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Cited by 806Genomics and Chromatin DynamicsChromatin Remodeling and CancerNuclear Structure and Function

The cohesin release factor WAPL restricts chromatin loop extension

Open access
Haarhuis, Judith H.I., van der Weide, Robin H., Blomen, Vincent A., Yáñez-Cuna, J. Omar, Amendola, Mario, van Ruiten, Marjon S., Krijger, Peter H.L., Teunissen, Hans +5 more·2017·Cell
DOI 10.1016/j.cell.2017.04.013PMC PMC5422210
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Abstract

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.

AI snapshot

Written from the paper’s full text.

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.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.cell.2017.04.013

Cites

77 of 77 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 36 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    ΔWAPL cells often develop pronounced corner-peaks at the intersection of the 5′ and 3′ boundaries of TADs.

    “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).”
    Quote in the paperSubstantial claim
  • Findingcitation

    ΔSCC4 cells display severely reduced SCC2 levels.

    “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).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Hinshaw et al., 2015 source

      Not checked in the free run.

    • cites Watrin et al., 2006 source

      Not checked in the free run.

  • Findingown data

    The median loop length increased by more than 200 kb in ΔWAPL cells compared to wild-type (575 kb versus 370 kb).

    “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).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Rao et al., 2014 source

      Not checked in the free run.

  • Findingown data

    The number of SMC1 peaks increased from 18,462 to 45,479 following WAPL knockout.

    “Our results show a strong increase in the number of SMC1 peaks following stabilization (from 18,462 to 45,479).”
    Quote in the paperSubstantial claim
  • Findingown data

    ΔWAPL cells only tolerated disruptive insertions up to and including the tenth exon of SCC2.

    “We found that ΔWAPL cells only tolerated disruptive insertions up to and including the tenth exon of SCC2 (Figure 4B).”
    Quote in the paperSubstantial claim
  • May combine two claims. 37
  • The quote only partly states this claim. 2
  • Classified as probably not a substantial claim. 24

  • May combine two claims.

    Findingown data

    ΔWAPL cells display the vermicelli cohesin-staining phenotype, but these thread-like structures are absent in ΔWAPL/ΔSCC4 cells.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    ΔWAPL cells tolerate gene-trap insertions in the genes encoding both subunits of the SCC2/SCC4 cohesin loader complex, whereas in wild-type cells SCC2 and SCC4 display strong essentiality for fitness.

    “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.”
    Quote in the paperSubstantial claim

  • May combine two claims. The quote only partly states this claim.

    Findingown data

    Wild-type HAP1 cells almost exclusively loop together convergent CTCF sites, whereas ΔWAPL cells contain many loops that violate the CTCF orientation rule and show an increase in tandem CTCF orientations.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    ΔSCC4 cells have a reduced amount of chromatin-associated cohesin and a more than 3-fold reduction in detected cohesin binding sites (from 18,462 peaks in wild-type to 5,974 in ΔSCC4).

    “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).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    Disrupting the SCC2 reading frame after its ATG led to loss of full-length SCC2 and yielded a shorter SCC2 product lacking the SCC4 binding domain.

    “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).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Braunholz et al., 2012 source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    WAPL deficiency severely impairs cohesin's turnover on chromatin, increases cohesin's association at DNA, and yields cells with vermicelli thread-like cohesin staining.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The SCC2 mutation led to a reduction of SCC1 binding to chromatin in wild-type and ΔWAPL backgrounds, loss of vermicelli cohesin staining in ΔWAPL cells, and no sister chromatid cohesion defect.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    WAPL deficiency leads to extension of chromatin loops and strongly increases interaction frequencies between nearby TADs.

    “Intriguingly, WAPL deficiency led to the extension of chromatin loops and strongly increased interaction frequencies between nearby TADs (Figures 1A–1C and S2A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Deleting the SCC2 coding sequence up to exon 11 yielded a truncated SCC2 protein lacking a large N-terminal region including its SCC4-binding domain and led to reduced SCC4 levels.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    SCC2-truncated cells, despite reduced SCC4 levels, harbored normal SCC1 levels on chromatin, displayed robust sister chromatid cohesion, and displayed vermicelli cohesin stainings in a ΔWAPL background.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The increase in signal at TAD corners in ΔWAPL cells is a global effect and is accompanied by a decrease in intra-TAD contact frequency.

    “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.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The SCC2 truncation was considerably less abundant than full-length SCC2 and led to a decrease in SCC4 levels.

    “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).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    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.

    “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).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The more diffuse TAD boundaries in ΔSCC4 cells were a global effect, and this defect was rescued in ΔWAPL/ΔSCC4 cells.

