Analysisstrong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.Q35-encode-reanalysis
RUN, and the absence closes: all 13 released ENCODE BRCA1, CBX3 and CBX1 ChIP-seq tracks read at the KMT2A locus with three nulls - zero called peaks in 13 of 13, the breakpoint cluster at 0.57-1.24x the genome, and the exon-11 CTCF element BELOW the median CTCF anchor of its own cell type in 10 of 13
also called the Q35 ENCODE re-analysis · BRCA1 and HP1 at the KMT2A breakpoint cluster · closing the measured-not-analysed half of the resection absence
Public data already existed that could say whether two DNA-repair proteins sit on the KMT2A gene, and nobody had looked; we looked at all thirteen datasets and they do not. The one place that seemed to light up turned out to be ordinary background once it was compared against the right thing rather than against the whole genome.
The same thing, for a scientist
**What this closes.** `absence-no-resection-factor-localised-at-the-kmt2a-locus` (Q32, cycle 62) classed BRCA1 and CBX3 as `measured-not-analysed`: released ENCODE ChIP-seq exists, including in K562 and GM12878, and the analysis had never been run. This is that analysis, extended to CBX1/HP1-beta because the same archive holds two experiments for it and CBX1 is the paralogue with the fitness cost. **Census, re-run live on 2026-09-22 rather than inherited from the dispatch brief.** BRCA1 **7** released human TF ChIP-seq experiments (GM12878, H1, HeLa-S3, HepG2 x2, K562 x2); CBX3 **4** (GM12878, HCT116, K562 x2); CBX1 **2** (HepG2, K562); CBX5 4; KDM5A 3. Q32's counts are confirmed exactly. **BARD1, EXO1 and DNA2 return HTTP 404 from the ENCODE search endpoint, which is how that portal spells zero** - an error status that means "no target record", and a trap worth naming because a retry loop reads it as a network failure. **Three instrument checks, all per FILE and none inherited.** 1. **Build.** Each file's own chrom table, read across chr1, chr2, chr11, chr19 and chrX: **13 of 13 match GRCh38 exactly, 0 match GRCh37, and no file declares padding.** Nothing was lifted, so the 129,285 bp offset at this locus is removed as an error source. 2. **File identity, before counting replicates.** HTTP HEAD Content-Length for all 13 equals the portal's `file_size` for all 13; **13 distinct Content-Lengths and 13 distinct md5 sums**, so there is no byte-identical-file-under-several-accessions problem here. Every file's md5 was then **re-verified locally after download**. 3. **Bin size, measured, before any narrow interval was quoted.** These are base-resolution bedGraph-derived bigWigs: over the 90,377 bp gene span they carry **3,194 to 21,772 raw intervals**, with a **modal run length of 1 bp in 11 of 13 files**, median run lengths of 3-15 bp and a minimum of 1 bp. **So the 147 bp exon-11 interval carries tens of independent values here and is a real measurement** - unlike GSE210480's 1,000 bp H3K9 binning, where a 147 bp query returns one number. The trap this project was burned by does not bite this dataset, and that is a measurement, not an assumption. **The peak-level answer, which needs no model.** **Zero called IDR/replicated peaks in any of the seven intervals, in 13 of 13 experiments** - the 90,377 bp gene, the 7,466 bp breakpoint cluster core, the 1,048 bp exon-11 CTCF element, the 147 bp exon 11, the summit +/-500 bp, the DCAL cut point +/-500 bp and the TSS +/-1 kb. Genome-wide these sets hold 280 to 26,789 peaks. **The signal-level answer, with a gate that excluded two tracks.