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Cited by 465Genomics and Chromatin DynamicsProtein Structure and DynamicsChromatin Remodeling and Cancer

The structural basis for cohesin–CTCF-anchored loops

Open access
Li, Yan, Haarhuis, Judith H. I., Sedeño Cacciatore, Ángela, Oldenkamp, Roel, van Ruiten, Marjon S., Willems, Laureen, Teunissen, Hans, Muir, Kyle W. +3 more·2020·Nature
DOI 10.1038/s41586-019-1910-zPMC PMC7035113
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Abstract

Cohesin catalyses the folding of the genome into loops that are anchored by CTCF1. The molecular mechanism of how cohesin and CTCF structure the 3D genome has remained unclear. Here we show that a segment within the CTCF N terminus interacts with the SA2–SCC1 subunits of human cohesin. We report a crystal structure of SA2–SCC1 in complex with CTCF at a resolution of 2.7 Å, which reveals the molecular basis of the interaction. We demonstrate that this interaction is specifically required for CTCF-anchored loops and contributes to the positioning of cohesin at CTCF binding sites. A similar motif is present in a number of established and newly identified cohesin ligands, including the cohesin release factor WAPL2,3. Our data suggest that CTCF enables the formation of chromatin loops by protecting cohesin against loop release. These results provide fundamental insights into the molecular mechanism that enables the dynamic regulation of chromatin folding by cohesin and CTCF. The crystal structure of the SA2–SCC1 subunits of human cohesin in complex with CTCF reveals the molecular basis of the cohesin–CTCF interaction that enables the dynamic regulation of chromatin folding.

AI snapshot

Written from the paper’s full text.

TL;DR

CTCF’s N-terminal YxF motif binds the SA2–SCC1 “conserved essential surface” (CES), and a 2.6 Å crystal structure explains the interface. Disrupting this interface abolishes CTCF-anchored loops while leaving TAD-like structures largely present, suggesting CTCF stabilizes cohesin at loop anchors rather than merely acting as a passive barrier.

Key findings

  • CTCF residues 222–231 bind SA2–SCC1 with Kd = 1.04 ± 0.20 μM; Y226 and F228 are the lead anchoring residues, and Y226A/F228A abolish binding in GST pulldowns.
  • In HAP1 cells with endogenous CTCF Y226A F228A, Hi-C loop calls drop from 2756 in wild type to 98 in mutant cells; TAD-like structures remain but have less-clear edges.
  • FRAP shows cohesin is more mobile in CTCF Y226A F228A cells, and ChIP-qPCR/ChIP-seq show reduced cohesin at CTCF sites, while CTCF binding itself is largely unaffected.
  • WAPL competes with CTCF for the SA2–SCC1 CES; the CTCF peptide binds more strongly than WAPL peptides (WAPL 423–463 Kd ≈ 32.8 μM), and RNA-seq shows >2000 genes affected by the CTCF mutation.

Methods

  • Biochemical binding assays: GST pulldowns, isothermal titration calorimetry, and peptide arrays using SA2–SCC1 and mutant complexes.
  • Structural analysis: crystals of SA2–SCC1 in complex with a CTCF 222–231 peptide; structure determined by molecular replacement at 2.6 Å (Rwork/Rfree 0.25/0.27).
  • Cell and genome-wide assays: CRISPR/Cas9-generated HAP1 CTCF Y226A F228A cells, HaloTagged SCC1 FRAP, Hi-C, ChIP-qPCR/ChIP-seq, and RNA-seq.

Limitations

  • The paper does not include a dedicated limitations section.
  • Evident from the text: key cellular conclusions rely on the human haploid HAP1 cell line and a single CTCF interface mutant (Y226A F228A), with no in vivo organismal validation.
  • Evident from the text: CTCF depletion was lethal in both control and CTCF Y226A F228A HAP1 cells, so essential CTCF functions independent of CES engagement and CTCF-anchored loops remain unresolved.

