Re-bound at full text: the H3K79me2 decay half-life is still unmeasured - one paper in 12.4 million full texts contains the phrase 'half-life of H3K79me2', it is an unnumbered assertion citing a 2010 review, and the MLL::AF9 degron time-course that could have measured it uses the word zero times
also called Q115 H3K79me2 half-life re-bound
How long the H3K79 chemical tag survives once the enzyme that writes it is switched off has never been put in a number, and searching the whole text of twelve million papers rather than just their summaries does not change that. The one sentence in the literature that calls the tag long-lived gives no figure and points at a 2010 review.
The same thing, for a scientist
`absence-h3k79me2-decay-half-life-never-measured` is bounded by an abstract-level search, which rule 80 says is not a bound. Re-run at full text against Europe PMC's `BODY:` index (12,362,145 full-text articles; negative control `BODY:"NOTAREALGENESYMBOLXYZ"` = 0; operands `BODY:"H3K79me2"` = 2,418 and `BODY:"half-life"` = 364,780): **`BODY:"half-life of H3K79me2"` returns exactly 1**, `BODY:"H3K79me2 half-life"` 0, `BODY:"decay of H3K79me2"` 0, `BODY:"H3K79" AND BODY:"decay rate"` 7 (all off topic on title check) [E1]. The single hit is PMID 41634341, opened in full: the sentence is *"The unusually long half-life of H3K79me2/3, arising from the absence of demethylases"*, **it states no value, no interval and no system, and its citation 22 is Barth & Imhof 2010, a Trends in Biochemical Sciences review** [E2]. The obvious place a number would live - the MLL::AF9 degron time-course of PMID 35245435, which the absence entry already cites - contains **zero** occurrences of `half-life`, `half life`, `decay` or `t1/2` across 113,077 characters of full text [E3]. **The absence survives, and it is now bounded by full texts rather than by abstracts.**
Why the loose conjunction is not the bound
BODY:"H3K79me2" AND BODY:"half-life" returns 170. That is a reading burden, not a result: half-life in a paper mentioning H3K79me2 is overwhelmingly a drug half-life, an mRNA half-life or a protein half-life, and the absence entry already records that three of its six abstract-level hits were about the DOT1L inhibitor's own pharmacokinetics. The phrase queries are the bound, because a measured decay constant for a histone mark is written as the half-life of H3K79me2 and essentially nothing else.
The positive control for the phrase form runs through the identical BODY:"half-life of <mark>" template: BODY:"half-life of H3K27me3" returns 1 - a 2015 J Biomol Screen high-throughput-microscopy paper. So the template can return a one, and returning a one for H3K27me3 and a one for H3K79me2 tells you something else worth knowing: this phrasing is rare for every mark, and a phrase-level zero would have been weak. It is a one, and the one is not a measurement.
What the single sentence actually rests on
Chain of custody, read rather than inferred: the claim "unusually long half-life of H3K79me2/3, arising from the absence of demethylases" carries superscript 22; reference 22 of PMID 41634341 is Barth TK, Imhof A, Fast signals and slow marks: the dynamics of histone modifications, Trends Biochem Sci 2010;35:618-626, PMID 20685123 - a review 2.
The same paper's discussion elsewhere says DOT1L inhibition shows "delayed gene downregulation owing to slow H3K79me turnover" citing references 31 and 32, which are Gilan et al., CRISPR-ChIP, Nat Struct Mol Biol 2023 (PMID 37679565) and Olsen et al., MLL::AF9 degradation, Mol Cell 2022 (PMID 35245435). Olsen was opened and contains no decay language at all 3. So three independent pointers in the field's most recent statement of the fact lead to a review and to two papers that do not contain the number.