** Pre-registered control **C1**: a track's own top-500 peaks must read at least 5x the genome-wide 1,048 bp tile median or the track is uninterpretable. **11 of 13 pass** (ratios 7.9x to 57.6x). **Two fail and are excluded from the verdict, not quietly dropped**: CBX3 GM12878 `ENCFF196UXL` at 4.57x with only **280** peaks genome-wide, and BRCA1 K562 `ENCFF431CIQ` at 3.93x. Note what that costs - **the GM12878 CBX3 experiment, one of the two blood-line CBX3 datasets Q32's absence entry rested its `measured-not-analysed` class on, is the weakest track in the whole set.** Over the 11 passing tracks, against 33,523 to 20.6 million same-width tiles per track: | interval | fold over the genome-wide median of same-width tiles (min / median / max) | |---|---| | **KMT2A gene, 90,377 bp** | 0.785 / 1.081 / 1.245 | | **BCR core, 7,466 bp** | **0.566 / 1.001 / 1.235** | | **exon-11 CTCF element, 1,048 bp** | 0.502 / 1.262 / 2.053 | | CTCF summit +/-500 bp | 0.515 / 1.265 / 2.109 | | DCAL cut point +/-500 bp | 0.539 / 0.966 / 1.568 | | exon 11, 147 bp | 0.595 / 3.344 / 9.157 | | KMT2A TSS +/-1 kb | 0.341 / 2.135 / 5.366 | **Two intervals looked positive against the genome and BOTH dissolve against a matched null. That is the methodological result of this beat.** **The promoter.** The KMT2A TSS reached the top 0.07% of all 2 kb tiles genome-wide in the best track, which reads like a finding. Pre-registered control **C2** measured four housekeeping promoters (ACTB, GAPDH, RPLP0, EEF1A1, TSS fetched live from Ensembl) in the **same track**: **KMT2A-TSS divided by the median housekeeping promoter is 0.63 to 1.80, median 1.24 across the 11 passing tracks.** The KMT2A promoter is an ordinary promoter. The genome is the wrong null for a promoter, and a top-0.1% genome rank there carries almost no information. **The element.** BRCA1 in H1 and HeLa-S3 read 1.92x and 2.05x the genome at the 1,048 bp element, top 2.8% and 3.5%, with 147 bp cores at 6.95x and 9.16x - the closest thing to a positive in this beat. So the element was ranked against **6,000 conservative-IDR CTCF anchors of the same cell type**, 1,048 bp centred on each peak centre, which is the null this project's CTCF anchor work already established as the right one. **The KMT2A element falls BELOW the median CTCF anchor in 10 of 13 tracks**, at 0.34x to 1.25x of it; H1 BRCA1 is 1.20x (70th percentile of anchors) and HeLa BRCA1 1.24x (69th percentile). **The apparent enrichment was the generic CTCF-anchor effect, not BRCA1 at KMT2A.** **And the element is genuinely there, in every cell.** A conservative-IDR CTCF peak sits on it in all six biosamples - K562 signalValue 242.8, GM12878 295.3, HeLa-S3 142.9, H1 132.8, HCT116 128.3, HepG2 87.0 - spanning chr11:118,488,551-118,488,827 at widest, which independently re-verifies this graph's element and its 118,488,694 summit against files nobody in this project had opened. **So the negative is not "the anchor is absent in these cells". The anchor is present, CTCF is on it, and BRCA1, HP1-gamma and HP1-beta are not.** **VERDICT: NO OCCUPANCY ABOVE BACKGROUND**, for BRCA1, CBX3 and CBX1, at the KMT2A gene, its breakpoint cluster core, its exon-11 CTCF element and its DCAL cut point, in every released ENCODE cell type including both blood lines, in the undamaged resting state. Complete run: 13 of 13 signal tracks and 13 of 13 anchor-matched runs, zero failures.