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

Integrity signals

Registry

Crossref · 10.1038/s41586-019-1910-z

Cites

76 of 76 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 33 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    CTCF F228 inserts into a pocket formed by SCC1 S334, I337, L341 and SA2 Y297, W334.

    “F228 inserts into a pocket comprising amino acids from SCC1 (S334, I337, L341) and SA2 (Y297, W334) (Extended Data Fig. 1f).”
    Quote in the paperSubstantial claim
  • Findingown data

    Mutating CTCF Y226A or F228A abolishes SA2-SCC1 binding in GST pulldown assays.

    “Mutagenesis of Y226A or F228A in CTCF abolished SA2-SCC1 binding in a GST pulldown assay (Fig. 1e).”
    Quote in the paperSubstantial claim
  • Findingown data

    The CTCF peptide binds to the convex surface of SA2.

    “The CTCF peptide is bound to the convex surface of SA2 (Fig. 1a,b).”
    Quote in the paperSubstantial claim
  • Findingcitation

    A similar binding motif occurs in several known and newly identified cohesin ligands, including WAPL.

    “A similar motif is present in a number of established and novel cohesin ligands, including the cohesin release factor WAPL2,3.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [2] Hara, K. et al. Structure of cohesin subcomplex pinpoints direct shugoshin–Wapl antagonism in centromeric cohesion. Nat. Struct. Mol. Biol. 21, 864–870 (2014). source

      Not checked in the free run.

    • cites [3] Shintomi, K. & Hirano, T. Releasing cohesin from chromosome arms in early mitosis: opposing actions of Wapl–Pds5 and Sgo1. Genes Dev. 23, 2224–2236 (2009). source

      Not checked in the free run.

  • Findingown data

    The CTCF-SA2-SCC1 interaction contributes to positioning cohesin at CTCF binding sites.

    “and contributes to the positioning of cohesin at CTCF binding sites”
    • Also stated in: § CTCF interaction promotes cohesin localization to CTCF sites · plain
      “CTCF interaction promotes cohesin localization to CTCF sites”
    Quote in the paperSubstantial claim
  • May combine two claims. 24
  • Classified as probably not a substantial claim. 25
  • The quote only partly states this claim. 16

  • May combine two claims.

    Findingown data

    CTCF E229 and E230 are secondary anchoring residues that likely contribute to binding specificity through salt bridges with SA2 R298 and SCC1 R338.

    “E229 and E230 of CTCF constitute secondary anchoring residues, which presumably contribute to binding specificity by forming salt bridges with R298 of SA2 and R338 of SCC1.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Mutating SA2 W334A, F371A or F367A, or SCC1 I337A/L341A, abolishes CTCF binding.

    “Likewise, mutation of critical amino acid residues in SA2, including W334A, F371A and F367A or in SCC1 I337A/L341A, abolished CTCF binding (Fig. 1f).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The crystal structure was determined by molecular replacement at 2.6 Å and an omit map showed clear density for the CTCF peptide.

    “determined the structure by molecular replacement at a resolution of 2.6 Å”
    • Also stated in: § Structure of the SA2-SCC1-CTCF complex · boosted
      “An Fo-Fc omit electron density Fourier map exhibited clear features corresponding to the CTCF peptide”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The CTCF binding surface is predominantly hydrophobic and includes residues from both SA2 and SCC1.

    “The CTCF binding surface is predominantly hydrophobic and composed of amino acids contributed by both SA2 and SCC1.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A peptide array assay showed clear binding of SA2-SCC1 to the CTCF peptide spanning residues 222-231, which was abolished by the SA2 F371A mutation.

    “We observed clear signal for the CTCF peptide spanning 222-231, which was abolished in the SA2 (F371A)-SCC1 mutant (Extended Data Fig. 7d,e).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Genome-wide ChIP-Seq shows the Y226A F228A mutation decreases cohesin localization to CTCF sites but has little to no effect at unrelated sites.

