What was searched, what came back empty, and what was read and not used - the P-TEFb reservoir beat's audit trail
also called 7SK reservoir enumeration · P-TEFb beat bounded absences
This is the working record behind the other entries in this beat: every literature search that was run, every one that returned nothing, and every paper that looked relevant and was then set aside with a reason. It exists so that someone repeating this work next year repeats the decisions, not only the searches.
The same thing, for a scientist
Three kinds of negative are recorded here, following this project's standing rule. **Bounded absences** - queries run, with their exact strings and dates, that return zero or near-zero. **Bounded rejections** - papers found, on topic, read at least at abstract level, and judged not usable, with the reason and what would change the judgement. **Unreadable or partially readable material** - identified, with the routes attempted. The headline numbers: `(MLL OR KMT2A) AND 7SK` returns **3**; `AND HEXIM1` returns **2**; `AND LARP7` and `AND MEPCE` return **1** each; `(MLL OR KMT2A) AND "free P-TEFb"` returns **0**; `"menin inhibitor"[tiab] AND (CDK9[tiab] OR "CDK9 inhibitor"[tiab])` returns **0**; `(CSNK2A2[tiab] OR "CK2 alpha prime"[tiab]) AND (leukemia[tiab] OR AML[tiab])` returns **0**; and **RN7SK returns zero rows in all 24,315,372 rows of the Human Protein Atlas cell-line RNA table across 1,206 lines** because the library is poly-A selected [E1][E2]. The last of these is the most consequential negative in the beat: the brake is not merely unstudied in this disease, it is invisible to the instruments the project already uses.
Bounded absences - every query, run 2026-09-20
| query | records | after title-check |
|---|---|---|
(MLL OR KMT2A) AND 7SK | 3 | 2 reviews, 1 HIV Tat purification; no measurement in a KMT2A cell |
(MLL OR KMT2A) AND HEXIM1 | 2 | one SEC phase-separation paper, one autophagy/BET paper |
(MLL OR KMT2A) AND LARP7 | 1 | a CDK9 review |
(MLL OR KMT2A) AND MEPCE | 1 | the same CDK9 review |
(MLL OR KMT2A) AND "free P-TEFb" | 0 | - |
7SK snRNP AND leukemia | 6 | none is a KMT2A study |
HEXIM1 AND leukemia | 20 | dominated by BET-inhibitor pharmacology |
"menin inhibitor"[tiab] AND (CDK9[tiab] OR "CDK9 inhibitor"[tiab]) | 0 | - |
| broad menin-inhibitor names x CDK9-inhibitor names | 1 | the Sharma synergy paper 3 |
(CDK13[tiab] OR CDC2L5[tiab] OR CHED[tiab] OR KIAA1791[tiab]) AND (leukemia OR leukaemia OR AML)[tiab] | 4 | 0 functional studies of CDK13 in leukaemia |
(CDK13 OR CDC2L5) AND (MLL OR KMT2A) | 1 | a developmental-disorder de novo mutation survey |
(CSNK2A2[tiab] OR "CK2 alpha prime"[tiab]) AND (leukemia[tiab] OR AML[tiab]) | 0 | - |
(CCNT2[tiab] OR "cyclin T2"[tiab]) AND (leukemia OR AML OR MLL OR KMT2A)[tiab] | 5 | 2 miRNA studies, 3 off-topic |
HPA rna_celline.tsv: any gene name containing 7SK or starting RN7S | 0 of 24,315,372 rows | poly-A selection excludes Pol III transcripts |
How these are bounded. Retired and alias symbols were included where HGNC lists them: CDK13 was searched as CDC2L5, CHED, CDC2L and KIAA1791, though PubMed silently dropped KIAA1791 from its query translation. CHED and CDC2L are short, word-like aliases, so every hit was title-checked rather than counted, per this project's precision rule. Query translations were read on the zero counts to confirm no [UID] rewriting. The queries that remain unbounded are complex-level ones: this project has repeatedly found that a paper framing its work at the level of 'the P-TEFb equilibrium' or 'the 7SK snRNP' is unreachable from any subunit symbol, so every count above is a lower bound on what exists 4.
