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Cohesin Loss Eliminates All Loop Domains
Open accessPublished version of a preprint
Abstract
SUMMARY The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci – almost always bound by CTCF and cohesin – lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation, but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes, and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although reformation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.
Overview
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Written from the paper’s full text.
TL;DR
Cohesin degradation in HCT-116 cells eliminates all loop domains while leaving compartment domains and histone marks intact, and cohesin restoration rapidly re-forms many loops. Loss of cohesin also strengthens superenhancer links and affects transcription of a small minority of genes, often near superenhancers.
Key findings
- Untreated cells had 3,170 loops, including 2,140 loop domains; after auxin-induced RAD21 degradation, only 9 loop domains were called and all were false positives. Compartmentalization was preserved (mean Pearson’s r = 0.968 across chromosomes).
- Loop-domain recovery varied widely: of 2,038 loop domains analyzed, fast domains (>95th percentile) were 159-fold more likely than slow domains (<5th percentile) to span superenhancers (2.94 vs. 0.02 SEs/Mb) and 26-fold more likely to contain strong NIPBL sites (4.23/Mb vs. 0.17/Mb). Many megabase-sized loops recovered in under an hour; a ~900 kb loop restored within 40 minutes implied extrusion of at least 375 bp/s, or at least 188 bp/s per subunit.
- Cohesin loss produced 61 cohesin-independent loops, with 203 interchromosomal links; their anchors were enriched for superenhancers (41 of 64 anchors overlapped the 387 HCT116 superenhancers, 37.5-fold enrichment; top 100 superenhancers showed 76-fold enrichment).
- Transcription changes were limited: among 14,853 unexpressed genes, 1% (216) were activated; among 12,222 expressed genes, 87% (10,615) changed by less than 30%, 64 genes (0.5%) showed 2-fold change, and 2 genes showed 5-fold change. Downregulated genes were enriched near superenhancers (23 of 49 within 500 kb, 4.8-fold enrichment).
Methods
- Used an auxin-inducible degron in HCT-116 RAD21-mAC cells to degrade RAD21 with 500 µM IAA; confirmed cohesin loss by microscopy and ChIP-Seq for RAD21/SMC1.
- Generated in situ Hi-C maps before and after 6 h auxin treatment (~6 billion contacts: 3.0B untreated, 2.9B treated), plus time-course Hi-C during treatment and withdrawal; analyzed with Juicer, HiCCUPS, Arrowhead, APA, and ADA.
- Performed ChIP-Seq for CTCF and histone modifications, PRO-Seq for nascent transcription with DESeq2 and Drosophila spike-in controls, and molecular dynamics simulations combining loop extrusion and compartmentalization.
Limitations
- The paper states that extrusion-speed estimates are lower bounds because they ignore auxin clearance and cohesin re-loading time; that modest transcriptional effects cannot be dismissed as unimportant; and that simulations do not rule out a central role for protein chaperones in vivo.
- The paper notes a higher false-discovery rate for loop calling after cohesin loss, karyotypic abnormalities/rearrangements in HCT-116, and the need for further in vivo and in vitro experiments on oligonucleosome-scale segregation.
- Evident from the text: findings rely mainly on one cell line (HCT-116), use a 6 h early timepoint for PRO-Seq, and include manually curated cohesin-independent loop lists, which may limit generalization.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Strikingly, the loop domains disappeared upon cohesin loss.”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains are rapidly lost after degradation of cohesin
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“and 26-fold more likely to contain strong NIPBL binding sites (4.23/Mb vs. 0.17/Mb) (Fig. S2E–F).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains spanning NIPBL and superenhancers recover more rapidly
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In the untreated cells, our algorithms annotated 3,170 loops, of which 2,140 were loop domains.”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains are rapidly lost after degradation of cohesin
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“or in the plaid pattern, as defined by the eigenvectors of the Hi-C correlation map (Fig. 3A; mean Pearson’s r = 0.968 across all chromosomes).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loss of cohesin is associated with stronger genome compartmentalization
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Following auxin treatment, there is no significant change in either the compartment domains, as defined by the presence of the corresponding squares along the diagonal in the Hi-C contact map (Fig. 3B; see Methods)”
§ Cohesin loss eliminates all loop domains > RESULTS > Loss of cohesin is associated with stronger genome compartmentalization
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Fast loop domains (recovery rate > 95th percentile) were 159-fold more likely than slow loop domains (<5th percentile) to span an SE (2.94 SEs/Mb vs. 0.02 SEs/Mb)”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains spanning NIPBL and superenhancers recover more rapidly
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The disappearance of the loop-domain links closely mirrored the depletion of cohesin levels in the samples during the treatment period, as ascertained by measuring mClover fluorescence (Fig. S1).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains are rapidly lost after degradation of cohesin
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In the paper
“By contrast, loop domains that recovered slowly were typically depleted for these features, but enriched for repressive marks like H3K27me3 and H3K9me3 (Fig. 2D–E, Fig. S2D–F, Data S1, II).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains spanning NIPBL and superenhancers recover more rapidly
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Cohesin loss had little effect on these features (Fig. 1C,D; Fig. S1C–E, see Methods).”