    “We then assessed cohesin distribution genome-wide by ChIP-Seq and found that the Y226A F228A mutation decreased cohesin localization to CTCF sites, but had little to no effect on cohesin localization at unrelated sites (Fig. 4c,d).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    TAD-like structures remain to a considerable degree in CTCF Y226A F228A cells but have less-clear edges.

    “found that these structures were, to a considerable degree, still present in CTCF Y226A F228A cells, but have less-clear edges (Fig. 3a).”
    • Also stated in: § CTCF-CES interaction is required for CTCF-anchored loops · boosted
      “Aggregate TAD analysis further confirmed that TAD-like structures do exist in CTCF Y226A F228A cells, but indeed have less-clear boundaries”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    siRNA-mediated depletion of CTCF is lethal to both control HAP1 cells and CTCF Y226A F228A mutant cells.

    “found that siRNA-mediated CTCF depletion was lethal to both control HAP1 cells and CTCF Y226A F228A mutant cells (Extended Data Fig. 7b,c).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The CTCF Y226F variant shows about 1.5-fold reduced binding, likely due to loss of the hydrogen bond between Y226 hydroxyl and SA2 D326.

    “A CTCF Y226F mutant showed ~1.5 fold reduced binding, apparently due to loss of the hydrogen bond between the hydroxyl group of CTCF Y226 and D326 of SA2 (Extended Data Table 2).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    WAPL peptides bind SA2-SCC1 considerably more weakly than CTCF, and no binding was detected for SGO1.

    “The WAPL peptides showed considerably weaker binding as compared to CTCF, while we could not detect binding for ligands such as SGO1 (see Methods and Extended Data Table 1a).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Among genes affected by the mutation, comparable numbers are up- and downregulated, but the most strongly impacted genes are more frequently downregulated.

    “While comparable numbers of genes were upregulated as were downregulated, the most strongly impacted genes were more frequently downregulated (Extended Data Fig. 7a).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In CTCF Y226A F228A cells, FRAP showed near-complete recovery, indicating cohesin is more mobile.

    “In CTCF Y226A F228A cells, however, we observed a near-complete recovery by FRAP, demonstrating that cohesin is more mobile in these cells (Fig. 2c,d).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Findingown data

    The SYCP1 peptide binds SA2-SCC1 with a Kd of 6.71 ± 3.18 μM.

    “SYCP1 | Human | Wild-type | Q15431 | 882 | RKMAFEFDINS | 6.71 ± 3.18†”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S1 (asserted), S4 (based). The quote only partly states this claim.

    Findingnone given

    The CTCF Y226A mutation abolishes binding to SA2-SCC1.

    “CTCF | Human | Y226A | P49711 | 222 | DVSVADFEEEQ | n.b.”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    Wapl residues 423-463 bind SA2-SCC1 with a Kd of 32.8 μM.

    “Wapl† | 423-463 | 32.8 | -6.66 | -0.54 | -6.11 | 0.62”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S1 (asserted), S4 (based). The quote only partly states this claim.

    Findingnone given

    The CTCF F228A mutation abolishes binding to SA2-SCC1.

    “CTCF | Human | F228A | P49711 | 222 | DVSVYDAEEEQ | n.b.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Findingown data

    The ZGPAT peptide binds SA2-SCC1 with a Kd of 4.03 ± 1.19 μM.

    “ZGPAT | Human | Wild-type | Q8N5A5 | 411 | PRNVFDFLNEK | 4.03 ± 1.19†”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    The CTCF Y226F mutation reduces binding affinity to SA2-SCC1 to a Kd of 1.60 ± 0.03 μM.

    “CTCF | Human | Y226F | P49711 | 222 | DVSVFDFEEEQ | 1.60 ± 0.03†”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Findingown data

    The SYCP3 peptide binds SA2-SCC1 with a Kd of 1.96 ± 0.26 μM.

    “SYCP3 | Human | Wild-type | Q8IZU3 | 21 | FTRAYDFETED | 1.96 ± 0.26†”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Findingown data

    The CENPU peptide binds SA2-SCC1 with a Kd of 4.03 ± 0.22 μM.