Bounded rejections - found, read, not used
PMID 37609817 - AFF4 globally affects the release of paused RNA polymerase II in HEL cells (Yi Chuan 2023). On-beat title and a well-designed study using RNA-seq, CUT&Tag, ChIP-seq and PRO-seq; it finds AFF4 knockdown increases promoter-proximal pausing on thousands of genes and that AFF4 promotes pause release by facilitating P-TEFb binding to Pol II. Not used because HEL is an erythroleukaemia line with no KMT2A rearrangement, and the authors themselves conclude the extent of AFF4's effect is cell-type dependent. Would change my mind: the same PRO-seq design run in a KMT2A::AFF1 line, which would speak directly to exp-pro-seq-pausing-index-kmt2a-aff1 5.
PMID 24985467 - A single point mutation in cyclin T1 eliminates binding to Hexim1, Cdk9 and RNA but not to AFF4 (Retrovirology 2014). The CycT1-V107E mutant is a genuinely useful separation-of-function reagent: it loses HEXIM1, CDK9 and 7SK binding while retaining AFF4 binding. Not used as a claim because every experiment is HIV transcription in T cells. Recorded because it is the reagent one would reach for to test whether a KMT2A fusion's P-TEFb requirement is reservoir-dependent 6.
PMID 26171280 - AF4 and AF4N protein complexes: recruitment of P-TEFb kinase, their interactome and potential functions (Am J Blood Res 2015). Same laboratory and journal as the DDX6 paper, and largely an overview of it. Not separately cited to avoid double-counting one laboratory's model as two sources.
PMIDs 22493297, 28409330, 33817287 - miRNA studies in AML naming CCNT2 as a target (miR-29a/miR-142-3p; miR-192; miR-212-5p). Not used: target-prediction plus luciferase evidence, with no measurement of cyclin T2's elongation function and no KMT2A genotype.
PMID 35651941 - a case report of ALL in a child with CDK13-related disorder. Not used: the authors state the leukaemia was probably coincidental, and n=1.
PMID 39259751 - Release of P-TEFb from the Super Elongation Complex promotes HIV-1 latency reversal (PLoS Pathog 2024). Interesting because it inverts the usual direction - release from the SEC rather than to it. Not used: an HIV latency study with no leukaemia content, but it is the paper to read first if anyone pursues SEC-to-free-pool flux.
Laboratories that publish repeatedly in this area and are cited nowhere else in this graph: Qiang Zhou (Berkeley), David H Price (Iowa), Olivier Bensaude (ENS Paris) and B Matija Peterlin (UCSF). Between them they produced most of the 7SK literature this beat rests on. Their work is almost entirely HeLa, HEK293 and HIV, which is why it had not previously entered a leukaemia knowledge graph - and is also why every claim in this beat carries a model-system caveat.
Read with difficulty, or not fully read
- PMID 26148704 (Devaraj 2016, Leukemia) carries no abstract in PubMed. Europe PMC
fullTextXMLreturned HTTP 500;efetch db=pmcreturned a document with a body and the paper was read from it. Under a two-route unreadable rule this beat's central HEXIM1-in-KMT2A result would have been lost. - PMID 27679741 (Mueck 2016, Am J Blood Res):
fullTextXMLHTTP 500,efetch db=pmcreturned no body, and the PMC HTML page returned 71,718 characters. Route 4 was required. This is the DDX6 paper, and without it this beat would have asserted that Tat is the only known directed extractor - which it very nearly did. - PMID 40979068 (Sharma 2025): full text read, but the individual Chou-Talalay combination index values live in Figure 5B and could not be read. Only 'CI < 1 in all four lines' is claimed.
- PMID 32270036 (Guo 2020, SEC phase separation): abstract only. The condensate entry is written from the abstract plus the general methodological literature, and says so.
