The ChIP-PCR is antibody-based at a single promoter and the isomer specificity of the reagents is not addressed, which for H4R3me1 versus symmetric H4R3me2 is the constraint that matters. 'Recruits' is the abstract's own word and conflates PRMT7 occupancy with mark deposition.

    Evidence that argues against this (1)
    • Because the same experiment reports both H4R3me1 and symmetric H4R3me2 at the promoter, and because a dedicated in vitro study says PRMT7 makes only monomethylarginine, the symmetric species could be deposited by a different enzyme acting on PRMT7-supplied monomethyl substrate. The result establishes PRMT7's requirement at the locus, not that PRMT7 is the symmetric writer. Zurita-Lopez CI et al. 2012
  5. E5weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.paper

    Histone H3 arginine 2 is symmetrically dimethylated by PRMT5 and PRMT7 to give H3R2me2s, present in euchromatic regions, a mark that excludes RBBP7 and whose effect on WDR5 binding distinguishes it from H3R2me2a.

    Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance. · Migliori V, Müller J, Phalke S, Low D, et al. · Nat Struct Mol Biol 2012
    What this evidence cannot show

    Abstract read from the eutils record 2026-09-22; full text not read. CONFIDENCE IS DELIBERATELY WEAK for the PRMT7 attribution specifically - it is a single clause naming PRMT7 alongside PRMT5 in a paper whose focus and downstream analyses are PRMT5-centred, it is not carried by UniProt, and it is contradicted in principle by the same-year type III study. 'H3R2me2s'[tiab] AND PRMT7[tiab] returns only 2 records, one of which is this paper, so no independent replication of the PRMT7 half was found. The claim about WDR5 binding was itself revised in 2020 (see mark-h3r2me2s).

    Evidence that argues against this (1)
    • UniProt's FUNCTION block for PRMT7 does not name H3R2 at all and assigns PRMT7's specific histone mark as H4R3me2s. Combined with the type III enzymology study and the absence of independent replication, this graph records PRMT7 as a weak H3R2me2s writer, and the dispatch brief's unqualified description of it as 'a second H3R2me2s writer' is not supported at that strength. UniProt 2026
  6. E6strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Genetic loss of Prmt7 and a small-molecule specific inhibitor of PRMT7 each delayed leukaemia development and impaired self-renewal of leukaemia stem cells in a CML mouse model and in primary human CML CD34+ cells, without affecting normal haematopoiesis; mechanistically, PRMT7 loss reduced expression of glycine decarboxylase, reprogramming glycine metabolism to generate methylglyoxal, which is detrimental to leukaemia stem cells.

    What this evidence cannot show

    Abstract read from the eutils record 2026-09-22; full text not read. CHRONIC MYELOID LEUKAEMIA, a BCR::ABL1 disease - not a KMT2A rearrangement and not lymphoid. 'Without affecting normal hematopoiesis' is a strong therapeutic-window claim made in an abstract and was not verified against the figures. The mechanism given is metabolic rather than chromatin, so this paper is a PRMT7 dependency result and NOT evidence about any histone arginine mark; the abstract's closing phrase 'links histone arginine methylation with glycine metabolism' is not supported by anything described in the abstract itself.

    Evidence that argues against this (1)
    • PRMT7 is not a DepMap dependency in cell-line screens - mean gene effect -0.1513 across 1,258 screened lines with only 1.67% of lines depleted below -0.5, and a lymphoid-tissue mean of -0.1039 over 97 lines. A stem-cell self-renewal requirement in a mouse model and in primary CD34+ cells is not contradicted by that, because LSC self-renewal is not what a proliferation screen measures, but it does mean no cell line should be expected to depend on PRMT7 and an in vitro cell-line experiment is the wrong assay. Open Targets Platform / DepMap 2026
  7. E7moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    Across haematological malignancies, PRMT7 mRNA is high in T-cell acute lymphoblastic leukaemia and particularly in the mature subtypes of T-ALL; CRISPR-Cas9 deletion of PRMT7 reduced colony formation of T-ALL cells and changed arginine monomethylation patterns in protein complexes associated with RNA and DNA processing and with T-ALL pathogenesis, among them RUNX1, whose target gene expression was consequently deregulated.

