Oncofusion

start / graph / ana-q115-the-kdm2b-rdna-intersection-survives-at-full-text-and-a-2026-deposit-makes-the-re-map-cheaper

Analysisstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.Q115-absence-rebound

Re-bound at full text: still no publication puts KDM2B's rDNA repression together with a KMT2A fusion's nucleolar residence - 27 records, 10 of them congress abstract books, the rest reviews - but KDM2B ChIP-seq in MLL-AF9 cells is now deposited, so the rDNA re-map has a second and better dataset

also called Q115 KDM2B rDNA re-bound

Three separate findings place three different proteins on the DNA that builds ribosomes, and no single paper has ever looked at more than one of them. Searching whole papers rather than summaries confirms that, and turns up a 2026 dataset that would make the missing experiment a computer job rather than a bench job.

The same thing, for a scientist

`absence-kdm2b-and-the-kmt2a-fusion-are-both-nucleolar-and-nobody-has-put-them-together` claims that no publication contains two of three nucleolar observations. Re-run as a three-way full-text intersection - `(KDM2B OR FBXL10 OR JHDM1B OR NDY1) AND (nucleolar OR nucleolus OR rDNA OR "ribosomal DNA") AND (KMT2A OR MLL-AF4 OR MLL-AF9 OR MLL-ENL OR MLL-rearranged OR "MLL fusion" OR KMT2A-rearranged)` - returns **27 records** [E1]. **Every title was read. Ten are congress abstract books and the remaining seventeen are review articles**: histone-demethylase surveys, epigenetic-therapy reviews, a *Cell* twenty-year retrospective on lysine demethylases, a chromatin-signalling review. **Not one is a primary study.** The breadth control `KDM2B x KMT2A` without the nucleolar clause returns 225 and the KDM2B alias group alone 1,893, so the conjunction is doing the work [E1]. **The absence survives at full text.** **What has changed is the cost of closing it.** PMID 41634341 performed **KDM2B and BCOR ChIP-seq in murine MLL-AF9 cells under DMSO, a DOT1L inhibitor and a menin inhibitor**, and deposited it in GSE260742 [E2]. The entry's own named prerequisite - re-mapping KMT2A-fusion ChIP-seq against an rDNA-containing assembly, for which it names GSE127508 raw reads - now has a companion: **the same cells with the reader and the fusion profiled together**, which is the pair the entry says nobody has assembled [E2].

Go deeper
What survives and what has to be said more carefully

The entry's claim is scoped to the nucleolus and rDNA, and that scope is what saves it. PMID 41634341 puts KDM2B and an MLL fusion in one paper, in one experiment, in the same cells - so the looser reading of the title, nobody has put them together, is no longer true in general. It remains true in the sense the entry means it: that paper says nothing about the nucleolus, rDNA or Pol I, and the standard genome assembly it used discards rDNA reads, which is the methodological point the entry itself makes.

So the entry is correct and its title is now ambiguous in a way it was not when written. The coordinator may wish to narrow the phrase nobody has put them together to nobody has put them together at rDNA. This beat did not edit that file.

The re-map, restated with the better dataset

The experiment the entry proposes is: in a KMT2A-rearranged line, perturb KDM2B and measure 47S pre-rRNA, H3K4me3 at rDNA, and fusion occupancy on an rDNA-containing assembly.

With GSE260742 the cheapest first step is smaller and needs no perturbation: re-map the existing KDM2B, BCOR and FLAG-MLLAF9 ChIP-seq reads against an rDNA-containing assembly and ask whether either protein has rDNA signal, and whether they overlap. That is a single alignment job on public data. A negative is informative - it would mean the shared compartment is not a shared locus - and a positive is the first co-occupancy observation in the family.

The SETD1A arm of the entry can be asked the same way: SETD1A x nucleolar x KMT2A clause returns 39 at full text, again all reviews and proceedings on title screen 1.