- Nothing in this beat was finally unreadable after all four routes.
| status | run |
|---|---|
| result summary | Eleven counted absences recorded with exact query strings and dates; six bounded rejections recorded with reasons and falsifying conditions; four papers recorded as requiring route 3 or route 4 of the full-text test or as only partially readable. The single most consequential negative is that RN7SK returns zero rows in all 24,315,372 rows of the HPA cell-line table, because the reservoir's central molecule is invisible to poly-A RNA-seq and therefore to every RNA resource this project currently uses. |
inputs
[ "NCBI E-utilities esearch/efetch/esummary, run 2026-09-20", "Human Protein Atlas rna_celline.tsv (1,206 cell lines)", "Open Targets Platform GraphQL depMapEssentiality", "analyses/depmap-kmt2a-selective-scan-full/results.json", "UniProt REST", "HGNC REST", "Ensembl REST" ]
counted absences — the numbers behind the chart
[
{
"query": "(MLL OR KMT2A) AND 7SK",
"records": 3,
"date": "2026-09-20"
},
{
"query": "(MLL OR KMT2A) AND HEXIM1",
"records": 2,
"date": "2026-09-20"
},
{
"query": "(MLL OR KMT2A) AND LARP7",
"records": 1,
"date": "2026-09-20"
},
{
"query": "(MLL OR KMT2A) AND MEPCE",
"records": 1,
"date": "2026-09-20"
},
{
"query": "(MLL OR KMT2A) AND \"free P-TEFb\"",
"records": 0,
"date": "2026-09-20"
},
{
"query": "7SK snRNP AND leukemia",
"records": 6,
"date": "2026-09-20"
},
{
"query": "\"menin inhibitor\"[tiab] AND (CDK9[tiab] OR \"CDK9 inhibitor\"[tiab])",
"records": 0,
"date": "2026-09-20"
},
{
"query": "eight menin-inhibitor terms AND seven CDK9-inhibitor terms",
"records": 1,
"date": "2026-09-20"
},
{
"query": "(CDK13[tiab] OR CDC2L5[tiab] OR CHED[tiab] OR KIAA1791[tiab]) AND (leukemia[tiab] OR leukaemia[tiab] OR AML[tiab])",
"records": 4,
"functional_studies": 0,
"date": "2026-09-20"
},
{
"query": "(CSNK2A2[tiab] OR \"CK2 alpha prime\"[tiab]) AND (leukemia[tiab] OR AML[tiab])",
"records": 0,
"date": "2026-09-20"
},
{
"query": "HPA rna_celline.tsv gene name contains 7SK or starts RN7S",
"rows": 0,
"of_rows": 24315372,
"date": "2026-09-20"
}
]bounded rejections — the numbers behind the chart
[
{
"pmid": "37609817",
"reason": "HEL erythroleukaemia, not KMT2A-rearranged; authors state the effect is cell-type dependent",
"would_change": "the same PRO-seq design in a KMT2A::AFF1 line",
"title": "AFF4 globally affects the release of paused RNA polymerase II in HEL cells.",
"authors": "Yang ZM, Zhang G, Wei G, et al.",
"venue": "Yi Chuan",
"year": 2023,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"pmid": "24985467",
"reason": "HIV transcription in T cells; recorded as a separation-of-function reagent (CycT1-V107E) rather than as evidence",
"would_change": "use of the mutant in a KMT2A-rearranged cell",
"title": "A single point mutation in cyclin T1 eliminates binding to Hexim1, Cdk9 and RNA but not to AFF4 and enforces repression of HIV transcription.",
"authors": "Kuzmina A, Verstraete N, Galker S, et al.",
"venue": "Retrovirology",
"year": 2014,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"pmid": "26171280",
"reason": "same laboratory and journal as PMID 27679741 and largely an overview of it; avoided double-counting one model as two sources",
"would_change": "independent replication of the AF4N/P-TEFb model",
"title": "AF4 and AF4N protein complexes: recruitment of P-TEFb kinase, their interactome and potential functions.",
"authors": "Scholz B, Kowarz E, Rössler T, et al.",
"venue": "Am J Blood Res",
"year": 2015,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"pmid": "22493297",
"reason": "miRNA target study naming CCNT2; no elongation measurement, no KMT2A genotype",
"would_change": "a functional cyclin T2 experiment in leukaemia",