    Arginine Methyltransferase PRMT7 Deregulates Expression of RUNX1 Target Genes in T-Cell Acute Lymphoblastic Leukemia. · Oksa L, Mäkinen A, Nikkilä A, Hyvärinen N, et al. · Cancers (Basel) 2022
    What this evidence cannot show

    Abstract read from the eutils record 2026-09-22; full text not read. T-lineage ALL, not B-lineage and not KMT2A-rearranged; the disease this project is about is infant B-ALL. The measured methylation change is arginine MONOmethylation, consistent with the type III reading of the enzyme and NOT a symmetric dimethyl result. Colony formation is a single functional readout. The RUNX1 link is 'among them' in a proteomic list plus a downstream expression change, not a demonstrated direct methylation event at a mapped residue.

    Evidence that argues against this (1)
    • That the measured consequence is monomethylation rather than symmetric dimethylation cuts against the histone-symmetric-dimethyl model of PRMT7 in a leukaemic cell, and points the mechanism at non-histone substrates in RNA and DNA processing complexes. A reader should not transfer this T-ALL dependency onto the H4R3me2s/KMT2D mechanism - they may be two different PRMT7 biologies. Szewczyk MM et al. 2020
  8. E8strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    SGC3027 is a potent, selective and cell-active chemical probe for PRMT7: a cell-permeable prodrug converted in cells to SGC8158, a potent SAM-competitive PRMT7 inhibitor; inhibition or knockout of cellular PRMT7 drastically reduces arginine monomethylation of HSP70-family stress-associated proteins, PRMT7-driven in vitro methylation of HSP70 at R469 requires an ATP-bound open conformation of HSP70, and SGC3027 decreases tolerance for perturbations of proteostasis including heat shock and proteasome inhibitors.

    Pharmacological inhibition of PRMT7 links arginine monomethylation to the cellular stress response. · Szewczyk MM, Ishikawa Y, Organ S, Sakai N, et al. · Nat Commun 2020
    What this evidence cannot show

    Abstract read from the eutils record 2026-09-22; full text not read. A chemical probe, NOT a clinical agent - no PRMT7-selective compound has entered a clinical trial as far as this beat established, and no trial registry search for PRMT7 was run. The cellular readout that validates target engagement is arginine MONOmethylation of HSP70, not any histone mark, so this probe's published pharmacodynamic does not report on H4R3me2s or H3R2me2s at all. The proteostasis phenotype is a general cell-biological effect and not leukaemia-specific.

    Evidence that argues against this (1)
    • A probe whose validated cellular pharmacodynamic is HSP70 monomethylation cannot be used to attribute a phenotype to a histone arginine mark without an independent chromatin measurement, and PRMT7 inhibition sensitises cells to proteasome inhibitors and heat shock - an on-target liability that would confound any combination study in a disease already treated with proteostasis-stressing agents. Liu C et al. 2022
  9. E9strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

    PRMT7 (ENSG00000132600) is NOT flagged essential in DepMap CRISPR (Chronos): mean gene effect -0.1513 across 1,258 screened cell lines with 1.67% of lines depleted below -0.5, and a lymphoid-tissue mean of -0.1039 over 97 lines; HGNC:25557 assigns PRMT7 to 16q22.1 with the single UniProt id Q9NVM4 and Ensembl gene ENSG00000132600; RCSB returns ZERO structures for Q9NVM4 and UniProt carries no PDB cross-reference, so there is no experimental structure of human PRMT7.

    What this evidence cannot show

    RULE 83: the API does NOT state a DepMap release, so the release is unverified and only the fetch date is recorded; DepMap ships quarterly and screens each gene in a gene-specific number of lines, so 1,258 is PRMT7's own screen count and not a corpus denominator. The RCSB query returned HTTP 204 (no content) for the accession-index search, which this beat reads as zero entries; that is a negative from one query form, and a structure deposited under a mouse or trypanosomal PRMT7 accession would not appear. No KMT2A-selectivity join was performed for PRMT7 because the mean effects are within 0.16 Chronos units of zero and any selectivity rank would be a ranking of noise.

