The DOI matches its Crossref record; 76 of the 76 references it cites were found in a registry or an index; 1 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 Not checked yet · 15 Own interpretation · 6 No basis given · 1 Supported
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
“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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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
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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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In the paper
“We demonstrate that this interaction is specifically required for CTCF-anchored loops”
- Also stated in: § CTCF-CES interaction is required for CTCF-anchored loops · plain
“CTCF-CES interaction is required for CTCF-anchored loops”
§ The structural basis for cohesin-CTCF anchored loops > Abstract
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- Also stated in: § CTCF-CES interaction is required for CTCF-anchored loops · plain
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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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“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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In the paper
“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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In the paper
“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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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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“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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“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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“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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“CTCF | Human | Y226F | P49711 | 222 | DVSVFDFEEEQ | 1.60 ± 0.03†”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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“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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“CENPU | Human | Wild-type | Q71F23 | 40 | PIDVFDFPDNS | 4.03 ± 0.22†”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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“MCM3 | Human | Wild-type | P25205 | 704 | SYDPYDFSDTE | 1.02 ± 0.05†”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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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
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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
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“CTCF | Human | Y226/F228A | P49711 | 222 | DVSVADAEEEQ | n.b.”
§ The structural basis for cohesin-CTCF anchored loops > Extended Data
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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
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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
- Not checked yetcites [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 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 [23] Roig, M. B. et al. Structure and function of cohesin’s Scc3/SA regulatory subunit. FEBS Lett. 588, 3692–3702 (2014). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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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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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.
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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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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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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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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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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.
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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.
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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.
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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.
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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.
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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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.
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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
“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.
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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.
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.
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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
“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.
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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.
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.
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- 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.
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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* |”
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STAG2 Promotes the Myelination Transcriptional Program in Oligodendrocytes
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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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