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Cited by 266Genomics and Chromatin DynamicsChromatin Remodeling and CancerNuclear Structure and Function

Recent evidence that TADs and chromatin loops are dynamic structures

Open access
Hansen, Anders S., Cattoglio, Claudia, Darzacq, Xavier, Tjian, Robert·2018·Nucleus
DOI 10.1080/19491034.2017.1389365PMC PMC5990973
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Abstract

Mammalian genomes are folded into spatial domains, which regulate gene expression by modulating enhancer-promoter contacts. Here, we review recent studies on the structure and function of Topologically Associating Domains (TADs) and chromatin loops. We discuss how loop extrusion models can explain TAD formation and evidence that TADs are formed by the ring-shaped protein complex, cohesin, and that TAD boundaries are established by the DNA-binding protein, CTCF. We discuss our recent genomic, biochemical and single-molecule imaging studies on CTCF and cohesin, which suggest that TADs and chromatin loops are dynamic structures. We highlight complementary polymer simulation studies and Hi-C studies employing acute depletion of CTCF and cohesin, which also support such a dynamic model. We discuss the limitations of each approach and conclude that in aggregate the available evidence argues against stable loops and supports a model where TADs are dynamic structures that continually form and break throughout the cell cycle.

AI snapshot

Written from the paper’s full text.

TL;DR

This review argues that CTCF/cohesin-dependent TADs and chromatin loops are dynamic structures that continually form and break, with mean lifetimes of minutes to tens of minutes, rather than stable structures. It integrates single-molecule imaging, polymer simulations, and acute CTCF/cohesin depletion Hi-C studies to support a loop-extrusion/dynamic LMC model.

Key findings

  • TADs are formed by cohesin-mediated loop extrusion and boundaries are established by CTCF; acute depletion of CTCF or cohesin causes TADs and loops to largely disappear, with CTCF loss having essentially no effect on genome-averaged contact probability and cohesin loss reducing contact probability at the tens-to-hundreds-of-kilobases scale. Cohesin loss increases epigenomic compartmentalization ∼2-fold.
  • Imaging in mES and U2OS cells yields CTCF chromatin residence times of ∼1–4 min and cohesin G1 residence times of ∼20–25 min; because cohesin eventually dissociates, the paper proposes that cohesin-mediated loops have mean lifetimes of a few to tens of minutes.
  • In ΔWAPL cells, average TAD size increases substantially and median loop size increases from 370 kb to 575 kb, supporting dynamic cohesin-controlled TADs. CTCF binds ∼2-fold more sites than cohesin (68,077 vs. 33,434 called peaks).
  • TADs emerge at the population level from many differently positioned extrusion complexes; even strong Hi-C loop anchors contact in only a small subset of cells, and insulation between adjacent TADs is only ∼2-fold.

Methods

  • Design: Extra View/review synthesizing recent studies on TAD and chromatin-loop structure and function, including the authors’ genomic, biochemical, and single-molecule imaging work plus complementary polymer simulation and Hi-C acute depletion studies.
  • Data/sample: live-cell imaging used CRISPR/Cas9-mediated homozygous HaloTag or SNAPf tagging of CTCF and cohesin in mouse embryonic stem cells and human U2OS cells, with ChIP-Seq, co-immunoprecipitation, single-molecule tracking at 225 Hz, FRAP, and PALM/STORM; cited Hi-C studies include ΔWAPL cells and auxin-AID-mediated acute Rad21 degradation.
  • Analysis: critical synthesis and evaluation of evidence across imaging, polymer modeling, and Hi-C perturbation approaches; the article is a review/synthesis rather than a new primary experimental study.

Limitations

  • Stated: imaging cannot identify which locus a molecule is bound to, reports genomic-average residence times, binding times are stochastic and exponentially distributed, very small (<5%) subpopulations with different binding times cannot be excluded, and using CTCF/cohesin binding dynamics to infer loop stability is indirect.
  • Stated: polymer modeling faces the problem that many mutually inconsistent models can fit the data, and fitting data does not prove mechanistic assumptions; acute cohesin degradation studies may not reflect normal turnover rates and have poor time resolution.
  • Stated/evident: final demonstration that TADs and loops are dynamic requires direct real-time observation of specific loci in live cells, and whether epigenomic compartments are stable or dynamic remains unknown; the review’s conclusion is an aggregate argument from indirect approaches.