    “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 ).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    More regions switched from B to A than from A to B in ΔWAPL cells (46.0 Mb B to A versus 22.8 Mb A to B), and compartment switches were strongly linked to a concomitant change in association with the nuclear periphery.

    “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).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingcitation

    Our data correspond with the report that cohesin depletion does not disrupt nuclear compartmentalization.

    “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.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    TADs in ΔSCC4 cells displayed more diffuse boundaries, and ΔSCC4 cells displayed severely decreased directionality index (DI) scores.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In ΔWAPL cells, A and B compartments are less clearly defined and the segregation between A and B compartments is less strict than in wild-type.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Extended loops are formed more frequently in ΔWAPL cells and are mostly formed between existing loop anchors rather than between de novo anchors.

    “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.”
    Quote in the paperSubstantial claim

  • May combine two claims. The quote only partly states this claim.

    Findingown data

    ΔWAPL cells show a striking decrease in the number of far-cis (>10 Mb) contacts, whereas ΔSCC4 cells display an increase in far-cis contacts compared to wild-type.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    SCC4 loss in ΔWAPL cells led to a reduction in extended loops, resulting in an overall loop length that strongly resembled that found in wild-type cells.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    SCC4 loss led to shorter loops in a wild-type background and also reduced loop length in ΔWAPL cells.

    “We found that SCC4 loss led to shorter loops in a wild-type background and also reduced loop length in ΔWAPL cells (Figure 5A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    Both vermicelli and mitotic chromosomes harbor virtually no far-cis interactions.

    “Both types of chromosomes harbor virtually no far-cis interactions, which presumably in both cases reflects the rigidity of these chromosomes.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    No exonic moderate- or high-impact mutations were found.

    “Using these annotations, we found no exonic moderate- or high-impact mutations.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    Both vermicelli and mitotic chromosomes display an axis of SMC complexes at the heart of each chromosome that spans its entire length.

    “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.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    In vermicelli chromosomes, the axis consists of cohesin complexes; in mitotic chromosomes, condensin has this axial localization.

    “In vermicelli chromosomes, this axis consists of cohesin complexes, while in mitotic chromosomes condensin has this axial localization.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    No ΔWAPL-specific mutations were found.

    “We found no ΔWAPL-specific mutations.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    In the absence of WAPL, cohesin is loaded onto DNA but does not turn over.

    “In the absence of WAPL, cohesin is loaded onto DNA, but does not turn over (Kueng et al., 2006, Tedeschi et al., 2013).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Kueng et al., 2006 source

      Not checked in the free run.

    • cites Tedeschi et al., 2013 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Cohesin is loaded onto DNA by the SCC2/SCC4 complex.

    “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).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Ciosk et al., 2000 source

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    • cites Gandhi et al., 2006 source

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    • cites Kueng et al., 2006 source

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  • May combine two claims.

    Interpretationreasoning

    Human SCC4 aids cohesin in the loading reaction, but cohesin can to some degree load onto DNA without SCC4.

    “It implies that human SCC4 aids cohesin in the loading reaction, but cohesin can, to some degree, load onto DNA without SCC4.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The specific convergent orientation of CTCF sites is required for the looping together of CTCF sites.

    “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).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites de Wit et al., 2015 source

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    • cites Guo et al., 2015 source

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    • cites Sanborn et al., 2015 source

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  • May combine two claims.

    Interpretationown data

    Cohesin turnover is not required for the formation of TADs and loops, but rather restricts the length of loops and intra-TAD interactions.

    “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.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    WAPL not only limits the extension of DNA loops per se but also counteracts the formation or maintenance of certain DNA loops.

    “Therefore, WAPL not only limits the extension of DNA loops per se but also counteracts the formation or maintenance of certain DNA loops.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Chromatin loops are formed almost exclusively between convergent CTCF sites.

    “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)”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Rao et al., 2014 source

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    • cites Vietri Rudan et al., 2015 source

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  • May combine two claims.

    Interpretationown data

    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.

    “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.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Many regulatory interactions are pre-formed.

    “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).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites de Laat and Duboule, 2013 source

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  • May combine two claims.

    Interpretationown data

    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.

    “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.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Stimulation with TNF-α does not drastically influence chromosome topology, despite substantial changes in gene expression.

    “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).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Jin et al., 2013 source

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  • Classified as probably not a substantial claim.

    Premisecitation

    Cohesin depletion does not evidently disrupt nuclear compartmentalization.

    “For example, cohesin depletion does not evidently disrupt nuclear compartmentalization (Seitan et al., 2013).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Seitan et al., 2013 source

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  • Classified as probably not a substantial claim.

