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The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension
Open accessAbstract
The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show here that chromatin loop size can be increased and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin's DNA release factor WAPL restricts this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.
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TL;DR
In HAP1 cells, WAPL loss stabilizes cohesin on DNA and extends chromatin loops (median 575 kb versus 370 kb in wild-type), while SCC2/SCC4 promotes loop extension; WAPL also enforces convergent CTCF looping and limits nuclear compartmentalization. The authors conclude that cohesin structures chromosomes by processive loop enlargement, balanced by WAPL and SCC2/SCC4.
Key findings
- WAPL restricts chromatin loop extension: ΔWAPL cells showed a median loop length increase of more than 200 kb (575 kb versus 370 kb in wild-type), increased inter-TAD contacts, and pronounced TAD corner peaks; SMC1 ChIP-seq peaks increased from 18,462 to 45,479.
- WAPL enforces the CTCF directionality rule: wild-type HAP1 cells almost exclusively looped convergent CTCF sites, whereas ΔWAPL cells formed loops between tandem-oriented CTCF sites, including at the NCAM2 locus by 4C-seq.
- SCC2/SCC4 promotes loop extension and TAD boundaries: ΔSCC4 cells had shorter loops, reduced cohesin binding sites (18,462 to 5,974), and diffuse TAD boundaries with decreased directionality index; ΔWAPL/ΔSCC4 cells restored loop length and wild-type-like contact maps. The C-terminal part of SCC2 was required for vermicelli cohesin staining.
- Cohesin limits nuclear compartmentalization: ΔWAPL cells had reduced far-cis (>10 Mb) contacts, less strict A/B compartment segregation, and fragmented lamina-associated domains; ΔSCC4 cells had increased far-cis contacts; ΔWAPL/ΔSCC4 resembled wild-type. B-to-A switches covered 46.0 Mb versus 22.8 Mb for A-to-B, and 1,009 genes were differentially expressed.
Methods
- HAP1 cells were used to generate CRISPR knockouts of WAPL, SCC4, and WAPL/SCC4, plus SCC2 truncation mutants; a haploid gene-trap synthetic viability screen compared control and ΔWAPL HAP1 cells.
- Chromosome organization was assayed by high-resolution Hi-C, 4C-seq, CTCF and SMC1 ChIP-seq, RNA-seq, Lamin B1 DamID, FRAP, immunofluorescence, and proliferation/colony-formation assays.
- Computational analyses included HiC-Pro, HICCUPS loop calling, HiCseg TAD calling, directionality index, aggregate peak analysis, PCA-based compartment scoring, and rank-product statistics.
Limitations
- The paper states that it remains unresolved how WAPL-mediated cohesin release enforces CTCF loop specificity, how WAPL/SCC2/SCC4/cohesin modulate specific gene expression changes, and whether SMC complexes provide topological anchors or directly extrude DNA. It also notes that illegally oriented loops remain relatively rare even in ΔWAPL cells.
- The paper states that SCC4 deletion causes near-complete loss of SCC2, so SCC4-deficient cells could not fully separate SCC4 from SCC2 function; SCC2 itself could not be knocked out even in a ΔWAPL background.
- Evident from the text: the work relies on HAP1 cells, which are haploid, p53-mutant, and cancer-derived, and WAPL-null proliferation was attributed to impaired p53 function; the loop-extrusion conclusion is inferred from Hi-C/4C/ChIP/FRAP data rather than direct single-molecule visualization, and only ∼1,000 genes changed expression despite genome-wide loop changes.
