SPEN / SHARP / MINT (Q96T58) - the RNA-binding corepressor that silences the X chromosome, in the pan-MLL-fusion core
also called SPEN · SHARP · MINT · KIAA0929 · Msx2-interacting protein · SMART/HDAC1-associated repressor protein
SPEN is a very large protein with RNA-binding arms at one end and a repression domain at the other; it is the protein the Xist RNA grabs to switch off an entire X chromosome, and it is also the switch that keeps Notch target genes off. It co-purifies with all seven MLL fusions tested and has never been studied in this disease.
The same thing, for a scientist
SPEN (Q96T58, 3,664 aa - the largest protein in this beat) carries N-terminal RRMs and a C-terminal SPOC domain that recruits the SMRT/NCoR-HDAC3 corepressor. It is the protein Xist binds directly to silence the inactive X, and it is the corepressor that occupies RBPJ in the Notch-off state. In Skucha 2018 it co-purified with all seven MLL fusions; the MLL-AF4 (= KMT2A::AFF1) call is p = 0.0532 with 3|5 spectra - marginally above 0.05 - while four other baits are between 1.6e-6 and 3.9e-6 with 12 to 46 spectra. So the pan-fusion signal is strong and the index-fusion measurement is not. SPEN is named in sixteen node files in this graph, none of them a gene entry, and none as an interactor of the fusion; a bounded search finds no publication connecting SPEN, SHARP or MINT to a KMT2A fusion.
The Skucha row
7 of 7 fusions. MLL-AF1p 0.00233 (8|6), MLL-AF4 0.0532 (3|5), MLL-AF9 2.75e-6 (34|26), MLL-CBP 3.3e-6 (12|46), MLL-EEN 1.61e-6 (37|38), MLL-ENL 3.93e-6 (23|35), MLL-GAS7 0.00201 (19|14); negative control 0|0 1. This is the clearest case in the beat of a protein whose pan-fusion evidence is strong - four baits in the 1e-6 range with tens of spectra - and whose index-fusion evidence is marginal (p = 0.0532, 3|5). The two statements must be kept apart.
What SPEN does
A purification of proteins interacting directly with Xist identified ten, of which SHARP (SPEN), SAF-A and LBR are required for Xist-mediated silencing; SHARP is required both for silencing and for exclusion of RNA polymerase II from the inactive X, and it acts through SMRT and HDAC3 2. Separately, the SPEN/SHARP SPOC-adjacent region binds RBPJ at the same site Notch intracellular domain uses, and the RBPJ-SHARP structure defines a conserved corepressor binding site 3. So SPEN is a repressor that is recruited both by a long non-coding RNA and by a sequence-specific DNA-binding factor.
Why an RNA-binding corepressor in this interactome is worth noticing, and why it is also a warning
This graph has already been burned by treating preys from a heterologous RNA-binding-protein atlas as established fusion interactors, and SPEN is an RNA-binding protein recovered from nuclear lysate. The relevant discipline is: SPEN's presence here is a hypothesis-generating observation about a repressive, RNA-coupled module in the MLL-fusion environment, not a demonstrated contact. What makes it more than noise is the pan-fusion consistency and the spectral depth at four baits, not the MLL-AF4 row.
| uniprot | Q96T58 |
|---|---|
| length AA | 3664 |
| accession resolution | Resolved live 2026-09-21: gene_exact:SPEN AND organism_id:9606 AND reviewed:true returns exactly one row, gene_primary SPEN, Q96T58, MINT_HUMAN, 3,664 aa, synonyms KIAA0929 MINT SHARP. Matches Skucha's table. The entry name MINT_HUMAN and the protein name 'Msx2-interacting protein' contain neither 'SPEN' nor 'SHARP', so reading the protein name back would make a correct record look wrong - the primary gene name is what settles it. |
| localization | Nucleus |
| subnuclear localization | No named compartment in the database. In the X-inactivation literature SPEN is recruited to the Xist-coated inactive X, which is a chromosome-scale domain rather than a body; nothing is published for a KMT2A-rearranged cell. |
| localization evidence | UniProt Q96T58, fetched 2026-09-21: a single location comment, Nucleus, with one ECO:0000269 experimental citation. No subnuclear annotation. |
| shown for fusion | KMT2A::AFF1 (MLL-AF4) by co-purification only and at p = 0.0532, plus the six other Skucha baits, four of them strongly. NO independent experiment ties SPEN, SHARP or MINT to a KMT2A fusion in any system. |
| graph context | SPEN is named in sixteen node files in this graph (grep -rl, 2026-09-21) - in mutation lists, in the AFF1 CHD-dimerisation experiment entry and in the target-list audit - and none is a gene entry or treats it as a fusion interactor. gene-rbm15, a SPEN-family paralogue, does have an entry. |
skucha 2018
{
"bait": "MLL-AF4 (= KMT2A::AFF1)",