§ Cohesin loss eliminates all loop domains > RESULTS > Histone modification patterns are unaffected by cohesin loss
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In the paper
“We examined the distribution of CTCF (associated with loop anchors) and the histone modifications H3K27me3, H3K36me3, H3K27Ac, H3K4me1, H3K4me3, H3K9me3, H4K16Ac, H4K20me3, H3K79me2, and H2.AZ (associated with compartment intervals). Cohesin loss had little effect on these features”
§ Cohesin loss eliminates all loop domains > RESULTS > Histone modification patterns are unaffected by cohesin loss
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Whereas loop domains disappear entirely after cohesin loss, compartmentalization is preserved (Fig. 3A).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loss of cohesin is associated with stronger genome compartmentalization
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In the paper
“After auxin was withdrawn, the APA signal quickly increased, largely recovering by 1 hour (Fig. 2B, S2B).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains are rapidly lost after degradation of cohesin
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In the paper
“Faster recovery was strongly associated with high levels of NIPBL binding between the loop anchors, as well as enrichment of promoter and enhancer elements, and of activating histone marks like H3K36me3 and H4K16Ac.”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains spanning NIPBL and superenhancers recover more rapidly
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Moreover, the algorithms found only 9 loop domains after auxin treatment. Upon close inspection, all were found to be false positives (see Methods).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains are rapidly lost after degradation of cohesin
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
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In the paper
“we were able to calculate individual recovery curves for 2038 of the 2140 loop domains observed in the untreated cells (Fig. 2C, see Methods).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains spanning NIPBL and superenhancers recover more rapidly
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
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In the paper
“The APA signal was initially strong, but was gone by 40 minutes after treatment, and remained absent throughout the rest of the treatment period (Fig. 2B, S2B).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains are rapidly lost after degradation of cohesin
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In the paper
“Strong effects were infrequent: 64 genes (0.5%) showed a 2-fold change, and 2 genes showed a 5-fold change (Fig. 7B).”
§ Cohesin loss eliminates all loop domains > RESULTS > Cohesin loss results in strong down-regulation of genes near superenhancers, but does not bring about widespread ectopic activation
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In the paper
“We also found that the superloops tend to occur simultaneously, forming hubs containing 3 or more loci.”
§ Cohesin loss eliminates all loop domains > RESULTS > Links between superenhancers strengthened after loss of cohesin
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
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In the paper
“By contrast, in the presence of cohesin, the majority of these superenhancers were located in the interior of cohesin-associated loop (in 13 of 19 cases) and the long-distance cohesin-independent links were much weaker.”
§ Cohesin loss eliminates all loop domains > RESULTS > Cohesin loss results in strong down-regulation of genes near superenhancers, but does not bring about widespread ectopic activation
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
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In the paper
“Whereas 1,030 such loops were annotated in untreated cells, only 72 were annotated after cohesin loss.”
§ Cohesin loss eliminates all loop domains > RESULTS > Links between superenhancers strengthened after loss of cohesin
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In the paper
“In the former case, the correlation in the genome-wide contact pattern on opposite sides of compartment boundaries showed a much greater decrease in treated vs. untreated cells—that is, the plaid pattern across the genome became much stronger in the absence of cohesin (Fig. 3C–E, Data S1,III).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loss of cohesin is associated with stronger genome compartmentalization
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“We identified 57 million unique “triples,” which bring together 3 loci; 32 million unique quadruples, and 130 thousand quintuples (Fig. 5B, see Methods).”
§ Cohesin loss eliminates all loop domains > RESULTS > Links between superenhancers strengthened after loss of cohesin
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“We found that histone tail interactions overcame constraints on the chromatin chain, leading either to focal contacts between short chromatin intervals or to global condensation, depending on the initial configuration and epigenetic state of the fiber (Fig S6C–E).”
§ Cohesin loss eliminates all loop domains > RESULTS > Molecular dynamics simulations integrating extrusion and compartmentalization can recapitulate Hi-C experimental results
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“In total, we identified 203 such interchromosomal links.”
§ Cohesin loss eliminates all loop domains > RESULTS > Links between superenhancers strengthened after loss of cohesin
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“Empirically, this max threshold removed peak annotations due to rearrangements; notably, nearly the same number of annotated peaks were removed from the untreated and the treated annotations, 277 and 269 respectively.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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“We annotated 9,845 domains in our untreated maps and 2,090 domains in our treated maps.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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“Notably, loops and links between superenhancers increase in strength rapidly following cohesin loss, reaching a plateau within hours.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Two classes of loops
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“In the end, we annotated 3,170 loops in our untreated maps and 81 loops in our treated maps.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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“We observed similar fractions of reads mapping to the Drosophila spike-in in the matched pairs of degron-expressing and control replicate experiments, indicating that there are not significant global changes in the total amount of transcription upon cohesin loss.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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“By contrast, our maps after auxin treatment show complete loss of APA signal and no visible focal enrichment, even when APA is performed on low resolution data sets (Fig. 2B, S2C).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“Similarly, the top 10% of loop domains by density of H3K27Ac peaks (>=54.4 peaks/Mb) showed 38% recovery by 40 minutes, while the bottom 10% of loop domains by density of H3K27Ac (<=2.76 peaks/Mb) showed only 8% recovery by 40 minutes (Fig. S2D).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“We then calculated the correlation of the eigenvector for each chromosome between untreated and treated maps. The mean correlation was 0.968.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“Of the 9, 8 were false positives due to rearrangements in HCT-116 cells and one was a false positive due to extensive compartmentalization that was mistakenly annotated as a loop by HiCCUPS.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“We identified 4,325 boundaries in untreated cells for a median compartment size of 425 kb and 4,424 boundaries in treated cells for a median compartment size of 475 kb.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“While the ADA scores for all domains show a sharp decline in the first 60 minutes after auxin treatment, they plateau above 1, indicating some residual domain signal from al domains.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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“High overlap (90%, 85% and 81% respectively) was seen for all three marks, indicating that the positions of active promoters and enhancers are largely unchanged after cohesin loss (Fig. S1D).