What this changes for the entry
The entry's headline stands. Two things should be added to it: the class of the bound moves from abstract-level to full-text, and the field's own justification for believing the mark is long-lived is now identified and is mechanistic rather than kinetic - no demethylase is known, therefore dilution by replication is assumed to be the only route. That is a testable premise and it is not the same claim as a measured half-life. mechanism-h3k79-demethylation-contested already holds the other side of it.
| script | none - Europe PMC BODY: queries plus two full-text reads, 2026-09-22 |
|---|---|
| status | run |
| verdict | SURVIVES at full text |
| entry re bounded | absence-h3k79me2-decay-half-life-never-measured |
| instrument before | abstract-level-literature-search |
| instrument after | full-text search of 12,362,145 Europe PMC full texts, plus two primary sources read in full |
| full text corpus denominator | 12362145 |
| monotonicity assertion | checked: BODY:"WDR5" = 4026, BODY:"TurboID" = 1755, their OR = 5766 (>= both disjuncts) and their AND = 15 (<= both), and 4026 + 1755 - 15 = 5766 exactly. |
| absence class | never-measured |
| absence class basis | Unchanged from the entry under test, and now bounded at full text rather than at abstract level. No archive holds a decay constant because no archive stores derived kinetic parameters; the closest deposited object is the degron time-course underlying PMID 35245435, which would make the class measured-not-reported IF a rate can be fitted from it. That fit was not attempted here. |
queries — the numbers behind the chart
[
{
"q": "BODY:\"half-life of H3K79me2\"",
"hits": 1,
"on_topic": 0,
"note": "the one hit asserts the fact without a value and cites a review"
},
{
"q": "BODY:\"H3K79me2 half-life\"",
"hits": 0
},
{
"q": "BODY:\"decay of H3K79me2\"",
"hits": 0
},
{
"q": "BODY:\"H3K79\" AND BODY:\"decay rate\"",
"hits": 7,
"on_topic": 0,
"note": "all seven title-checked"
},
{
"q": "BODY:\"H3K79me2\" AND BODY:\"half-life\"",
"hits": 170,
"role": "reading burden, not a bound"
},
{
"q": "BODY:\"half-life of H3K27me3\"",
"hits": 1,
"role": "positive control, identical phrase template"
},
{
"q": "BODY:\"H3K79me2\"",
"hits": 2418,
"role": "operand control"
},
{
"q": "BODY:\"half-life\"",
"hits": 364780,
"role": "operand control"
},
{
"q": "BODY:\"NOTAREALGENESYMBOLXYZ\"",
"hits": 0,
"role": "negative control, same URL template"
}
]papers opened
[
{
"pmid": "41634341",
"pmcid": "PMC12904788",
"chars": 142856,
"route": "EPMC fullTextXML"
},
{
"pmid": "35245435",
"pmcid": "PMC9044330",
"chars": 113077,
"route": "efetch db=pmc after EPMC fullTextXML returned HTTP 500"
}
]chain of custody for the claim
[ "PMID 41634341 asserts the long half-life, cites ref 22", "ref 22 = PMID 20685123, Barth & Imhof 2010, Trends Biochem Sci - a REVIEW", "the same paper cites refs 31 and 32 for slow turnover: PMID 37679565 and PMID 35245435", "PMID 35245435 opened: zero occurrences of half-life / decay / t1/2" ]
not read
[ "20685123 (the review at the end of the chain)", "37679565 (Gilan CRISPR-ChIP)", "24826939 (Proteomics 2014 site-specific methylation stability - the nearest miss)" ]
- If the long half-life is an inference from 'no demethylase is known' rather than a measurement, then the pharmacological argument built on it - that DOT1L inhibitor effect is set by integrated exposure rather than occupancy - inherits that assumption. A demethylase discovered tomorrow would not change any published data and would change the dosing logic completely.
- A mark whose clearance is assumed to be division-coupled predicts that a quiescent leukaemic cell clears it slowly or not at all, which would make DOT1L inhibition weakest exactly in the population that survives therapy.
- Can a decay constant be fitted from the published H3K79me2 time-course in PMID 35245435? If yes this absence is measured-not-reported and closes in an afternoon; if no, the entry's never-measured class is confirmed by a stronger route than a query.
- Does Barth & Imhof 2010 tabulate an H3K79 turnover rate? It is the terminus of the citation chain and nobody in this graph has opened it.