Facts and figures
scriptnone - Europe PMC BODY: queries and one full-text read, 2026-09-22
statusrun
verdictSURVIVES at full text in its rDNA-scoped form; the looser reading of its title does not
entry re boundedabsence-kdm2b-and-the-kmt2a-fusion-are-both-nucleolar-and-nobody-has-put-them-together
instrument beforeabstract-level intersection of publication sets - the form most exposed to rule 80
instrument afterthree-way full-text intersection over 12,362,145 full texts, all 27 titles read
title ambiguity reported to the coordinatorThe entry's title ends 'and nobody has put them together'. PMID 41634341 puts KDM2B and an MLL fusion together genome-wide in one experiment. The entry's CLAIM is rDNA-scoped and survives; the TITLE reads more broadly than the claim. Recommend narrowing to 'nobody has put them together at rDNA'. NOT EDITED BY THIS BEAT.
absence classmeasured-not-analysed
absence class basisUNCHANGED in class, strengthened in evidence. The entry already carried GSE127508 as the raw-read source for an rDNA re-map. GSE260742 is a second and better source because it profiles KDM2B and the fusion in the same cells; verified live 2026-09-22 at the GEO SOFT endpoint. The analysis has still never been run.
queries
KDM2B aliases AND nucleol…27.0KDM2B aliases AND nucleolar terms AND KMT2A clause: 27SETD1A AND nucleolar term…39.0SETD1A AND nucleolar terms AND KMT2A clause: 39KDM2B aliases AND nucleol…176.0KDM2B aliases AND nucleolar terms: 176KDM2B aliases AND KMT2A c…225.0KDM2B aliases AND KMT2A clause (breadth control, no nucleolar clause): 225KDM2B aliases alone1,893KDM2B aliases alone: 1893
queries — the numbers behind the chart
[
  {
    "q": "KDM2B aliases AND nucleolar terms AND KMT2A clause",
    "hits": 27,
    "primary_studies": 0,
    "proceedings": 10,
    "reviews": 17
  },
  {
    "q": "SETD1A AND nucleolar terms AND KMT2A clause",
    "hits": 39,
    "primary_studies": 0,
    "proceedings": 7
  },
  {
    "q": "KDM2B aliases AND nucleolar terms",
    "hits": 176
  },
  {
    "q": "KDM2B aliases AND KMT2A clause (breadth control, no nucleolar clause)",
    "hits": 225
  },
  {
    "q": "KDM2B aliases alone",
    "hits": 1893,
    "role": "operand control"
  }
]
kdm2b aliases
[
  "KDM2B",
  "FBXL10",
  "JHDM1B",
  "NDY1"
]
nucleolar terms
[
  "nucleolar",
  "nucleolus",
  "rDNA",
  "ribosomal DNA"
]
nucleolar terms NOT tried
[
  "nucleolus-associated domain",
  "47S",
  "pre-rRNA",
  "Pol I",
  "RNA polymerase I",
  "rRNA transcription"
]
new dataset for the re map
{
  "accession": "GSE260742",
  "pmid": "41634341",
  "contents": "KDM2B, BCOR, FLAG-MLLAF9, H2AK119ub, H3K27me3, H3K4me3 ChIP-seq in murine MLLAF9 cells under DMSO / SGC0946 / VTP50469",
  "why_it_matters": "the reader and the fusion in the SAME cells, which is the pairing the entry says nobody has assembled",
  "what_is_still_missing": "any rDNA-containing assembly; the paper used a standard one, which discards these reads by construction",
  "companion_accession_already_named_by_the_entry": "GSE127508"
}
How this could bite us back
  • If the fusion and KDM2B do share rDNA territory, then a menin inhibitor that drives KDM2B and BCOR onto fusion target genes may also drive them onto rDNA - and a treatment-induced change in ribosome biogenesis is a toxicity nobody is monitoring, in an infant, in the tissue that is growing fastest.
Still open
  1. Do the GSE260742 KDM2B and FLAG-MLLAF9 libraries retain rDNA-mapping reads? One look at the file list decides whether the re-map is a desk job or needs new sequencing.
  2. Would widening the nucleolar clause to 'Pol I', 'pre-rRNA' and '47S' find a primary study the four-term clause missed? That is the most likely way this re-bound is wrong.
  3. Does PMID 40185081, the 2025 Cell twenty-year retrospective on histone lysine demethylases, mention KDM2B at rDNA in a leukaemia context? It is the highest-quality review in the hit list and was not opened.
Every source behind this entry (2)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

    The three-way full-text intersection of KDM2B aliases, nucleolar/rDNA terms and a seven-term KMT2A clause returns 27 records, of which 10 are congress abstract books and the remainder are review articles with no primary study among them; the SETD1A form returns 39 with the same composition; breadth controls are 225 (KDM2B x KMT2A) and 1,893 (KDM2B aliases alone).

    What this evidence cannot show

    Europe PMC BODY: reaches only the 12,362,145 full texts the index holds. A congress abstract book is one document containing thousands of unrelated abstracts and therefore matches almost any conjunction; across this beat's 18 fully-read intersections 83 of 321 records (25.9%, range 0-50%) are proceedings. Screening was at TITLE level unless a paper is listed as opened. Judging seventeen records as reviews was done from titles and journal names (Chem Rev, Adv Cancer Res, Signal Transduct Target Ther, Curr Opin Chem Biol, Cold Spring Harb-style surveys); none was opened. A review can contain an unpublished-elsewhere observation, and one of them - PMID 40185081, a Cell twenty-year retrospective on histone lysine demethylases - is the kind that sometimes does.

    Evidence that argues against this (1)
    • The nucleolar clause uses four terms and no others. A paper writing 'nucleolus-associated domain', 'NAD', '47S', 'pre-rRNA' or 'Pol I' without any of the four would not match, and a Pol I study is quite likely to write 'rRNA transcription' rather than 'rDNA'. The absence is bounded by those four terms and that list is the weak point. Europe PMC 2026
  2. E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

    KDM2B and BCOR ChIP-seq were performed in murine MLL-AF9 cells under DMSO, SGC0946 and VTP50469 and deposited in GSE260742, so the reader and the fusion have now been profiled in the same cells - but with no rDNA analysis and against a standard assembly.

    PMID 41634341DOI
    What this evidence cannot show

    Read in full (PMC12904788, 142,856 characters) on 2026-09-22. The words nucleolus, nucleolar, rDNA and Pol I were not searched for exhaustively in that text; what is asserted here is that the paper's subject is H2AK119ub at MLL-fusion target genes and that its figures name KDM2B, BCOR, H2AK119ub and H3K27me3 at those genes. Whether the deposited reads retain rDNA-mapping sequence depends on the library and the submitter's trimming, and that was not checked.

    Evidence that argues against this (1)
    • Most ChIP-seq libraries do contain rDNA reads - they are discarded at alignment, not at sequencing - but a submitter who uploaded only aligned BAMs against a standard assembly would have removed them irrecoverably. GSE260742's file-level contents were not inspected, so 'the re-map is possible' is an expectation, not a verified fact, and checking it is one look at the supplementary file list. NCBI Gene Expression Omnibus 2026
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