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

Integrity signals

Registry

Crossref · 10.1080/19491034.2017.1389365

Cites

78 of 78 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 184 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    CTCF IP pulled down all the subunits of the cohesin complex.

    “We next performed co-immunoprecipitation (IP) experiments and found that CTCF IP pulled down all the subunits of the cohesin complex consistent with earlier reports,61”
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  • Findingown data

    In mES cells, ∼50% of all CTCF molecules are bound to cognate sites.

    “in mES cells, ∼50% of all CTCF molecules are bound to cognate sites.”
    Quote in the paperSubstantial claim
  • Findingown data

    Co-IP, ChIP-Seq and STORM studies strongly suggested that CTCF and cohesin form an LMC protein complex.

    “our co-IP, ChIP-Seq and STORM studies strongly suggested that CTCF and cohesin form an LMC protein complex”
    Quote in the paperSubstantial claim
  • Findingown data

    CTCF and cohesin exhibit very distinct diffusion dynamics.

    “We found that CTCF and cohesin also exhibit very distinct diffusion dynamics”
    Quote in the paperSubstantial claim
  • Findingown data

    The CTCF search mechanism involves ∼35% non-specific chromatin interactions (sliding or hopping) and ∼65% 3D diffusion.

    “the search mechanism involves large amounts of non-specific chromatin interactions (such as sliding or hopping; ∼35%) in addition to 3D diffusion (∼65%).”
    Quote in the paperSubstantial claim
  • May combine two claims. 50
  • Classified as probably not a substantial claim. 13

  • May combine two claims.

    Findingown data

    ChIP-Seq showed that although CTCF binds ∼2-fold more sites than cohesin (68,077 vs. 33,434 called peaks), essentially all cohesin ChIP-Seq peaks co-localize with CTCF peaks.

    “We additionally performed ChIP-Seq and found that although CTCF binds ∼2-fold more sites than cohesin (68,077 vs. 33,434 called peaks; note that cohesin extrusion likely “spreads out” its ChIP signal and thus results in fewer “peaks”), essentially all cohesin ChIP-Seq peaks co-localize with CTCF peaks.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Kinetic modeling of FRAP data using a reaction dominant model yielded a CTCF FRAP residence time of ∼3-4 min in mES cells, and it is somewhat longer in U2OS cells.

    “Kinetic modeling of the FRAP data using a “reaction dominant” model yielded a FRAP residence time of ∼3-4 min in mES cells and somewhat longer in U2OS cells.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In G1, cohesin's FRAP and kinetic modeling residence time is ∼20-25 min, about 10-fold more stable than CTCF.

    “FRAP and kinetic modeling revealed a G1 residence time of ∼20-25 min, ∼10-fold more stable than CTCF”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In mES cells, the average CTCF SMT residence time for specific binding events at cognate sites is ∼1 min, and it is somewhat longer in U2OS cells.

    “we found an average CTCF SMT residence time of ∼1 min in mES cells for specific binding events at cognate sites and somewhat longer in U2OS cells.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Both CTCF and cohesin form small clusters.

    “We found that both CTCF and cohesin form small clusters”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Both CTCF and cohesin form small protein clusters.

    “we showed that both CTCF and cohesin form small protein clusters7”
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  • May combine two claims.

    Findingcitation

    Average residence times for CTCF (~1-4 min) and cohesin (~20-25 min in G1) in mESCs are genomic averages.

    “although we can report average residence times for CTCF (∼1–4 min) and cohesin (∼20-25 min in G1) in mESCs, these numbers are genomic averages.”
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  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    TADs may emerge at the population level when averaged over many heterogeneous single-cell genome topologies.

    “TADs may emerge at the population level when averaged over many heterogeneous single-cell genome topologies.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Active chromatin tends to associate with active chromatin and vice versa, giving rise to a plaid pattern in Hi-C maps.

