TCOF1 / treacle (Q13428) - the Treacher Collins nucleolar phosphoprotein in the MLL-fusion nucleolar block, the block's only link to rDNA damage signalling through NBS1, and the only member whose loss causes a named human developmental syndrome

TCOF1 IS in the MLL-AF4 column, at combined p = 0.163, recovered by 5 of the seven baits (MLL-AF1p, MLL-AF4, MLL-AF9, MLL-ENL, MLL-GAS7). Negative control: ZERO spectra. AND THIS ROW IS ABOVE p = 0.05 IN THE INDEX COLUMN. It is listed only because the paper's inclusion rule is a rank cutoff - the top 300 preys per bait - and 63.9% of the MLL-AF4 column exceeds 0.05, with a maximum of 0.175. So membership of that column is a statement about rank, and for this protein the index-fusion p-value does not support an association on its own. Say so in the claim, not only here. SPECIFIC TO THIS PROTEIN: 0.163 against a column maximum of 0.175 means TCOF1 sits near the very bottom of the retained ranking for the index bait. This entry is justified by what TCOF1 does, not by this measurement, and the measurement must not be quoted as support. FUNCTIONAL SCREEN. Supplementary Data 2 (MOESM5) is the shRNA library for the negative-selection screen: 768 data rows, 128 unique gene symbols, EXACTLY six shRNAs each -- counted with openpyxl by this beat on 2026-09-21, and this protein's symbol IS in it with six shRNAs. So it was functionally tested against an MLL fusion (MLL-AF9 in MOLM-13), which is more than a co-purification. But per-gene scores are published only as the heatmaps in Fig. 2c/2d with no table anywhere in the paper or its five supplementary files, so the outcome for this protein is not recoverable: measured-not-reported. THE BLOCK, re-measured by this beat on 2026-09-21 by re-running analyses/mll-fusion-interactome-complexes/run.py. A 26-subunit nucleolar / ribosome-biogenesis set returns 15 of 26 present in the 960-protein network against 1.25 expected by chance, hypergeometric p = 6.99e-14, q(BH) = 8.39e-13 across the twelve complexes tested -- the TOP-RANKED complex in the whole interactome, ahead of the CCT/TRiC negative control (q = 1.4e-09) and the SEC positive control (q = 1.5e-09). The fifteen are FBL, FTSJ3, GNL2, LYAR, NOLC1, NOP2, NOP58, PA2G4, RRP12, RRP9, TBL3, TCOF1, UTP14A, UTP18, WDR18. BUT THE BACKGROUND IS THE ~20,000-PROTEIN PROTEOME, not the ~4,600 proteins the study actually recovered before filtering, so every q here is an UPPER BOUND on significance and it is loosest for a complex of abundant nuclear proteins -- which this one is, more than any other row in that table. AND THE POOLED NUMBER IS NOT THE PER-BAIT NUMBER. Subunits of the block recovered per bait, out of 26: MLL-AF1p 8, MLL-AF4 7, MLL-AF9 12, MLL-CBP 10, MLL-EEN 12, MLL-ENL 11, MLL-GAS7 7. The index fusion is TIED LAST. In its column there are seven members and only four at p<0.05 -- GNL2, NOP2, PA2G4 and TBL3; LYAR (0.141), NOLC1 (0.134) and TCOF1 (0.163) are above it. So the strongest complex-level signal in this entire interactome is weakest in the fusion this project studies. SYSTEM: the AP-MS host is JURKAT, a human T-ALL line, while KMT2A::AFF1 disease is B-lineage infant leukaemia; a partner requiring 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 at an FRT/Flp cassette, not the endogenous fusion. Prey came from bulk nuclear lysate after a single STREP-Tactin step, 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: "All the identified bait-prey pairs were ranked by the combined p-value. The 300 most significant interactions per bait were retained."). In the MLL-AF4 column 186 of 291 listed p-values (63.9%) exceed 0.05; the pooled rate over all baits is 26.6%, and the pooled rate must NOT be quoted for a per-bait claim. BAIT DEPTH: MLL-AF4 is the shallowest of the seven baits by spectral counts, so a low or absent MLL-AF4 count is a property of the bait (transgene expression, purification depth, normalisation) and must not be read as a weaker association. ABUNDANCE IS THE LEADING ALTERNATIVE EXPLANATION. The nucleolus is the densest compartment in the nucleus, every bait here is a tagged nuclear protein, and the complex-level analysis in this repo exists to make exactly that point: its strongest per-bait signature in the index fusion's own column is CCT/TRiC, a canonical AP-MS contaminant, at 8 of 9 subunits with 6 at p<0.05 -- BETTER represented in MLL-AF4's column than the nucleolar block is. Complex-wide enrichment is not by itself evidence of specific binding. THE ARGUMENT ON THE OTHER SIDE: all thirteen members of the nucleolar block, this protein included, have a negative control of ZERO spectra. A non-specific sticky abundant protein would be expected to appear in the control purification too, and none of them does. That is the strongest single fact about this block and it is not explained by abundance alone. SELECTIVITY: the paper's own named NON-selectivity controls are RFC1, SF3A3 and CCT3 -- knockdown inhibited MLL-wild-type K562 and HL-60 as much as MOLM-13 -- against MEN1 as the selective positive. This protein is not among them. That is NOT evidence of selectivity: only 40 of the 128 entered the MLL-r versus MLL-wild-type re-screen and the paper does not say which 40, so absence from the control list is equally consistent with never having reached the second screen. Recorded as UNKNOWN. This entry does not nominate a target. Per-bait membership re-derived by this beat on 2026-09-21 by re-running analyses/skucha-mll-fusion-interactome/run.py (both controls PASS: 128 shared by >=5 baits, 42 by all seven, MEN1 present with all seven) and analyses/mll-fusion-interactome-complexes/run.py. n_fusions and the MLL-AF4 p-value were supplied pre-verified by the coordinator from the cached MOESM4 xlsx and were independently reproduced by this beat's re-run of the complex analysis.

