Cited by 880Genomics and Chromatin DynamicsChromatin Remodeling and CancerNuclear Structure and Function

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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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Wutz, Gordana, Várnai, Csilla, Nagasaka, Kota, Cisneros, David A, Stocsits, Roman R, Tang, Wen, Schoenfelder, Stefan, Jessberger, Gregor, Muhar, Matthias, Hossain, M Julius, Walther, Nike, Koch, Birgit, Kueblbeck, Moritz, Ellenberg, Jan, Zuber, Johannes, Fraser, Peter, Peters, Jan‐Michael·2017·The EMBO Journal

DOI 10.15252/embj.201798004PMC PMC5730888

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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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Additional file 4 of RAD21 is the core subunit of the cohesin complex involved in directing genome organization
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Additional file 8 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
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Additional file 4 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality
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Additional file 10 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
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Additional file 2 of CTCF and cohesin promote focal detachment of DNA from the nuclear lamina
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Additional file 1 of PDS5A and PDS5B differentially affect gene expression without altering cohesin localization across the genome
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Additional file 11 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Figshare · doi:10.6084/m9.figshare.26709290
Additional file 2 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Figshare · doi:10.6084/m9.figshare.26709263
Additional file 3 of Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin
Cuadrado, A., Giménez-Llorente, D., Koninck, M. D., Ruiz‐Torres, M., Kojic, A., Rodríguez-Corsino, M., & Losada, A. (2022) · Figshare · doi:10.6084/m9.figshare.21622965
Additional file 2 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality
Kamalyan, S., Kyrchanova, O., Klimenko, N., Babosha, V., Vasileva, Y., Belova, E., Фурсенко, Д. В., Maksimenko, O., & Georgiev, P. G. (2024) · Figshare · doi:10.6084/m9.figshare.26700011
Additional file 1 of Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation
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Additional file 5 of Wheat chromatin architecture is organized in genome territories and transcription factories
Concia, L., Veluchamy, A., Ramirez-Prado, J. S., Martin-Ramirez, A., Huang, Y., Perez, M., Domenichini, S., Rodriguez‐Granados, N. Y., Kim, S., Blein, T., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12218897
Additional file 1 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Figshare · doi:10.6084/m9.figshare.26709260
Additional file 1 of Sensitivity of cohesin–chromatin association to high-salt treatment corroborates non-topological mode of loop extrusion
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Additional file 2 of PDS5A and PDS5B differentially affect gene expression without altering cohesin localization across the genome
Arruda, N. L., Bryan, A. F., & Dowen, J. M. (2022) · Figshare · doi:10.6084/m9.figshare.20521075
Additional file 2 of RAD21 is the core subunit of the cohesin complex involved in directing genome organization
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Additional file 4 of Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation
Nishana, M., Ha, C. J., Rodriguez-Hernaez, J., Ranjbaran, A., Chio, E., Nora, E. P., Badri, S., Kloetgen, A., Bruneau, B. G., Tsirigos, A., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12284861
Additional file 6 of Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures
Hao, X., Parmar, J. J., Lelandais, B., Aristov, A. I., Ouyang, W., Weber, C., & Zimmer, C. (2021) · Figshare · doi:10.6084/m9.figshare.14576666
Additional file 3 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Figshare · doi:10.6084/m9.figshare.26709266
Additional file 3 of CTCF and cohesin promote focal detachment of DNA from the nuclear lamina
van Schaik, T., Liu, N. Q., Manzo, S. G., Peric‐Hupkes, D., de Wit, E., & van Steensel, B. (2022) · Figshare · doi:10.6084/m9.figshare.20787025
Additional file 1 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality
Kamalyan, S., Kyrchanova, O., Klimenko, N., Babosha, V., Vasileva, Y., Belova, E., Фурсенко, Д. В., Maksimenko, O., & Georgiev, P. G. (2024) · Figshare · doi:10.6084/m9.figshare.26700008
Additional file 2 of Sensitivity of cohesin–chromatin association to high-salt treatment corroborates non-topological mode of loop extrusion
Golov, A. K., Golova, A., Gavrilov, A. A., & Razin, S. V. (2021) · Figshare · doi:10.6084/m9.figshare.15071428
Additional file 4 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Figshare · doi:10.6084/m9.figshare.26709269
Additional file 1 of CTCF and cohesin promote focal detachment of DNA from the nuclear lamina
van Schaik, T., Liu, N. Q., Manzo, S. G., Peric‐Hupkes, D., de Wit, E., & van Steensel, B. (2022) · Figshare · doi:10.6084/m9.figshare.20787019
Additional file 1 of Wheat chromatin architecture is organized in genome territories and transcription factories
Concia, L., Veluchamy, A., Ramirez-Prado, J. S., Martin-Ramirez, A., Huang, Y., Perez, M., Domenichini, S., Rodriguez‐Granados, N. Y., Kim, S., Blein, T., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12218867
Additional file 5 of Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin
Cuadrado, A., Giménez-Llorente, D., Koninck, M. D., Ruiz‐Torres, M., Kojic, A., Rodríguez-Corsino, M., & Losada, A. (2022) · Figshare · doi:10.6084/m9.figshare.21622974
