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Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins
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Abstract
Mammalian genomes are spatially organized into compartments, topologically associating domains (TADs), and loops to facilitate gene regulation and other chromosomal functions. How compartments, TADs, and loops are generated is unknown. It has been proposed that cohesin forms TADs and loops by extruding chromatin loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here, we show that cohesin suppresses compartments but is required for TADs and loops, that CTCF defines their boundaries, and that the cohesin unloading factor WAPL and its PDS5 binding partners control the length of loops. In the absence of WAPL and PDS5 proteins, cohesin forms extended loops, presumably by passing CTCF sites, accumulates in axial chromosomal positions (vermicelli), and condenses chromosomes. Unexpectedly, PDS5 proteins are also required for boundary function. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.
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“Contacts between convergent CTCF binding sites are established by the extrusion of chromatin loops with cohesin [42,46,48,93].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [48]
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“Convergent binding sites for the versatile transcription factor CTCF (CCCTC-binding factor) located at TAD borders [46] block the movement of loop extruders [47,48,49].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [48]
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“The CTCF Y226A F228A mutation, like CTCF depletion, only slightly affects the contact probability profile.”
From The structural basis for cohesin–CTCF-anchored loops (2020) · cites this paper as [12]
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Requirement of Nek2a and cyclin A2 for Wapl-dependent removal of cohesin from prophase chromatin
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“…extrudes ever longer loops of DNA (Nasmyth, 2001), an activity thought to be responsible for creating the Topologically Associated Domains (TADs) observed using HiC (Fudenberg et al., 2016; Haarhuis et al., 2017; Rao et al., 2017; Sanborn et al., 2015; Schwarzer et al., 2017; Wutz et al., 2017).”
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Ishiguro, K., & Fujiwara, Y. (2026) · Advances in experimental medicine and biology · doi:10.1007/978-981-92-1439-6_5 · Cited by 1
A splicing factor-cohesin association links RNA processing to cohesin-dependent genome folding
Wu, T., Cui, S., Zhang, Z., Yin, Z., Wang, Y., Xu, H., Zhang, H., Wang, W., Gu, W., & Guo, Y. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.118008 · Cited by 1
Cornelia de Lange Syndrome mutations in SMC1A cause cohesion defects in yeast
Chen, J., Floyd, E. N., Dawson, D., & Rankin, S. (2023) · Genetics · doi:10.1093/genetics/iyad159 · Cited by 1
STAG2-RAD21 complex: A unidirectional DNA ratchet mechanism in loop extrusion
Ros‐Pardo, D., Gómez‐Puertas, P., & Marcos‐Alcalde, Í. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.133822 · Cited by 1
“Additionally, other associated proteins, including NIPBL, PDS5, and WAPL, play crucial roles in the cohesin complex functions [4 – 6].”
The Three-Dimensional Chromatin Architecture in Fungi
Polisetty, S. D., & Sanyal, K. (2024) · The mycota · doi:10.1007/978-3-031-75666-5_2 · Cited by 1
Extrusion of chromatin loops by a composite loop extrusion factor
Yan, H., Surovtsev, I. V., Williams, J. F., Bailey, M. L. P., King, M. C., & Mochrie, S. G. J. (2021) · Physical review. E · doi:10.1103/physreve.104.024414 · Cited by 1
Functional diversity of chromosome cohesion proteins
Lu, Y., Zhou, C., & Xiong, B. (2021) · Scientia Sinica Vitae · doi:10.1360/ssv-2021-0068 · Cited by 1
BET proteins loop and compartmentalize the 3D genome
Eagen, K. P. (2022) · Nature Genetics · doi:10.1038/s41588-022-01031-0 · Cited by 1
How the Genome Folds, Divides, Lives, and DiesPreprint
Johnson, W. L., Xie, K. T., Kwon, M., Liu, S., & Pellman, D. S. (2017) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2017.82.035527 · Cited by 1
“Hi-C analysis revealed that WAPL-depleted chromosomes show extensive looping which can even extend beyond CTCF boundaries (presumably due to the increased lifetime of cohesin on chromatin after its removal factor has been depleted) (Haarhuis et al. 2017; Wutz et al. 2017).”
