ELOA / TCEB3, Elongin A (Q14241) - a Pol II elongation factor in the pan-MLL-fusion core, ALONE, with none of its own complex and a non-zero negative control

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 (buffer C420, 420 mM NaCl) 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."). Measured by this beat from the cached MOESM4 xlsx on 2026-09-21: 545 of the 2,049 per-bait p-values in the table (26.6%) exceed 0.05; within the MLL-AF4 column alone it is 186 of 291 (63.9%), and that column's maximum p is 0.175. MEASURED BY THIS BEAT, 2026-09-21, from the cached MOESM4 xlsx: across all 42 pan-fusion proteins the MLL-AF4 column carries the LOWEST total spectral counts of the seven baits for 34 of 42, and is sixth or seventh for 40 of 42. That is a bait-level property (transgene expression, purification depth or the DDX5/DDX17 GLM normalisation), not a statement about any one prey, so a low MLL-AF4 count must not be read as a weaker association than the same protein's count under another bait. For TCEB3 the MLL-AF4 total (13 spectra over two replicates) is rank 6 of the seven baits, against a maximum of 33 under another bait. All seven per-bait values, p (replicate spectral counts): MLL-AF1p 0.0280 (8|3); MLL-AF4 0.0059 (7|6); MLL-AF9 0.0015 (14|13); MLL-CBP 0.0093 (4|11); MLL-EEN 0.0619 (12|7); MLL-ENL 0.0006 (13|20); MLL-GAS7 0.0081 (14|11). SPECIFIC TO THIS PROTEIN, AND IT IS THE MOST IMPORTANT CAVEAT HERE: the negative control for TCEB3 is 0|1, not 0|0 - one control replicate returned a spectrum. Only ten of the 42 pan-fusion proteins have a non-zero negative control and this is one of them. Separately, MLL-EEN's p of 0.0619 is the only value above 0.05 anywhere in this tranche's per-bait table and is present only because of the rank cutoff. And ELOB, ELOC and CUL5 are absent from the network at any n, so the subunit recovered is the one that is not active on its own. SELECTIVITY: the paper's 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. Only 40 of the 128 ('the 40 candidate genes with the highest confidence') entered that MLL-r versus MLL-wild-type re-screen, and the paper does not list which 40. This protein is not named among the controls, but that is NOT evidence of selectivity: it is equally consistent with the protein never having reached the second screen. Recorded as unknown, and this entry must not be read as nominating a target. Values re-read from the cached xlsx on 2026-09-21 and cross-checked against analyses/skucha-mll-fusion-interactome/results.json, whose two controls (128 proteins shared by >=5 baits and 42 by all seven, both matching the paper; MEN1 present with all seven) both PASS on today's re-run.

• 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 'either frequently observed contaminants or ... not detected in human hematopoietic cell lines', which concedes that the rank cutoff lets contaminants through - and ACTB survived that filter, sitting in the pan-fusion 42 with a NON-ZERO negative control (3|3). Ten of the 42 carry a non-zero negative control: PSIP1 0|5, MCM2 0|2, ACTB 3|3, CSNK2A1 2|0, RUNX1 0|2, SF3A3 0|3, TCEB3 0|1, CHD4 2|2, SMARCC1 1|0, ZNF512 0|2 - counted by this beat from the xlsx neg_ctrl column, 2026-09-21. ProteomeXchange/PRIDE 2018
• The paper states that 'more than one third of proteins in the network of conserved MLL-fusion protein interaction partners were identified as essential in recent genome-wide screens'. Abundance and essentiality both raise the odds of recovery in an AP-MS experiment, so membership in the conserved core is partly a statement about how much of a protein is present in a nucleus, not only about what it binds. Skucha A et al. 2018

1995 Science; a reconstituted in vitro transcription system with recombinant subunits, which is the right assay for the claim but says nothing about occupancy or rate in a living cell - and the 2021 in vivo study below reports that EloA does NOT substantially enhance Pol II elongation rate in cells. Not haematopoietic, not a fusion system. Read from the abstract. The subunit architecture is the load-bearing part for this entry, because ELOB and ELOC are absent from the interactome.

• In mouse embryonic stem cells EloA localises broadly to Pol II genes and active enhancers but does NOT substantially enhance elongation rate in vivo; its deletion causes accumulation of transcripts from a subset of enhancers rather than a global elongation defect. So the in vitro pausing-suppression activity should not be carried straight into a cellular mechanism. Ardehali MB et al. 2021

MOUSE embryonic stem cells, 2021; not human, not haematopoietic, not a fusion system. The condensate claim is in vitro, and this project's standing rule applies: in-cell punctate behaviour is compatible with binding to spatially clustered sites, and neither 1,6-hexanediol nor classical FRAP distinguishes the two - the discriminating assay (calibrated half-bleaching for internal mixing) was not performed. Read from the abstract. Cited here mainly for the negative - that EloA is broadly distributed across active transcription and does NOT act as a rate-limiting elongation factor in vivo - because that is the leading alternative explanation for its presence in a chromatin-bait purification.

• If EloA is at thousands of genes and many enhancers, then any chromatin-associated bait purified from nuclear lysate has a high prior probability of recovering it, and the pan-fusion pattern (seven structurally different baits, all positive) is exactly what a broadly distributed chromatin protein produces. The in vitro pausing activity is what makes the story attractive and is not what the cellular data show. Aso T et al. 1995

1996 Science; in vitro transcription assays. Cited here for ONE thing: that the founding characterisation of a KMT2A fusion partner explicitly frames it as the functional counterpart of Elongin, which is why an Elongin subunit in a KMT2A-fusion purification is worth writing down rather than discarding. It is an analogy between two elongation factors, not evidence that ELOA does anything in this disease, and this entry does not treat it as more. Note also that ELL's own biology in this graph is as a FUSION PARTNER, a different phenomenon from being an interactor. Read from the abstract.

• The functional resemblance runs the wrong way for the inference one would like to make: ELL matters in this disease because it is FUSED to KMT2A and contributes its own domains to a chimera, not because wild-type ELL binds KMT2A. A shared biochemical activity between ELL and Elongin A says nothing about whether Elongin A associates with a KMT2A fusion for a reason. Skucha A et al. 2018