    “CENPU | Human | Wild-type | Q71F23 | 40 | PIDVFDFPDNS | 4.03 ± 0.22†”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing), S4 (based). The quote only partly states this claim.

    Findingown data

    The MCM3 peptide binds SA2-SCC1 with a Kd of 1.02 ± 0.05 μM.

    “MCM3 | Human | Wild-type | P25205 | 704 | SYDPYDFSDTE | 1.02 ± 0.05†”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    Shugoshin residues 331-349 with T346 phosphorylation bind SA2-SCC1 with a Kd of 2.32 μM.

    “Shugoshin† | 331-349(pT346)§ | 2.32 | -20.00 | -12.30 | -7.69 | 0.89”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    CTCF residues 86-267 bind SA2-SCC1 with a Kd of 0.62 μM.

    “CTCF† | 86-267 | 0.62 | -13.16 | -4.61 | -8.54 | 0.78”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S1 (asserted), S4 (based). The quote only partly states this claim.

    Findingnone given

    The CTCF Y226/F228A double mutation abolishes binding to SA2-SCC1.

    “CTCF | Human | Y226/F228A | P49711 | 222 | DVSVADAEEEQ | n.b.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    CTCF engages a composite binding surface containing residues from both SCC1 and SA2, so prior mapping with isolated SA2 may have been misleading.

    “As CTCF engages a composite binding surface containing amino acids from SCC1 and SA2, prior mapping studies using isolated SA2 may have been misleading20.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [20] Xiao, T., Wallace, J. & Felsenfeld, G. Specific sites in the C terminus of CTCF interact with the SA2 subunit of the cohesin complex and are required for cohesin-dependent insulation activity. Mol. Cell. Biol. 31, 2174–2183 (2011). source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    SA2 contains an 86-amino-acid stromalin conservative domain/CES that is conserved from fungi to mammals and overlaps the CTCF binding pocket.

    “SA2 contains an 86 amino acid motif, termed the ‘stromalin conservative domain’21,22 or ‘conserved essential surface’ (CES)2,23, which is conserved from fungi to mammals and coincides with the CTCF binding pocket.”
    Quote in the paperSubstantial claim0 of 4 sources checked
    • cites [21] Pezzi, N. et al. STAG3, a novel gene encoding a protein involved in meiotic chromosome pairing and location of STAG3-related genes flanking the Williams-Beuren syndrome deletion. FASEB J. 14, 581–592 (2000). source

      Not checked in the free run.

    • cites [22] Orgil, O. et al. A conserved domain in the Scc3 subunit of cohesin mediates the interaction with both Mcd1 and the cohesin loader complex. PLoS Genet. 11, e1005036 (2015). source

      Not checked in the free run.

    • cites [2] Hara, K. et al. Structure of cohesin subcomplex pinpoints direct shugoshin–Wapl antagonism in centromeric cohesion. Nat. Struct. Mol. Biol. 21, 864–870 (2014). source

      Not checked in the free run.

    • cites [23] Roig, M. B. et al. Structure and function of cohesin’s Scc3/SA regulatory subunit. FEBS Lett. 588, 3692–3702 (2014). source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    CTCF and WAPL compete directly for the CES, and this binding event is proposed to stabilize chromatin loops.

    “As CTCF directly competes with WAPL for binding to the CES (Fig. 2a,b), we propose that this interaction stabilizes chromatin loops.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    CTCF is not merely a passive barrier to loop extrusion; it interacts with the CES to stabilize cohesin at CTCF loci and prevent loop disruption.

    “Thus, CTCF does not simply present a passive barrier to cohesin-mediated loop extrusion, but specifically interacts with the CES to stabilize cohesin at these loci, and to prevent loop disruption.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    CTCF acts on cohesin through two separable mechanisms: stopping cohesin at CTCF sites and stabilizing it at the base of CTCF-anchored loops.