    “In mammalian nuclei, active chromatin tends to associate with active chromatin and vice versa giving rise to a “plaid” pattern in maps obtained by genome-wide chromosome conformation capture studies (Hi-C).5”
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    Premisecitation

    TADs were identified through Hi-C and their existence has been confirmed by alternative methods such as intrinsic 3C (i3C) and Genome Architecture Mapping (GAM).

    “TADs were identified through Hi-C3,4 and their existence have since been confirmed by alternative methods such as intrinsic 3C (i3C),18 which avoids the cross-linking step and Genome Architecture Mapping (GAM),19 which avoids the ligation step.”
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    Premisecitation

    TADs often have a nested, hierarchical configuration, where smaller TADs can make up larger TADs, and range in size from ∼40 kb to ∼3 MB with a median size of ∼185 kb.

    “Moreover, TADs often have a nested, hierarchical configuration, where smaller TADs can make up larger TADs, and range in size from ∼40 kb to ∼3 MB with a median size of ∼185 kb16, though these numbers depend somewhat on the resolution of the Hi-C data used to identify them”
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    Premisecitation

    Loss of a TAD boundary between limb enhancers and the wnt6 gene is sufficient to upregulate wnt6 expression and cause developmental defects in both mice and humans.

    “loss of a TAD boundary between limb enhancers and the wnt6 gene is sufficient to upregulate wnt6 expression and cause developmental defects in both mice and humans.28”
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    Premisecitation

    Deletion of a boundary between two TADs causes ectopic contacts between previously insulated loci and can cause aberrant gene expression through improper enhancer-promoter contact.

    “Accordingly, deletion of a boundary between two TADs causes ectopic contacts between previously insulated loci3 and can cause aberrant gene expression through improper enhancer-promoter contact.27,28”
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    Premisecitation

    Compartments composed of repressed chromatin tend to be located near the nuclear envelope through lamina association and are referred to as Lamina-Associated Domains (LADs).

    “In contrast, compartments composed of repressed chromatin tend to be located near the nuclear envelope through lamina association and are also referred to as Lamina-Associated Domains (LADs)17”
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  • May combine two claims.

    Interpretationnone given

    TADs appear as triangles in Hi-C maps, within which there are more frequent chromatin contacts, and are often marked by cornerpeaks, suggesting that they are held together by a chromatin loop.

    “TADs appear as triangles, within which there are more frequent chromatin contacts and are often marked by “cornerpeaks”, suggesting that they are held together by a chromatin loop.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: The presence of CTCF and cohesin bound corner peaks in Hi-C maps corresponds to a chromatin loop held together by CTCF and cohesin.

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

    Premisecitation

    Epigenomic compartments range in size from 6 kb to more than 5 Mb.

    “These epigenomic compartments range in size from 6 kb to more than 5 Mb.16”
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  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    TAD and loop boundaries are almost always bound by CTCF and cohesin.

    “Below, simulated CTCF and cohesin ChIP-Seq tracks illustrating that TAD and loop boundaries are almost always bound by CTCF and cohesin.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    TADs likely regulate enhancer-promoter contacts and gene expression.

    “Thus, TADs likely regulate enhancer-promoter contacts and gene expression.”
    Quote in the paperNot a substantial claim

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

    Premisecitation

    TADs are characterized by preferential contacts between loci inside the same TAD and insulation from loci in adjacent TADs.

    “First, chromatin is organized into Topological Associating Domains (TADs) that are characterized by preferential contacts between loci inside the same TAD and insulation from loci in adjacent TADs.3,4”
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    Premisecitation

    Closely related SMC-condensin complexes were recently found to extrude at ∼50 kb/min in B. subtilis and ∼16-19 kb/min in Caulobacter.

    “Third, although it requires cohesin extrusion to be quite fast, closely related SMC-condensin complexes were recently found to extrude at ∼50 kb/min in B. subtilis52 and ∼16-19 kb/min in Caulobacter.53”
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  • May combine two claims.

    Interpretationreasoning

    Although the loop extrusion model remains a hypothesis, it has proved remarkably resilient to testing.

