The DOI matches its Crossref record; 76 of the 76 references it cites were found in a registry or an index; 8 of the 33 sources its claims cite were checked for support.
The structural basis for cohesin–CTCF-anchored loops
Open accessAbstract
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.
Overview
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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.
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Claims the paper makes
60 Own result · 16 Own method · 15 Own interpretation · 13 Not checked yet · 6 No basis given · 2 Partly supported · 1 Supported · accuracy not yet measured
Every source the paper cites for this claim was checked and supports it.
In the paper
“Similarly, titration of a SGO1 phospho-T346 peptide, previously reported to preclude WAPL binding2, also displaced SA2-SCC1 from GST-CTCF (Extended Data Fig. 2d).”
§ The structural basis for cohesin-CTCF anchored loops > Results > CTCF stabilizes cohesin on chromatin
What the sources say
- Supportedcites [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
The citation is attached to the statement that the phospho-T346 SGO1 peptide precludes WAPL binding, not to the citing authors’ GST-CTCF displacement result. In Results, “Sgo1 competes with Wapl for cohesin binding,” the source reports dose-dependent reduction of SA2–Scc1 binding to GST-Wapl-M by the phosphorylated peptide. (LLM, conf=0.92)
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In the paper
“Stabilization of cohesin by engagement of the CTCF N-terminus may in fact explain why TAD boundaries arise preferentially when CTCF binding sites are convergently oriented9,13–16,38,39.”
§ The structural basis for cohesin-CTCF anchored loops > Discussion
What the sources say
- Not checked yetcites [9] Sanborn, A. L. et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc. Natl Acad. Sci. USA 112, E6456–E6465 (2015).
- Partly supportedcites [13] Guo, Y. et al. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function. Cell 162, 900–910 (2015). sourceExperimental — accuracy not yet measured
The Results section, under “Directional CTCF Binding in Genome-wide DNA Looping Specificity” (page unavailable), reports preferential orientations of CTCF-site pairs at TAD boundaries and links CTCF/cohesin occupancy to directional looping. It does not propose that engagement of the CTCF N-terminus stabilizes cohesin or explains that orientation preference. (LLM, conf=0.86)
- Not checked yetcites [14] de Wit, E. et al. CTCF binding polarity determines chromatin looping. Mol. Cell 60, 676–684 (2015). source
- Partly supportedcites [15] Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014). sourceExperimental — accuracy not yet measured
The Results report that 92% of examined loop-anchor CTCF motif pairs are convergent, and the Discussion says loops often demarcate domains. But the Discussion proposes CTCF dimerization as a possible mechanism; it does not attribute the orientation preference to stabilization of cohesin by the CTCF N-terminus. No page number is available in our copy. (LLM, conf=0.87)
- Partly supportedcites [16] Vietri Rudan, M. et al. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep. 10, 1297–1309 (2015). sourceExperimental — accuracy not yet measured
The Results (section “Conserved CTCF Sites Are Directional and Interact with Other Conserved Sites”; page unavailable) link CTCF motif orientation to directional contacts and report oppositely oriented sites anchoring domain-defining interactions. But the paper does not propose stabilization through the CTCF N-terminus; the Discussion instead says cohesin interacts with CTCF primarily through its C-terminal tail. (LLM, conf=0.88)
- Not checked yetcites [38] Sedeño Cacciatore, Á. & Rowland, B. D. Loop formation by SMC complexes: turning heads, bending elbows, and fixed anchors. Curr. Opin. Genet. Dev. 55, 11–18 (2019). source
- Partly supportedcites [39] Tang, Z. et al. CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell 163, 1611–1627 (2015). sourceExperimental — accuracy not yet measured
Results II reports that most chromatin-contact-domain boundaries have inward-facing CTCF motifs and that cohesin co-occupies many CTCF interaction anchors. The Discussion links convergent CTCF loops to CCD/TAD boundaries. Neither passage attributes that preference to engagement of the CTCF N-terminus stabilizing cohesin. (LLM, conf=0.85)
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In the paper
“F228 inserts into a pocket comprising amino acids from SCC1 (S334, I337, L341) and SA2 (Y297, W334) (Extended Data Fig. 1f).”
§ The structural basis for cohesin-CTCF anchored loops > Results > Structure of the SA2-SCC1-CTCF complex
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In the paper
“Mutagenesis of Y226A or F228A in CTCF abolished SA2-SCC1 binding in a GST pulldown assay (Fig. 1e).”