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“We observed positive APA scores (>1) and visible focal enrichment in all experiments generated in previous studies, before and after cohesin or CTCF depletion (Fig. S2C).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“We observed similar enrichments of activating factors, and especially strong NIPBL sites and superenhancers at the loop domains that recovered more quickly vs those that recovered more slowly.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“We found that the top 10% of loop domains by density of NIPBL peaks (>=24 peaks/Mb) showed 38% recovery by 40 minutes, while the bottom 10% of loop domains by density of NIPBL peaks (0 peaks/Mb) showed only 11% recovery by 40 minutes.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“After withdrawal of auxin, loop domains form similarly quickly, with strong loop domain signal by 60 minutes after withdrawal.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“When we visually examined these loops, we found that 66 were false positives, with 55 of the false positives due to assembly issues, issues with repetitive elements or structural rearrangements.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“there was a stronger increase in compartmentalization strength at transitions spanned by loop domains (0.01 increase in sliding correlation in untreated vs. 0.03 dip in treated).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“In contrast, when we identified 389 compartment boundaries in treated cells that were positioned at loop domain anchors annotated in untreated cells (within 25kb), we found that there a much more modest increase in compartment strength after treatment: 0.35 decrease in the sliding correlation score in untreated cells vs. 0.53 in treated cells (Fig. 3E).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“However, while there was very little change in the compartmentalization strength at transitions at loop domain boundaries (0.29 dip in sliding correlation in untreated vs. 0.33 in treated),”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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In the paper
“We also found that superenhancers were strongly enriched at loop anchors generated from the 88 loop list automatedly called with low resolution HiCCUPS; the top 100 superenhancers were 47-fold enriched (present at 30/115 loop anchors).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“After visual examination, we found that 46 of these loops corresponded to true positives while the other 42 were false positives (22 were due to issues with repetitive regions and 15 were due to other forms of structure in the contact map, for instance interactions between broad compartment intervals).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We saw an 0.41 decrease in the sliding correlation score in untreated cells vs. 0.50 decrease in treated cells for H3K27Ac transitions spanned by loops, and an 0.10 decrease in the sliding correlation score in untreated cells versus an 0.26 decrease in treated cells for H3K27Ac transitions at loop anchors (Fig S3B).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“This annotation yielded 88 loops.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
What the sources say
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. The quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We also performed the analyses listed above on automated lists of cohesin-independent loops without any manual curation. We found that the results showing a lack of CTCF binding at cohesin-independent loop anchors and a lack of CTCF orientation preference were similar (Fig. S4A).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Similar results were seen for H3K27me3 transitions spanned by all loops: we identified 391 H3K27me3 transitions in untreated cells that were spanned by loops and at least 100kb away from either loop anchor, and we identified 469 H3K27me3 transitions in untreated cells that were positioned at loop anchors.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we identified 593 compartment boundaries in treated cells that were spanned by loops and at least 100kb away from either loop anchor, and we identified 503 compartment boundaries in treated cells that were positioned at loop anchors.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We first identified the loop anchors contributing to the cohesin-independent loops. We merged all adjacent loci involved in one of the 61 loops annotated above. We then expanded all loop anchor loci to be 100kb in size, yielding a list of 64 loop anchor loci.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Similar results were seen for H3K27Ac transitions spanned by all loops: we identified 426 H3K27Ac transitions in untreated cells that were spanned by loops and at least 100kb away from either loop anchor, and we identified 381 H3K27Ac transitions in untreated cells that were positioned at loop anchors.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found that while 90% of cohesin-associated loop anchors were associated with CTCF binding, only 20% of cohesin-independent loop anchors were associated with CTCF binding.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We then analyzed the corner scores for each of these sets of domains separately in treated cells and found that while the median score for compartment domains was 89th percentile of the random corner scores, the median score for non-compartment domains was only 72nd percentile of the random corner scores.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“More over, while 95% of unique CTCF motifs in cohesin-associated loop anchors pointed towards the interior of the loop (consistent with the convergent rule), the unique CTCF motifs in cohesin-independent loops did not exhibit any such bias (56% pointing towards the interior of the loop) (Fig. 4C).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“To test this, we identified 974 contact domains whose boundaries overlapped a compartment interval boundary (within 25 kb), i.e. compartment domains. Additionally, we identified 410 contact domains whose boundaries were not within 100 kb of a compartment boundary even after using a relaxed threshold for identifying compartment boundaries, i.e. a high confidence set of non-compartment domains.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We saw an 0.11 decrease in the sliding correlation score in untreated cells vs. 0.37 decrease in treated cells for compartment boundaries spanned by loops, and an 0.38 decrease in the sliding correlation score in untreated cells versus an 0.54 decrease in treated cells for compartment boundaries at loop anchors (Fig S3D).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Using this procedure, we annotated 81 loops in treated RAD21-mAC cells.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
What the sources say
- Not checked yetcites Durand et al., 2016b
- Not checked yetcites Rao et al., 2014 source
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. The quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We observed that the boundaries contained within loop domains showed a strong increased in compartment strength (larger dip in the sliding correlation score) after the elimination of loop domains: 0.10 decrease in the sliding correlation score in untreated cells vs. 0.31 in treated cells.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We saw an 0.27 decrease in the sliding correlation score in untreated cells vs. 0.31 decrease in treated cells for H3K27me3 transitions spanned by loops, and an 0.03 decrease in the sliding correlation score in untreated cells versus an 0.12 decrease in treated cells for H3K27me3 transitions at loop anchors (Fig S3C).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As seen in the contact maps and corresponding images in Fig. S6E, demarcated zones emerge in the ensemble of the alternating constructs: the wt nucleosomes segregate from the other nucloeosmes as well tend to associate with one another, while the folded-tail nucleosomes segregate separately.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“APA analysis clearly demonstrated that while cohesin-independent links (both intra and interchromosomal) were weakly present before auxin treatment, they were ~2-fold strengthened after auxin-treatment (Fig S4C,D).