WAC — the adaptor that hands RNF20/RNF40 to RNA polymerase II, and the only member of this axis whose knockdown alone killed MLL-rearranged ALL cells

This is a prediction, not a measurement. No one has seen this protein in this shape. The colours say how much the software trusts itself, and that is worth reading before anything else — the orange stretches are places the model is effectively saying this part has no fixed shape.

• Germline heterozygous WAC loss causes an intellectual disability syndrome. Pharmacological WAC inhibition in infants - the population this disease affects - would be targeting a gene whose partial loss during development is known to damage the brain.
• WAC has no KMT2A selectivity in DepMap, so the case for it rests entirely on one knockdown clause in one paper.
• WAC also participates in mTORC1 regulation through R2TP/TTT chaperone complexes, so it is not a clean single-pathway node and an inhibitor would have metabolic effects unrelated to chromatin.
• Because WAC couples the ligase to Pol II, inhibiting it removes H2Bub preferentially from the most actively transcribed genes - which in a proliferating normal progenitor are the ribosomal and cell-cycle genes, not the leukaemic programme.

1. Is the WAC knockdown lethality in MLL-rearranged ALL selective? The single reported experiment has no non-MLL comparator, and DepMap says it is not - the cleanest resolution is a WAC knockdown in matched KMT2A-rearranged and germline-KMT2A B-ALL lines with the same guide.
2. Do the domains split the function? A WW-domain point mutant that cannot bind Pol II would separate transcription-coupled H2Bub from bulk H2Bub, and would say whether it is the coupling or the mark that MLL-rearranged cells need.
3. Do individuals with DeSanto-Shinawi syndrome have any measurable haematopoietic phenotype? Ten reported individuals is enough to notice a gross abnormality and not enough to exclude a subtle one; the cohort exists and could be asked.

1. E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

   WAC was identified by protein affinity purification as a functional partner of RNF20/40; depletion of WAC abolishes H2B ubiquitination; WAC interacts with RNF20/40 through its C-terminal coiled-coil region and promotes RNF20/40 E3 ligase activity for H2B ubiquitination; the N-terminal WW domain of WAC recognises RNA polymerase II; and during transcription WAC targets RNF20/40 to associate with the Pol II complex for H2B ubiquitination at active transcription sites.

   WAC, a functional partner of RNF20/40, regulates histone H2B ubiquitination and gene transcription. · Zhang F, Yu X · Mol Cell 2011
   PMID 21329877DOI
   ▸What this evidence cannot show

   Abstract read in full; full text not read. Non-leukaemic human cells. 'Abolishes' is the abstract's word for the effect of WAC depletion on H2Bub; whether that means complete loss or loss below detection is not resolvable from the abstract.

   ▸Evidence that argues against this (1)

   • WAC depletion abolishing H2B ubiquitination identifies WAC as required for the modification in that system, and the entry uses it to position WAC as a regulatory partner. Abolition is a strong phenotype that is equally consistent with WAC being structurally required for complex integrity, which the later interface work supports. Nucleic Acids Research 2026
2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   In MLL-rearranged ALL, panobinostat's anti-leukaemic activity involves depletion of H2B ubiquitination via suppression of the RNF20/RNF40/WAC E3 ligase complex, described as a pivotal pathway for MLL-rearranged leukaemic maintenance, and knockdown of WAC phenocopies loss of H2B ubiquitination with concomitant cell death induction.

   The HDAC inhibitor panobinostat (LBH589) exerts in vivo anti-leukaemic activity against MLL-rearranged acute lymphoblastic leukaemia and involves the RNF20/RNF40/WAC-H2B ubiquitination axis. · Garrido Castro P, van Roon EHJ, Pinhancos SS, Trentin L, Schneider P, Kerstjens M, Te Kronnie G, Heidenreich O, Pieters R, Stam RW · Leukemia 2018
   PMID 28690313DOI
   ▸What this evidence cannot show

   Abstract read in full; full text not read. The WAC knockdown experiment is described in one clause of the abstract with no cell lines, no comparator non-MLL line and no effect size. Cell death after knocking down a transcription-coupled cofactor is not specific to MLL-rearranged cells unless a comparator shows otherwise, and none is described.