§ The structural basis for cohesin-CTCF anchored loops > Results > Analysis of the CTCF binding interface
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In the paper
“The CTCF peptide is bound to the convex surface of SA2 (Fig. 1a,b).”
§ The structural basis for cohesin-CTCF anchored loops > Results > Structure of the SA2-SCC1-CTCF complex
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None of the sources cited for this claim have been checked yet.
In the paper
“A similar motif is present in a number of established and novel cohesin ligands, including the cohesin release factor WAPL2,3.”
§ The structural basis for cohesin-CTCF anchored loops > Abstract
What the sources say
- Not checked yetcites [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 yetcites [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
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“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”
§ The structural basis for cohesin-CTCF anchored loops > Abstract
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- Also stated in: § CTCF interaction promotes cohesin localization to CTCF sites · plain
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In the paper
“The lead ‘anchoring’ amino acids of CTCF, which bury the largest solvent-accessible surface area upon binding, are Y226 and F228 (Fig. 1b).”
§ The structural basis for cohesin-CTCF anchored loops > Results > Structure of the SA2-SCC1-CTCF complex
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In the paper
“A 2.6Å crystal structure of SA2-SCC1 in complex with CTCF reveals the molecular basis of the interaction.”
- Also stated in: § Structure of the SA2-SCC1-CTCF complex · plain
“we produced crystals of the SA2-SCC1 complex in the presence of a peptide comprising the CTCF binding motif and determined the structure by molecular replacement at a resolution of 2.6 Å”
§ The structural basis for cohesin-CTCF anchored loops > Abstract
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- Also stated in: § Structure of the SA2-SCC1-CTCF complex · plain
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In the paper
“The hydroxyl group of Y226 hydrogen bonds with D326 of SA2 in a deep hydrophobic pocket lined by L329, L366 and F367 (Fig. 1c,d).”
§ The structural basis for cohesin-CTCF anchored loops > Results > Structure of the SA2-SCC1-CTCF complex
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- It may state two separate claims as one. 24
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The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“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.”
§ The structural basis for cohesin-CTCF anchored loops > Results > Analysis of the CTCF binding interface
What the sources say
- Not checked yetcites [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
- Partly supportedcites [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). sourceExperimental — accuracy not yet measured
The Results section identifies a conserved stromalin conserved domain (SCD) in yeast Scc3, and the Discussion describes SA2 as a human Scc3 homolog. The paper gives the yeast SCD as residues 367–457; it does not establish an 86-amino-acid motif in SA2, call it the CES, or locate a CTCF-binding pocket overlapping it. (LLM, conf=0.84)
- Partly supportedcites [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). sourceExperimental — accuracy not yet measured
The Results section on the Sgo1-binding site identifies an SA2 motif conserved in SA proteins from yeast to humans. It does not identify an 86-amino-acid stromalin conservative domain or CES, or say that such a domain coincides with a CTCF-binding pocket (pages unavailable in our copy). (LLM, conf=0.79)
- Partly supportedcites [23] Roig, M. B. et al. Structure and function of cohesin’s Scc3/SA regulatory subunit. FEBS Lett. 588, 3692–3702 (2014). sourceExperimental — accuracy not yet measured
The structure and CES-function sections describe a highly conserved surface in Scc3 orthologs, including mammalian SA2, and identify it as the conserved essential surface. However, our copy does not specify an 86-amino-acid motif, call it the stromalin conservative domain, or establish that it coincides with a CTCF-binding pocket. (LLM, conf=0.85)
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In the paper
“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.”
§ The structural basis for cohesin-CTCF anchored loops > Results > Structure of the SA2-SCC1-CTCF complex
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In the paper
“Likewise, mutation of critical amino acid residues in SA2, including W334A, F371A and F367A or in SCC1 I337A/L341A, abolished CTCF binding (Fig. 1f).”
§ The structural basis for cohesin-CTCF anchored loops > Results > Analysis of the CTCF binding interface
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“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”
§ The structural basis for cohesin-CTCF anchored loops > Results > Structure of the SA2-SCC1-CTCF complex
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In the paper
“The CTCF binding surface is predominantly hydrophobic and composed of amino acids contributed by both SA2 and SCC1.”
§ The structural basis for cohesin-CTCF anchored loops > Results > Structure of the SA2-SCC1-CTCF complex
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In the paper
“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).”