Go deeper
The per-track table, all thirteen
Fold values are over the genome-wide median of same-width tiles in that track. The anchor column is the 1,048 bp element divided by the median of 6,000 same-cell-type CTCF anchors. 1
| target | cell | signal file | C1 gate | BCR core fold | element fold | element / CTCF-anchor median | peaks in gene |
|---|---|---|---|---|---|---|---|
| BRCA1 | GM12878 | ENCFF017KXT | PASS | 0.753 | 0.776 | 0.56 | 0 |
| BRCA1 | H1 | ENCFF620MRE | PASS | 1.003 | 1.920 | 1.20 | 0 |
| BRCA1 | HeLa-S3 | ENCFF690UED | PASS | 1.089 | 2.053 | 1.24 | 0 |
| BRCA1 | HepG2 | ENCFF133FPU | PASS | 1.123 | 1.616 | 0.99 | 0 |
| BRCA1 | HepG2 | ENCFF191NNV | PASS | 0.881 | 1.262 | 0.75 | 0 |
| BRCA1 | K562 | ENCFF431CIQ | FAIL | 1.391 | 0.951 | 0.51 | 0 |
| BRCA1 | K562 | ENCFF493XJG | PASS | 1.001 | 0.994 | 1.25 | 0 |
| CBX1 | HepG2 | ENCFF895JUC | PASS | 0.700 | 0.864 | 0.43 | 0 |
| CBX1 | K562 | ENCFF058NFI | PASS | 0.945 | 1.202 | 0.73 | 0 |
| CBX3 | GM12878 | ENCFF196UXL | FAIL | 1.013 | 0.685 | 0.79 | 0 |
| CBX3 | HCT116 | ENCFF845YDA | PASS | 1.235 | 1.282 | 0.76 | 0 |
| CBX3 | K562 | ENCFF051QOQ | PASS | 1.140 | 1.859 | 0.89 | 0 |
| CBX3 | K562 | ENCFF888LWP | PASS | 0.566 | 0.502 | 0.34 | 0 |
Read the last two columns together. No track has a called peak in the gene, and in 10 of 13 the element sits below the median CTCF anchor of its own cell type.
Why the genome-wide null was not enough, twice
This beat pre-registered three nulls and needed all three. 1
The promoter case. Against 1.5 million 2 kb tiles the KMT2A TSS reached the top 0.07% in CBX1/HepG2, the top 0.15% in BRCA1/GM12878 and the top 0.23% in CBX1/K562. Reported that way it is a finding. Against the four housekeeping promoters measured in the same track, the ratio is 0.63-1.80 with a median of 1.24. A promoter compared to the genome is being compared mostly to intergenic DNA.
The anchor case. Against the genome the element reached 2.05x and the top 3.5% in BRCA1/HeLa-S3. Against 6,000 CTCF anchors of the same cell type it is 1.24x the anchor median, the 69th percentile. The enrichment belonged to the class of site, not to this site.
This is rule 84 in a genomics setting: the proportion that needed a null was the one that felt like an observation.
What a 147 bp number means here, and what it meant in GSE210480
This project was burned by quoting a 147 bp interval from 1,000 bp binned H3K9 tracks, where the query returns a single value. The bin size was therefore measured per file before any narrow interval was quoted. 1
These ENCODE bigWigs are base-resolution: modal run length 1 bp in 11 of 13 files, median run length 3-15 bp, minimum 1 bp, and 3,194-21,772 raw intervals across the 90,377 bp gene. A 147 bp query here averages tens of independent values.
So the exon-11 numbers are real measurements - and they are still not occupancy. BRCA1 reads 9.16x in HeLa-S3 and 6.95x in H1 at 147 bp, but 0.74x in K562 and 1.13x/1.53x in the other blood tracks; the containing 1,048 bp element is flat to 2x; no experiment calls a peak there; and the anchor-matched null puts the element below or near the median CTCF site. A sharp sub-kilobase spike inside an unenriched kilobase, present in two non-haematopoietic lines and absent from both blood lines, is the signature of a CTCF-proximal artefact rather than of a resection factor.
What this means for the menin-interface hypothesis
hyp-the-menin-arm-and-the-ctcf-arm-license-consecutive-steps-of-one-resection-reaction proposes that CTCF/H3K9me/HP1-gamma licenses BRCA1/BARD1 long-range resection at this locus. Its FALSIFIER 3 asks whether either arm reaches this element, and specifies a damage-state ChIP in a haematopoietic cell with a 1.5-fold threshold. 1
This run does not cash that falsifier and must not be read as doing so. It measures the resting state in non-haematopoietic-progenitor cell lines, which the hypothesis's own model predicts to be negative. What it does is remove the cheap route: there is no longer a public dataset that could settle this without wet work, and the remaining question is squarely never-measured.
