AKAP95's subnuclear addresses - nuclear matrix, nucleolus, and dynamic foci - and the finding that the famous one is the one its MLL-linked function does not need
also called AKAP95 subnuclear localization · AKAP8 nucleolus · AKAP95 NMTS
AKAP95 sits in three places inside the nucleus: on the nuclear scaffold, in the nucleolus where ribosomes are built, and in small mobile droplets. The scaffold address is the one it is famous for, and it is the one it can do without when it helps switch genes on.
The same thing, for a scientist
Three distinct subnuclear pools, from three different experiments, and they dissociate. (1) **Nuclear matrix**, ECO:0000269 from Collas 1999, which is also the source of the nuclear matrix targeting site (**NMTS**) concept [E1][E2]. (2) **Nucleolus**, ECO:0000269 from Marstad 2016: a subpopulation of AKAP95 targets the nucleolus during interphase, co-localises with UBF, is associated with ribosomal chromatin by ChIP, shows Pol I- and Pol II-dependent nucleolar trafficking by FRAP, prefers GC-rich DNA by SELEX, and its expression is reciprocally related to 47S rRNA [E3]. (3) **Dynamic nuclear foci**, from an endogenous Flag-mEGFP-AKAP95 CRISPR knock-in in HeLa: discrete foci with **FRAP T1/2 = 4.12 +/- 1.31 s** over 8 cells [E4]. **The dissociation is the finding.** Deleting the NMTS (residues **111-140**) does **not** impair AKAP95's coactivation of a chromosomal reporter, while deleting the NLS or the two zinc fingers does [E2]. A localisation field that recorded only *nucleus matrix* would point a reader at the wrong domain.
A correction this beat owes the corpus: the nucleolus is NOT in the 2013 MLL paper
The brief that dispatched this beat listed 'localisation to nuclear matrix and nucleolus' among the full-text claims of PMID 23995757. It is not there. The string nucleol occurs zero times in the entire full text of PMC3813012, Methods and figure legends included. nuclear matrix occurs twice: once in the Introduction, citing prior work (the paper's reference 30, the p68/nuclear-matrix study), and once as the expansion of the NMTS acronym. That paper performs no localisation experiment of any kind.
The corpus entry was right and the brief was wrong. interface-kmt2a-akap8-a-prey-only-grade-on-a-direct-mll-coactivator attributes both locations to UniProt O43823, correctly, in its evidence item E3. The error was introduced when the coordinator's dispatch brief re-described that UniProt-sourced claim as a full-text claim.
The general lesson is worth more than the instance. A localisation fact and a mechanism fact sat in the same entry, sourced to a database and a paper respectively, and one re-telling merged them. The entry's own support_location fields distinguished them; the prose summary did not. When an entry mixes a database annotation with a paper's experiments, the summary must say which is which, because the summary is what gets quoted.
Why the nucleolar pool is worth its own line in this graph
This graph already runs a nucleolar thread: localization-nucleolus-kmt2a-fusion holds the direct published images of a KMT2A fusion in the nucleolus, and absence-kdm2b-and-the-kmt2a-fusion-are-both-nucleolar-and-nobody-has-put-them-together records that three CXXC-pathway activities converge on rDNA - KDM2B represses Pol I, KMT2A and SETD1A are at rDNA.
AKAP95 is a fourth, and it is the one with a direct functional readout on Pol I: manipulating AKAP95 expression in U2OS cells changes 47S rRNA reciprocally 3. It also has the GC-preference that the CXXC story turns on, though by SELEX rather than by a CXXC domain - AKAP95 reaches GC-rich DNA through C2H2 zinc fingers (392-414, 481-504), a completely different chemistry from KMT2A's CXXC.
That convergence is either a real shared address or a systematic artefact of nucleolar proteomics, and this beat cannot tell which. The honest statement is that the nucleolus is the compartment where non-specific retention of nucleic-acid-binding proteins is most likely, and that every member of the convergence is a nucleic-acid binder.