BackgroundHou, H. (2019) · TSpace (University of Toronto) · Cited by 1
CONTEXT-INDEPENDENT FUNCTION OF A CHROMATIN BOUNDARY IN VIVOPreprint
Willemin, A., Lopez‐Delisle, L., Bolt, C. C., Gadolini, M.-L., Duboule, D., & Rodríguez-Carballo, E. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.11.430727 · Cited by 1
Kueblbeck, M., Callegari, A., Serrano‐Solano, B., & Ellenberg, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.23.449557 · Cited by 1
Self-citationSSIM can robustly identify changes in 3D genome conformation mapsPreprint
Ing‐Simmons, E., Machnik, N., & Vaquerizas, J. M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.18.464422 · Cited by 1
“Data from Wutz et al. 2017 7 was downloaded from the 4D Nucleome website as .mcool files.”
MethodRad21 is the core subunit of the cohesin complex involved in directing genome organizationPreprint
Sun, Y., Sun, Y., Xu, X., Zhao, W., Zhang, Y., Chen, K., Li, Y., Wang, X., Zhang, M., Xue, B., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-1120640/v1 · Cited by 1
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
Gil, D. A., Cuadrado, A., Giménez-Llorente, D., Rodríguez-Corsino, M., & Losada, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.29.518367 · Cited by 1
Waldman, T. A., Kim, J.-S., Xu, W., Yang, T., Ya, A., Tallon, L. J., Sadzewicz, L., Harris, B. T., Sarkaria, J. N., & Jin, F. (2023) · Research Square · doi:10.21203/rs.3.rs-3673198/v1 · Cited by 1
Reply to: Revisiting the use of structural similarity index in Hi-C
Ing‐Simmons, E., Machnik, N., & Vaquerizas, J. M. (2023) · Nature Genetics · doi:10.1038/s41588-023-01595-5 · Cited by 1
Unique territorial and compartmental organization of chromosomes in the holocentric silkmothPreprint
Gil, J., Navarrete, E., Rosin, L. F., Chowdhury, N., Abraham, S., Cornilleau, G., Lei, E. P., Mozziconacci, J., Mirny, L., Muller, H., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4732646/v1 · Cited by 2
“A length-dependent contact preference can also be identified among B. mori chromosomes, with a group of small chromosomes (Chr02, 28, 26, 20, and 16) having the highest average inter-chromosomal contact frequency (Figures 1F, S2A).”
BackgroundPDS5s control the Arabidopsis 3D genome by suppressing the formation of TAD-like domainsPreprint
Göbel, A.-M., Zhou, S., Wang, Z., Tzourtzou, S., Himmelbach, A., Zheng, S., Pradillo, M., Liu, C., & Jiang, H. L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.31.606105 · Cited by 1
Karpińska, M. A., Zhu, Y., Ghazvini, Z. F., Ramasamy, S., Barbieri, M., Cao, T. B. N., Varahram, N., Aljahani, A., Lidschreiber, M., Papantonis, A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.20.624447 · Cited by 1
Replisomes restrict SMC-mediated DNA-loop extrusion in vivo
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Evolutionary trajectories of cohesin gatekeepers across the Tree of LifePreprint
Quiroz, D., Pierce, A., & Monroe, J. G. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.08.652912 · Cited by 1
“After DNA replication, cohesin is further stabilized through SMC3 acetylation, a process indirectly promoted by PDS5 via recruitment of CDCA5 (Sororin), which displaces WAPL (Morales et al., 2020; Nishiyama et al., 2010; Wutz et al., 2017).”
HDAC1 has a role in double strand break repair by regulating γH2AX signallingPreprint
Marqueta-Gracia, J. J., Bejarano-Franco, M., Spaag, S., Silva, S. D. R., Aguilera, A., & Gómez‐González, B. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.18.689006 · Cited by 1
“It is therefore formally possible that the reduced levels of cohesin recruitment observed at CBSs upon HDAC1 depletion (Figure S1) could contribute to explain the HR defect by affecting g H2AX signalling.”