"p_value": 0.0532,
"spectral_counts": "3|5",
"n_fusions_of_seven": 7,
"negative_control_counts": "0|0",
"per_bait": {
"MLL-AF1p": "0.00233 (8|6)",
"MLL-AF4": "0.0532 (3|5)",
"MLL-AF9": "2.75e-06 (34|26)",
"MLL-CBP": "3.3e-06 (12|46)",
"MLL-EEN": "1.61e-06 (37|38)",
"MLL-ENL": "3.93e-06 (23|35)",
"MLL-GAS7": "0.00201 (19|14)"
},
"index_bait_warning": "p = 0.0532, marginally above conventional significance; the pan-fusion signal is carried by four baits in the 1e-6 range.",
"source": "analyses/skucha-mll-fusion-interactome/results.json, re-derived from the cached MOESM4 xlsx on 2026-09-21"
}cell types and states
[ "Jurkat (human T-ALL) - AP-MS host, nuclear lysate", "mouse embryonic stem cells - Xist-mediated silencing, Pol II exclusion", "structural/biochemical systems - RBPJ corepressor interface", "no KMT2A-rearranged cell of any kind" ]
bounded literature
{
"query": "SPEN[tiab] AND (KMT2A[tiab] OR MLL[tiab] OR \"MLL-AF4\"[tiab] OR \"MLL-AF9\"[tiab])",
"querytranslation": "\"SPEN\"[Title/Abstract] AND (\"KMT2A\"[Title/Abstract] OR \"MLL\"[Title/Abstract] OR \"MLL-AF4\"[Title/Abstract] OR \"MLL-AF9\"[Title/Abstract])",
"count": 4,
"on_topic_after_title_check": 0,
"rejected": "PMID 40678837 (nasopharyngeal carcinoma genomic database), 33793001 (KMT2D in gastric cancer ctDNA), 33297669 (post-transplant plasmablastic lymphoma), 32598477 (mantle cell lymphoma meta-analysis) - all mutation-panel papers in which SPEN and a KMT2 gene appear as separate rows.",
"alias_queries": "SHARP[tiab] AND (KMT2A[tiab] OR MLL[tiab]) returns 8, title-checked to 0 on topic - every hit uses 'sharp' as an ordinary word or an unrelated acronym (machine-learning augmentation, X-ray diffraction, sturgeon antimutagenesis). MINT[tiab] AND (KMT2A[tiab] OR MLL[tiab]) returns 4, title-checked to 0 - all four are animal-nutrition papers about Mentha piperita essential oil.",
"names_tried": [
"SPEN",
"SHARP",
"MINT"
],
"date": "2026-09-21",
"tool": "NCBI esearch db=pubmed",
"positive_control": "the identical query shape with MEN1 returns 85",
"collision_note": "SHARP and MINT are both ordinary English words and neither is usable as a search token without title-checking every hit. Neither is in data/symbol-collisions.json as of 2026-09-21.",
"bound": "Titles and abstracts only; supporting figures not searched."
}functionally screened in the source paper
{
"_added": "king, cycle 48, 2026-09-21, after Q86 flagged that cycle-47 entries understate the record. Verified by me directly from the supplementary file, not from the paper's prose.",
"screened": true,
"library_symbol": "SPEN",
"shrnas_for_this_gene": 6,
"design": "Supplementary Table 6 / MOESM5 is 768 data rows, 128 unique gene symbols, EXACTLY 6 shRNAs each -- counted with openpyxl on 2026-09-21. Negative-selection RNAi screen in MLL-AF9-expressing MOLM-13.",
"what_this_DOES_establish": "Every one of the 128 conserved MLL-fusion interactors, this protein included, was functionally tested against an MLL fusion. An entry saying 'nothing in the paper validates this prey' is true of BINDING and understates the record.",
"what_this_does_NOT_establish": "A per-gene result. Scores are presented as heatmaps (Fig. 2c/2d) and no per-gene depletion value is tabulated, so for any individual gene the outcome is measured-not-reported. It is also MLL-AF9 MOLM-13, a myeloid line, not the index fusion and not B-lineage.",
"absence_class_for_the_per_gene_score": "measured-not-reported"
}- SPEN is required for X inactivation and for Notch-off states across development; it is not a plausible therapeutic target in an infant on any current modality.
- A 3,664-residue RNA-binding scaffold has no druggable pocket in the ordinary sense, and the one structurally defined interface (RBPJ) is a general developmental switch.
- If the association is RNA-mediated, then every intervention aimed at it is really aimed at an RNP, with consequences far beyond the fusion.
- Is SPEN's association with MLL fusions RNA-dependent? An RNase-treated co-IP would separate a protein contact from a shared RNP, and this graph has an existing reason to ask - the AFF1 arm of the fusion is itself RNA-associated.
- Are SMRT/NCoR2 or HDAC3 in the Skucha 960-protein network? SPEN plus its corepressor would be a module; SPEN alone is a protein.
- Does the index-fusion association reach significance in a repeat experiment, given p = 0.0532?
- SPEN and CSNK2B, two of these twelve, both touch Notch. Is there a Notch-repression module in the MLL-fusion environment, or is this a base-rate coincidence? The null needs writing down before the pattern is believed.