Additional file 5 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Figshare · doi:10.6084/m9.figshare.26709272
Additional file 6 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Figshare · doi:10.6084/m9.figshare.26709275
Additional file 12 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Figshare · doi:10.6084/m9.figshare.26709293
Additional file 7 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Figshare · doi:10.6084/m9.figshare.26709278
Additional file 3 of RAD21 is the core subunit of the cohesin complex involved in directing genome organization
Sun, Y., Xu, X., Zhao, W., Zhang, Y., Chen, K., Li, Y., Wang, X., Zhang, M., Xue, B., Yu, W., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26600446
Additional file 1 of RAD21 is the core subunit of the cohesin complex involved in directing genome organization
Sun, Y., Xu, X., Zhao, W., Zhang, Y., Chen, K., Li, Y., Wang, X., Zhang, M., Xue, B., Yu, W., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26600440
Additional file 2 of Chromosomal localization of cohesin is differentially regulated by WIZ, WAPL, and G9a
Justice, M., Bryan, A. F., Limas, J. C., Cook, J. G., & Dowen, J. M. (2022) · Figshare · doi:10.6084/m9.figshare.19696032
Additional file 3 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality
Kamalyan, S., Kyrchanova, O., Klimenko, N., Babosha, V., Vasileva, Y., Belova, E., Фурсенко, Д. В., Maksimenko, O., & Georgiev, P. G. (2024) · Figshare · doi:10.6084/m9.figshare.26700014
Additional file 9 of Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Camerino, M. J., Chang, W. K., & Cvekl, A. (2024) · Figshare · doi:10.6084/m9.figshare.26709284
Additional file 4 of Contribution of variant subunits and associated factors to genome-wide distribution and dynamics of cohesin
Cuadrado, A., Giménez-Llorente, D., Koninck, M. D., Ruiz‐Torres, M., Kojic, A., Rodríguez-Corsino, M., & Losada, A. (2022) · Figshare · doi:10.6084/m9.figshare.21622971
Chromosome organization by Structural Maintenance of Chromosomes complexes in C. elegans
Erkan, S., Ghadage, K., & Meister, P. (2026) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2025.102430
Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compactionPreprint
Wu, G., Meister, M. F., Reissner, S., Mueller, P. J., & Kappes, F. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.19.700267
Dissecting the contribution of transposable elements to interphase chromosome structure
Shi, L., Xiao, Z., Babarinde, I. A., Xiuling, F., Ma, G., Huang, Z., Sun, L., Zhou, X., He, J., Strunnikov, A. V., et al. (2026) · Genome biology · doi:10.1186/s13059-026-03945-y · Cited by 1
“ETFs bind to TEs [35, 46, 47], and can both promote [12, 48, 49] and impair [24] chromatin contacts.”
Potential Mechanisms by Which Reverse-Transcriptase L1 ORF2p Precisely Recognizes and Cleaves Genomic Target Site for Targeted Gene Editing and Related Pathophysiological SignificancePreprint
Sui, Y., & Shuanghong, P. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.6067427
HiCInterpolate: 4D Spatiotemporal Interpolation of Hi-C Data for Genome Architecture AnalysisPreprint
Chowdhury, H. M. A. M., & Oluwadare, O. (2026) · bioRxiv · doi:10.64898/2026.02.06.704438
“We validated predicted loops with RAD21 (for DMSO) and CTCF (for HeLa-S3) ChIP-seq data and HiCInterpiolate preserved almost all biologically meaningful loops. and HeLa-S3 predicted loops with CTCF ChIP-seq data [27] to biologically quantify HiCInterpolate predicted Hi-C contact matrix.”
Noncanonical loops regulated by EMF1 and cohesin-associated factors shape the distinct 3D genome architecture in plantsPreprint
Wang, D., Xiao, S., Luo, L., Wei, J., Shu, J., Tian, G., 刘亚丽, Yang, M., Yang, T., Calonje, M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.08.704707
NSD3 stabilizes nuclear compartmentalization and promotes megabase-scale chromatin interactionsPreprint
Chen, Y., Collette, J. R., Sampat, K., Yonchev, I. D., Hawkins, C. E., Ponne, C., Rosencrance, C. D., & Eagen, K. P. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.07.704091
Role of nuclear ATPases in nuclear mechanics and cell migration through confined spaces: Opposite effects of BRG1 and cohesin
Suprewicz, Ł., Byfield, F. J., Dutta, T. T., & Janmey, P. A. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.02.011
Nested TAD hierarchy defines cohesion zones on replicated chromosomes
Takács, Z., Mylarshchikov, D. E., Kolesnikova, S., Langer, C. C. H., Goloborodko, A. A., & Gerlich, D. W. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00902-0
“We selected HeLa cells because multiple validated degron-tagged cell lines are available for the acute depletion of cohesin regulators, together with extensive reference datasets on cohesin distribution and chromosome conformation (Batty et al, 2023; Wutz et al, 2017, 2025; Mitter et al, 2020).”
Influential
Zscan4 enables the formation of the Z compartment.
Lalsare, A., & Grow, E. J. (2026) · Nature Structural & Molecular Biology · doi:10.1038/s41594-026-01764-0

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: Wutz, Gordana
Várnai, Csilla
Nagasaka, Kota
Cisneros, David A
Stocsits, Roman R
Schoenfelder, Stefan
Muhar, Matthias
Hossain, M Julius
Walther, Nike
Koch, Birgit
Kueblbeck, Moritz
Ellenberg, Jan
Zuber, Johannes
Fraser, Peter
Peters, Jan‐Michael
Venue: The EMBO Journal
Publisher: Springer Science and Business Media LLC
Published: 2017-12-07
Volume: 36
Issue: 24
Pages: 3573-3599
ISSN: 0261-4189 (ISSN-L)
1460-2075
DOI: 10.15252/embj.201798004
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
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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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Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins

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