   ▸Evidence that argues against this (1)

   • DepMap gives WAC no KMT2A selectivity at all (difference -0.011, rank 7,779 of 17,728). If WAC knockdown kills MLL-rearranged ALL cells because of an MLL-specific requirement, that requirement is not visible across 11 KMT2A-rearranged versus 43 other leukaemia lines. Broad Institute DepMap; Cellosaurus; Open Targets Platform; analysis run by this project 2026
3. E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

   A crystal structure of yeast Bre1-Lge1 and an AlphaFold model of RNF20/RNF40 bound to WAC reveal extensive interfaces sharing structural homology but completely different sets of key electrostatic interactions that encode binding specificity, and these interactions are critical for the Bre1-catalysed H2B monoubiquitination reaction and the processes it regulates.

   Structural insights into the Bre1-Lge1 and RNF20/RNF40-WAC interactions critical for H2B ubiquitination. · Shi M, Wang X, Zhang H, Wen Y, Liu Q, Chen P, Chen X, Xiang S · Nucleic Acids Res 2026
   PMID 41533567DOI
   ▸What this evidence cannot show

   Abstract read in full; full text not read. The human RNF20/RNF40-WAC structure is an **AlphaFold prediction**, not experimental; only the yeast complex was crystallised, and the functional validation described is in yeast. No PDB id is asserted because the abstract states none and this beat did not verify one.

   ▸Evidence that argues against this (1)

   • The RNF20/RNF40-WAC arrangement is an AlphaFold model, not an experimental structure, and 'extensive interfaces sharing structural features' with the yeast complex is a comparison between a prediction and a crystal structure. The entry should mark which half is observed. Nucleic Acids Research 2026
4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset

   In the genome-wide DepMap KMT2A-selectivity scan, WAC has a KMT2A-rearranged mean gene effect of -0.393 against -0.383 in other leukaemia lines, a difference of -0.011 and a rank of 7,779 of 17,728, on a pan-essentiality of -0.389 across 1,208 lines.

   DepMap CRISPR (Chronos) genome-wide KMT2A-selectivity scan of 17,728 protein-coding genes, 11 Cellosaurus-annotated KMT2A-rearranged leukaemia lines vs 43 other leukaemia lines · Broad Institute DepMap; Cellosaurus; Open Targets Platform; analysis run by this project (analyses/depmap-kmt2a-selective-scan-full) · Database and derived analysis 2026
   ▸What this evidence cannot show

   Eleven KMT2A-rearranged lines, AML-weighted, none infant-derived; the panobinostat result that motivates interest in WAC is from infant/paediatric B-ALL models that this panel does not contain.

   ▸Evidence that argues against this (1)

   • SCAN CONFOUND: this number comes from the project's genome-wide KMT2A-selectivity scan, whose index arm is MYELOID-ENRICHED (8 AML lines against 5 B-ALL). A gene whose requirement differs by lineage is mis-scored in BOTH directions by that design — CEBPA ranks 25 genome-wide with no dependency at all in KMT2A-rearranged B-ALL, and conversely a gene required in one lineage and not the other can average to apparent non-selectivity. See `ana-lineage-confound-myeloid-tf-dependencies`. WAC at -0.393 against -0.383 is a difference of 0.01, which is within noise on this scale regardless of lineage composition — so this item's real content is that the scan cannot resolve WAC either way, not that WAC is non-selective. Oncofusion knowledge graph (internal analysis) 2026
5. E5established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper

   Ten individuals with de novo WAC mutations, all but one expected to cause loss of function, share mild intellectual disability, hypotonia, behavioural problems and distinctive facial dysmorphism, defining a clinically recognisable syndrome overlapping the 10p12p11 microdeletion syndrome; neuronal knockdown of the Drosophila orthologue impairs habituation learning.

   De novo loss-of-function mutations in WAC cause a recognizable intellectual disability syndrome and learning deficits in Drosophila. · Lugtenberg D, Reijnders MR, Fenckova M, Bijlsma EK, Bernier R, van Bon BW, Smeets E, Vulto-van Silfhout AT, Bosch D, Eichler EE, Mefford HC, Carvill GL, Bongers EM, Schuurs-Hoeijmakers JH, Ruivenkamp CA, et al. · Eur J Hum Genet 2016
   PMID 26757981DOI
   ▸What this evidence cannot show

   Abstract read in full; full text not read. Germline heterozygous loss from conception is not a model for pharmacological inhibition in an infant already born, and the absence of a reported haematological phenotype in ten individuals is weak evidence of haematological safety. The syndrome is now commonly called DeSanto-Shinawi syndrome; that name is not used in this paper's abstract.