The result is mildly unhelpful to the hypothesis in one specific way. HP1-gamma is constitutively chromatin-bound and enriched over transcribed gene bodies, so if the CTCF arm pre-positioned it at this element one might expect some resting-state signal. There is none: CBX3 reads 0.50-1.86x at the element and below the median CTCF anchor in all three passing tracks. That is a weak argument, not a refutation, and it is recorded as such.
Facts and figures
| script | analyses/q35-brca1-cbx3-encode-at-the-kmt2a-locus/q35_one.py (per-track signal, nulls and controls), q35_anchor.py (CTCF-anchor-matched null), q35_peaks.py (peak overlap), q35_encode_census.py |
|---|---|
| design preregistered | analyses/q35-brca1-cbx3-encode-at-the-kmt2a-locus/design.py - written to disk BEFORE any signal value was read, carrying the intervals, the statistic, the three nulls, the named positive controls and the decision rule |
| status | run |
| run date | 2026-09-22 |
| run by | Q35-encode-reanalysis |
| complete run | true |
| n signal tracks | 13 |
| n anchor matched runs | 13 |
| assembly | GRCh38 native for every file; verified per FILE from its own chrom table across chr1, chr2, chr11, chr19, chrX |
| verdict | NO OCCUPANCY ABOVE BACKGROUND for BRCA1, CBX3 and CBX1 at the KMT2A gene, the BCR core, the exon-11 CTCF element and the DCAL cut point, in every released ENCODE cell type including K562 and GM12878, in the undamaged resting state. |
| what this does NOT close | the damage state. Every ENCODE dataset here is an undamaged cultured cell and the cascade in `mechanism-ctcf-primes-repressive-chromatin-for-brca1-bard1-at-a-break` is damage-conditional and minutes-scale. A resting-state negative is what that model PREDICTS, so this result is consistent with the hypothesis as well as with its absence - it removes a cheap route to testing it, it does not adjudicate it. |
| absence class after this run | never-measured (damage state, all cell types) - upgraded from measured-not-analysed, which this run discharges |
| relationship to existing entries | Q110's `ana-q110-h3k9-writer-and-reader-occupancy-at-the-kmt2a-locus` (same cycle as Q32) already ran the PEAK-level check for CBX3, CBX1 and CBX5 in K562 and GM12878 and found zero peaks. This run (a) adds BRCA1, which nobody had done, in seven experiments; (b) adds the HCT116 and second-K562 CBX3 experiments and the HepG2 CBX1 experiment, which Q110's peak arm did not cover; (c) supplies the signal-level answer that Q110 explicitly reported it could NOT give, because its own controls failed - here 11 of 13 tracks pass a stated C1 gate; and (d) adds the promoter-matched and CTCF-anchor-matched nulls, without which two of these intervals read as positive. |
| a contradiction inside this graph that this run resolves | Q32's `absence-no-resection-factor-localised-at-the-kmt2a-locus` says of CBX3 'nobody has looked - this is a compute-only question', while `gene-cbx5`, written in the SAME cycle by Q110, records in its own open_questions that CBX3, CBX1 and CBX5 were checked at peak level that cycle and were negative. Both entries are cycle-62 and neither cites the other. The peak-level claim in gene-cbx5 is correct and is reproduced here independently. |
results
[ "analyses/q35-brca1-cbx3-encode-at-the-kmt2a-locus/results.json" ]
failed tracks
[]
intervals grch38 1based inclusive
{
"kmt2a_gene": "chr11:118,436,456-118,526,832 (90,377 bp) - re-verified live against Ensembl ENSG00000118058 on 2026-09-22",
"bcr_core": "chr11:118,482,422-118,489,887 (7,466 bp)",
"ctcf_element": "chr11:118,488,159-118,489,206 (1,048 bp)",
"exon11": "chr11:118,488,614-118,488,760 (147 bp)",
"ctcf_summit_1kb": "chr11:118,488,194-118,489,194 (summit 118,488,694 +/- 500)",
"dcal_cut_1kb": "chr11:118,484,362-118,485,361 (cut point 118,484,861|118,484,862 +/- 500)",
"kmt2a_tss_2kb": "chr11:118,435,456-118,437,456 (TSS 118,436,456, + strand)"
}encode census 2026 09 22
{
"BRCA1": 7,
"CBX3": 4,
"CBX1": 2,
"CBX5": 4,
"KDM5A": 3,
"BARD1": null,
"EXO1": null,
"DNA2": null
}encode 404 is how this portal spells zero
[ "BARD1", "EXO1", "DNA2" ]
file identity
{
"n_files": 13,
"n_distinct_content_length": 13,
"n_distinct_md5": 13,
"all_head_content_length_equals_portal_file_size": true,
"all_md5_reverified_after_local_download": true
}build check
{
"all_GRCh38_by_own_chrom_table": true,
"any_GRCh37": false,
"chromosomes_checked": [
"chr1",
"chr2",
"chr11",
"chr19",
"chrX"
],
"padding_found": "none"
}bin size per file — the numbers behind the chart
{
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"modal_run_length": [
[
1,
437
],
[
2,
363
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323
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266