§ The structural basis for cohesin-CTCF anchored loops > Results > Identification of CES ligands
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“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).”
§ The structural basis for cohesin-CTCF anchored loops > Results > CTCF interaction promotes cohesin localization to CTCF sites
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“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”
§ The structural basis for cohesin-CTCF anchored loops > Results > CTCF-CES interaction is required for CTCF-anchored loops
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- Also stated in: § CTCF-CES interaction is required for CTCF-anchored loops · boosted
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In the paper
“found that siRNA-mediated CTCF depletion was lethal to both control HAP1 cells and CTCF Y226A F228A mutant cells (Extended Data Fig. 7b,c).”
§ The structural basis for cohesin-CTCF anchored loops > Results > CTCF interaction promotes cohesin localization to CTCF sites
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“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).”
§ The structural basis for cohesin-CTCF anchored loops > Results > Identification of CES ligands
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“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).”
§ The structural basis for cohesin-CTCF anchored loops > Results > Identification of CES ligands
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“While comparable numbers of genes were upregulated as were downregulated, the most strongly impacted genes were more frequently downregulated (Extended Data Fig. 7a).”
§ The structural basis for cohesin-CTCF anchored loops > Results > CTCF interaction promotes cohesin localization to CTCF sites
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“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).”
§ The structural basis for cohesin-CTCF anchored loops > Results > CTCF stabilizes cohesin on chromatin
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In the paper
“SYCP1 | Human | Wild-type | Q15431 | 882 | RKMAFEFDINS | 6.71 ± 3.18†”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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In the paper
“CTCF | Human | Y226A | P49711 | 222 | DVSVADFEEEQ | n.b.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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In the paper
“Wapl† | 423-463 | 32.8 | -6.66 | -0.54 | -6.11 | 0.62”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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In the paper
“CTCF | Human | F228A | P49711 | 222 | DVSVYDAEEEQ | n.b.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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“ZGPAT | Human | Wild-type | Q8N5A5 | 411 | PRNVFDFLNEK | 4.03 ± 1.19†”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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In the paper
“CTCF | Human | Y226F | P49711 | 222 | DVSVFDFEEEQ | 1.60 ± 0.03†”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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In the paper
“SYCP3 | Human | Wild-type | Q8IZU3 | 21 | FTRAYDFETED | 1.96 ± 0.26†”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“CENPU | Human | Wild-type | Q71F23 | 40 | PIDVFDFPDNS | 4.03 ± 0.22†”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. The quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“MCM3 | Human | Wild-type | P25205 | 704 | SYDPYDFSDTE | 1.02 ± 0.05†”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plaincorrelational- Asserted: fails — The authors may not put it forward as true.
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Probably not a substantial claim. The authors may not put it forward as true. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. The quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Shugoshin† | 331-349(pT346)§ | 2.32 | -20.00 | -12.30 | -7.69 | 0.89”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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The quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“CTCF† | 86-267 | 0.62 | -13.16 | -4.61 | -8.54 | 0.78”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The quote only partly states this claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“CTCF | Human | Y226/F228A | P49711 | 222 | DVSVADAEEEQ | n.b.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plaindirect- Asserted: fails — The authors may not put it forward as true.
- Checkable: passes — It can be checked against evidence.
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- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The authors may not put it forward as true. The paper may give no reason why it holds. The quote only partly states this claim.
In the paper
“As CTCF engages a composite binding surface containing amino acids from SCC1 and SA2, prior mapping studies using isolated SA2 may have been misleading20.”
§ The structural basis for cohesin-CTCF anchored loops > Results > Structure of the SA2-SCC1-CTCF complex
What the sources say
- Not checked yetcites [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
hedgedconditional- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As CTCF directly competes with WAPL for binding to the CES (Fig. 2a,b), we propose that this interaction stabilizes chromatin loops.”
§ The structural basis for cohesin-CTCF anchored loops > Discussion
hedgedconditional- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ The structural basis for cohesin-CTCF anchored loops > Discussion
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ The structural basis for cohesin-CTCF anchored loops > Results > CTCF interaction promotes cohesin localization to CTCF sites
hedgeddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
In the paper
“This antagonism arises as a result of direct competition for binding to the CES of SA2-SCC12.”
