The structural basis for cohesin–CTCF-anchored loops

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.

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Fig. 1: Structure of the SA2–SCC1–CTCF complex.
Fig. 2: CTCF interaction stabilizes cohesin on DNA.
Fig. 3: CTCF–CES interaction is required for CTCF-anchored loops.
Fig. 4: CTCF–CES interaction promotes localization of cohesin to CTCF sites.

Data availability

Coordinates are available from the PDB under accession number 6QNX for the SA2–SCC1–CTCF complex. The generated Hi-C, RNA sequencing and ChIP–seq data have been deposited in GEO, accession number GSE126637. Any other relevant data are available from the corresponding authors upon reasonable request.

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Acknowledgements

This work was funded by EMBL. J.H.I.H., Á.S.C. and B.D.R. were supported by an ERC CoG (772471 ‘CohesinLooping’), M.S.v.R. was supported by the Boehringer Ingelheim Fonds and H.T. and E.d.W. were supported by an ERC StG (637587 ‘HAP-PHEN’). H.T. and E.d.W. are part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. We thank the staff at the ESRF beamline Massif-1; T. Gibson for advice concerning short linear motifs; J. Rhodes and K. Nasmyth for reagents and advice on Halo tagging; R. van der Weide for advice and bioinformatic analyses; and R. Kerkhoven and the NKI Genomics Core Facility for sequencing.

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Contributions

Y.L. and K.W.M. initiated the project and proposed the CES motif. Y.L. performed biochemical studies and structural analyses with support from K.W.M. J.H.I.H., R.O., M.S.v.R., L.W. and H.T. performed wet-laboratory cell-based experiments and Á.S.C. performed bioinformatic analyses. K.W.M., E.d.W., B.D.R. and D.P. provided supervision. Y.L., K.W.M., B.D.R. and D.P. were involved in conceptualization, project administration and wrote the original and revised draft with input from all authors.

Corresponding authors

Correspondence to Kyle W. Muir or Elzo de Wit or Benjamin D. Rowland or Daniel Panne.

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Peer review information Nature thanks Victor Corces, Karl-Peter Hopfner and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Fig. 1 Biochemical analysis of CTCF binding to SA2–SCC1.

a, Domain architecture of CTCF. CTCF fragments tested for SA2–SCC1 binding by GST pulldown analysis are indicated. The region that retains SA2–SCC1 is highlighted in magenta. b, Summary data showing results of GST pulldowns. The input and the bound fractions were analysed by SDS–PAGE. CTCF fragments that bind SA2–SCC1 are shown in magenta. The experiment was repeated once. c, ITC curves. The binding stoichiometry (N) and dissociation constants (Kd) are indicated. The experiment was repeated three times, with consistent results. d, Fo − Fc omit electron-density Fourier map contoured at 3σ. e, LIGPLOT representation of the interaction between the CTCF peptide and SA2–SCC1. The CTCF peptide is shown in magenta, SA2 in blue and SCC1 in green bonds.

Extended Data Fig. 2 Analysis of the SA2–SCC1–CTCF structure.

a, Multiple sequence alignment of SA2 (here denoted STAG2) orthologues and paralogues. *Key amino-acid residues that engage CTCF. b, Missense mutation frequencies plotted onto the SA2 structure. R370 (a hotspot in SA2) is indicated. The inset shows an overview of the mutation hotspots R370 of SA2), Y226 and F228 of CTCF, and S334, K335, R338 and L341 of SCC). c, ITC progress curves of binding between WAPL(423–463) and SA2–SCC1. d, Competition between SGO1 and CTCF for SA2–SCC1 binding. SA2–SCC1 was incubated with GST–CTCF(86–267). Increasing amounts (lanes 4–8) (molar ratios are indicated) of the SGO1 phosphorylated at T346 peptide (spanning residues 331–349) were added and the input and the bound fraction analysed by SDS–PAGE. The experiment was repeated twice. One representative example is shown. e, Domain architecture and sequence alignments of cohesin regulators that contain F/YXF motifs. Putative CES-interacting residues are highlighted in red. f, Regular expression motif used to query the human and yeast proteomes for factors containing F/YXF motifs. Regular expression syntax: letters denote a specific amino acid; square brackets denote a subset of allowed amino acids; curly brackets denote length variability.

Extended Data Fig. 3 Generation of CTCFY226A/F228A cells.

a, Schematic of CRISPR–Cas9-based generation of CTCFY226A/F228A cells. The guide targets cleavage of exon 1 of the CTCF gene. The repair oligonucleotide renders the gene noncleavable by Cas9, and simultaneously introduces mutations in the codons that encode Y226 and F228. b, The CTCFY226A/F228A mutation was confirmed by Sanger sequencing, including a silent mutation at position 229. c, Western blot depicting Halo-tagged SCC1 in wild-type and CTCFY226A/F228A cells. The parental wild-type cells are included as a control. This experiment was performed once. d, Representative images of cells in G1 and G2, as indicated by their nuclear and cytoplasmic localization of DHB–iRFP, respectively. e, Chromatin-bound levels of CTCF and SMC1 analysed by western blot. Histone H4 is used as a control for the chromatin fraction. The CTCFY226A/F228A mutation does not evidently affect overall CTCF and cohesin levels on chromatin. WCE, whole-cell extract; CB, chromatin-bound fraction. This experiment was performed twice with similar results. f, Relative SCC1–Halo fluorescence intensity quantified in the unbleached area directly after photobleaching, as a proxy for the chromatin-bound fraction of SCC1. This nondiffusive fraction is not evidently affected by the CTCFY226A/F228A mutation. Individual cells of three independent experiments are plotted as dots and their mean is indicated (21 wild-type cells and 17 CTCFY226A/F228A cells were scored).