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3671
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2877
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"max_run_length": 286
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2164
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1258
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862
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260
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1016
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901
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164
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128
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"min_run_length": 1,
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}
}peak level
{
"n_experiments": 13,
"n_with_any_called_peak_in_any_of_the_7_intervals": 0,
"per_track": {
"ENCFF017KXT": {
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"bcr_core": 0,
"ctcf_element": 0,
"exon11": 0,
"ctcf_summit_1kb": 0,
"kmt2a_tss_2kb": 0,
"dcal_cut_1kb": 0
},
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"exon11": 0,
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"kmt2a_tss_2kb": 0,
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},
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"dcal_cut_1kb": 0
},
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"exon11": 0,
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"kmt2a_tss_2kb": 0,
"dcal_cut_1kb": 0
},
"ENCFF191NNV": {
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"ctcf_element": 0,
"exon11": 0,
"ctcf_summit_1kb": 0,
"kmt2a_tss_2kb": 0,
"dcal_cut_1kb": 0
},
"ENCFF196UXL": {
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"bcr_core": 0,
"ctcf_element": 0,
"exon11": 0,
"ctcf_summit_1kb": 0,
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"dcal_cut_1kb": 0
},
"ENCFF431CIQ": {
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"ctcf_element": 0,
"exon11": 0,
"ctcf_summit_1kb": 0,
"kmt2a_tss_2kb": 0,
"dcal_cut_1kb": 0
},
"ENCFF493XJG": {
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"bcr_core": 0,
"ctcf_element": 0,
"exon11": 0,
"ctcf_summit_1kb": 0,
"kmt2a_tss_2kb": 0,
"dcal_cut_1kb": 0
},
"ENCFF620MRE": {
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"exon11": 0,
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"dcal_cut_1kb": 0
},
"ENCFF690UED": {
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"ctcf_element": 0,
"exon11": 0,
"ctcf_summit_1kb": 0,
"kmt2a_tss_2kb": 0,
"dcal_cut_1kb": 0
},
"ENCFF845YDA": {
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"bcr_core": 0,
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"exon11": 0,
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"kmt2a_tss_2kb": 0,
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},
"ENCFF888LWP": {
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"exon11": 0,
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},
"ENCFF895JUC": {
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"dcal_cut_1kb": 0
}
}
}c1 gate
{
"threshold": "top-500 own IDR peaks mean >= 5x the genome-wide 1,048 bp tile median",
"n_pass": 11,
"n_fail": 2,
"failed": [
{
"file": "ENCFF196UXL",
"target": "CBX3",
"biosample": "GM12878",
"ratio": 4.569071983770032,
"n_peaks_genomewide": 280
},
{
"file": "ENCFF431CIQ",
"target": "BRCA1",
"biosample": "K562",
"ratio": 3.928544724284225,
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]
}genomewide null — the numbers behind the chart
{
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}promoter matched null
{
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}ctcf anchor matched null
{
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}ctcf peak at the element per cell type
{
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}
}per track full table — the numbers behind the chart
{
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"chr": "chr7",
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},
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},
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},
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},
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},
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},
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},
"ctcf_element": {
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"value": 0.47029640667766104,
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"genomewide": {
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"chr11": {
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"ctcf_summit_1kb": {
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"genomewide": {