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In the paper
“Importantly, we often found TADs that developed pronounced corner-peaks, i.e., peaks at the intersection of the 5′ and 3′ boundary of a TAD, in ΔWAPL cells (Figure 2A).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL-Deficient Cells Accumulate Contacts at TAD Corners
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In the paper
“Notably, ΔSCC4 cells displayed severely reduced SCC2 levels (Figure 3C), presumably due to reduced SCC2 stability in the absence of its binding partner (Hinshaw et al., 2015, Watrin et al., 2006).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL Deficiency Compensates for Impaired SCC2/SCC4 Function
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Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIn the paper
“When we performed systematic loop calling on the full-genome contact maps (Rao et al., 2014), we found that the median loop length increased by more than 200 kb in the ΔWAPL cells compared to the wild-type (575 kb versus 370 kb).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL Restricts Chromatin Loop Extension
What the sources say
- Not checked yetcites Rao et al., 2014 source
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In the paper
“Our results show a strong increase in the number of SMC1 peaks following stabilization (from 18,462 to 45,479).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL Enforces the Specificity of Chromosomal Loops
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In the paper
“We found that ΔWAPL cells only tolerated disruptive insertions up to and including the tenth exon of SCC2 (Figure 4B).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The C-Terminal Part of SCC2 Drives the Formation of Vermicelli Chromosomes
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In the paper
“Importantly, this truncated SCC2 product was highly abundant, which would indicate that the deleted N-terminal region harbors a sequence that, when unbound to SCC4, destabilizes SCC2.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The C-Terminal Part of SCC2 Drives the Formation of Vermicelli Chromosomes
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In the paper
“However, those TADs that contained differentially expressed genes showed significantly stronger interactions (Figure 1D), suggesting that the aberrant interaction between TADs can affect the expression of genes within these domains.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL Restricts Chromatin Loop Extension
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In the paper
“We should note that even though WAPL deficiency affects loop length genome-wide, only ∼1,000 genes are differentially expressed.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > Cohesin and Nuclear Architecture
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In the paper
“In addition, we found that SCC4 deficiency caused a reduction in contact frequency between loop anchors identified in wild-type cells.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The SCC2/SCC4 Complex Promotes Loop Extension
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In the paper
“We do find extended loops genome-wide in ΔWAPL cells.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > WAPL and Illegal Loops
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In the paper
“We then studied cohesin staining patterns and found that whereas ΔWAPL cells clearly displayed the vermicelli cohesin-staining phenotype, these thread-like structures were absent in ΔWAPL/ΔSCC4 cells (Figure 4A).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The C-Terminal Part of SCC2 Drives the Formation of Vermicelli Chromosomes
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In the paper
“To our surprise, we found that ΔWAPL cells tolerated gene-trap insertions in the genes encoding both subunits of the SCC2/SCC4 cohesin loader complex (Figure 3B), while in wild-type cells, SCC2 and SCC4 displayed strong essentiality for fitness.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL Deficiency Compensates for Impaired SCC2/SCC4 Function
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“Based on the CTCF ChIP data, we assigned an orientation to the loop anchors and found that wild-type HAP1 cells almost exclusively looped together convergent CTCF sites (Figures 2C–2E). However, when we characterized the chromatin loops in ΔWAPL cells, we found many examples of loops that violated the CTCF orientation rule (Figure 2C).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL Enforces the Specificity of Chromosomal Loops
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“Using immunofluorescence microscopy, we found a reduced amount of chromatin-associated cohesin (Figure 3F), and ChIP-seq analysis showed a more than 3-fold reduction in the amount of detected cohesin binding sites (from 18,462 peaks in wild-type to 5,974 in ΔSCC4) (Figure 3G).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > SCC4-Independent Cohesin Loading
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In the paper
“This led to loss of expression of full length SCC2 and yielded a shorter SCC2 product that lacked the SCC4 binding domain (Braunholz et al., 2012).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The C-Terminal Part of SCC2 Drives the Formation of Vermicelli Chromosomes
What the sources say
- Not checked yetcites Braunholz et al., 2012 source
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In the paper
“As expected, WAPL deficiency severely impaired cohesin’s turnover on chromatin, led to a marked increase of cohesin’s association at DNA, and yielded cells that displayed the vermicelli thread-like cohesin staining pattern (Figure S1).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL Restricts Chromatin Loop Extension