"title": "MicroRNA-29a and microRNA-142-3p are regulators of myeloid differentiation and acute myeloid leukemia.",
"authors": "Wang XS, Gong JN, Yu J, et al.",
"venue": "Blood",
"year": 2012,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"pmid": "28409330",
"reason": "as above (miR-192/CCNT2)",
"would_change": "as above",
"title": "MicroRNA-192 regulates cell proliferation and cell cycle transition in acute myeloid leukemia via interaction with CCNT2.",
"authors": "Ke S, Li RC, Lu J, et al.",
"venue": "Int J Hematol",
"year": 2017,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"pmid": "33817287",
"reason": "as above (miR-212-5p/CCNT2)",
"would_change": "as above",
"title": "Decitabine shows anti-acute myeloid leukemia potential via regulating the miR-212-5p/CCNT2 axis.",
"authors": "Xing L, Ren J, Guo X, et al.",
"venue": "Open Life Sci",
"year": 2020,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"pmid": "35651941",
"reason": "n=1 case report; authors call the leukaemia probably coincidental",
"would_change": "a cohort of CDK13-related disorder patients with leukaemia incidence",
"title": "Case Report: Hemophagocytic Lymphohistiocytosis Prior to the Onset of Leukemia in a Boy With CDK13-Related Disorder.",
"authors": "Cui D, Wang S, Zhang A, et al.",
"venue": "Front Genet",
"year": 2022,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"pmid": "39259751",
"reason": "HIV latency; no leukaemia content",
"would_change": "anyone pursuing SEC-to-free-pool flux should read this first",
"title": "Release of P-TEFb from the Super Elongation Complex promotes HIV-1 latency reversal.",
"authors": "Cisneros WJ, Soliman SHA, Walter M, et al.",
"venue": "PLoS Pathog",
"year": 2024,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
}
]read with difficulty — the numbers behind the chart
[
{
"pmid": "26148704",
"issue": "no PubMed abstract; EPMC fullTextXML HTTP 500",
"resolved_by": "efetch db=pmc, body present",
"title": "HEXIM1 induction is mechanistically involved in mediating anti-AML activity of BET protein bromodomain antagonist.",
"authors": "Devaraj SG, Fiskus W, Shah B, et al.",
"venue": "Leukemia",
"year": 2016,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"pmid": "27679741",
"issue": "fullTextXML HTTP 500; efetch db=pmc returned no body",
"resolved_by": "PMC HTML page, 71,718 characters",
"title": "DDX6 transfers P-TEFb kinase to the AF4/AF4N (AFF1) super elongation complex.",
"authors": "Mück F, Bracharz S, Marschalek R",
"venue": "Am J Blood Res",
"year": 2016,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"pmid": "40979068",
"issue": "individual combination index values are in Figure 5B",
"resolved_by": "not resolved; only 'CI<1 in all four lines' is claimed",
"title": "Targeting CDK9 inhibits the growth of KMT2A-rearranged infant leukemia and demonstrates synergy with menin inhibition.",
"authors": "Sharma R, Zhang C, Shah R, et al.",
"venue": "Blood Neoplasia",
"year": 2025,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
},
{
"pmid": "32270036",
"issue": "read at abstract level only",
"resolved_by": "not resolved; the condensate entry says so explicitly",
"title": "ENL initiates multivalent phase separation of the super elongation complex (SEC) in controlling rapid transcriptional activation.",
"authors": "Guo C, Che Z, Yue J, et al.",
"venue": "Sci Adv",
"year": 2020,
"title_provenance": "Title/authors/venue backfilled from PubMed esummary on 2026-09-20 because this citation stored a bare PMID with no title, which made it unscoreable by verify-citations.py. BACKFILLING IS NOT VERIFICATION: it confirms the PMID resolves to a real paper, not that this is the right paper for the claim. That still requires reading."