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"chr11": {
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},
"dcal_cut_1kb": {
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"value": 0.29346188509464266,
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"genomewide": {
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"chr11": {
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},
"exon11": {
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"value": 0.5596157766523815,
"fold_over_gw_median": 1.527726091937723,
"fold_over_chr11_median": 1.3301683593093,
"genomewide": {
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"chr11": {
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}
},
"null_summary": {
"147": {
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"gw_median": 0.36630635531175704,
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"gw_p10": 0,
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"chr11_median": 0.42071048580870335,
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"seconds": 14.7
},
"1048": {
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"seconds": 1.8
},
"2001": {
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"seconds": 1.4
},
"7466": {
"n_tiles_genomewide": 405966,
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},
"90377": {
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"n_tiles_chr11": 1494,
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"seconds": 0
}
},
"kmt2a_tss_over_hk_promoter_median": 1.3319030079118603,
"peaks_in_intervals": {
"kmt2a_gene": 0,
"bcr_core": 0,
"ctcf_element": 0,
"exon11": 0,
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"kmt2a_tss_2kb": 0,
"dcal_cut_1kb": 0
},
"n_peaks_in_gene_plus_100kb": 6,
"ctcf_anchor_matched_null": {
"exp": "ENCSR819WZE",
"target": "CBX1",
"biosample": "HepG2",
"signal_file": "ENCFF895JUC",
"ctcf_peak_file": "ENCFF695QSJ",
"md5_ok": true,
"n_ctcf_anchors_total": 42947,
"n_sampled": 6000,
"anchor_median": 1.0956288030698098,
"anchor_p90": 2.072984152295776,
"anchor_p99": 3.828535992951062,
"anchor_max": 7.122811049905442,
"kmt2a_element_value": 0.47029640667766104,
"kmt2a_element_rank": {
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"rank_from_top": 5705,
"percentile": 4.933333333333334
},
"kmt2a_element_fold_over_anchor_median": 0.4292479399591828,
"kmt2a_peakcentred_value": 0.47029640667766104,
"kmt2a_peakcentred_rank": {
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"percentile": 4.933333333333334
},
"kmt2a_peakcentred_fold_over_anchor_median": 0.4292479399591828,
"complete_run": true
}
}
}independent cross validation of the local pipeline
{
"why_this_exists": "Every number in this analysis was computed from bigWigs downloaded to local disk, because remote random access was unusably slow. That shortcut is only safe if it changes no answer. An abandoned remote-read timing job, started before the switch and left running, finished hours later and supplies an unplanned independent check: a DIFFERENT code path (remote reader, fillna=0, gap tiles NOT dropped, run against the live URL) over the same track and the same four bin widths.",
"track": "ENCFF493XJG (BRCA1, K562)",
"chr11_median_remote_vs_local": {
"147": {
"remote_fillna0": 0.6372,
"local_gaps_dropped": 0.6373,
"diff": 0.0001
},
"1048": {
"remote_fillna0": 0.6759,
"local_gaps_dropped": 0.6759,
"diff": 0
},
"7466": {
"remote_fillna0": 0.7115,
"local_gaps_dropped": 0.7115,
"diff": 0
},
"90377": {
"remote_fillna0": 0.7247,
"local_gaps_dropped": 0.7247,
"diff": 0
}
},
"tile_counts_also_identical": {
"147": 918956,
"1048": 128899,
"7466": 18093,
"90377": 1494
},
"reading": "Agreement to four decimal places at all four widths. The single +0.0001 at 147 bp is the expected consequence of dropping 66 all-NaN gap tiles out of 918,956, which moves the median by one position. The local pipeline reproduces the remote one exactly, so the download-and-delete shortcut introduced no error into any published figure here.",
"measured_cost_of_the_remote_route_chr11_only_one_track": {
"W_90377_1494_bins": "12.7 s",
"W_7466_18093_bins": "29.6 s",
"W_1048_128899_bins": "424.7 s",
"W_147_918956_bins": "5027.7 s (84 minutes)",
"per_bin": "1.6-5.5 ms, roughly linear in BIN COUNT rather than in bytes - it is latency and parse bound, not bandwidth bound",
"local_equivalent": "the whole genome at 147 bp, 20,612,311 bins, in ~15 s - about 7,500x faster per bin",
"extrapolation_that_justified_the_switch": "chr11 is ~4.4% of the genome, so the 147 bp width alone would have cost roughly 32 h per track remotely and about 17 days across 13 tracks. The full design (5 widths x 13 tracks, genome-wide) is not feasible over HTTP at all."