§ The structural basis for cohesin-CTCF anchored loops > Results > Analysis of the CTCF binding interface
What the sources say
- Not checked yetcites [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
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
In the paper
“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).”
§ The structural basis for cohesin-CTCF anchored loops > Discussion
What the sources say
- Not checked yetcites [39] Tang, Z. et al. CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell 163, 1611–1627 (2015). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ The structural basis for cohesin-CTCF anchored loops > Results > CTCF-CES interaction is required for CTCF-anchored loops
hedgeddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Three independent experiments were done with consistency.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As the CES interface is conserved between SA isoforms, we anticipate that ligand binding will affect all cohesin variants in a similar manner.”
§ The structural basis for cohesin-CTCF anchored loops > Discussion
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The experiment was repeated three times with consistency.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This experiment was performed twice with similar results.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The quote only partly states this claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The mean of two independent ChIP experiments is shown.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The experiment was repeated twice. One representative example is shown.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
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- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Individual cells of three independent experiments are plotted as dots and their mean is indicated”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
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- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The experiment was repeated once.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This experiment was performed once.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plainSingle case- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The quote only partly states this claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The mean of three independent ChIP experiments is shown with the standard deviation.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The CTCF Y226A F228A mutation was confirmed by Sanger sequencing, including a silent mutation at position 229.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“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.”
§ The structural basis for cohesin-CTCF anchored loops > Discussion
What the sources say
- Not checked yetcites [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
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This experiment was performed twice with similar results.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The quote only partly states this claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“SCC1 ChIP was performed three times, and on each ChIP three qPCRs were performed in duplicate.”
§ The structural basis for cohesin-CTCF anchored loops > Methods > ChIP-qPCR
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This experiment was performed four times with similar results.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The quote only partly states this claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Aggregate peak analysis as in Fig. 3c, using two independent library preps per genotype.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The mean of two independent ChIP experiments is shown.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“For CTCF and IgG, two ChIPs were performed in duplicate.”
§ The structural basis for cohesin-CTCF anchored loops > Methods > ChIP-qPCR
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
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.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“We found the motif of chromatin architecture factor, CTCF as the highest enriched in the Rad21 dataset (Figure 5g), which is consistent with the cooperativity between Ctcf and Cohesin32.”
From Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues (2021) · cites this paper as [32]
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.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ The structural basis for cohesin-CTCF anchored loops > Methods > Crystallization and structure determination
“The CTCF-containing model was refined to 2.6 Å resolution with an Rwork and an Rfree of 25% and 27%, respectively”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
“| Resolution (Å) | 45.81–2.70 |”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
“| CTCF Y226A F228A | 1 | 63339779 | 62197640 | 47164621 | 75,83 | 72900092 | 39874529 | 5,47 |”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
Reported 47164621 · recomputed 112774621
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ The structural basis for cohesin-CTCF anchored loops > Methods > Crystallization and structure determination
“amino acid residues 222-231 of CTCF (Uniprot ID: Q8NI51; DVSVYDFEEE)”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
“| 1 | CTCF | Human | Wild-type | P49711 | 222 | DVSVYDFEEEQ | 1.04 ± 0.16* |”
Citations
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Items 301–400 of 465
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Substrate recognition by human separase
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MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops
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Loop Extrusion Machinery Impairments in Models and Disease
Ryzhkova, A. S., Maltseva, E., Баттулин, Н. Р., & Kabirova, E. (2024) · Cells · doi:10.3390/cells13221896 · Cited by 2
Multilayered Mechanisms for Long-range Regulatory Interactions in Eukaryotic Transcription
Fukaya, T. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169311 · Cited by 3
Regulation of loop extrusion on the interphase genome
Shin, H., & Kim, Y. (2023) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2023.2182273 · Cited by 4
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Competition between transcription and loop extrusion modulates promoter and enhancer dynamicsPreprint
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Replication stress underlies genomic instability at CTCF/cohesin-binding sites in cancerPreprint
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Cooperative CTCF-nucleosome oligomerization stabilizes chromatin loop anchorsPreprint