    “Although the loop extrusion model remains a hypothesis, it has proved remarkably resilient to testing.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: In the loop extrusion model, cohesin spontaneously engages chromatin and begins extruding a DNA loop.
    • The authors state this as an assumption: Loop extrusion continues until cohesin spontaneously falls off or until it encounters an occupied CTCF binding site in the convergent orientation.

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

    Premisecitation

    Cohesin is thought to topologically entrap DNA, enabling it to mediate sister chromatid cohesion and homologous recombination.

    “Cohesin is thought to topologically entrap DNA (Fig. 2C),34 a structural feature that enables cohesin to mediate multiple functions including sister chromatid cohesion and homologous recombination.35”
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  • May combine two claims.

    Premisecitation

    Almost all TADs are demarcated by CTCF ChIP-Seq peaks, but only around one-third of CTCF ChIP-Seq peaks flank TADs.

    “Since almost all TADs are demarcated by CTCF ChIP-Seq peaks,16 but only around one-third of CTCF ChIP-Seq peaks flank TADs,1,7”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [1] Merkenschlager M, 2017, Annu Rev Genomics Hum Genet

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  • May combine two claims.

    Premisecitation

    DNA FISH and single-cell Hi-C studies show that genome organization is highly variable between cells and that even strong Hi-C loop anchors only contact in a small subset of cells.

    “Both DNA FISH3,9,36–39 and single-cell Hi-C40,41 studies show that genome organization is highly variable between cells and that even strong Hi-C loop anchors only contact in a small subset of cells”
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  • May combine two claims.

    Premisecitation

    ∼18% of TAD boundaries appear to be partially resistant to CTCF loss, suggesting that additional boundary factors, such as active promoters and alternative architectural factors, may also play a role.

    “Finally, ∼18% of TAD boundaries appear to be partially resistant to CTCF loss,10 suggesting that additional boundary factors, such as active promoters4 since engaged RNA Pol II can block cohesin extrusion46 as well as alternative architectural factors, may also play a role.”
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  • May combine two claims.

    Interpretationcitation

    CTCF is the passive partner that predominantly sits bound to its cognate sites and waits for extruding cohesin complexes, whereas cohesin plays the active role by constantly moving along and extruding DNA until it finds CTCF.

    “Using slightly anthropomorphic imagery, CTCF is the “passive” partner and predominantly sits bound to its cognate sites and “waits” for extruding cohesin complexes, whereas cohesin plays the “active” role by constantly moving along and extruding DNA until it “finds” CTCF.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: In the loop extrusion model, cohesin spontaneously engages chromatin and begins extruding a DNA loop.
    • The authors state this as an assumption: Loop extrusion continues until cohesin spontaneously falls off or until it encounters an occupied CTCF binding site in the convergent orientation.

  • May combine two claims.

    Premisereasoning

    TADs and well-defined Hi-C loops largely disappear when either CTCF or cohesin is strongly depleted, but for different reasons.

    “In accordance with the extrusion model, TADs and well-defined Hi-C loops largely disappear when either CTCF10,14 or cohesin11,13–15 is strongly depleted, but for different reasons.”
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    • cites [14] Wutz G, 2017, bioRxiv

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    • cites [13] Rao S, 2017, bioRxiv

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    • cites [15] Gassler J, 2017, bioRxiv

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  • May combine two claims.

    Premisecitation

    CTCF loss has only a small effect on epigenomic compartments, whereas cohesin loss increases the degree of epigenomic compartmentalization ∼2-fold.

    “Likewise, CTCF loss has only a small effect on epigenomic compartments,10 whereas cohesin loss increases the degree of epigenomic compartmentalization ∼2-fold.11,13”
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  • May combine two claims.

    Premisecitation

    CTCF loss has essentially no effect on genome-averaged contact probability at any distance scale, whereas cohesin loss significantly reduces contact probability at the scale of tens to hundreds of kilobases.