| compartment | nucleus |
|---|---|
| functionally required region | NLS (289-306) and both zinc fingers (392-414, 481-504); NOT the NMTS (111-140) and NOT the RII-binding region (572-589) |
| shown for fusion | PARTIAL - the condensate pool partially co-localises with MLL1 N-terminal fragments in THP-1 (KMT2A::MLLT3) and with mCherry-MLL1T in HeLa. The nucleolar and nuclear-matrix pools have NEVER been examined in any KMT2A-rearranged cell. |
| correction recorded | The brief dispatching this beat attributed nuclear matrix AND nucleolus to the full text of PMID 23995757. Both are UniProt annotations from other papers; the string 'nucleol' occurs zero times in PMC3813012. The corpus entry interface-kmt2a-akap8-... sourced them correctly to UniProt in its E3; only the re-telling was wrong. |
subnuclear pools
[
{
"pool": "nuclear matrix",
"evidence": "ECO:0000269 PMID 10601332",
"functionally_required_for_coactivation": false,
"region": "NMTS 111-140"
},
{
"pool": "nucleolus",
"evidence": "ECO:0000269 PMID 26683827; UBF co-localisation, rDNA ChIP, 47S rRNA reciprocity",
"functionally_required_for_coactivation": null,
"region": "not mapped"
},
{
"pool": "dynamic nuclear foci / condensates",
"evidence": "endogenous mEGFP knock-in, PMID 41501053; FRAP T1/2 4.12 s",
"functionally_required_for_coactivation": true,
"region": "IDR1 101-390; PS-mutant abolishes"
}
]measurements — the numbers behind the chart
[
{
"quantity": "half_time",
"subject": "FRAP recovery of endogenous Flag-mEGFP-AKAP95 nuclear foci",
"value": 4.12,
"units": "s",
"n": 8,
"universe": "8 individual HeLa knock-in cells, PMID 41501053 Fig 3a",
"null": null,
"note": "+/- 1.31 s SD; whole-focus bleach, no half-bleach control"
},
{
"quantity": "count",
"subject": "occurrences of the string 'nucleol' in the full text of PMC3813012",
"value": 0,
"units": "occurrences",
"n": 1,
"universe": "complete NCBI PMC OAI text of PMC3813012, 49,400 characters, including Methods and figure legends; literal case-insensitive grep",
"null": null,
"note": "THE ABSENCE IS THE SUPPORT. This is the measurement that corrects the dispatch brief."
},
{
"quantity": "count",
"subject": "occurrences of the string 'nuclear matrix' in the full text of PMC3813012",
"value": 2,
"units": "occurrences",
"n": 1,
"universe": "same text; one in the Introduction citing prior work, one as the NMTS acronym expansion",
"null": null,
"note": "neither is an experiment performed in that paper"
}
]- AKAP95's nucleolar function is regulation of 47S rRNA production. Any agent that removes AKAP95 or dissolves its condensates is a candidate ribosome-biogenesis perturbant, and ribosome biogenesis is the toxicity that ends epigenetic drug programmes in regenerating tissue.
- The subnuclear annotation a reader keys on - nuclear matrix - is the one shown to be dispensable for the function that matters here. A target-validation package built from the database annotation would pick the wrong domain to drug.
- The condensate pool is the functionally required one and it is characterised by a single whole-focus FRAP in HeLa. If the liquid interpretation is wrong, the entire JD-PI95 rationale - dissolve the condensate, lose the function - loses its mechanism while keeping its phenotype.
- Are the nucleolar AKAP95 pool and the MLL1T co-condensate pool the same object seen two ways? Both are dynamic, both are GC/nucleic-acid driven, and nobody has imaged AKAP95 foci against a nucleolar marker in the same cells where the MLL1T co-localisation was scored.
- Does the AKAP95 nucleolar pool overlap the KMT2A-fusion nucleolar pool this graph already records? Two proteins independently reported nucleolar in different papers and different cell types is weak evidence for co-residence; a single two-colour image in a KMT2A-rearranged line would settle it and costs a day.
- What does the NMTS (111-140) actually do? It is dispensable for coactivation, has no UniProt feature, and sits inside both the DDX5-interaction region (109-201) and IDR1 (101-390) - so a construct deleting it also perturbs two mapped functions, and nobody has asked whether the published dNMTS result is clean.
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
UniProtKB O43823 records four subcellular locations: Nucleus (ECO:0000269, PubMed 19277197 and 26683827), Nucleus matrix (ECO:0000269, PubMed 10601332), Nucleus nucleolus (ECO:0000269, PubMed 26683827) and Cytoplasm (ECO:0000250, by similarity to Q9DBR0). There is no NMTS feature in the feature table.
UniProtKB entry O43823 (AKAP8_HUMAN), subcellular location comment and feature table, retrieved live 2026-09-24 by q166 · UniProt Consortium 2026What this evidence cannot show
Rule 91 requires the cited papers be opened rather than trusted as pointers, and both were: PMID 10601332 (Collas 1999, J Cell Biol) is titled for AKAP95's role in chromatin condensation at mitosis and is a genuine localisation and function paper; PMID 26683827 (Marstad 2016, FEBS J) is a dedicated nucleolar study. Both pass. The expected_absent_terms entry records that the NMTS, which the 2013 paper treats as a named region, has no UniProt feature at all - so its coordinates exist only in that paper's Methods.
Evidence that argues against this (1)
- UniProt presents four locations as a flat list, but they come from three papers spanning 1999 to 2016 in different cell types and different cell-cycle states - a mitotic chromatin-condensation study, an interphase nucleolar study in U2OS, and a HeLa study. AKAP95's distribution is itself cell-cycle dependent; that is the title of its cloning paper. So the annotation is a UNION over conditions and describes no single cell, and any entry that reads it as a simultaneous address list is over-reading the record. Eide T et al. 1998
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
In PMID 23995757 the nuclear-matrix targeting site is deleted by the construct dNMTS = 1-110 + 141-692, i.e. the NMTS is residues 111-140; deleting it does NOT impair AKAP95 coactivation of the chromosomal Gal4-VP16 luciferase reporter, whereas deleting the NLS or the two zinc fingers does. The string 'nucleol' does not appear anywhere in the full text, and 'nuclear matrix' appears only in the Introduction (citing prior work on p68 RNA helicase) and as the expansion of the NMTS acronym. The paper reports no localisation experiment.