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“Notably, the SCC2 mutation led to the same phenotype as did SCC4 deletion, namely a reduction of SCC1 binding to chromatin, both in wild-type and in a ΔWAPL background, to a loss of the vermicelli cohesin staining pattern of ΔWAPL cells, and these cells did not display a sister chromatid cohesion defect (Figures 4E–4G).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The C-Terminal Part of SCC2 Drives the Formation of Vermicelli Chromosomes
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In the paper
“Intriguingly, WAPL deficiency led to the extension of chromatin loops and strongly increased interaction frequencies between nearby TADs (Figures 1A–1C and S2A).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL Restricts Chromatin Loop Extension
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In the paper
“This yielded a truncated SCC2 protein that lacked a large N-terminal region including its SCC4-binding domain and again led to reduced SCC4 levels (Figure 4D).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The C-Terminal Part of SCC2 Drives the Formation of Vermicelli Chromosomes
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“We found that these SCC2-truncated cells, despite their reduced SCC4 levels, harbored normal SCC1 levels on chromatin, displayed robust sister chromatid cohesion, and importantly, also displayed vermicelli cohesin stainings in a ΔWAPL background (Figures 4E–4G).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The C-Terminal Part of SCC2 Drives the Formation of Vermicelli Chromosomes
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“When we calculated the average contact profile of the TADs that we identified in wild-type cells, we observed that this was a global effect (Figures 2B and S2C). The increase in signal at the corners of TADs was accompanied by a decrease in the intra-TAD contact frequency.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL-Deficient Cells Accumulate Contacts at TAD Corners
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“This truncation was considerably less abundant than full length SCC2 was in the parental cells, and it also led to a decrease in SCC4 levels (Figure 4D).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The C-Terminal Part of SCC2 Drives the Formation of Vermicelli Chromosomes
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“Interestingly, we found that a B to A switch often coincided with an increase in gene expression, whereas gene expression was not evidently affected for regions switching from A to B (Figure S4E).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > Cohesin Limits Nuclear Compartmentalization
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“To quantify this on a genome-wide level, we aligned the DI for all TAD boundaries, which revealed that the more diffuse boundaries in ΔSCC4 cells were a global effect, and this defect was rescued in ΔWAPL/ΔSCC4 cells (Figures 5E, 5F, and S6D ).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The SCC2/SCC4 Complex Promotes Loop Extension
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“When we quantified the regions that switched from A to B or vice versa, we found that more regions switched from B to A (46.0 Mb B to A versus 22.8 Mb A to B), and the compartment switches were strongly linked to a concomitant change in the association with the nuclear periphery (Figure 6E).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > Cohesin Limits Nuclear Compartmentalization
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“Our data are in correspondence with this report, and we would suggest that high levels of cohesin stably associated with DNA actually counteract compartmentalization, and WAPL-mediated cohesin turnover provides the necessary chromosomal flexibility for nuclear compartmentalization.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > Cohesin and Nuclear Architecture
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“Our Hi-C data also revealed that TADs in ΔSCC4 cells displayed more diffuse boundaries (Figure 5D, left). We then calculated the directionality index (DI), which is a measure for TAD partition, and found that ΔSCC4 cells indeed displayed severely decreased DI scores (Figure 5D, right).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The SCC2/SCC4 Complex Promotes Loop Extension
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“Although they are less clearly defined in ΔWAPL cells, we can to some degree identify A and B nuclear compartments and they generally overlap with those found in wild-type, but the distribution of the scores is not as strongly bimodal as in the wild-type. This indicates that the segregation between A and B compartments is less strict in ΔWAPL cells (Figures 6C and S4B).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > Cohesin Limits Nuclear Compartmentalization
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“The APA confirmed our observation that extended loops are formed more frequently in ΔWAPL cells and showed that extended loops are mostly formed between existing loop anchors, rather than being formed between de novo anchors.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The SCC2/SCC4 Complex Promotes Loop Extension
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“When we compared the whole-chromosome contact maps for wild-type and ΔWAPL cells, we saw a striking decrease in the number of far-cis (>10 Mb) contacts in the ΔWAPL cells. (Figure 6A).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > Vermicelli Chromosomes Harbor Reduced Far-cis Contacts