   ▸Evidence that argues against this (1)

   • De novo WAC loss-of-function causing an intellectual disability syndrome is a germline developmental phenotype. It shows the gene is dose-sensitive in human development and carries no information about whether a KMT2A-rearranged blast requires it. European Journal of Human Genetics 2016
6. E_q95_wac_loc1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

   WAC's UniProt compartment annotation is a CIRCULAR two-record loop: human Q9BTA9 carries 'Nucleus speckle' on a single ECO:0000250 attributed to mouse Q924H7, and mouse Q924H7 carries 'Nucleus' on a single ECO:0000250 attributed straight back to human Q9BTA9 - each record cites the other for one of its two terms. The mouse record's speckle call is the only one with an experimental code, ECO:0000269 PubMed 11827461, and the human record's note 'In distinct nuclear speckles. Colocalizes with pre-mRNA processing complexes' is itself by-similarity from mouse. The two proteins are 647 and 646 residues, one residue apart.

   UniProtKB Q9BTA9 (WAC_HUMAN) and Q924H7 (WAC_MOUSE), SUBCELLULAR LOCATION comments with evidence codes and sources, both fetched live 2026-09-22 · UniProt Consortium · Databases 2026
   ▸What this evidence cannot show

   A statement about the two database records, not about the biology. The one-residue length difference means verify-accessions.py cannot detect a human-for-mouse substitution in this pair, which is the same exposure tranche 5 recorded for CTR9/Ctr9 (both 1,173 aa) and CSNK2A2/Csnk2a2 (both 350 aa) - now the third such pair in this series, and the tightest.

   ▸Evidence that argues against this (1)

   • AND HERE THE CHAIN INVERTS IN THE PROTEIN'S FAVOUR, WHICH IS THE OPPOSITE OF THE CTR9 CASE AND THE SECOND INSTANCE OF A SHAPE TRANCHE 5 FOUND FOR NASP. Opening the by-similarity chain does not lead to a weak rodent observation; it leads to a paper whose TITLE IS THE LOCALISATION RESULT and whose subject is the HUMAN gene: 'WAC, a novel WW domain-containing adapter with a coiled-coil region, is colocalized with splicing factor SC35', which identifies WAC at human chromosome 10p11.2-10p12.1 and colocalises it by immunofluorescence with SC35, the canonical nuclear-speckle marker. So a human experimental result reaches the human record only as an ECO:0000250 propagation from mouse. A strict discard-by-similarity filter would throw away a real human measurement of the exact compartment claimed - which is precisely the error tranche 5 caught itself about to make on NASP. Xu GM et al. 2002
7. E_q95_wac_loc2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   WAC's nuclear-speckle residence is now domain-resolved and mechanistic: WAC is localised to nuclear speckles VIA ITS WW DOMAIN, forms biomolecular condensates via its C-terminal coiled-coil domain, and acts as a scaffold that integrates RBM12 into nuclear speckles where RBM12 potentially interacts with the spliceosomal U5 snRNP; knockdown of RBM12 or deletion of the WAC coiled-coil domain alters splicing outcomes and raises the short BECN1-S variant, which upregulates mitophagy.

   Nuclear Condensates of WW Domain-Containing Adaptor With Coiled-Coil Regulate Mitophagy via Alternative Splicing. · Wang J, Fan Y, Luo G, Xiong L, Wang L, Wu Z, Wang J, Peng Z, Rosen CJ, Lu K, Jing J, Yuan Q, Zhang Z, Zhou C · Adv Sci (Weinh) 2025
   PMID 39840526DOI
   ▸What this evidence cannot show

   The two functional halves of WAC now sit in two different compartments by two different domains, and this entry must not collapse them: the WW domain both recognises RNA polymerase II for the RNF20/40 H2B-ubiquitination function and targets WAC to speckles, while the coiled-coil both binds RNF20/40 and drives condensate formation. That is a genuine ambiguity in the primary literature rather than a gap - no source has asked whether the Pol-II-bound and the speckle-resident pools are the same molecules.