    “Consistent with their different roles, CTCF loss has essentially no effect on genome-averaged contact probability at any distance scale,10 whereas cohesin loss significantly reduces contact probability at the scale of tens to hundreds of kilobases,11”
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    Study design and conductown data

    Control experiments verified that tagging CTCF and cohesin did not affect their function or expression levels.

    “First, we performed a series of control experiments to verify that tagging CTCF and cohesin – both essential proteins – did not affect their function or expression levels.”
    Quote in the paperSubstantial claim

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    Interpretationcitation

    Chromatin is still compacted and extruded by cohesin, but without sharp boundaries, TADs disappear in Hi-C maps.

    “Thus, chromatin is still compacted and extruded by cohesin, but without sharp boundaries, TADs disappear in Hi-C maps.10,14”
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    Interpretationcitation

    The CTCF/cohesin anchored loop domain matching the Hi-C corner-peak actually only exists in a small subset of cells, consistent with high cell-to-cell variability in contact probability observed in DNA FISH studies.

    “The CTCF/cohesin anchored loop domain matching the Hi-C corner-peak actually only exists in a small subset of cells, which is also consistent with the high levels of cell-to-cell variability in contact probability observed in DNA FISH studies.3,9,36–39”
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    Premisecitation

    TADs and loops are absent in mitosis, but present in G1-phase.

    “What has been clear is that TADs and loops are absent in mitosis, but present in G1-phase.54,55”
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    Study design and conductnone given

    Hi-C provides a static snapshot derived from the average of a large cell population, so Hi-C based methods are necessarily limited in their ability to reveal dynamics and heterogeneity.

    “Since Hi-C provides a static snapshot derived from the average of a large cell population, Hi-C based methods are necessarily limited in their ability to reveal dynamics and heterogeneity.”
    Quote in the paperSubstantial claim

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

    Study design and conductnone given

    A unique advantage of live-cell imaging is that single protein molecules can be followed over time and their dynamics can thus be directly observed at the single-cell level.

    “A unique advantage of live-cell imaging is that single protein molecules can be followed over time and their dynamics can thus be directly observed at the single-cell level.”
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  • May combine two claims.

    Study design and conductreasoning

    Single-cell methods such as single-cell Hi-C and DNA-FISH can report on cell-to-cell variability, but they still provide a terminal snapshot and thus can only give limited dynamic information.

    “While single-cell methods such as single-cell Hi-C and DNA-FISH can report on cell-to-cell variability, they still provide a terminal snapshot and thus can only give limited dynamic information.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationcitation

    Recent studies employing induced CTCF and cohesin degradation now strongly support a model where cohesin forms TADs and CTCF establishes TAD boundaries.

    “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.”
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  • May combine two claims.

    Interpretationcitation

    CTCF and cohesin are required for chromatin looping, form a biochemically stable protein complex, and both bind chromatin at loop anchors.

    “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.”
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  • May combine two claims.

    Interpretationreasoning

    The result that CTCF loss has small effect on compartments while cohesin loss increases compartmentalization argues against a hierarchical model where TADs are the building blocks of compartments and demonstrates that TADs and epigenomic compartments are formed by distinct and mutually antagonistic mechanisms.

    “This result also argues against a hierarchical model where TADs are the building blocks of compartments and demonstrates that TADs and epigenomic compartments are formed by distinct and mutually antagonistic mechanisms.”
    Quote in the paperSubstantial claim

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    Premisecitation

    Cohesin loss has no apparent effect on CTCF binding to chromatin, consistent with CTCF functioning upstream of cohesin.

    “Cohesin loss has no apparent effect on CTCF binding to chromatin,13 consistent with CTCF functioning upstream of cohesin.”
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    • cites [13] Rao S, 2017, bioRxiv

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    Interpretationnone given

    After cohesin dissociation, previously held-together chromatin will likely only move apart slowly even though the loop is broken.

    “after cohesin dissociation, previously held-together chromatin will likely only move apart slowly even though the loop is broken”
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    Interpretationcitation

    These results are consistent with our imaging results showing that CTCF binding is stochastic and less stable than cohesin.