}
]labs publishing here and uncited elsewhere in this graph
[ "Qiang Zhou (UC Berkeley)", "David H Price (Iowa)", "Olivier Bensaude (ENS Paris)", "B Matija Peterlin (UCSF)" ]
- Would a total-RNA (rRNA-depleted) reanalysis of any published KMT2A-rearranged dataset recover 7SK? Some deposited libraries are total RNA and nobody has looked.
- Are there conference abstracts reporting menin-inhibitor plus CDK9-inhibitor combinations that PubMed does not index?
- Does the Marschalek laboratory's DDX6/AF4N model appear anywhere outside that laboratory? No replication was found, and the absence of replication is itself worth a targeted search.
- E1moderate confidence 3 of 5: One strong study, or several smaller consistent ones.review
PubMed returns three records for (MLL OR KMT2A) AND 7SK, two for AND HEXIM1, one each for AND LARP7 and AND MEPCE, and zero for (MLL OR KMT2A) AND "free P-TEFb", all run 2026-09-20; none of the retrieved records reports a measurement of the P-TEFb partition in a KMT2A-rearranged cell.
CDK9: a signaling hub for transcriptional control. · Bacon CW, D'Orso I · Transcription 2019What this evidence cannot show
Counted absences bounded by PubMed's own MLL/KMT2A expansion and by the literal strings 7SK, HEXIM1, LARP7 and MEPCE. A paper framing its work at the level of the complex rather than a named subunit would be missed, and this project has documented that failure mode explicitly. The cited record is the review that appears in three of these result sets.
Evidence that argues against this (1)
- A near-zero count over subunit symbols is exactly the signature this project has learned to distrust; the honest reading is that these are lower bounds, and the finding is the absence of any measurement in the retrieved set rather than proof that none exists. HUGO Gene Nomenclature Committee 2026
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
Filtering the Human Protein Atlas cell-line RNA table (rna_celline.tsv, 24,315,372 rows, 1,206 cell lines, downloaded 2026-09-20) for any gene name containing 7SK or beginning RN7S returns zero rows, because the library is poly-A selected and 7SK is a non-polyadenylated Pol III transcript.
Human Protein Atlas cell-line RNA nTPM, rna_celline.tsv (24,315,372 rows, 1,206 cell lines), downloaded and filtered for this beat on 2026-09-20 · Human Protein Atlas · Database 2026What this evidence cannot show
An absence in one resource, bounded by the exact filter run. It generalises to poly-A libraries in principle rather than by having been checked in every dataset, and it says nothing about whether 7SK is present in these cells - only that the instrument cannot see it.
Evidence that argues against this (1)
- A dataset annotating the locus only by an RNAcentral or Rfam identifier rather than by an HGNC symbol would also return zero under this filter, so the mechanism of the absence is inferred from the library chemistry rather than proven by the filter alone. HUGO Gene Nomenclature Committee 2026
- E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
A broad PubMed query naming eight menin-inhibitor terms against seven CDK9-inhibitor terms returned exactly one record on 2026-09-20, and the narrow query 'menin inhibitor'[tiab] AND (CDK9[tiab] OR 'CDK9 inhibitor'[tiab]) returned zero; the single record is the enitociclib plus MI-463 synergy study.
Targeting CDK9 inhibits the growth of KMT2A-rearranged infant leukemia and demonstrates synergy with menin inhibition. · Sharma R, Zhang C, Shah R, Frigault MM, Johnson AJ, Mangum DS, Maese LD, Lacayo NJ, Narendran A · Blood Neoplasia 2025What this evidence cannot show
Bounded by the drug names enumerated. Conference abstracts are frequently unindexed, and the menin-inhibitor combination literature is currently abstract-heavy, so the true number of tested-but-unreported combinations is unknown.