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:boosted· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Using our triple dataset as well as the Poisson projection of our quadruples, we identified 11 contacts that fell within the center voxel of the 3D-APA sub-tensor in our auxin-treated dataset, where as we saw none in our untreated dataset.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Results with only H4 tails folded (mimicking H4K16Ac) are very similar to the case of all-folded tails (data not shown).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Stronger effects were seen, but less frequently: 64 genes (0.5%) showed a 2-fold change, and 2 genes showed a 5-fold change (Fig. 7B).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“APA scores for cohesin-independent links rapidly increased upon auxin treatment and rapidly dropped upon auxin withdrawal (Fig. 4E).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We noticed that our 64 cohesin-independent loop anchors determined from our 61 loop intrachromosomal list often formed focal interchromosomal links between pairs of loop anchors and that there were large cliques of interactions between anchors (Fig. 4A,E, 5A).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“With this procedure, we obtained 32M triples, 18M quadruples, and 75K quintuples in our untreated data set, and 25M triples, 14M quadruples and 55K quintuples in our treated data set.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Similar results were seen upon performing the time course APA at 100kb resolution using all intrachromosomal pairs of the 47 superenhancer overlapping anchors in the 88-loop automated list from above (Fig. S4E).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“The alternating construct tends to adopt an overall figure-8 shaped fold or hierarchical loop (Grigoryev et al., 2016).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
What the sources say
- Not checked yetcites Grigoryev et al., 2016 source
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“1.4% of these genes were significantly downregulated (>1.3-fold change), but it is unclear what reductions in expression at such low levels of expression mean biologically.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While we did not observed many quintuples, we did observe high rates of quadruples, so we devised several strategies to project quadruples onto triple space in order to use them along with our triples in searching for hubs.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“With this procedure, we obtained 32M triples, 18M quadruples, and 75K quintuples in our untreated data set, and 25M triples, 14M quadruples and 55K quintuples in our treated data set.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“To look for signs of ectopic activation, we examined the 14,853 genes that were not expressed (RPKM<0.5) in untreated cells. We identified 2,145 genes that were significantly (adjusted p<0.05) changed by DESeq2.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The most dense regions in the contact maps of the alternating constructs come from wt/wt local and nonlocal interactions. These are followed by the local folded/folded and wt/folded interactions.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Using this procedure, we identified 203 interchromosomal cohesin-independent links.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesThe quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Stronger effects were seen, but less frequently: 64 genes (0.5%) showed a 2-fold change, and 2 genes showed a 5-fold change (Fig. 7B).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We next looked for changes in the 12,191 genes that were expressed (RPKM>0.5) in untreated cells (Fig. 5B). We identified 4,251 genes that were significantly changed (adjusted p<0.05) changed by DESeq2.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The overall distribution of distance to the nearest superenhancer was shifted significantly closer compared to randomly selected genes (Fig. S7D).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesThe quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Stronger effects were seen, but less frequently: 86 genes (1%) showed a 2-fold change, and 3 genes showed a 5-fold change (Fig. S7C).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. The quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In addition, 7% of these genes (1179) exhibited “leaky” transcription in treated cells: a larger PRO-Seq signal (p<0.05, >1.3 fold change difference) that fell short of the threshold for an expressed gene (i.e., RPKM was still below 0.5).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We identified 43 genes that were 2-fold downregulated with p<0.05 after auxin treatment.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The remaining genes (15%, 1861) showed a larger transcriptional effect (p<0.05, >30% change in RPKM).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“1.8% of these genes were strongly downregulated (>1.3-fold change), but it is unclear what reductions in expression at such low levels of expression mean biologically.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of those 15 loops and the 12 genes associated with them, 9 were not expressed in HCT-116 (of the other three, two were downregulated, and one was upregulated).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We noticed that many of the genes that were downregulated (by >2-fold) were located within 500kb of superenhancers (28 of 43).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Stronger effects were seen, but less frequently: 86 genes (1%) showed a 2-fold change, and 3 genes showed a 5-fold change (Fig. S7C).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. The quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of these genes, 49% (21 of 43) were located with 500kb of one of the top 100 superenhancers.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of those 15 loops and the 12 genes associated with them, 9 were not expressed in HCT-116 (of the other three, two were downregulated, and one was upregulated).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Our data is consistent with a previous report that genome compartmentalization is preserved after depletion of cohesin (Seitan et al., 2013) or CTCF (Nora et al., 2017).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loss of cohesin is associated with stronger genome compartmentalization
What the sources say
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Consistent with this, deletion of CTCF sites interferes with loop and contact domain formation (Guo et al., 2015; Sanborn et al., 2015; de Wit et al., 2015).”
§ Cohesin loss eliminates all loop domains > INTRODUCTION
What the sources say
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“(The time-resolved maps were not sufficiently deep to assess the 102 loop domains shorter than 100kb.)”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains spanning NIPBL and superenhancers recover more rapidly
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Taken together, these results indicate that the rate of loop domain re-formation varies greatly across the genome, and is associated with factors ranging from cohesin loading to local regulatory activity.”
§ Cohesin loss eliminates all loop domains > RESULTS > Loop domains spanning NIPBL and superenhancers recover more rapidly
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“This suggests that these proteins help regulate genome folding (Merkenschlager and Nora, 2016).”
§ Cohesin loss eliminates all loop domains > INTRODUCTION
What the sources say
- Not checked yetcites Merkenschlager and Nora, 2016
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None of the sources cited for this claim have been checked yet.
In the paper
“Many studies have shown that the insulator protein CTCF and the ring-shaped cohesin complex colocalize on chromatin (Wendt et al., 2008) and lie at the anchors of loops (Rao et al., 2014; Splinter et al., 2006) and the boundaries of contact domains”
§ Cohesin loss eliminates all loop domains > INTRODUCTION
What the sources say
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In any case, it is unclear what effect NIBPL depletion would be expected to have on loop domain formation because, although NIPBL facilitates cohesin loading, it may not be essential for cohesin loading.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Comparison with other studies
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of course, these findings do not rule out a central role for protein chaperones in vivo.”