    “these results are consistent with our imaging results showing that CTCF binding is stochastic and less stable than cohesin.7”
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    Premisecitation

    The best agreement with experimental Hi-C data was obtained when cohesin extrudes for ∼120-240 kb before falling off and a mean separation of ∼120 kb between extrusion complexes.

    “The best agreement with experimental Hi-C data16 was obtained when cohesin extrudes for ∼120-240 kb before falling off and a mean separation of ∼120 kb between extrusion complexes (note that these are average numbers).8”
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    Premisecitation

    Upon auxin treatment, near-complete loss of Rad21 was achieved in 1 hour in Rao et al. or ∼20 min in Wutz et al.

    “Upon auxin treatment, near-complete loss of Rad21 was achieved in 1 hour in Rao et al.13 or ∼20 min in Wutz et al..14”
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    Premisecitation

    The loop extrusion model introduced by Fudenberg and Imakaev et al. explicitly favored dynamic loops and argued against static loops.

    “the loop extrusion model introduced by Fudenberg and Imakaev et al.8 explicitly favored dynamic loops and convincingly argued against static loops.”
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  • May combine two claims.

    Interpretationreasoning

    CTCF's residence time is quite stable compared to conventional transcription factors (∼2-15 seconds) but very dynamic compared to the cell cycle (15-30 hours).

    “which is quite stable compared to conventional transcription factors (∼2-15 seconds),62 but very dynamic compared to the cell cycle (15-30 hours).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [62] source

      Not checked in the free run.

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

    Interpretationreasoning

    Assuming no change in cohesin's extrusion speed, increased cohesin residence time would increase cohesin extrusion processivity.

    “which – assuming no change in cohesin's extrusion speed – would increase cohesin extrusion processivity.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: In ΔWAPL cells, cohesin's extrusion speed does not change.

  • May combine two claims.

    Premisecitation

    The average TAD size increased substantially in ΔWAPL cells and the median loop size increased from 370 kb to 575 kb.

    “the average TAD size increased substantially in ΔWAPL cells12,14,15 and the median loop size increased from 370 kb to 575 kb.12”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [12] source

      Not checked in the free run.

    • cites [14] Wutz G, 2017, bioRxiv

      Not checked in the free run.

    • cites [15] Gassler J, 2017, bioRxiv

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    CTCF can form large foci upon senescence, which causes genome reorganization.

    “a recent study found that CTCF can form large foci upon senescence, which causes genome reorganization.74”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [74] Zirkel A, 2017, bioRxiv

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    The mechanisms by which TADs and loops are formed and broken down are both quite fast, which argues against stable TADs and favors dynamic TADs.

    “Taken together, these studies13,14 suggest that the mechanisms by which TADs and loops are formed and broken down are both quite fast, which argues against stable TADs and favors dynamic TADs.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [13] Rao S, 2017, bioRxiv

      Not checked in the free run.

    • cites [14] Wutz G, 2017, bioRxiv

      Not checked in the free run.

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

    Interpretationreasoning

    Dynamically extruding cohesin complexes are likely functionally important by facilitating dynamic and repeated enhancer-promoter scanning in cis.

    “We note that dynamically extruding cohesin complexes are also likely to be functionally important by facilitating dynamic and repeated enhancer-promoter scanning in cis.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Wutz et al. found that 96% of loops, but only 53% of TADs were lost 15 min after auxin addition, whereas TADs were fully lost at later time points.

    “Similarly, Wutz et al. found that 96% of loops, but only 53% of TADs were lost 15 min after auxin addition, whereas TADs were fully lost at later time points.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [14] Wutz G, 2017, bioRxiv

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationcitation

    The ability of a particular model to fit data does not prove that the model's mechanistic assumptions are also true.

    “Nevertheless, it must be noted that the ability of a particular model to fit data does not prove that the model's mechanistic assumptions are also true.68”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [68] source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    Loops and TADs rapidly disappear at a timescale of a few to tens of minutes after acute cohesin loss, which is consistent with the notion that cohesin binding dynamics control TAD dynamics.