   ▸Evidence that argues against this (1)

   • THE CONDENSATE HALF OF THIS CLAIM DOES NOT MEET THIS GRAPH'S OWN STANDARD AND SHOULD NOT BE PROPAGATED AS PHASE SEPARATION. The paper frames its result as liquid-liquid phase separation, but the methodology this project holds itself to is that 1,6-hexanediol sensitivity and classical FRAP recovery BOTH fail to distinguish LLPS from binding to spatially clustered sites, and that only model-free calibrated half-bleaching measuring internal mixing discriminates them; worse in a chromatin context, 1,6-hexanediol rapidly immobilises and condenses chromatin in living cells, doing something close to the opposite of what the assay assumes. Nuclear speckles are also among the most site-dense structures in the nucleus - a splicing-factor-rich compartment is exactly where clustered binding looks like a droplet. So this entry adopts the SPECKLE assignment, which rests on marker colocalisation and domain mapping, and records the condensate interpretation as the authors' rather than as established. Muzzopappa F et al. 2022
8. E_q95_wac_loc3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

   WAC's functional address on chromatin is OCCUPANCY at active transcription sites and it is a different quantity from the speckle compartment: WAC's N-terminal WW domain recognises RNA polymerase II, WAC targets RNF20/40 to associate with the Pol II complex for H2B ubiquitination at active transcription sites, WAC depletion abolishes H2B ubiquitination, and WAC-dependent transcription is required for cell-cycle checkpoint activation in response to genotoxic stress - and the abstract of that paper, which is UniProt's only ECO:0000269 for human WAC's 'Nucleus', describes no microscopy at all.

   WAC, a functional partner of RNF20/40, regulates histone H2B ubiquitination and gene transcription. · Zhang F, Yu X · Mol Cell 2011
   PMID 21329877DOI
   ▸What this evidence cannot show

   Affinity purification, ubiquitination assays and transcription readouts - so this establishes where WAC ACTS along a gene, not which compartment it occupies, and the two answers are not interchangeable (the same distinction this tranche records for SPT6). Brief rule 80 applies to the claim that the paper contains no microscopy: that is bounded by the abstract, and a colocalisation panel could exist in a figure.

   ▸Evidence that argues against this (1)

   • THESE TWO ADDRESSES ARE IN TENSION AND THE TENSION IS SUBSTANTIVE RATHER THAN BOOKKEEPING. Nuclear speckles are classically depleted of active Pol II transcription units at their cores and enriched in splicing factors at their peripheries, while H2B ubiquitination by RNF20/40 happens on the bodies of genes being transcribed. A protein cannot be doing both jobs in the same place at the same time, so either the speckle pool is a reservoir that the WW domain also uses for Pol II capture at speckle peripheries, or there are two pools. The measurement that would settle it - endogenous WAC co-stained for SC35 and for elongating Pol II (Ser2P), with quantification of overlap - has never been done, and both published addresses came from experiments that could not see the other one. Wang J et al. 2025
9. E_q95_wac_loc4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database

   Bounded 2026-09-22: no WAC compartment has been measured in any KMT2A-fusion context, and WAC's entire subnuclear literature is two papers. The gene clause over WAC and KIAA1844 returns 617 records and intersects the nine-term KMT2A/MLL fusion clause at 3; with a localisation clause it returns 20 and with the fusion clause added 0; with a subnuclear clause it returns 2 - which ARE the two speckle papers, 11827461 and 39840526 - and with the fusion clause added 0. The speckle-plus-SC35 sub-query also returns exactly those 2.

   NCBI E-utilities esearch db=pubmed; every count stored with the querytranslation read back, in data.localization_bounded_absence · NCBI E-utilities · Databases 2026
   ▸What this evidence cannot show

   Titles and abstracts only; supporting figures not searched (rule 80). WAC is a short, word-like token and the 617 records include unrelated uses, but the direction of that error is inflation of the operand control rather than of any positive claim: the subnuclear count of 2 was title-checked to 2 of 2 on topic, and the fusion-context zeros stand against a wider net than labelled.

