NOP2 / NSUN1 / p120 (P46087) - the 28S rRNA m5C4447 methyltransferase in the MLL-fusion nucleolar block, present in the index fusion's column at p = 0.0223, and the gene whose PubMed token is two-thirds contaminated by its NSUN paralogues

NOP2 IS in the MLL-AF4 column, at combined p = 0.0223, recovered by 5 of the seven baits (MLL-AF1p, MLL-AF4, MLL-AF9, MLL-EEN, MLL-ENL). Negative control: ZERO spectra. Second-lowest MLL-AF4 p-value of the eleven nucleolar-block proteins this beat wrote, and one of only four block members below 0.05 in that column. 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, 2022 Nucleic Acids Research, miCLIP-seq plus complex purification. Not leukaemia, not a fusion, no haematopoietic system. Read from the abstract only - the substrate position and the non-catalytic snoRNP finding are the abstract's own stated results, and the supporting figures were not opened. Cited for what NOP2 does, which is the independent credential this entry needs; it says nothing about KMT2A. The box C/D link is used here to argue that the nucleolar block has internal structure, which is a statement about the block and not about the fusion.

• A protein that forms complexes with box C/D snoRNPs is a protein that travels with a large, abundant, tightly associated particle. FBL and NOP58 - the box C/D cores - are themselves in this same 960-protein network. That makes the nucleolar block MORE likely to be recovered as a unit by any nuclear bait, specifically bound or not, and so the internal coherence of the block cuts in favour of the abundance explanation as much as against it. Recovering a whole coherent particle is what a contaminant complex does: the CCT/TRiC chaperonin is in this network at 8 of 9 subunits for exactly that reason. Skucha A et al. 2018

Database record fetched live 2026-09-21. The location comment reads 'Localizes predominantly in the nucleolus and to a smaller extent in the nucleus', ECO:0000269 citing PubMed 12429849, 26196125, 36161484 and 8089149 - none of which this beat opened except 36161484, so per rule 91 the codes establish that a curator read an experiment, not that any of those papers is the founding observation. NO sub-nucleolar assignment - no fibrillar centre, no dense fibrillar component, no granular component - is given by UniProt, and this beat found none in the literature it read. That is a BOUNDED ABSENCE recorded as such, and it is a real gap for a protein whose substrate is 28S rRNA, which is processed in the DFC and GC.

• Recorded as an explicit non-contradiction rather than a dispute: UniProt's own record gives NOP2 a general nuclear pool as well as the nucleolar one (ECO:0000269 PubMed 36161484), so a protein pool outside the nucleolus exists and a nuclear-lysate co-purification could in principle have captured that pool rather than the nucleolar one. Nothing in the AP-MS experiment distinguishes them. Skucha A et al. 2018

Measured live 2026-09-21 by this beat, counts quoted above. The 67.3% figure is an intersection count against a fixed paralogue name list (NSUN2, NSUN4, NSUN5, NSUN6, NSUN7 and the literal phrase 'NOP2/Sun'), so it is a FLOOR on contamination, not a point estimate: an NSUN paper that names neither a paralogue nor the family string is not counted. The one returned KMT2A-intersection record, PMID 41816830, was FETCHED AND TITLE-CHECKED, not assumed - its title is 'NSUN2-FOSB reciprocity facilitates leukemogenesis in an m5C-dependent manner by increasing BCL2L1 expression', it studies NSUN2 in an MLL-AF9 murine model, and it matched only because its first sentence spells out 'NOP2/Sun RNA methyltransferase family member 2 (NSUN2)'. Bounded by titles and abstracts only.

• This is a RETRIEVAL finding, not a biological one, and it must not be over-read in the other direction either. NSUN2 is a genuine paralogue with a genuine MLL-AF9 leukaemia stem-cell phenotype, and the existence of that result is a reason to ask whether NOP2/NSUN1 has been tested in the same system - not a reason to treat the family as interchangeable. NSUN2's substrate is mRNA m5C; NOP2's is 28S rRNA position 4447. They are different enzymes. Zhou B et al. 2026