Effects of CTCF on the regulatory landscape of the mouse Sox2 locusPreprint
Eder, M., Moene, C. J. I., Kaagman, M., Braccioli, L., de Wit, E., & van Steensel, B. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.16.711995 · Cited by 1
A dual role for CTCF in developmentPreprint
Saiz, N. A., Martinovic, M., Rubio, M., Samal, P., Giselbrecht, S., Braccioli, L., & de Wit, E. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.17.712290 · Cited by 3
Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cellsPreprint
Wang, P., Meng, L., Jiang, L., Li, Y., Huang, J., Tiancheng, Y. U., Chai, H., Kim, M., Wang, X., & Ruan, Y. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.01.722300 · Cited by 1
Conserved lifestyle-associated chromosome architectures across mammalian symbiontsPreprint
Viehboeck, T., Krause, N., Weber, P., Shea, E., Noetzel, V., Pende, N., Gölles-Kirth, H., Varoquaux, N., Boccard, F., Junier, I., et al. (2026) · bioRxiv · doi:10.64898/2026.07.20.739713 · Cited by 1
“These loops are observed as corner peaks at TAD boundaries and result from the structural maintenance of chromosomes (SMC) cohesin complexes and the CCCTC-binding factor (CTCF) binding the DNA at specific sites (Busslinger et al., 2017; Wutz et al., 2017; Sanborn et al., 2015).”
The intriguing dynamics of chromatin folding and assemblyPreprint
Yang, Z., Miao, W., & Mofrad, M. R. K. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.18.953398
“mechanism(10, 12, 20, 33, 34), chromatin loops are extruded to form chromosomal domains until loop extrusion process is delayed by binding sites(extrusion model).”
BackgroundAllyn-Feuer, A. (2018) · Deep Blue (University of Michigan)
Characterization of the Cohesin Complex in the Model Organism Neurospora Crassa
Hart, C. M. (2019) · Scholars' Bank (University of Oregon)
Mechanistic Modelling of Chromatin Folding to Understand FunctionPreprint
Brackley, C. A., Marenduzzo, D., & Gilbert, N. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2010.06413
Effects of forced cohesin eviction and retention on X-inactivation and autosomesPreprint
Kriz, A. J., Colognori, D., Sunwoo, H., Nabet, B., & Lee, J. T. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.13.426565
Dissecting the molecular mechanism and spatiotemporal dynamics controlling senescence entry
Sofiadis, K. (2021) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-8409
Eukaryotic Genome in Three Dimensions
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Rearrangement of T Cell Genome Architecture Regulates GVHDPreprint
Sun, Y., Dotson, G. A., Muir, L. A., Ronquist, S., Oravecz-Wilson, K. I., Peltier, D., Seike, K., Li, L., Meixner, W., Rajapakse, I., et al. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3981900
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Metadata
- Authors
- Wutz, G., Várnai, C., Nagasaka, K., Cisneros, D. A., Stocsits, R. R., Tang, W., Schoenfelder, S., Jessberger, G., Muhar, M., Hossain, M. J., Walther, N., Koch, B., Kueblbeck, M., Ellenberg, J., Zuber, J., Fraser, P., & Peters, J.
- Affiliations
- Research Institute of Molecular Pathology (AT)
- Babraham Institute (GB)
- European Molecular Biology Laboratory (DE)
- Florida State University (US)
- Corresponding author
- Peters, Jan‐Michael
- ORCID
- Venue
- The EMBO Journal
- Published
- 2017-12-07
- Volume
- 36
- Issue
- 24
- Pages
- 3573-3599
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC5730888
- OpenAlex
- W2775505403
- Cited by
- 864
- References
- 97
- Citations by year
- 2026: 83 · 2025: 77 · 2024: 102 · 2023: 97 · 2022: 119 · 2021: 127 · 2020: 112 · 2019: 87 · 2018: 49 · 2017: 11
- FWCI
- 29.61
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- The EMBO Journal (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ePrints Soton (University of Southampton) (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
- Funders
- Boehringer Ingelheim
- Austrian Research Promotion Agency (FFG‐834223)
- UK Biotechnology and Biological Sciences Research Council (BB/J004480/1)
- European Research Council Advanced Grant (DEVOCHROMO)
- EMBO Long Term Fellowship (ALTF 1335‐2016)
- Austrian Science Fund (SFB F34, Z196‐B20)
- Human Frontier Science Program (LT001527/2017)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- topologically associating domains, chromatin looping, cohesin, CTCF, WAPL, Pds5, loop extrusion, chromatin compartments, long-range chromatin interactions, chromosome condensation, vermicelli, 3D genome organization
- MeSH terms
- CCCTC-Binding Factor, Cohesins, Carrier Proteins, Chromatin, Chromosomal Proteins, Non-Histone, Chromosomes, DNA-Binding Proteins, HeLa Cells, Humans, Nuclear Proteins, Proto-Oncogene Proteins, Transcription Factors, Genome, Human, Cell Cycle Proteins
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