    “These results show that loops and TADs rapidly disappear at a timescale of a few to tens of minutes after acute cohesin loss, which is consistent with the notion that cohesin binding dynamics control TAD dynamics.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Dynamic loop extrusion models can explain recent perturbation experiments where CTCF binding sites have been added or deleted and also explain the loss of either CTCF or cohesin.

    “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”
    Quote in the paperSubstantial claim0 of 10 sources checked
    • cites [9] source

      Not checked in the free run.

    • cites [49] source

      Not checked in the free run.

    • cites [50] source

      Not checked in the free run.

    • cites [51] source

      Not checked in the free run.

    • cites [10] source

      Not checked in the free run.

    • cites [11] source

      Not checked in the free run.

    • cites [12] source

      Not checked in the free run.

    • cites [13] Rao S, 2017, bioRxiv

      Not checked in the free run.

    • cites [14] Wutz G, 2017, bioRxiv

      Not checked in the free run.

    • cites [15] Gassler J, 2017, bioRxiv

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    About 18% of TAD boundaries were not sensitive to CTCF loss and could have different dynamics.

    “(∼18% of TAD boundaries were not sensitive to CTCF loss10 and could have different dynamics)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [10] source

      Not checked in the free run.

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

    Interpretationcitation

    Genome organization dynamics could be different in some cell types, such as post-mitotic olfactory sensory neurons, which exhibit a highly unusual and specialized nuclear organization.

    “(genome organization dynamics could be different in some cell types, e.g. in post-mitotic olfactory sensory neurons, which exhibit a highly unusual and specialized nuclear organization69,70)”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [69] source

      Not checked in the free run.

    • cites [70] source

      Not checked in the free run.

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

    Interpretationreasoning

    Almost certainly, some binding sites will exhibit longer and shorter binding times.

    “Almost certainly, some binding sites will exhibit longer and shorter binding times.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Binding times to cognate sites are highly stochastic and exponentially distributed such that few events exhibit the mean value.

  • May combine two claims.

    Premisecitation

    TADs are somewhat conserved between different cell types, but several do change.

    “although TADs are somewhat conserved between different cell types,1 several do change.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [1] Merkenschlager M, 2017, Annu Rev Genomics Hum Genet

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Recent studies show that TADs and loops are lost within tens of minutes after acute cohesin degradation and quickly reformed after cohesin replenishment.

    “recent studies13,14 showing that TADs and loops are lost within tens of minutes after acute cohesin degradation and quickly reformed after cohesin replenishment”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [13] Rao S, 2017, bioRxiv

      Not checked in the free run.

    • cites [14] Wutz G, 2017, bioRxiv

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Recent polymer studies of presumably cohesin-motor driven loop extrusion were able to quantitatively account for Hi-C data, but so was a mechanistically distinct model by Benedetti et al., where supercoiling drives the formation of TADs.

    “recent polymer studies8,9 of presumably cohesin-motor driven loop extrusion were able to quantitatively account for Hi-C data, but so was a mechanistically distinct model by Benedetti et al., where supercoiling drives the formation of TADs.66”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [8] source

      Not checked in the free run.

    • cites [9] source

      Not checked in the free run.

    • cites [66] source

      Not checked in the free run.

61 of 61

  • The authors state this as an assumption.

    The presence of CTCF and cohesin bound corner peaks in Hi-C maps corresponds to a chromatin loop held together by CTCF and cohesin.

    “The presence of CTCF and cohesin bound “corner peaks” in Hi-C maps are generally assumed to correspond to a chromatin loop held together by CTCF and cohesin as sketched.”

  • The authors state this as an assumption.

    TADs are formed by cohesin-mediated extrusion, which stops at occupied CTCF binding sites.

    “This picture assumes that TADs are formed by cohesin-mediated extrusion, which stops at occupied CTCF binding sites.”

  • The authors state this as an assumption.

    CTCF binds its cognate sites and recruits cohesin, which then folds the in-between chromatin into a loop structure.

    “This readily suggested a model wherein CTCF binds its cognate sites and recruits cohesin, which then folds the in-between chromatin into a loop structure.”

  • The authors state this as an assumption.

    In the loop extrusion model, cohesin spontaneously engages chromatin and begins extruding a DNA loop.