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“SCC4 loss in ΔWAPL cells also led to a reduction in extended loops, resulting in an overall loop length that strongly resembled those found in wild-type cells (Figure 5C).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The SCC2/SCC4 Complex Promotes Loop Extension
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In the paper
“We found that SCC4 loss led to shorter loops in a wild-type background and also reduced loop length in ΔWAPL cells (Figure 5A).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The SCC2/SCC4 Complex Promotes Loop Extension
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“Both types of chromosomes harbor virtually no far-cis interactions, which presumably in both cases reflects the rigidity of these chromosomes.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > SMC Complexes and Loop Formation
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“Using these annotations, we found no exonic moderate- or high-impact mutations.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > STAR★Methods > Method Details
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“Another crucial shared feature of vermicelli and mitotic chromosomes is that both display an axis of SMC complexes at the heart of each chromosome that spans its entire length.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > SMC Complexes and Loop Formation
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“In vermicelli chromosomes, this axis consists of cohesin complexes, while in mitotic chromosomes condensin has this axial localization.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > SMC Complexes and Loop Formation
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“We found no ΔWAPL-specific mutations.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > STAR★Methods > Method Details
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“In the absence of WAPL, cohesin is loaded onto DNA, but does not turn over (Kueng et al., 2006, Tedeschi et al., 2013).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Introduction
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In the paper
“Cohesin is loaded onto DNA by the SCC2/SCC4 complex (also known as NIPBL and MAU2, respectively), and DNA release is driven by cohesin’s antagonist WAPL (Ciosk et al., 2000, Gandhi et al., 2006, Kueng et al., 2006).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Introduction
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In the paper
“It implies that human SCC4 aids cohesin in the loading reaction, but cohesin can, to some degree, load onto DNA without SCC4.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > SCC4-Independent Cohesin Loading
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In the paper
“and this specific orientation is required for the looping together of CTCF sites (de Wit et al., 2015, Guo et al., 2015, Sanborn et al., 2015).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Introduction
What the sources say
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In the paper
“These results show that cohesin turnover is not required for the formation of TADs and loops, but rather restricts the length of loops and intra-TAD interactions.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL Restricts Chromatin Loop Extension
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In the paper
“Therefore, WAPL not only limits the extension of DNA loops per se but also counteracts the formation or maintenance of certain DNA loops.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > WAPL Enforces the Specificity of Chromosomal Loops
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“Recent work has shown that chromatin loops are formed almost exclusively between “convergent” CTCF sites (i.e., sites with consensus CTCF motifs pointing toward each other) (Rao et al., 2014, Vietri Rudan et al., 2015)”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Introduction
What the sources say
Strength:plain· not yet calibratedCausal:correlational· 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 find that the size of chromatin loops is under control of cohesin, and the dynamics of cohesin’s DNA entrapment state determines the length of these loops.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > Processive Loop Enlargement
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“Stimulation with tumor necrosis factor alpha (TNF-α) does not drastically influence chromosome topology, despite substantial changes in gene expression (Jin et al., 2013), suggesting that many regulatory interactions are pre-formed (de Laat and Duboule, 2013).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > Cohesin and Nuclear Architecture
What the sources say
- Not checked yetcites de Laat and Duboule, 2013 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
“We propose that nuclear compartmentalization requires a certain degree of flexibility of chromosomes, and WAPL is required to limit the amount of cohesin on chromatin to provide this flexibility.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > Cohesin Limits Nuclear Compartmentalization
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“Stimulation with tumor necrosis factor alpha (TNF-α) does not drastically influence chromosome topology, despite substantial changes in gene expression (Jin et al., 2013), suggesting that many regulatory interactions are pre-formed (de Laat and Duboule, 2013).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > Cohesin and Nuclear Architecture
What the sources say
- Not checked yetcites Jin et al., 2013 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.
