RRP9 / U3-55K (O43818) - the U3 snoRNP-specific core protein in four MLL-fusion interactomes but NOT the index fusion's, and the block's only member with a published acetylation switch

THE INDEX FUSION DID NOT RECOVER THIS PROTEIN. RRP9 is absent from the MLL-AF4 column of Supplementary Table 5 entirely -- there is no p-value and no spectral count for it under the index bait. It is an MLL-FUSION interactor, not a demonstrated KMT2A::AFF1 interactor, and nothing in this entry should be read as a KMT2A::AFF1 contact. The 4 baits that did recover it are MLL-AF9, MLL-CBP, MLL-EEN, MLL-ENL. Negative control: ZERO spectra. THE HEADLINE OF THIS ENTRY, AND IT BELONGS IN EVERY QUOTATION OF IT: this protein is NOT in the MLL-AF4 column. It is an MLL-FUSION interactor and NOT a demonstrated KMT2A::AFF1 interactor. Six of the eleven nucleolar-block proteins written by this beat are in that position - RRP12, WDR18, UTP14A, RRP9, UTP18 and FTSJ3. The 'thirteen-protein nucleolar block' is a POOLED statement over seven baits; in the index fusion's own column there are seven members and four below p = 0.05. AND IT IS BELOW THE SCREEN THRESHOLD TOO: the source paper's shRNA library covers only the 128 interactors shared by at least five baits, so this protein was never functionally tested against any MLL fusion either. Both of its records - binding and function - are empty for the index fusion. SPECIFIC TO THIS PROTEIN: its per-bait pattern is IDENTICAL to UTP14A's. That may be a shared sub-network across those four fusions or a shared detection-depth pattern across those four purifications, and this beat cannot distinguish them. Note also that the U3 snoRNP cores FBL and NOP58 are in this network but under DIFFERENT baits (MLL-CBP and MLL-AF1p respectively), so the U3 particle is not recovered as a unit under any single bait. FUNCTIONAL SCREEN -- NOT SCREENED. The shRNA library (MOESM5) covers the 128 interactors shared by at least five of the seven baits: 768 rows, 128 symbols, exactly six shRNAs each, counted with openpyxl by this beat on 2026-09-21. This protein's symbol is NOT in that library, because it falls below the five-bait threshold. So unlike the seven-plus-bait members of this block it has never been functionally tested against any MLL fusion, even in the source paper. That is a stronger absence than 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, 2016 Nature Communications. Not leukaemia, not a fusion, not haematopoietic, and no KMT2A protein appears in it. Read from the abstract only. Cited for what RRP9 is and how it is regulated. The adjacency to this graph's acetylation-cycle work is noted deliberately as an ADJACENCY: SIRT7 has no entry in this graph, no fusion appears in this paper, and the index fusion did not recover RRP9, so nothing here is a link.

• An acetylation switch on an RNA-binding contact is a general ribosome-biogenesis regulatory mechanism present in every cell, so its existence gives no reason to expect a relationship with a leukaemia fusion. The temptation this entry is guarding against is specific and named: this graph is full of acetylation biology, and a deacetylase acting on a protein in the fusion interactome is exactly the kind of coincidence that gets written up as a convergence without a test. Skucha A et al. 2018

Database record fetched live 2026-09-21. The location comment is a single line, 'Nucleus, nucleolus', with ECO:0000269 citing PubMed 12429849, 26867678, 34516797 and 9418896 - four experimental citations, more than most members of this block, but this beat opened only 26867678, so per rule 91 the codes establish that curators read experiments and not that any of these is the founding or best observation. NOTE the entry name is U3IP2_HUMAN and the protein name contains neither 'RRP9' nor the string 'U3-55K' in the leading position - reading the entry name back would make a correct lookup look wrong, which is rule 69's DPF2/REQU_HUMAN failure mode. NO sub-nucleolar assignment: a bounded absence.

• Four experimental citations for 'nucleolus' is a well-supported compartment call and simultaneously shows how little a compartment call delivers here: the same four citations produce no sub-compartment, no condition-dependence and no cell-type resolution. For a block whose entire interest is sub-nuclear, the depth of the nucleolar call is not the quantity that matters. Chen S et al. 2016

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). The hyphenated form 'U3-55K' was searched as a quoted phrase; per the hyphenation rule the unhyphenated 'U355K' is a different string and was NOT searched separately, which is a stated limit of this bound. The complex-name form was also considered: 'U3 snoRNP' as a phrase was not run against the KMT2A clause, so per rule 64 this absence is bounded at the subunit level and not at the complex level. Bare operand 31.

• As for UTP14A, the usual 'screened but not reported' counter does NOT apply: RRP9 is at four baits, below the five-bait library threshold, so it was never functionally tested against an MLL fusion at all. Its absence class is never-measured, not measured-not-reported. Skucha A et al. 2018