    “In this model, cohesin spontaneously engages chromatin and begins extruding a DNA loop.”

  • The authors state this as an assumption.

    Loop extrusion continues until cohesin spontaneously falls off or until it encounters an occupied CTCF binding site in the convergent orientation.

    “Loop extrusion then continues until cohesin spontaneously falls off or until it encounters an occupied CTCF binding site in the convergent orientation.”

  • The authors state this as an assumption.

    The orientation of the CTCF binding site determines the orientation of the CTCF protein.

    “Since the orientation of the CTCF binding site determines the orientation of the CTCF protein, this may explain how an extruding cohesin complex distinguishes between convergent and divergent CTCF binding sites.”

  • The authors state this as an assumption.

    In ΔWAPL cells, cohesin's extrusion speed does not change.

    “assuming no change in cohesin's extrusion speed”

  • The authors state this as an assumption.

    CTCF positions cohesin at its convergent cognate binding sites and cohesin holds together two strands of chromatin.

    “Cohesin functions to hold together two strands of chromatin and CTCF positions cohesin at its convergent cognate binding sites as previously proposed.”

  • The paper relies on this without support.

    The main function of cohesin in G1 is loop extrusion.

    “the main function of cohesin in G1 is loop extrusion”

  • The paper relies on this without support.

    Binding times to cognate sites are highly stochastic and exponentially distributed such that few events exhibit the mean value.

    “Moreover, the binding times to cognate sites are highly stochastic and exponentially distributed such that few events exhibit the mean value.”

  • The paper relies on this without support.

    Replenishment of cohesin involves translation of enough Rad21 protein, incorporation into cohesin complexes, loading onto chromatin, initiation and continuation of extrusion, and re-formation of TADs.

    “For example, replenishment of cohesin involves translation of enough Rad21 protein, incorporation into cohesin complexes, loading onto chromatin, initiation and continuation of extrusion, and re-formation of TADs.”
11 of 11

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?

Cites

Flagged first, then by citations

Research works printed but not linked: 7

  1. Merkenschlager M, 2017, Annu Rev Genomics Hum Genet, 17, 1
  2. Rao S, 2017, bioRxiv
  3. Wutz G, 2017, bioRxiv
  4. Gassler J, 2017, bioRxiv
  5. Finn E, 2017, bioRxiv
  6. Hansen AS, 2017, bioRxiv
  7. Zirkel A, 2017, bioRxiv

Cited by

Sorted by citations

Related

Authors
Hansen, A. S., Cattoglio, C., Darzacq, X., & Tjian, R.
Affiliations
  • Howard Hughes Medical Institute (US)
  • University of California, Berkeley (US)
Corresponding author
Hansen, Anders S.
ORCID
Venue
Nucleus
Publisher
Informa UK Limited
Published
2017-12-14
Volume
9
Issue
1
Pages
20-32
ISSN
  • 1949-1034 (ISSN-L)
  • 1949-1042
DOI
10.1080/19491034.2017.1389365
PMC
PMC5990973
OpenAlex
W2767110090
Semantic Scholar
105d85c2ba436e44587d8b60f1d342ae96d7e316
Cited by
266
References
78
Citations by year
2026: 14 · 2025: 24 · 2024: 31 · 2023: 24 · 2022: 42 · 2021: 35 · 2020: 44 · 2019: 32 · 2018: 17 · 2017: 2
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleus (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
Funders
  • California Institute of Regenerative Medicine (LA1-08013)
  • Siebel Stem Cell Institute
  • National Institutes of Health (DK 107980)
  • National Institute of Diabetes and Digestive and Kidney Diseases (U54DK107980)
  • National Institute of Biomedical Imaging and Bioengineering (U01EB021236)
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
topologically associating domains, chromatin looping, loop extrusion, cohesin, CTCF, 3D genome organization, enhancer-promoter interactions, loop dynamics, cell cycle, Hi-C, polymer simulation, single-molecule imaging
MeSH terms
Animals, Chromatin, Humans, Models, Molecular, Chromatin Assembly and Disassembly

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 2026-10-10.

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

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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