In the paper
“For example, cohesin depletion does not evidently disrupt nuclear compartmentalization (Seitan et al., 2013).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > Cohesin and Nuclear Architecture
What the sources say
- Not checked yetcites Seitan et al., 2013 source
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
In the paper
“Earlier studies have found that chromosome topology can be remarkably refractory to changes (Lin et al., 2012).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > Cohesin and Nuclear Architecture
What the sources say
- Not checked yetcites Lin et al., 2012 source
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“Indeed, cohesin can slide along chromatin in vitro, and this requires the topological entrapment of DNA inside cohesin’s lumen (Davidson et al., 2016, Kanke et al., 2016, Stigler et al., 2016).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > Processive Loop Enlargement
What the sources say
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“The local and temporal protection against WAPL also plays an important role during mitosis and allows the WAPL-dependent removal of most cohesin complexes from chromosome arms but not centromeres that leads to the classical X-shape of mitotic human chromosomes (Haarhuis et al., 2014).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > To the Boundary and Beyond
What the sources say
- Not checked yetcites Haarhuis et al., 2014 source
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
“Considering that the SCC2/SCC4 complex contributes to the extension of chromatin loops, and it is also required for the formation of defined TAD boundaries, these two phenotypes are presumably functionally linked.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Results > The SCC2/SCC4 Complex Promotes Loop Extension
Strength:hedged· 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
“Recent work in B. subtilis indicates that the SMC complex found in this species slides along DNA, and this movement coincides with the tethering together of DNA elements at the sites that it passes (Wang et al., 2017).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > Processive Loop Enlargement
What the sources say
- Not checked yetcites Wang et al., 2017 source
Strength:hedged· not yet calibratedCausal:correlational· 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.
None of the sources cited for this claim have been checked yet.
In the paper
“Fundamentally different chromosome topologies have so far primarily been observed when comparing different developmental lineages (Dixon et al., 2015, Krijger et al., 2016).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > Cohesin and Nuclear Architecture
What the sources say
Strength:plain· not yet calibratedCausal:correlational· 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 finding that WAPL deficiency also leads to the formation or maintenance of loops between incorrectly oriented CTCF sites indicates that WAPL not only restricts chromatin loop extension, but also enforces the “CTCF directionality looping rule.””
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > WAPL and Illegal Loops
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
“We created two templates for wild-type and the three mutant cell lines to control for differences in template generation.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > STAR★Methods > Method Details
Strength:plain· not yet calibratedn = 3Tests✓ 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
“As we previously showed that p53 depletion allows proliferation of WAPL deficient cells (Haarhuis et al., 2013), we could efficiently generate ΔWAPL HAP1 clones.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > STAR★Methods > Method Details
What the sources say
- Not checked yetcites Haarhuis et al., 2013 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.
In the paper
“A fundamental difference, however, is that condensed mitotic chromosome arms are almost completely devoid of cohesin (Haarhuis et al., 2014), and mitotic condensation is, to a large degree, dependent on the condensin complex (Hirano, 2016).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > SMC Complexes and Loop Formation
What the sources say
- Not checked yetcites Haarhuis 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.
In the paper
“The processive loop enlargement model was originally proposed as an explanation for how condensin drives mitotic condensation, and at the time, it was suggested that cohesin may act in a similar manner (Nasmyth, 2001).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > SMC Complexes and Loop Formation
What the sources say
- Not checked yetcites Nasmyth, 2001 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.
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
“Both types of chromosomes harbor virtually no far-cis interactions, which presumably in both cases reflects the rigidity of these chromosomes.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > SMC Complexes and Loop Formation
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✗ Based: failsProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
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 minimize confounding from diploid cells carrying heterozygous mutations, the fixed cells were stained using DAPI for DNA content and sorted for haploid cells in the G1 phase of the cell cycle on an Astrios Moflo.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > STAR★Methods > Method Details
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“Cohesin and condensin are highly related SMC complexes that can entrap DNA inside their lumens (Cuylen et al., 2011, Haering et al., 2008).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > SMC Complexes and Loop Formation
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. It 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
“Overlapping gene regions on opposite strands were disregarded (since orientation bias in that region is not readily interpretable)”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > 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.