    “Our data therefore support the model that CTCF influences cohesin in two distinct ways: i) it halts cohesin at CTCF sites and ii) it stabilizes cohesin at the base of CTCF-anchored loops.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    WAPL and SGO1 have opposing functions, and their antagonism arises from direct competition for the SA2-SCC1 CES.

    “This antagonism arises as a result of direct competition for binding to the CES of SA2-SCC12.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [2] Hara, K. et al. Structure of cohesin subcomplex pinpoints direct shugoshin–Wapl antagonism in centromeric cohesion. Nat. Struct. Mol. Biol. 21, 864–870 (2014). source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    SA2, SCC1 and CTCF are frequently mutated in several tumour types, and the mutations cluster in the CES.

    “SA2, SCC1 as well as CTCF are frequently mutated in a number of different tumour types39 and the mutations cluster in the CES (Extended Data Fig. 2b).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [39] Tang, Z. et al. CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell 163, 1611–1627 (2015). source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    In CTCF Y226A F228A cells, cohesin can still form loops along DNA that make up contacts within TADs, but is not stabilized at CTCF sites to form or maintain CTCF-anchored loops.

    “Our results therefore support the notion that in CTCF Y226A F228A cells cohesin can still form the loops along DNA that make up the contacts within TADs, but that cohesin is not stabilized at CTCF sites to allow for the formation or maintenance of CTCF-anchored loops.”
    Quote in the paperSubstantial claim

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

    Study design and conductown data

    The peptide array experiments were performed three times with consistent results.

    “Three independent experiments were done with consistency.”
    Quote in the paperNot a substantial claim

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

    Interpretationreasoning

    The CES interface is conserved between SA isoforms, so ligand binding is anticipated to affect all cohesin variants similarly.

    “As the CES interface is conserved between SA isoforms, we anticipate that ligand binding will affect all cohesin variants in a similar manner.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    The ITC experiment was repeated three times with consistency.

    “The experiment was repeated three times with consistency.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Study design and conductown data

    The Western blot assessing CTCF and SMC1 knockdown was performed twice with similar results.

    “This experiment was performed twice with similar results.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    The CTCF ChIP-qPCR analysis at loci 8 to 12 was based on two independent ChIP experiments.

    “The mean of two independent ChIP experiments is shown.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    The competition experiment was repeated twice.

    “The experiment was repeated twice. One representative example is shown.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    The SCC1-Halo fluorescence quantification was based on three independent experiments.

    “Individual cells of three independent experiments are plotted as dots and their mean is indicated”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    The GST pulldown experiment was repeated once.

    “The experiment was repeated once.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Study design and conductown data

    The Western blot for Halo-tagged SCC1 was performed once.

    “This experiment was performed once.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    The SCC1 ChIP-qPCR analysis was based on three independent ChIP experiments.

    “The mean of three independent ChIP experiments is shown with the standard deviation.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    The CTCF Y226A F228A mutation was verified by Sanger sequencing, which also revealed a silent mutation at position 229.

    “The CTCF Y226A F228A mutation was confirmed by Sanger sequencing, including a silent mutation at position 229.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Shugoshin carries an F/YxF motif and safeguards centromeric cohesion by blocking WAPL from the SA2-SCC1 CES.

    “A number of other genome regulatory factors contain F/YxF motifs including Shugoshin (Extended Data Fig. 7d,e), which protects centromeric chromatid cohesion by antagonizing WAPL binding to the CES of SA2-SCC12.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [2] Hara, K. et al. Structure of cohesin subcomplex pinpoints direct shugoshin–Wapl antagonism in centromeric cohesion. Nat. Struct. Mol. Biol. 21, 864–870 (2014). source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Study design and conductown data

    The chromatin-bound levels experiment was repeated twice with similar results.

    “This experiment was performed twice with similar results.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    SCC1 ChIP was performed three times, with three qPCRs per ChIP in duplicate.