Evidence that argues against this (1)
- The one retrieved study uses a tool menin inhibitor rather than a clinical one, so even the single positive does not establish that any clinical menin inhibitor has been combined with a CDK9 inhibitor anywhere. Sharma R et al. 2025
- E4established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
Alias and retired-symbol coverage was applied where HGNC lists them - CDK13 as CDC2L5, CHED, CDC2L and KIAA1791; CDK12 as CRKRS, CRK7, CRKR, KIAA0904; CSNK2A2 as CK2 alpha prime - and HGNC additionally lists CSNK2A1 as an alias symbol of CSNK2A2, which is a symbol-resolution trap.
HGNC REST records fetched 2026-09-20 for RN7SK (HGNC:10037), CDK13 (7p14.1, previous symbol CDC2L5, aliases CHED/CDC2L/KIAA1791), CDK12, CCNT2 and CSNK2A2; used to bound the alias sets in the counted absences below · HUGO Gene Nomenclature Committee · Database 2026What this evidence cannot show
PubMed silently dropped KIAA1791 from the CDK13 query translation, so that alias was effectively not searched. Alias precision cuts the other way for short symbols: CHED and CDC2L are word-like, so raw counts were title-checked before being recorded.
Evidence that argues against this (1)
- Database nomenclature records are opposable on scope: they say what a symbol is called, not what has been studied under it, and older literature frequently uses spellings HGNC no longer lists at all. HUGO Gene Nomenclature Committee 2026
- E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
AFF4 knockdown in HEL cells decreased cellular and chromatin-bound Pol II CTD Ser2 phosphorylation and increased promoter-proximal pausing on several hundred heat-shock and thousands of non-heat-shock genes, with the authors concluding that the extent of AFF4's effect on pause release is likely context- or cell-type dependent.
AFF4 globally affects the release of paused RNA polymerase II in HEL cells. · Yang ZM, Zhang G, Wei G, Jing LL, Yu M · Yi Chuan 2023What this evidence cannot show
HEL is an erythroleukaemia line with no KMT2A rearrangement. Published in Yi Chuan; the English abstract was read and the full text was not. Recorded here as a bounded rejection, not as support for any claim in this beat.
Evidence that argues against this (1)
- A separate study cited by these authors found that in DLD-1 cells the SEC regulates pause release only of heat-shock genes while the BRD4/P-TEFb complex handles the rest, which is a materially different division of labour in a different cell type. Yang ZM et al. 2023
- E6established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
The cyclin T1 V107E point mutant loses binding to HEXIM1, CDK9, HIV TAR and 7SK snRNA while retaining strong binding to AFF4, and enforces repression of HIV transcription in human T cell lines and primary CD4+ cells.
A single point mutation in cyclin T1 eliminates binding to Hexim1, Cdk9 and RNA but not to AFF4 and enforces repression of HIV transcription. · Kuzmina A, Verstraete N, Galker S, Maatook M, Bensaude O, Taube R · Retrovirology 2014What this evidence cannot show
All experiments are HIV transcription in T cells; nothing in the paper concerns leukaemia. Recorded as an available separation-of-function reagent, not as evidence for any claim in this beat.
Evidence that argues against this (1)
- A mutant that also loses CDK9 binding is not a clean reservoir-only separation, since it removes the kinase from the cyclin as well; its usefulness for the experiment suggested here is therefore limited and would need a better allele. Kuzmina A et al. 2014
the counted absence that shows 7SK is invisible to every poly-A resource this project uses
establishes that no measurement of the partition exists in this disease
alias-aware search finds no functional CDK13 study in leukaemia
one record in the entire menin-inhibitor x CDK9-inhibitor query space
recovered only by route 4 of the full-text test, and it overturned this beat's draft conclusion