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
“To reduce noise, we concatenated GATC fragments in 50Kb windows, with each 50Kb-extended GATC fragment starting and finishing in a GATC motif.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > STAR★Methods > Method Details
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.
In the paper
“A fundamental difference, however, is that condensed mitotic chromosome arms are almost completely devoid of cohesin (Haarhuis et al., 2014), and mitotic condensation is, to a large degree, dependent on the condensin complex (Hirano, 2016).”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > SMC Complexes and Loop Formation
What the sources say
- Not checked yetcites Hirano, 2016 source
Strength:plain· 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
“Considering the large degree of conservation between these complexes and their similar distribution at chromosome axes, it is a likely scenario that they act in fundamentally the same manner.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > Discussion > SMC Complexes and Loop Formation
Strength:hedged· not yet calibratedCausal:correlational· 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
“A non-parametric analysis is appropriate since the distributions of R and Δ do not follow a normal distribution.”
§ The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension > STAR★Methods > Method Details
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✗ Based: failsProbably not a substantial claim. The paper may give no reason why it holds.
The paper relies on this without support.
Looping factors are important for cellular viability, and in the absence of WAPL, factors that promote looping may become less important.
“We reasoned that looping factors are important for cellular viability, and that in the absence of WAPL, factors that promote looping may become less important.”
The paper relies on this without support.
Any defect in loop formation may be compensated for by WAPL deficiency.
“Any defect in loop formation may thereby be compensated for by WAPL deficiency.”
The authors state this as an assumption.
There must be a linear scanning mechanism that, by tracing the DNA, can communicate the orientation of the contacting CTCF sites.
“One would therefore assume that there must be a linear scanning mechanism that, by tracing the DNA, can communicate the orientation of the contacting CTCF sites.”
The authors state this as an assumption.
The looped DNA passes through cohesin during loop formation.
“In this model, the looped DNA does, in fact, pass through cohesin during loop formation.”
The authors state this as an assumption.
In the 4C analysis, contact frequency decreases monotonically with distance.
“The main assumption in our 4C analysis is that the contact frequency decreases monotonically with the distance.”
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?
In the citing 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).”
From Cohesin Loss Eliminates All Loop Domains (2017) · cites this paper as Haarhuis et al., 2017
In the citing paper
“Similarly, deletion of WAPL appears to increase the processivity of the Xcom, and thus increases the size of loops (Haarhuis et al., 2017).”
From Cohesin Loss Eliminates All Loop Domains (2017) · cites this paper as Haarhuis et al., 2017
In the citing 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).”
From Cohesin Loss Eliminates All Loop Domains (2017) · cites this paper as Haarhuis et al., 2017
In the citing paper
“Consistent with our observations, these larger loops are associated with extensive mixing, which obscures long-range compartment patterns.”