§ Cohesin loss eliminates all loop domains > RESULTS > Molecular dynamics simulations integrating extrusion and compartmentalization can recapitulate Hi-C experimental results
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, while cohesin plays a role in preventing ectopic activation, most genes remain inactivated even in the absence of cohesin and loop domains.”
§ Cohesin loss eliminates all loop domains > RESULTS > Cohesin loss results in strong down-regulation of genes near superenhancers, but does not bring about widespread ectopic activation
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None of the sources cited for this claim have been checked yet.
In the paper
“In many respects, the cohesin-independent loops resemble the superloops we previously observed on the inactive X chromosome (Darrow et al., 2016; Rao et al., 2014): they are very large (up to 77Mb), the intervals they span do not form contact domains, and their anchors tend to form cliques and are marked by H3K27 acetylation (Fig. S4F).”
§ Cohesin loss eliminates all loop domains > RESULTS > Links between superenhancers strengthened after loss of cohesin
What the sources say
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Finally, an exciting recent experiment demonstrated that deletion of WAPL, a cohesin antagonist that removes cohesin from chromatin, results in the formation of thousands of new loops and loop domains, which are larger than those found when WAPL is intact (Haarhuis et al., 2017).”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Comparison with other studies
What the sources say
- Not checked yetcites Haarhuis et al., 2017 source
Strength:boosted· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We find that cohesin is required for the establishment and maintenance of loop domains.”
§ Cohesin loss eliminates all loop domains > DISCUSSION
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In the paper
“Our data for cohesin depletion is consistent with is study.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Comparison with other studies
What the sources say
- Not checked yetcites Nora et al., 2017 source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The discrepancy may be due to (i) the fact that low resolution Hi-C analysis cannot not distinguish between loop domains, which are sensitive to cohesin depletion, and compartment domains, which are not; and (ii) the possibility that the cohesin depletion was incomplete (Fig. S2C).”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Comparison with other studies
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“—suggesting that cohesin-associated loops may both facilitate activation of promoters by their distal enhancer elements and block activation by inappropriate enhancers, with the former being somewhat more common.”
§ Cohesin loss eliminates all loop domains > RESULTS > Cohesin loss results in strong down-regulation of genes near superenhancers, but does not bring about widespread ectopic activation
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“(ii) compartment structure is strengthened in the absence of cohesin, as loop domains spanning multiple compartment intervals lead to mixing among loci in different compartments;”
§ Cohesin loss eliminates all loop domains > DISCUSSION
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None of the sources cited for this claim have been checked yet.
In the paper
“Indeed, cohesin loading independent of NIPBL has been observed in vitro, albeit at low efficiency (Davidson et al., 2016; Stigler et al., 2016).”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Comparison with other studies
What the sources say
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Our data is consistent with the observation that genome compartmentalization is weakened in cells where the cohesin-antagonist WAPL is knocked out, leading to larger loop domains (Haarhuis et al., 2017).”
§ Cohesin loss eliminates all loop domains > RESULTS > Loss of cohesin is associated with stronger genome compartmentalization
What the sources say
- Not checked yetcites Haarhuis et al., 2017 source
Strength:hedged· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Similarly, RNA polymerase II can push cohesin along DNA (Davidson et al., 2016) but elongation rate estimates (9–90 bp/s; (Jonkers and Lis, 2015)) are slower than what we observe.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > The speed of loop extrusion
What the sources say
- Not checked yetcites Davidson et al., 2016 source
- Not checked yetcites Jonkers and Lis, 2015
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“In order to ensure that our results were not due to the HCT-116 cells stalling in mitosis, we also repeated our Hi-C experiments after cell synchronization and arrest of the cells at the G1/S boundary.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > EXPERIMENTAL MODEL AND SUBJECT DETAILS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Similar results were obtained with Hi-C libraries from synchronized and arrested cells (Data. S1, I)”
§ Cohesin loss eliminates all loop domains > STAR METHODS > METHOD DETAILS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We show that loop domains disappear shortly after auxin-induced cohesin loss, and reappear shortly after auxin withdrawal, implying that (i) they require cohesin both for formation and maintenance; and (ii) they do not represent stable states of chromosome condensation.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > The speed of loop extrusion
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In the paper
“Our data is therefore less consistent with a model where where superenhancer loops form by extrusion, and more consistent with the presence of an alternative mechanism, perhaps based on some form of facilitated diffusion or phase separation (Sanborn et al., 2015).”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Two classes of loops
What the sources say
- Not checked yetcites Sanborn et al., 2015 source
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Loop extrusion cannot create links between loci on different chromosomes.
None of the sources cited for this claim have been checked yet.
In the paper
“We (Sanborn et al., 2015) and others (Alipour and Marko, 2012; Fudenberg et al., 2016; Nasmyth, 2001) have hypothesized that the underlying physical process is the formation of loops by extrusion.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Two mechanisms that guide genome folding
What the sources say
Strength:hedged· not yet calibratedTests✗ Asserted: fails✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The authors may not put it forward as true. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our results are consistent with these findings.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Comparison with other studies
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Finally, for H3K4me1 and H3K27Ac, we filtered peaks called by MACS by requiring an adjusted -log10 p-value of at least 7 and 5 respectively in order to ensure that we had a high quality peak annotation.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“All ChIP-Seq experiments were processed in parallel with whole cell extract input controls.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > METHOD DETAILS
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“These estimates are similar to ones obtained studying the SMC complex in B. subtilis [500–1000 bp/s] (Wang et al., 2017).”
§ Cohesin loss eliminates all loop domains > DISCUSSION > The speed of loop extrusion
What the sources say
- Not checked yetcites Wang et al., 2017 source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our study suggests a model where cohesin-associated looping, by increasing the frequency of contact between loci within loop domains and by disturbing patterns of compartmentalization, facilitates mixing between elements (such as genes and superenhancers) that would otherwise be segregated.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > The interplay between cohesin and gene regulation
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, this loop is extruded at an average rate of no less than 375 bp/s, with each Xcom subunit sliding at no less than 188 bp/s.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > The speed of loop extrusion
Strength:plain· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“earlier studies, using similar methods, that showed a strong correlation between the presence of a loop domain and many-fold increases in the expression of genes at the loop domain anchor (Kagey et al., 2010; Rao et al., 2014).”