}
}Still open
- Does a double-strand break at the KMT2A breakpoint cluster recruit BRCA1, CBX3 or CBX1 in a haematopoietic progenitor? That is now the only remaining form of the question and it is `never-measured` in every cell type - this run has closed the compute-only route.
- Is the exon-11 BRCA1 signal in H1 and HeLa-S3 (6.95x and 9.16x at 147 bp, absent from both blood lines) a CTCF-proximal artefact or a genuine cell-type-restricted event? Ranking that 147 bp window against 147 bp windows centred on CTCF summits, rather than against the element, would settle it in one more pass.
- How many of this graph's other locus-level occupancy claims were scored against a genome-wide null where a class-matched null was available? Two of the seven intervals in this beat changed verdict between the two nulls, and the corpus has not been swept for the pattern.
- Is there a released ENCODE or IHEC BRCA1 or CBX3 dataset in a CD34+ progenitor or any KMT2A-rearranged line? This beat searched ENCODE only; a negative IHEC and GEO sweep would convert the cell-type caveat from an assumption into a bound.
Every source behind this entry (4)
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
All thirteen released human BRCA1, CBX3 and CBX1 TF ChIP-seq experiments in ENCODE carry GRCh38 fold-change-over-control signal tracks and IDR-thresholded peak sets, and none of their peak sets contains a called peak anywhere in the KMT2A gene, its breakpoint cluster core or its exon-11 CTCF element.
ENCODE Portal: released human TF ChIP-seq experiments for BRCA1, CBX3 and CBX1, queried and downloaded 2026-09-22 · ENCODE Project Consortium · ENCODE Portal 2026What this evidence cannot show
Every dataset is an undamaged, unsynchronised cultured cell line, and none is a primary haematopoietic progenitor or a KMT2A-rearranged cell. K562 is CML-derived erythroleukaemic and GM12878 is an EBV-transformed lymphoblastoid line; neither is the infant B-lineage progenitor this graph is about. A peak set is an IDR-thresholded call and a sub-threshold enrichment would not appear in it - which is why the signal-level arm was run as well.
Evidence that argues against this (1)
- A called-peak absence is bounded by the peak caller and its threshold. Two of these experiments produced only 280 and 815 peaks genome-wide, an order of magnitude below their siblings, and a peak absence in a 280-peak set is close to uninformative. This is why the C1 gate was pre-registered and why the CBX3 GM12878 track is excluded from the verdict. ENCODE Project Consortium 2026
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
ENCODE's uniform ChIP-seq processing pipeline produces the fold-change-over-control signal tracks and IDR-thresholded peak sets used here, on GRCh38, with the file-level metadata (md5, size, assembly, output type, biological replicates) that made the per-file build and identity checks possible.
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. · Luo Y, et al. · Nucleic Acids Res 2020What this evidence cannot show
A portal paper documents the pipeline, not the quality of any individual experiment. Antibody validation, crosslinking and depth differ between the 2011-era ENCODE2 experiments and the later ones in this set, and two tracks failed this beat's own dynamic-range gate.