From Cohesin Loss Eliminates All Loop Domains (2017) · cites this paper as Haarhuis et al., 2017
In the citing paper
“It is known that architectural proteins such as CTCF and cohesin play a role (Haarhuis et al., 2017, Nora et al., 2017, Phillips-Cremins et al., 2013)”
From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Haarhuis et al., 2017
In the citing paper
“complementary polymer simulation studies and Hi-C studies employing acute depletion of CTCF and cohesin, which also support such a dynamic model.”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [12]
In the citing paper
“In conclusion, recent studies10–15 employing induced CTCF and cohesin degradation now strongly support a model where cohesin forms TADs and CTCF establishes TAD boundaries.”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [12]
In the citing paper
“In summary, CTCF and cohesin are required for chromatin looping,10–15 form a biochemically stable protein-complex and both bind chromatin at loop anchors.”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [12]
In the citing paper
“cohesin's residence time is prolonged in ΔWAPL cells,12,14”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [12]
In the citing paper
“the average TAD size increased substantially in ΔWAPL cells12,14,15 and the median loop size increased from 370 kb to 575 kb.12”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [12]
In the citing paper
“Thus, the ΔWAPL Hi-C studies12,14,15 support our conclusion that CTCF binds more dynamically than cohesin.7”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [12]
In the citing paper
“Wapl removes cohesin from chromatin.”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [12]
In the citing paper
“Notably, a key advantage of dynamic loop extrusion models is that they can explain recent perturbation experiments where CTCF binding sites have been added or deleted9,49-51 and also explain the loss of either CTCF or cohesin.10-15”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [12]
In the citing paper
“although CTCF and cohesin both appear absolutely required for the formation of most TADs10-15”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [12]
Citations
Cites
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
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Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668
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Host Factor Experiment (E_R_HTBE_H3N2)
J. Craig Venter Institute, & University of Chicago (2016) · Influenza Research Database · doi:10.35094/mymm-6046
Host Factor Experiment (E_R_HTBE_H5N1)
J. Craig Venter Institute, & University of Chicago (2016) · Influenza Research Database · doi:10.35094/75fn-m776
Host Factor Experiment (E_R_MDM_H3N2)
J. Craig Venter Institute, & University of Chicago (2017) · Influenza Research Database · doi:10.35094/v8rq-cq54
Host Factor Experiment (E_R_MDM_H1N1)
J. Craig Venter Institute, & University of Chicago (2017) · Influenza Research Database · doi:10.35094/mmxd-df62
Host Factor Experiment (E_R_HTBE_H1N1)
J. Craig Venter Institute, & University of Chicago (2016) · Influenza Research Database · doi:10.35094/m5t3-gz96
Metadata
- Authors
- Haarhuis, J. H. I., van der Weide, R. H., Blomen, V. A., Yáñez-Cuna, J. O., Amendola, M., van Ruiten, M. S., Krijger, P. H. L., Teunissen, H., Medema, R. H., van Steensel, B., Brummelkamp, T. R., de Wit, E., & Rowland, B. D.
- Affiliations
- The Netherlands Cancer Institute (NL)
- Hubrecht Institute for Developmental Biology and Stem Cell Research (NL)
- Corresponding author
- Rowland, Benjamin D.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2017-05
- Volume
- 169
- Issue
- 4
- Pages
- 693-707.e14
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC5422210
- OpenAlex
- W2610160407
- Semantic Scholar
- ccf9ed3bd806d283989c2c5795aebea3f20dbe1e
- Cited by
- 793
- References
- 77
- Citations by year
- 2026: 60 · 2025: 67 · 2024: 66 · 2023: 70 · 2022: 101 · 2021: 126 · 2020: 100 · 2019: 95 · 2018: 72 · 2017: 36
- FWCI
- 34.19
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Cell (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Institutional Research Information System University of Ferrara (University of Ferrara) (submittedVersion)
- Funders
- Dutch Cancer Society (NKI 2010-4706, NKI 2011-5103, NKI 2015-7657)
- European Research Council (ERC Starting Grant 637587 HAP-PHEN, ERC Advanced Grant 293662)
- Cancer Genomics Center (CGC.nl)
- EMBO (Long Term Fellowship)
- 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, WAPL, CTCF, topologically associating domains, 3D genome organization, chromatin looping, nuclear compartmentalization
- MeSH terms
- Gene Editing, CCCTC-Binding Factor, Fatty Acid Elongases, Cohesins, Acetyltransferases, Carrier Proteins, Cell Nucleus, Chromatin, Chromosomal Proteins, Non-Histone, DNA-Binding Proteins, Humans, Nuclear Proteins, Proto-Oncogene Proteins, Repressor Proteins, Cell Cycle Proteins, Multiprotein Complexes
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).
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