§ Cohesin loss eliminates all loop domains > DISCUSSION > The interplay between cohesin and gene regulation
What the sources say
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
In the paper
“In this model, loop domains form when a hypothetical cohesin-based extrusion complex (“Xcom”), which comprises two physically tethered subunits, binds chromatin at a particular location; subsequently, the subunits slide in opposite directions until they arrive at a bound CTCF protein.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Two mechanisms that guide genome folding
What the sources say
- Not checked yetcites Sanborn et al., 2015 source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“By performing PRO-Seq on CMV-OsTIR1 cells with and without auxin treatment, we could control for transcriptional effects of the auxin treatment itself on HCT-116 cells, as well as any consequences of tagging the RAD21 protein.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > METHOD DETAILS
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
In the paper
“For example, modest increases in the expression of receptor tyrosine kinase genes can have meaningful effects on cell proliferation (Flavahan et al., 2016).”
§ Cohesin loss eliminates all loop domains > DISCUSSION > The interplay between cohesin and gene regulation
What the sources say
- Not checked yetcites Flavahan et al., 2016 source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“(Given the correlation between loop reformation speed and Nipbl, loading time may be a significant consideration.)”
§ Cohesin loss eliminates all loop domains > DISCUSSION > The speed of loop extrusion
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, the disappearance of cohesin can eliminate all loop domains without influencing CTCF binding.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Two mechanisms that guide genome folding
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The data presented above are consistent with several models of this process.”
§ Cohesin loss eliminates all loop domains > DISCUSSION > Two mechanisms that guide genome folding
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Similarly, deletion of WAPL appears to increase the processivity of the Xcom, and thus increases the size of loops (Haarhuis et al., 2017).”
§ Cohesin loss eliminates all loop domains > DISCUSSION > The interplay between loop extrusion and compartmentalization
What the sources say
- Not checked yetcites Haarhuis et al., 2017 source
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“We showed in (Rao et al., 2014) that this method does not capture compartment structure accurately at high resolutions; however it is useful for comparing gross compartmentalization patterns.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
What the sources say
- Not checked yetcites Rao et al., 2014 source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Taken together, this suggests that a major confound of previous studies was the incomplete depletion of cohesin or CTCF, and along with the low resolution of the Hi-C experiments, likely explains the limited effects seen.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“indicating that cohesin is required for active maintenance of loop domain structures, not just establishment.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“In addition, we confirmed that the loss of loops/loop domains was not a result of any cell cycle effects; we visually observed loss of loop domains after auxin treatment in G1/S arrested cells (Data S1, I.H-L) and observed similar results to above via APA (Fig. S2C).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This data supports a model in which cohesin is a member of an extrusion complex that slides across DNA, whereas CTCF finds it binding sites independently of the extrusion complex and acts as an oriented brake to halt extrusion complex translocation.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This demonstrates that there is no true hierarchy between compartmentalization and loop domain formation, contrary to what has been suggested in the literature.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Load-bearingStrength:boosted· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, while loop domains are completely eliminated, contact domain structure arising from genome compartmentalization is still present after auxin treatment, although the domains are weaker than those found in untreated cells.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This indicates that cohesin facilitates mixing of distinct compartment states and causes decreases in compartmentalization unless it is halted at the compartment boundary.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This indicates that contact domains were significantly weakened after auxin treatment. However, there was still some residual signal.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“These are very likely conservative upper bounds on the true median compartment size, since we utilized stringent peak calling and compartment structure can be difficult to detect in maps that are not extremely high resolution (Rao et al., 2014).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
What the sources say
- Not checked yetcites Rao et al., 2014 source
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Taken together, these results suggest that cohesin facilitates mixing of chromatin with different histone modification states and loss of cohesin leads to better correspondence of genome compartmentalization with histone modification patterns and gene activity.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This strongly suggests that cohesin-independent loops and links form via a mechanism other than extrusion, since extrusion cannot occur on two topologically distinct molecules..”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The extrusion mechanism cannot act across two separate DNA molecules.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Given the sparsity of our higher-order data set, we were unable to call individual hubs.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“That such a striking segregation effect arises from simple alternating fiber constructs suggests that short chromatin intervals separate in sequence can spontaneously separate in space in specific patterns due to charge effects that alter the intrinsic histone-tail flexibility of specfiic nucleosomes.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:hedged· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
- Rests on an assumption: Alterations in histone-tail flexibility can be caused by chemical modifications of histone tails, DNA, or linker histones, as well as by protein anchoring, which can restrict interactions to specific domains.
In the paper
“Already, we have shown that such domain segregation naturally emerges from nucleosome-free or depleted regions (Bascom, Kim, and Schlick 2017), but here the nucleosome spacing is uniform.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
What the sources say
- Not checked yetcites Bascom, Kim, and Schlick 2017
Strength:boosted· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In fact, it may be the case that some other regulatory event catalyzes both loop formation and gene activation, or that gene activation itself enables loop formation.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✗ Checkable: fails✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, even if this were the case, the fact that we do not see large-scale expression changes between our untagged HCT-116 cells (above) and the auxin-treated RAD21-mAC cells (only 3 genes with a greater than 5-fold change in expression), suggests that the association between loop appearance and strong (>10-fold) gene activation may not be such that loop formation causes gene activation.”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“Our previous analyses (Rao et al 2014) have suggested that a subset of cell-type specific loops is associated with very strong gene activation (>10-fold upregulation of gene expression in the cell type where the loop is present).”