    “SCC1 ChIP was performed three times, and on each ChIP three qPCRs were performed in duplicate.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Study design and conductown data

    The colony formation assay was performed four times with similar results.

    “This experiment was performed four times with similar results.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    The aggregate peak analysis used two independent library preparations per genotype.

    “Aggregate peak analysis as in Fig. 3c, using two independent library preps per genotype.”
    Quote in the paperNot a substantial claim

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

    Study design and conductown data

    The CTCF ChIP-qPCR analysis at loci 1 to 7 was based on two independent ChIP experiments.

    “The mean of two independent ChIP experiments is shown.”
    Quote in the paperNot a substantial claim

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

    Study design and conductnone given

    For CTCF and IgG, two ChIPs were performed in duplicate.

    “For CTCF and IgG, two ChIPs were performed in duplicate.”
    Quote in the paperNot a substantial claim
50 of 50

  • The paper relies on this without support.

    TADs previously defined for wild type HAP1 cells are applicable to CTCF Y226A F228A cells for aggregate TAD analysis.

    “For this analysis we employed TADs previously defined for wild type HAP1 cells10.”

  • The paper relies on this without support.

    The non-diffusive fraction of SCC1-Halo fluorescence is a valid proxy for the chromatin-bound fraction of SCC1.

    “as a proxy for the chromatin-bound fraction of SCC1”

  • The paper relies on this without support.

    Histone H4 is a valid control for the chromatin fraction.

    “Histone H4 is used as a control for the chromatin fraction.”
3 of 3

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Crystal-structure resolution differs between Methods and table

    Minor

    The Methods report refinement to 2.6 Å, whereas the crystallographic statistics table reports 2.70 Å.

  • Mutant Hi-C cis-contact counts do not add up

    Minor

    For CTCF Y226A F228A replicate 1, the reported short- and long-range cis contacts sum to 112,774,621, exceeding the reported 47,164,621 total cis contacts. The short-range count appears to contain an extra digit.

    Reported 47164621 · recomputed 112774621

  • CTCF has conflicting UniProt identifiers

    Minor

    The Methods identify the CTCF peptide with UniProt ID Q8NI51, while the peptide-array table identifies CTCF as P49711.

3 of 3

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Authors
Li, Y., Haarhuis, J. H. I., Sedeño Cacciatore, Á., Oldenkamp, R., van Ruiten, M. S., Willems, L., Teunissen, H., Muir, K. W., de Wit, E., Rowland, B. D., & Panne, D.
Affiliations
  • European Molecular Biology Laboratory (FR)
  • The Netherlands Cancer Institute (NL)
  • MRC Laboratory of Molecular Biology (GB)
  • University of Leicester (GB)
Corresponding author
  • Muir, Kyle W.
  • Rowland, Benjamin D.
  • Panne, Daniel
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2020-01-06
Volume
578
Issue
7795
Pages
472-476
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-019-1910-z
PMC
PMC7035113
OpenAlex
W2998399076
Semantic Scholar
3965c92cc2688a322bb6f724613fab45b8ff49d2
Cited by
459
References
75
Citations by year
2026: 55 · 2025: 70 · 2024: 84 · 2023: 75 · 2022: 70 · 2021: 63 · 2020: 42
FWCI
20.91
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • Figshare (submittedVersion, cc-by)
Funders
  • European Molecular Biology Laboratory (EMBL001)
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek (016.161.316)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords
cohesin, CTCF, chromatin looping, 3D genome organization, protein-protein interaction, WAPL, chromatin folding, crystal structure
MeSH terms
CCCTC-Binding Factor, Cohesins, Binding Sites, Carrier Proteins, Chromatin, Chromosomal Proteins, Non-Histone, DNA, Humans, Ligands, Models, Molecular, Nuclear Proteins, Peptide Fragments, Protein Binding, Proto-Oncogene Proteins, Crystallography, X-Ray, Cell Cycle Proteins, Protein Subunits, Protein Stability

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.

What counts as a claim ›How we measure confidence ›How we check this ›

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