- PMID 24826939 measures site-specific H3 methylation stability by mass spectrometry and reports fast K4me3 turnover. Does its supporting data include K79? That single lookup could overturn this entry.
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
In Europe PMC's full-text index of 12,362,145 articles, BODY:"half-life of H3K79me2" returns 1, BODY:"H3K79me2 half-life" 0, BODY:"decay of H3K79me2" 0 and BODY:"H3K79" AND BODY:"decay rate" 7, against operands of 2,418 for H3K79me2 and 364,780 for half-life and a negative control of 0.
Europe PMC RESTful search, BODY: full-text field, queries run 2026-09-22 · Europe PMC 2026What this evidence cannot show
BODY: searches only the open-access and author-manuscript full texts Europe PMC holds (12,362,145 of them), not the whole literature: a paywalled paper with the number in a supplementary figure legend remains invisible. All seven records of the decay-rate query were title-checked and none is about H3K79 turnover (a stochastic epigenetic-memory model, a NAT10 mESC paper, a noise/expression modelling paper, a UBR7 hepatocellular paper, a 2014 H3 methylation stability paper reporting FAST K4me3 turnover, a USP49 paper and an O-GlcNAc platform paper).
Evidence that argues against this (1)
- PMID 24826939 (Proteomics 2014, 'Site-specific human histone H3 methylation stability: fast K4me3 turnover') is in the decay-rate hit list and is the nearest miss in the corpus: it measures site-specific methylation stability by mass spectrometry. Its title names K4, and this beat did not open it. If it reports an H3K79 rate in a supporting table the absence falls, and that is the single cheapest way to refute this entry. Proteomics 2014
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
The one full text containing the phrase states 'The unusually long half-life of H3K79me2/3, arising from the absence of demethylases' with no value and cites reference 22, which is Barth & Imhof 2010, a Trends in Biochemical Sciences review.
DOT1L provides transcriptional memory through PRC1.1 antagonism. · Nature Cell Biology 2026What this evidence cannot show
Read in full through Europe PMC fullTextXML (PMC12904788, 142,856 characters) on 2026-09-22. The reference was resolved by parsing the <ref> elements of that XML and indexing to position 22 of 69, not by a windowed regex - this corpus has twice manufactured a number by reading a serialised blob with a sliding window.
Evidence that argues against this (1)
- A review can itself contain a primary measurement, and Barth & Imhof 2010 was not opened by this beat. If it tabulates an H3K79 turnover rate from a pulse-chase study, the chain ends in a number and the absence is weaker than stated here. Trends in Biochemical Sciences 2010
- E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
The MLL::AF9 degron time-course paper contains zero occurrences of 'half-life', 'half life', 'decay' or 't1/2' in 113,077 characters of full text.
MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape. · Molecular Cell 2022What this evidence cannot show
Retrieved 2026-09-22. Europe PMC fullTextXML returned HTTP 500 for PMC9044330 and `efetch db=pmc` recovered it, which is the documented route-2 rescue; the <body> element was present. A word count is not a reading: the paper plots H3K79me2 loss over a degron time-course and a half-life could be READ OFF those curves by a reader. What it does not do is state one.
Evidence that argues against this (1)
- That is precisely the counter-argument. If the published time-course contains the data from which a decay constant can be fitted, the correct class for this absence is measured-not-reported, not never-measured, and it becomes an afternoon's work on a published figure rather than an experiment. This beat did not fit it. Molecular Cell 2022
SURVIVES: re-bound from abstract level to 12.4 M full texts; the single phrase hit states no value and cites a 2010 review
identifies what the field's belief in a long half-life actually rests on: the absence of a known demethylase, cited to a review, not a measured rate
- related to →Nobody has convincingly found the H3K79 eraser - and that constraint sets the clock on every DOT1L inhibitor
the no-demethylase premise is the load-bearing half of the long-half-life claim, and that premise is contested in this graph already
the unmeasured kinetic parameter that sets how long a DOT1L inhibitor must be held to clear the mark
the contamination measurement that qualifies every full-text count written by this beat