§ Cohesin loss eliminates all loop domains > STAR METHODS > QUANTIFICATION AND STATISTICAL ANALYSIS
What the sources say
- Not checked yetcites Rao et al 2014 source
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
The authors state this as an assumption.
Phase separation leads to the compartmentalization of chromatin intervals bearing similar patterns of histone marks.
“The above simulations assume that phase separation leads to the compartmentalization of chromatin intervals bearing similar patterns of histone marks.”
The paper relies on this without support.
Loop extrusion cannot create links between loci on different chromosomes.
“whereas loop extrusion cannot form interchromosomal links.”
The paper relies on this without support.
HiCCUPS false positives arise from data artifacts that are independent of cohesin-mediated looping.
“as one might expect false positives to arise from artifacts in the data that are independent of cohesin-mediated looping”
The paper relies on this without support.
The extrusion mechanism cannot act across two separate DNA molecules.
“since extrusion cannot occur on two topologically distinct molecules..”
The paper relies on this without support.
The convergent rule—that CTCF motifs at loop anchors point toward the loop interior—is a valid expectation for extrusion-based loops.
“consistent with the convergent rule”
The paper relies on this without support.
Segregated interactions between short chromatin intervals, such as the cohesin-independent loop anchors observed, have not previously been reported.
“Segregated interactions between short chromatin intervals, such as the cohesin-independent loop anchors we observed, have not previously been reported, and require the strength of the interaction between similarly-decorated nucleosomes to overcome the stiffness of the local chromatin fiber.”
The paper relies on this without support.
The biophysical consequences of the H4K16Ac mark are well understood as more rigid tails that inhibit tail/tail internucleosome interactions and disrupt stabilization of condensed chromatin fiber.
“(The biophysical consequences of the H4K16Ac mark have been studied in detail, and are well understood in terms of more rigid tails, which in turn inhibit tail/tail internucleosome interactions and thus disrupt crucial stabilization of condensed chromatin fiber).”
The paper relies on this without support.
Compartment transitions can only be defined in Hi-C maps at coarse resolutions of 25kb and above.
“Because compartment transitions can only be defined in Hi-C maps at coarse resolutions (25kb and above), the compartment transition of each simulation replicate was varied randomly within 30kb (30 monomers) of defined transition points.”
The paper relies on this without support.
Alterations in histone-tail flexibility can be caused by chemical modifications of histone tails, DNA, or linker histones, as well as by protein anchoring, which can restrict interactions to specific domains.
“Such alterations in tail flexibility can be caused by chemical modifications of the histone tails, DNA, or linker histones, as well as by protein anchoring, which can restrict the range of interactions to specific domains.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Finally, the temporary disruption of 3D loops on a genome-wide scale through cohesin depletion was found to have minimal lasting effect on gene expression155,156.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [155]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Surprisingly however, deletion or degradation of cohesin or CTCF in differentiated cells has only mild effects on gene expression [344–349].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [347]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“rapid depletion of cohesin or CTCF quickly abolishes TADs but, as mentioned above, has only relatively mild effects on gene expression [301, 345–347, 448].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [347]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“In mammals and other vertebrates, TADs are formed by the dynamic extrusion of DNA loops [42,43], mediated by cohesin motors [44,45].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [44]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“The A/B compartment structure does not disappear (and is in fact even strengthened) upon cohesin/CTCF depletion [344, 346–348], but, like TADs, dissolves in mitosis [459].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [347]
In the citing paper
“Cohesin binding has been associated with loop formation38, so we further filtered the predictions using the presence of Rad21 binding on both sides of the loop (promoter and enhancer), which resulted in approximately 5,000 loops.”
From Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues (2021) · cites this paper as [38]
In the citing paper
“The cohesin complex is an important architectural protein that organizes the 3D genome and is also important in DSB repair”
From Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration (2023) · cites this paper as [77]
In the citing paper
“loop extrusion mediated by cohesin and CTCF mediates the formation of chromatin loops and self-interacting Topologically Associating Domains (TADs)”
From Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration (2023) · cites this paper as [77]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Ectopic-activation percentage is understated for the control comparison
MinorOf the 14,884 initially unexpressed genes, 255 is 1.71%, which rounds to 2%, not the reported 1%.
Reported 1 · recomputed 1.713249
“Of these genes, 1% (255) were ectopically activated after treatment”
Compartment domains are described as both unaffected and weaker
MinorThe abstract says compartment domains are unaffected by cohesin loss, whereas the Methods say the retained compartment domains are weaker than those in untreated cells.
“All loop domains are eliminated, but neither compartment domains nor histone marks are affected.”
“contact domain structure arising from genome compartmentalization is still present after auxin treatment, although the domains are weaker than those found in untreated cells.”
Histone-mark name differs within the broad-domain analysis
MinorThe analysis lists H4K17Ac among the broad-source marks examined, but gives the resulting boundary count for H4K16Ac. These designate different histone residues.
“Finally, we examined the positions and enrichments of broad source marks (H3K27me3, H3K9me3, H2AZ, H3K36me3, H4K17Ac, H3K79me2).”
“2515 boundaries for H4K16Ac”
Leaky-transcription percentage is understated for the control comparison
MinorThe reported 1,179 genes out of 14,884 constitute 7.92%, which rounds to 8%, not 7%.
Reported 7 · recomputed 7.921258
“In addition, 7% of these genes (1179) exhibited “leaky” transcription in treated cells”
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Wapl is an essential regulator of chromatin structure and chromosome segregation
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Transferable model for chromosome architecture
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Biochemical reconstitution of topological DNA binding by the cohesin ring
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SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing
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Self-citationBacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus
Wang, X., Brandão, H. B., Le, T. B. K., Laub, M. T., & Rudner, D. Z. (2017) · Science · doi:10.1126/science.aai8982 · Cited by 293 · cited 1×
“These estimates are similar to ones obtained studying the SMC complex in B. subtilis [500– 1000 bp/s] (Wang et al., 2017).”