   ▸Evidence that argues against this (1)

   • RULE 64 CHANGES WHAT THIS ZERO MEANS AND THE COMPLEX FORM WAS RUN. WAC reaches this project as the adaptor that hands RNF20/RNF40 to Pol II, so the question a KMT2A::AFF1 argument needs is not where WAC sits but whether the H2B-ubiquitination axis is engaged by the fusion - and that literature is reachable only through RNF20/RNF40, H2Bub and the complex name, never through WAC. This entry's own body already records that WAC knockdown alone kills the mark. So the defensible statement is narrow: nobody has published a WAC-resolved compartment or occupancy measurement in a fusion-driven cell. The broader-sounding 'the H2Bub axis is unstudied in KMT2A leukaemia' would be false, and the ATXN7L3 entry amended in this same tranche is the DUB side of the same axis. Zhang F et al. 2011

• causes →H2BK120ub (H2Bub1) — the ubiquitin tag on histone H2B that licenses H3K79 methylation, and the mark this graph was missing

  adaptor required for H2B ubiquitination; depletion abolishes the mark

• binds →RNF20 (BRE1A) — the H2B ubiquitin ligase that MLL-rearranged leukaemia needs, and that DepMap says every other cancer line needs just as much

  C-terminal coiled-coil of WAC binds RNF20/RNF40 and promotes ligase activity

• part of →Mechanism class 1 — chromatin and elongation hijack (KMT2A-r, NUP98-r)

  WW domain binds Pol II, coupling H2B ubiquitination to elongation

• ← inhibitsPanobinostat lowers H2B ubiquitination in MLL-rearranged ALL by suppressing RNF20/RNF40/WAC — the only clinical-stage agent that reaches this axis, and its one ALL trial was stopped for lack of efficacy

  panobinostat suppresses the RNF20/RNF40/WAC complex; WAC knockdown phenocopies H2Bub loss and kills

• related to →Nuclear speckles — the compartment everyone assumes KMT2A::AFF1 uses, on evidence that skips AFF1 itself

  A REAL speckle assignment, and the counter-example to CTR9 in tranche 5. WAC's UniProt speckle term is ECO:0000250 from mouse, but opening the chain leads to a HUMAN paper titled for the result - WAC colocalised with SC35 by immunofluorescence (PMID 11827461) - and a 2025 study localises WAC to speckles via its WW DOMAIN and has it scaffold RBM12 there (PMID 39840526). The LLPS framing is not adopted (Q95 2026-09-22)

• related to →Transcription factories and Pol II clusters - no KMT2A::AFF1 imaging, condensate evidence for SEC and MLL-ENL, and 3D-FISH that actively contradicts the factory story for t(4;11)

  WAC's SECOND address, in tension with the speckle one: its WW domain recognises RNA polymerase II and targets RNF20/40 to the Pol II complex for H2B ubiquitination at active transcription sites (PMID 21329877). Speckle cores are depleted of active transcription units, so either there are two pools or the WW domain works at speckle peripheries - nobody has co-stained SC35 and Ser2P Pol II for WAC (Q95 2026-09-22)

• related to →CTR9 — a PAF1C subunit the field assumes is a fusion partner, with no paper that tested it

  Third cross-species two-step compartment chain in this series and the tightest length pair: human WAC 647 aa against mouse Wac 646 aa, ONE residue apart, so verify-accessions.py cannot catch a swap (CTR9 was 1,173/1,173, CSNK2A2 350/350). WAC's chain INVERTS in the protein's favour where CTR9's did not - the source is a human paper titled for the localisation (Q95 2026-09-22)

• ← related toATXN7L3 — the shared adaptor that actually sets H2Bub levels, and a KMT2A-selectivity hit nobody in this field has looked at

  ERASER-ADAPTOR AND WRITER-ADAPTOR OF ONE MARK, and neither has a compartment measurement. ATXN7L3 is the SAGA DUB-module adaptor that sets H2Bub1 levels; WAC is the adaptor that hands RNF20/RNF40 to Pol II to deposit it. Both amended in this tranche; WAC has nuclear speckles by marker colocalisation, ATXN7L3 has nothing subnuclear at all (1 record, containing no compartment) (Q95 2026-09-22)