• IntAct has never curated this dataset, so no independent curator has re-examined these calls and no interactome-coverage metric built on IntAct can see them; the raw spectra at ProteomeXchange PXD009338 have not been reanalysed here. The authors themselves removed seven proteins from the shared set by hand as frequently observed contaminants, which concedes that a rank cutoff lets contaminants through. ProteomeXchange/PRIDE 2018
• The same paper that motivates the nucleolar reading supplies its null hypothesis: MLL-AF4 is reported predominantly nucleolar, so every abundant nucleolar protein becomes a high-probability co-purification partner on compartment grounds alone. And the prediction that reading makes fails -- if nucleolar residency of the bait drove recovery, the index fusion should pull MORE of the block than the other six baits, and it pulls the FEWEST (7 of 26, tied last with MLL-GAS7). The report is also an ectopic-overexpression system, which this project treats as weak evidence about an endogenous protein. Siemund AL et al. 2022

HUMAN cultured cells, 2014 Nature Cell Biology. Not leukaemia, not a fusion, not haematopoietic, and no KMT2A protein appears anywhere in it. Read from the abstract only; the in-trans mechanism and the treacle-dependence of NBS1 nucleolar accumulation are the abstract's own stated results and the supporting figures were not opened. Cited because it is the one function in this entire nucleolar block that is a priori relevant to KMT2A fusion biology rather than generically relevant to cell growth - and that relevance is a reason to investigate, NOT a finding. No experiment anywhere connects this mechanism to any KMT2A fusion.

• The relevance argument cuts the other way too. Damage-induced rDNA silencing is a general genome-integrity response present in every cell type, so its presence in a leukaemia is expected rather than informative. And this graph has a documented failure mode of treating a mechanism that COULD connect to the index disease as though it did: the entry that flagged it is the standing nucleolar-convergence absence, which is classified measured-not-analysed precisely because the connection has never been tested on data that exist. Skucha A et al. 2018

XENOPUS OOCYTES and MOUSE embryos, 2005 Human Molecular Genetics. Not human cells, not leukaemia, not a fusion. Read from the abstract only. The UBF interaction and the rDNA-transcription role are stated in this paper's own background as established prior knowledge rather than as its result, so for those two facts this citation is a secondary pointer and the primary source was not traced by this beat - flagged rather than hidden. Its own result is the 2'-O-methylation finding, and the Tcof1+/- mouse strains used exhibit a lethal phenotype, so the methylation deficit is measured in a severely affected background.

• Treacle's best-known consequence in humans is Treacher Collins syndrome, a craniofacial disorder from haploinsufficiency - a neural-crest phenotype with no reported haematopoietic component. So unlike TBL3, whose zebrafish mutant loses T cells and HSPCs, TCOF1's loss-of-function phenotype gives NO reason to expect a blood-specific requirement, and this entry does not claim one. Larsen DH et al. 2014

A counted negative with a date, the exact query, the querytranslation and the tool. Bounded by TITLES AND ABSTRACTS ONLY - supporting figures not searched (rule 80), which matters more than usual here because a damage-induced rDNA-silencing panel is exactly the kind of supporting figure a paper is not titled after. Bounded also by the name list: TCOF1, treacle, Treacher Collins. 'Treacle' is an ordinary English word and was included deliberately for recall; the intersection is empty so no title-screening was needed. The bare operand returns 249, so the instrument works for this symbol.

• An absence of publication is not an absence of measurement. TCOF1 is one of the 128 conserved interactors shRNA-screened in MLL-AF9 MOLM-13 with six shRNAs in the source paper itself: measured-not-reported, not never-measured. Skucha A et al. 2018

Database record fetched live 2026-09-21. The subcellular-location comment is a single line, 'Nucleus, nucleolus', with one ECO:0000269 citation (PubMed 12777385) which this beat did NOT open - so per rule 91 it establishes that a curator read an experiment and nothing more. Note the entry name is TCOF_HUMAN, not TCOF1_HUMAN. Recorded here chiefly as a BOUNDED ABSENCE on the sub-nucleolar question: for a protein that works with UBF at rDNA, a fibrillar-centre assignment is what the function implies, and neither UniProt nor the literature this beat read states it. This beat therefore does NOT assert it.

• The single-citation localisation is thinner than it looks for a protein this large and this well studied, and TCOF1's 1488 residues with extensive phospho-regulated repeats make it a protein whose distribution could plausibly differ between conditions. A one-line database localisation should not be the basis of a sub-nuclear claim in either direction. Larsen DH et al. 2014