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Cohesin bridging as a physical principle of enhancer-promoter communicationPreprint
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Biomolecular Condensates in the Regulation of Transcription and Chromatin Architecture
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Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum
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Jpx RNA controls Xist induction through spatial reorganization of the mouse X-inactivation center
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CTCF barrier breaking by ZFP661 promotes protocadherin diversity in mammalian brainsPreprint
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You shall not pass! Unveiling the barriers for cohesin-mediated loop extrusion
Meyer‐Nava, S., & Rivera‐Mulia, J. C. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.06.028 · Cited by 1
Identifying deleterious noncoding variation through gain and loss of CTCF binding activity
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Tiukacheva, E. A., Luzhin, A. V., Kruglova, N. A., Shtompel, A. S., Antonov, G., Tvorogova, A. V., Vassetzky, Y. S., Ulianov, S. V., & Razin, S. V. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26157446 · Cited by 1
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Chaturvedi, P., Ghosh, P., Zhang, L., Zhang, M., Zhao, H., & Belmont, A. S. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.07.025 · Cited by 1
CTCF’s loop-independent functions prevail over chromatin looping in the acute degradation system
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Exuberant long noncoding RNA expression may sculpt Igh locus topology
Drake, E., Naiyer, S., Qu, X., Bhat, K. H., Farooq, H., Maienschein‐Cline, M., Liang, J., & Kenter, A. L. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1678105 · Cited by 1
CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igκ repertoire
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A phospho-switch to trigger mitotic chromosome condensation
Borsellini, A. (2026) · Biology Direct · doi:10.1186/s13062-025-00714-y · Cited by 1
A functional overlap between actively transcribed genes and chromatin insulator elements
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Folding a broken genome: the versatile roles of cohesin in genome maintenance
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Key roles of CCCTC-binding factor in cancer evolution and development
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STAG2-RAD21 complex: A unidirectional DNA ratchet mechanism in loop extrusion
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CTCF-anchored chromatin loop dynamics during human meiosis
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Cohesin modulates DNA replication to preserve genome integrityPreprint
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Hi-TrAC reveals fine-scale chromatin structures organized by transcription factorsPreprint
Liu, S., Cao, Y., Cui, K., Tang, Q., & Zhao, K. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.01.494329 · Cited by 1
Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2Preprint
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What AlphaFold tells us about cohesin’s retention on and release from chromosomesPreprint
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Systematic discovery of directional regulatory motifs associated with human insulator sitesPreprint
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AT-hook-dependent DNA loop extrusion by STAG1 drives 3D genome foldingPreprint
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Self-citationA dual role for CTCF in developmentPreprint
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Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cellsPreprint
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Introductory Chapter: Gene Expression in Eukaryotic Cells
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Distal transcriptional enhancers and repressors of bidirectional promoters
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Zhang, S. (2022) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-9632
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Self-citationDependency of 3D chromatin folding on RNA polymerase II at different cell cycle stages
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Lifting the curtain on loop extrusion barriers: Single-molecule insights into cohesin stalling
Braccioli, L., & de Wit, E. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.07.025
What AlphaFold tells us about cohesin’s retention on and release from chromosomesPreprint
Nasmyth, K., Lee, B., Roig, M. B., & Löwe, J. (2023) · eLife · doi:10.7554/elife.88656.2
Mechanism of ZNF143 in chromatin looping and 3D genome organizationPreprint
Zhang, M., Huang, H., Li, J., & Wu, Q. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.27.559875
Cohesin preserves genome stability through regulating DNA replication timing
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What AlphaFold tells us about cohesin’s retention on and release from chromosomes
Nasmyth, K. A., Lee, B.-G., Roig, M. B., & Löwe, J. (2023) · doi:10.7554/elife.88656.3
Additional file 7 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435840
Additional file 6 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435837
Additional file 2 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435825
Additional file 5 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435834
Additional file 8 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435843
Additional file 4 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435831
Additional file 3 of Acute depletion of CTCF rewires genome-wide chromatin accessibility
Xu, B., Wang, H., Wright, S., Hyle, J. W., Zhang, Y., Shao, Y., Niu, M., Fan, Y., Rosikiewicz, W., Djekidel, M. N., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16435828
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Memory and epigenetics: Influence of sex and estrogens
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Cohesin-dependent loop extrusion: molecular mechanics and role in cell physiology
Golov, A. K., & Gavrilov, A. A. (2024) · Biochemistry (Moscow) · doi:10.31857/s0320972524040024
Metadata
- 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
- Venue
- Nature
- Published
- 2020-01-06
- Volume
- 578
- Issue
- 7795
- Pages
- 472-476
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- 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
- green
- www.ncbi.nlm.nih.gov
- 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
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