- E1moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
SPEN co-purified with all seven Strep-HA-tagged MLL fusions in isogenic Jurkat cells; the MLL-AF4 (= KMT2A::AFF1) call is p = 0.0532 with 3|5 spectral counts, while MLL-AF9, MLL-CBP, MLL-EEN and MLL-ENL are all in the 1e-6 range with 12 to 46 spectra.
MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity. · Skucha A, Ebner J, Schmoellerl J, Roth M, Eder T, Cesar-Razquin A, Stukalov A, Vittori S, Muhar M, Lu B, Aichinger M, Jude J, Mueller AC, Gyorffy B, Vakoc CR, Valent P, Bennett KL, Zuber J, Superti-Furga G, Grebien F · Nature Communications 2018What this evidence cannot show
SYSTEM: the AP-MS host is JURKAT, a T-ALL line, whereas KMT2A::AFF1 disease is B-lineage infant leukaemia, so a partner that needs a B-cell or infant proteome cannot appear here and a T-lineage partner can appear spuriously. The bait is a Strep-HA-tagged, SINGLE-COPY, doxycycline-INDUCED transgene, not the endogenous fusion. Prey was recovered from bulk nuclear lysate, so co-purification is not evidence of a direct contact. INCLUSION RULE: the paper kept the top 300 interactions per bait by combined p-value rather than applying a p threshold (Methods, verbatim: "The 300 most significant interactions per bait were retained"). Measured by this beat by reading the cached Supplementary Table 5 xlsx directly on 2026-09-21: 545 of the 2,049 per-bait p-values in the table (26.6%) exceed 0.05, to a maximum of 0.175. This graph's own king analysis ana-the-index-fusion-interactome-is-not-distinctive-and-two-earlier-answers-were-artifacts found the MLL-AF4 column reaches deepest into the weak tail of the seven, so an MLL-AF4 p-value is systematically weaker than the same protein's p-value under another bait and should not be read as a weaker interaction. The index-fusion p-value of 0.0532 is above 0.05; the strength of this row is in the other four baits, not in MLL-AF4. SPEN is a large RNA-binding protein and this graph has previously mis-promoted RNA-binding-protein preys from a heterologous system to interactor status - the same caution applies here. Values re-read from the cached xlsx on 2026-09-21.
Evidence that argues against this (1)
- IntAct has never curated this dataset (pubid:29777171 returns 0 rows against a working positive control), so no independent curator has re-examined these calls, and the raw data at ProteomeXchange PXD009338 have not been reanalysed here. Nothing in the paper validates this particular prey by an orthogonal assay: of the twelve proteins in this beat, only SETD2 is mentioned anywhere in the paper's body text (counted by regex over the PMC full text, 2026-09-21; SF3A3 appears once, as a named non-selective control). ProteomeXchange/PRIDE 2018
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
SHARP/SPEN interacts directly with the Xist long non-coding RNA and is required for Xist-mediated transcriptional silencing and for exclusion of RNA polymerase II from the inactive X, acting through the SMRT corepressor and HDAC3.
The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. · McHugh CA, Chen CK, Chow A, Surka CF, Tran C, et al. · Nature 2015What this evidence cannot show
Mouse embryonic stem cells with a quantitative-mass-spectrometry lncRNA purification method; X inactivation, not leukaemia and not a fusion. Read from the abstract.
Evidence that argues against this (1)
- SPEN's best-characterised role is in a chromosome-wide silencing pathway that has no obvious counterpart in a KMT2A fusion's activating programme; that mismatch is a reason to suspect the co-purification rather than to explain it. Yuan Z et al. 2019
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
SHARP/SPEN binds RBPJ through a conserved corepressor binding site, the structural basis of Notch target-gene repression in the absence of Notch signalling.
Structural and Functional Studies of the RBPJ-SHARP Complex Reveal a Conserved Corepressor Binding Site. · Yuan Z, VanderWielen BD, Giaimo BD, Pan L, Collins CE, Turkiewicz A, Hein K, Oswald F, Borggrefe T, Kovall RA · Cell Rep 2019What this evidence cannot show
Structural and functional work on the RBPJ-SHARP interface, not in a haematopoietic or leukaemic system. Read from the abstract and title. Recorded here partly as a cross-link: this beat's CSNK2B entry records a NOTCH2-dependent B-cell phenotype, so two of the twelve pan-fusion proteins touch Notch from different directions, which is a coincidence worth noting and not yet a finding.
Evidence that argues against this (1)
- Notch repression is a general developmental mechanism; its presence in two entries of this beat is at least as likely to reflect how much of the nuclear proteome touches Notch as anything about the fusion. McHugh CA et al. 2015
supplies the epigenetics record gene-spen lacks: SPOC recruits NCoR/SMRT and NuRD to active enhancers
co-purified with MLL-AF4 at p=0.0532 (3|5) - marginal; four other baits at 1e-6 with 12-46 spectra
- related to →RBM15 — m6A adaptor, AMKL fusion partner, and a named hit in the only KMT2A-biased RNA-protein CRISPR screen
SPEN-family paralogue; both are SPOC-domain RNA-binding corepressors
pan-fusion Skucha interactor with no gene entry before cycle 47