ResultLiu, T. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0512-6_4 · Cited by 284
Genome-wide map of regulatory interactions in the human genome
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Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture
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Self-citationLong-Range Chromatin Interactions
Dekker, J., & Misteli, T. (2015) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a019356 · Cited by 255
Rapid movement and transcriptional re-localization of human cohesin on DNA
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An Overview of Genome Organization and How We Got There: from FISH to Hi-C
Fraser, J., Williamson, I., Bickmore, W. A., & Dostie, J. (2015) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00006-15 · Cited by 232
Single-molecule imaging reveals a collapsed conformational state for DNA-bound cohesin
Stigler, J., Çamdere, G. Ö., Koshland, D. E., & Greene, E. C. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.003 · Cited by 229 · cited 2×
“Indeed, cohesin loading independent of NIPBL has been observed in vitro, albeit at low efficiency (Davidson et al., 2016; Stigler et al., 2016).”
BackgroundChromatin Insulators: Linking Genome Organization to Cellular Function
Phillips‐Cremins, J. E., & Corces, V. G. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.04.018 · Cited by 222
A CTCF Code for 3D Genome Architecture
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Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?
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Identifying dispersed epigenomic domains from ChIP-Seq data
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Cohesin acetylation and Wapl-Pds5 oppositely regulate translocation of cohesin along DNA
Kanke, M., Tahara, E., Huis in't Veld, P. J., & Nishiyama, T. (2016) · The EMBO Journal · doi:10.15252/embj.201695756 · Cited by 136
Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes
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Self-citationCohesin Mediates Chromatin Interactions That Regulate Mammalian β-globin Expression
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Self-citationCause and Consequence of Tethering a SubTAD to Different Nuclear Compartments
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Causes and consequences of nuclear gene positioning
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Multistep assembly of DNA condensation clusters by SMC
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Linking Chromatin Fibers to Gene Folding by Hierarchical Looping
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Self-citationSmall chromosomal regions position themselves autonomously according to their chromatin classPreprint
van de Werken, H. J. G., Haan, J. C., Feodorova, Y., Bijos, D. A., Weuts, A., Theunis, K., Holwerda, S. J. B., Meuleman, W. R. A., Pagie, L., Thanisch, K., et al. (2017) · Genome Research · doi:10.1101/gr.213751.116 · Cited by 43
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Self-citationTwo independent modes of chromosome organization are revealed by cohesin removalPreprint
Schwarzer, W., Abdennur, N., Goloborodko, A., Pękowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C., Mirny, L., et al. (2016) · bioRxiv · doi:10.1101/094185 · Cited by 39
Regulatory Domains and Their MechanismsPreprint
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Coactivator condensation at super-enhancers links phase separation and gene control
Sabari, B. R., Dall’Agnese, A., Boija, A., Klein, I. A., Coffey, E. L., Shrinivas, K., Abraham, B. J., Hannett, N. M., Zamudio, A. V., Manteiga, J. C., et al. (2018) · Science · doi:10.1126/science.aar3958 · Cited by 2,595
HiGlass: web-based visual exploration and analysis of genome interaction maps
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Organizational principles of 3D genome architecture
Rowley, M. J., & Corces, V. G. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0060-8 · Cited by 1,171
Two independent modes of chromatin organization revealed by cohesin removal
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Long-range enhancer–promoter contacts in gene expression control
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Metadata
- Authors
- Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., Huang, X., Shamim, M. S., Shin, J., Turner, D., Ye, Z., Omer, A. D., Robinson, J. T., Schlick, T., Bernstein, B. E., Casellas, R., Lander, E. S., & Aiden, E. L.
- Affiliations
- Baylor College of Medicine (US)
- Broad Institute (US)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (US)
- New York University (US)
- National Institutes of Health (US)
- Corresponding author
- Aiden, Erez Lieberman
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2017-10
- Volume
- 171
- Issue
- 2
- Pages
- 305-320.e24
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC5846482
- OpenAlex
- W2761461280
- Semantic Scholar
- 45bcad8c7fa58b22fa0f17655bcee52b1f47a10a
- Cited by
- 1,883
- References
- 97
- Citations by year
- 2026: 160 · 2025: 210 · 2024: 192 · 2023: 218 · 2022: 217 · 2021: 238 · 2020: 245 · 2019: 237 · 2018: 146 · 2017: 18
- FWCI
- 72.64
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- UWA Profiles and Research Repository (UWA) (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-nd)
- PMC
- Funders
- Paul and Daisy Soros Fellowship
- Fannie and John Hertz Foundation Fellowship
- Cornelia de Lange Syndrome Foundation
- Stanford Medical Scholars Fellowship
- NIGMS (R01GM055164)
- NIH New Innovator Award (1DP2OD008540-01)
- NSF Physics Frontier Center (PHY-1427654)
- NHGRI Center for Excellence for Genomic Sciences (HG006193)
- Welch Foundation (Q-1866)
- NVIDIA Research Center Award
- IBM University Challenge Award
- Google Research Award
- Cancer Prevention Research Institute of Texas Scholar Award (R1304)
- McNair Medical Institute Scholar Award
- NIH 4D Nucleome (U01HL130010)
- NIH Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375)
- President’s Early Career Award in Science and Engineering (4DP2OD008540)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- cohesin, loop domains, 3D genome organization, chromatin looping, CTCF, histone modifications, super-enhancers, loop extrusion, gene expression regulation, chromatin folding
- MeSH terms
- CCCTC-Binding Factor, Cohesins, Cell Nucleus, Chromosomal Proteins, Non-Histone, Chromosomes, DNA-Binding Proteins, Enhancer Elements, Genetic, Humans, Nuclear Proteins, Nucleosomes, Phosphoproteins, Repressor Proteins, Genome, Human, Cell Cycle Proteins, Histone Code, Cell Line, Tumor
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-07, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-07 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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