Extended Data Fig. 4 TAD analyses and Hi-C replicates.

a, Schematic of a Hi-C matrix displaying DNA–DNA contacts across a genomic region that includes two TADs. TADs in general are flanked by inwards-pointing CTCF sites (magenta arrows). Signal close to the diagonal line reflects short-range contacts, and contacts that span longer distances are found further away from the diagonal. The contacts within a TAD are formed by cohesin complexes (blue circles). Cohesin builds loops that it can enlarge until it encounters CTCF. Some TADs are enriched for contacts between the two CTCF sites that lie at their boundaries. These contacts are referred to as CTCF-anchored loops. b, Aggregate TAD analysis depicting the average contact frequency across TADs defined in wild-type cells. c, Heat map of the insulation score61 at TAD borders, as defined for wild-type cells. d, Aggregate peak analysis as in Fig. 3c, using two independent library preparations per genotype. e, Aggregate TAD analysis for wild-type and CTCFY226A/F228A cells as in b. f, Heat map of insulation scores at TAD borders for wild-type and CTCFY226A/F228A cells as in c.

Extended Data Fig. 5 CTCFY226A/F228A mutation has little effect on CTCF levels at CTCF sites.

a, Hi-C contact matrix of region chromosome 16: 77000000–78300000 at 10-kb resolution for the wild-type cell line (bottom triangles) and the CTCFY226A/F228A cell line (top triangles). CTCF sites are depicted below; those selected for qPCR are shown in colour. Red triangles indicate sites with a forward motif and blue triangles indicate sites with a reverse motif. The numbers underneath indicate the qPCR primer pairs shown in b. Primer pair 11 (indicated with *) is at a locus devoid of SCC1 and CTCF. b, ChIP–qPCR analysis of SCC1 (cohesin) enrichment at the aforementioned CTCF sites and control locus (*) in wild-type and CTCFY226A/F228A cells. The mean of three independent ChIP experiments is shown with the s.d. c, ChIP–seq tracks for SCC1 and CTCF at region chromosome 16: 77000000–78300000 in wild-type and CTCFY226A/F228A cells. The loci used for ChIP–qPCR analysis are indicated below the SCC1 ChIP–seq tracks. RPKM, reads per kilobase per million reads. d, ChIP–qPCR analysis of CTCF abundance at loci 1–7, as described in Fig. 3d. Analysis includes IgG as a control. The mean of two independent ChIP experiments is shown. Details of replicates are given in the Methods. e, ChIP–qPCR analysis of CTCF abundance at loci 8–12, as described in Extended Data Fig. 4a. Analysis includes IgG as a control. The mean of two independent ChIP experiments is shown. Details of replicates are given in the extended methods.

Extended Data Fig. 6 Compartmentalization is largely maintained in cells that contain the CTCFY226A/F228A mutation.

a, Hi-C contact matrices of the q-arm of chromosome 2 at 500-kb resolution. The corresponding compartment scores are plotted above. b, Genome-wide comparison of compartment scores for wild-type and CTCFY226A/F228A cells. Pearson correlation = 0.97. c, Saddle plots representing the interaction between A and B compartments. d, A region of chromosome 1 (55500000–59500000) at 10-kb resolution that contains no obvious CTCF-anchored loops. e, Relative contact probability profiles for wild-type and CTCFY226A/F228A mutant cells (left), compared to previously published12 contact profiles upon degradation of CTCF (middle) or SCC1 (right). The contact probability profile is affected only slightly in the CTCFY226A/F228A mutants, similar to the effects of CTCF depletion.

Extended Data Fig. 7 Identification of CES ligands.

a, Plot depicting the log2-transformed fold change in gene expression in relation to the mean of the normalized counts for each gene. Differentially expressed genes (adjusted P value < 0.05, two-tailed Wald test adjusted for multiple testing using the Benjamini–Hochberg procedure) are shown in red. Gene names are included for the 40 genes with the highest fold change. b, Western blot assessing knockdown of CTCF and the cohesin subunit SMC1 upon transfection with a control siRNA targeting luciferase (luc) or siRNAs targeting CTCF or SMC1A. This experiment was performed twice with similar results. c, Colony-formation assay of wild-type and CTCFY226A/F228A cells upon transfection with a control siRNA targeting luciferase or siRNAs targeting CTCF or SMC1A. CTCF remains essential for viability in CTCFY226A/F228A cells. This experiment was performed four times with similar results. d, Peptide array annotation (top left), binding of SA2–SCC1 (top right) or SA2(F371A)–SCC1 mutant (bottom left) and antibody control (bottom right). Three independent experiments were done, with consistent results. One representative example is shown. e, Amino acid sequences of the peptides. Predicted lead-anchoring residues are coloured red.

Extended Data Table 1 Summary of ITC data, and X-ray data collection and refinement statistics
Extended Data Table 2 Quantification of peptide arrays
Extended Data Table 3 Primers and Hi-C statistics

Supplementary information

Supplementary Figure 1

Uncropped images of western blots shown in Extended Data Fig. 3 and Extended Data Fig. 7. The relevant sections used for generating the figures are boxed

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Li, Y., Haarhuis, J.H.I., Sedeño Cacciatore, Á. et al. The structural basis for cohesin–CTCF-anchored loops. Nature 578, 472–476 (2020). https://doi.org/10.1038/s41586-019-1910-z

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