Regulation of transcription by the MLL2 complex and MLL complex-associated AKAP95. · Jiang H, Lu X, Shimada M, Dou Y, Tang Z, Roeder RG · Nat Struct Mol Biol 2013What this evidence cannot show
Full text read via PMC3813012; supplementary figures unavailable, and the NMTS/NLS/ZF dissection result is reported across Fig 5D and Supplementary Fig 3C, so the supplementary half is the main text's description. The absence claims in expected_absent_terms were verified by literal grep over the whole downloaded text, not by reading impression - the ABSENCE IS THE SUPPORT for the correction this entry records.
Evidence that argues against this (1)
- A deletion of 30 residues that does not change a reporter readout does not prove the protein still reaches the nuclear matrix without them, nor that matrix association is irrelevant - only that this assay does not require that region. No imaging of the dNMTS construct is reported. Jiang H et al. 2013
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
A subpopulation of AKAP95 targets the nucleolus during interphase and is involved in regulating rRNA production: it co-localises with the nucleolar upstream binding factor UBF; SELEX and in vitro binding show a preference for GC-rich DNA, as for other C2H2 zinc-finger proteins; FRAP shows AKAP95 to be a highly mobile protein with RNA polymerase I- and II-dependent nucleolar trafficking; ChIP shows association with ribosomal chromatin in vivo; and manipulating AKAP95 expression in U2OS cells reveals a reciprocal relationship between AKAP95 and 47S rRNA.
A-kinase anchoring protein AKAP95 is a novel regulator of ribosomal RNA synthesis. · Marstad A, Landsverk OJ, Stromme O, Otterlei M, Collas P, Kuntziger T, Kuntziger T · FEBS J 2016What this evidence cannot show
Abstract read; full text not obtained. The author list here is truncated from the PubMed record and should be re-pulled before this citation is used in a manuscript. This is the UniProt ECO:0000269 source for the nucleolar location, so the annotation and this paper are the same evidence and must not be double-counted as two sources.
Evidence that argues against this (1)
- The nucleolus is the compartment in which non-specific retention of nucleic-acid-binding proteins is most common, and AKAP95's nucleolar residence is explicitly a SUBPOPULATION with Pol-dependent trafficking - i.e. dynamic and partial, not a resident pool. A reciprocal expression relationship with 47S rRNA in an osteosarcoma line is a correlation in an over/under-expression experiment, not a demonstrated regulatory mechanism. Marstad A et al. 2016
- E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
An endogenous Flag-mEGFP-AKAP95 CRISPR knock-in in HeLa cells shows discrete nuclear foci in two independent positive clones, with FRAP half-recovery of 4.12 +/- 1.31 s measured over 8 individual cells. The endogenous tag was made with an sgRNA targeting the AKAP95 N-terminus and an mEGFP donor flanked by 800-bp homology arms.
AKAP95 condensates regulate transcription and can be targeted in MLL-fusion driven oncogenesis. · Yan X, Luan Y, Zhu Y, Cai Y, Ye F, Yang L, Zhu K, Hu J, Luo S, Lin J, Wang Y, Huang Y, Sun P, Yang Z, Shi B, Jiang H, et al. · Nat Commun 2026What this evidence cannot show
Full text read; the FRAP panel itself was not inspected. n = 8 cells, one clone's worth of measurement, no half-bleach control and no 1,6-hexanediol test reported - which this project's `localization-condensate-evidence-standards` treats as the discriminating assays. The endogenous tag is a genuine strength: this is not an over-expression focus. The imaging is in HeLa, not a leukaemia cell.
Evidence that argues against this (1)
- A fast whole-focus FRAP recovery is consistent with a liquid condensate but also with a rapidly exchanging binding site on a static scaffold, which is precisely what a nuclear-matrix protein with a defined NMTS might be. Without a half-bleach - which distinguishes internal rearrangement from exchange with the nucleoplasm - the liquid interpretation is not established. This project's own audit of NUP98 FG condensates makes the same point. this project 2026
three subnuclear pools; the functionally required one is not the annotated one
- related to →The nucleolus — the one compartment with direct published images of a KMT2A fusion inside it
a fourth nucleolar member of the rDNA convergence this graph already tracks, and the only one with a direct 47S rRNA readout
AKAP95's nuclear-matrix pool and its NMTS at 111-140, which its MLL-linked function does not require
the AKAP95 condensate call rests on one whole-focus FRAP in HeLa with no half-bleach and no 1,6-hexanediol
claim 7 scored NOT-FOUND - 'nucleol' occurs zero times in PMC3813012
the same zinc fingers carry the GC-rich DNA preference behind the nucleolar pool, which is why the ZF-mutant is not a clean RNA-binding reagent