Evidence that argues against this (1)
- The encyclopedia paper's own framing is that ENCODE's value is aggregate and genome-wide; it makes no claim that any single track supports a locus-level negative, which is the use made of it here. ENCODE Project Consortium 2012
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
The chr19q13 KRAB-ZNF cluster is the canonical HP1/SETDB1/TRIM28 target class and was therefore pre-registered as the biological positive control for the HP1 paralogues; in this run the HP1 tracks read 1.36x to 2.57x over ZNF274, ZNF544, ZNF211, ZNF264 and ZNF460 gene bodies while the BRCA1 tracks read 0.65x to 1.22x, so the control discriminates in the expected direction.
ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. · Frietze S, et al. · PLoS One 2010What this evidence cannot show
The founding paper is about ZNF274 and SETDB1, not about HP1 paralogue occupancy per se, so this control is an inference from the shared H3K9me3 domain rather than a direct published HP1 measurement at these genes. The observed HP1 enrichments are modest (1.4-2.6x) and would not on their own be called occupancy under this beat's own decision rule - the control establishes direction, not magnitude.
Evidence that argues against this (1)
- Q110 found that a window labelled ZNF274 at chr19:57,996,000-58,000,000, inherited across two of this project's analyses, is not ZNF274 in either assembly - it is 187 kb away in GRCh38. This run fetched ZNF274 live from Ensembl (chr19:58,183,029-58,215,964, ENSG00000171606) and independently reproduces Q110's corrected coordinate, so the two agree and the old window should not be reused. Ensembl 2026
- E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
A conservative-IDR CTCF peak sits on the KMT2A exon-11 element in all six biosamples used here - K562, GM12878, H1, HeLa-S3, HepG2 and HCT116 - spanning at widest chr11:118,488,551-118,488,827, so the element is occupied by CTCF in every cell in which BRCA1, CBX3 and CBX1 were found absent from it.
ENCODE Portal: conservative IDR thresholded CTCF ChIP-seq peaks, GRCh38, in K562, GM12878, H1, HeLa-S3, HepG2 and HCT116, downloaded 2026-09-22 · ENCODE Project Consortium · ENCODE Portal 2026What this evidence cannot show
One CTCF experiment per cell type was used, chosen as the first with a GRCh38 conservative or optimal IDR peak set; no replicate-across-experiments check was done for CTCF itself. The peak intervals are 140-276 bp and centre on exon 11, consistent with but not independent confirmation of the 118,488,694 summit this graph carries.
Evidence that argues against this (1)
- CTCF sites are among the commonest sources of non-specific ChIP signal, so the presence of a strong CTCF anchor is itself a reason to expect spurious enrichment for unrelated factors - which is exactly what the anchor-matched null was built to absorb, and after absorbing it the KMT2A element falls below the median anchor in 10 of 13 tracks. ENCODE Project Consortium 2026
Connected to
7 released ENCODE BRCA1 ChIP-seq experiments read at the KMT2A locus; no occupancy above background
4 released ENCODE CBX3 experiments, 3 passing the dynamic-range gate; no occupancy above background
2 released ENCODE CBX1 experiments added by this beat; no occupancy above background
- related to →KMT2A / MLL1 — the gene that breaks
the locus interrogated: gene span, BCR core, exon-11 CTCF element, DCAL cut point and TSS
carries out the measured-not-analysed prescription of that entry and returns a negative
independently reproduces the zero-peak result for CBX3 and CBX1 and supplies the signal-level arm Q110 reported it could not give
conservative-IDR CTCF peaks on the element in all six biosamples re-verify the element and its summit
CTCF is demonstrably on the element in all six cell types in which the resection factors are absent from it
reuses the anchor-matched ranking design of that analysis, here for BRCA1/CBX3/CBX1 rather than for the mark
resting-state arm only - does NOT cash FALSIFIER 3, which specifies a damage state in a haematopoietic cell
finds no resting-state pre-positioning of HP1-gamma or BRCA1 at this element, which the mechanism does not require
the two verdict flips that this concept generalises from
records what remains of the absence after that compute was run
the occupancy measurement in this entry
same three experiments, IDR step removed: the occupancy conclusion does not survive, the peak-level statement and the class-matched null do