    Evidence that argues against this (1)
    • A cell-line proliferation screen is the wrong assay for a stem-cell self-renewal dependency. Prmt7 loss impairs leukaemia-stem-cell self-renewal in a CML mouse model and in primary human CML CD34+ cells while sparing normal haematopoiesis - a phenotype invisible to DepMap by construction. 'Not a DepMap dependency' must not be read as 'not a therapeutic target'. Liu C et al. 2022
  10. E10strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

    PubMed esearch 2026-09-22 with querytranslation read back and zeros re-run: PRMT7[tiab] = 172; PRMT7[tiab] AND KMT2A[tiab] = 0 (re-run 0, warninglist outputmessages ['No items found.']); AND MLL[tiab] = 1 (22231400, where 'MLL' names a WDR5-containing coactivator complex); AND menin[tiab] = 1 (32859041, a GLI arginine-methylation review); AND leukemia[tiab] = 9 (41157668, 40619015, 35675797, 35565298, 35508169, 28874563, 26179907, 23249737, 19089452); AND 'H3R2me2s'[tiab] = 2 (22231400, 33980975); AND H3R2[tiab] = 3; AND SGC3027[tiab] = 5. Operand control KMT2A[tiab] = 1652.

    What this evidence cannot show

    Bounds TITLES AND ABSTRACTS only. The nine leukaemia records were title-checked; 23249737 enters only through the legacy phrase 'mixed-lineage leukemia 4' in the enzyme's name and is a stem-cell differentiation paper, and 19089452 is an etoposide-cytotoxicity genome-wide association study, so counting nine as a PRMT7 leukaemia literature would overstate it - the substantive ones are 35508169, 35565298 and 26179907. No Europe PMC full-text sweep was run, so a PRMT7 measurement inside a KMT2A-fusion paper's supplementary data would be invisible here.

    Evidence that argues against this (1)
    • A zero against the modern symbol is not a zero against the literature: this beat measured H4R3[tiab] AND KMT2A[tiab] = 0 while H4R3[tiab] AND MLL[tiab] = 3, so arginine-methylation work touching this gene family is old enough to use the legacy symbol. For PRMT7 both symbols were run and both are effectively empty, which is why this absence is recorded as strong rather than provisional. NCBI PubMed 2026
  11. E11moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    The founding characterisation of PRMT7 is titled 'PRMT7, a new protein arginine methyltransferase that synthesizes symmetric dimethylarginine' - the source of the type II assignment, and the single publication behind both of UniProt's ECO:0000269 subcellular-location values for PRMT7 (Cytoplasm/cytosol and Nucleus).

    PRMT7, a new protein arginine methyltransferase that synthesizes symmetric dimethylarginine. · Lee JH, Cook JR, Yang ZH, Mirochnitchenko O, et al. · J Biol Chem 2005
    What this evidence cannot show

    Title and bibliographic record fetched from the eutils record 2026-09-22; the ABSTRACT WAS NOT READ for this item and no experimental detail from it is asserted here - it is cited to identify the source of the type II assignment and of UniProt's localisation evidence code, which is a bibliographic claim. Whether the paper contains a localisation experiment at all was NOT verified, which is precisely the rule-91 gap being flagged: an ECO:0000269 code means a curator saw an experiment somewhere in the paper, not that the paper is about subcellular localisation.

    Evidence that argues against this (1)
    • This paper's central conclusion - that PRMT7 synthesises symmetric dimethylarginine - was directly contradicted seven years later by a dedicated product-specificity study. Since the same paper is UniProt's sole experimental support for PRMT7's subcellular location, a reader should note that the localisation annotation and the disputed enzymology rest on one source and are not equally durable. Zurita-Lopez CI et al. 2012
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