    Premisecitation

    Chromosome topology can be remarkably refractory to changes.

    “Earlier studies have found that chromosome topology can be remarkably refractory to changes (Lin et al., 2012).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Lin et al., 2012 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Cohesin can slide along chromatin in vitro, and this requires the topological entrapment of DNA inside cohesin's lumen.

    “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).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Davidson et al., 2016 source

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    • cites Kanke et al., 2016 source

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    • cites Stigler et al., 2016 source

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  • May combine two claims.

    Premisecitation

    Local and temporal protection against WAPL plays an important role during mitosis and allows WAPL-dependent removal of most cohesin complexes from chromosome arms but not centromeres, leading to the classical X-shape of mitotic human chromosomes.

    “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).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Haarhuis et al., 2014 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The contribution of the SCC2/SCC4 complex to loop extension and its requirement for defined TAD boundaries are presumably functionally linked.

    “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.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The SMC complex in B. subtilis slides along DNA, and this movement coincides with the tethering together of DNA elements at the sites that it passes.

    “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).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Wang et al., 2017 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Fundamentally different chromosome topologies have so far primarily been observed when comparing different developmental lineages.

    “Fundamentally different chromosome topologies have so far primarily been observed when comparing different developmental lineages (Dixon et al., 2015, Krijger et al., 2016).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Dixon et al., 2015 source

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    • cites Krijger et al., 2016 source

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  • May combine two claims.

    Interpretationown data

    WAPL not only restricts chromatin loop extension, but also enforces the "CTCF directionality looping rule."

    “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.””
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Two templates were created for wild-type and the three mutant cell lines to control for differences in template generation.

    “We created two templates for wild-type and the three mutant cell lines to control for differences in template generation.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    p53 depletion allows proliferation of WAPL deficient cells.

    “As we previously showed that p53 depletion allows proliferation of WAPL deficient cells (Haarhuis et al., 2013), we could efficiently generate ΔWAPL HAP1 clones.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Haarhuis et al., 2013 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Condensed mitotic chromosome arms are almost completely devoid of cohesin.

    “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).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Haarhuis et al., 2014 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The processive loop enlargement model was originally proposed as an explanation for how condensin drives mitotic condensation, and it was suggested that cohesin may act in a similar manner.

    “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).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Nasmyth, 2001 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    The lack of far-cis interactions in both vermicelli and mitotic chromosomes presumably reflects the rigidity of these chromosomes.

    “Both types of chromosomes harbor virtually no far-cis interactions, which presumably in both cases reflects the rigidity of these chromosomes.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    Sorting fixed cells for haploid cells in G1 phase by DAPI staining minimizes confounding from diploid cells carrying heterozygous mutations in the synthetic viability screens.

    “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.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Cohesin and condensin are highly related SMC complexes that can entrap DNA inside their lumens.

    “Cohesin and condensin are highly related SMC complexes that can entrap DNA inside their lumens (Cuylen et al., 2011, Haering et al., 2008).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Cuylen et al., 2011 source

      Not checked in the free run.

    • cites Haering et al., 2008 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    Gene regions overlapping on opposite strands were disregarded in the analysis because orientation bias in those regions is not readily interpretable.

    “Overlapping gene regions on opposite strands were disregarded (since orientation bias in that region is not readily interpretable)”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Concatenating GATC fragments into 50Kb windows, each starting and finishing at a GATC motif, reduces noise in DamID profile analyses.

    “To reduce noise, we concatenated GATC fragments in 50Kb windows, with each 50Kb-extended GATC fragment starting and finishing in a GATC motif.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Mitotic condensation is, to a large degree, dependent on the condensin complex.

    “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).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hirano, 2016 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    It is a likely scenario that cohesin and condensin act in fundamentally the same manner.

    “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.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Study design and conductnone given

    The distributions of R and Δ do not follow a normal distribution.

    “A non-parametric analysis is appropriate since the distributions of R and Δ do not follow a normal distribution.”
    Quote in the paperNot a substantial claim
58 of 58

  • 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.”
5 of 5

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 data are consistent with the observation that genome compartmentalization is weakened in cells where WAPL is knocked out, leading to larger loop domains.

    “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

  • WAPL deletion seems to raise Xcom processivity, enlarging loops.

    “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

  • Deletion of WAPL results in formation of thousands of new loops and loop domains, which are larger than those found when WAPL is intact.

    “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

  • Bigger loops show widespread mixing that blurs long-range compartment patterns.

    “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

  • Architectural proteins such as CTCF and cohesin play a role in domain formation.

    “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

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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)
DOI
10.1016/j.cell.2017.04.013
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
Licence
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.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-07.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-07.

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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