What AlphaFold tells us about cohesin’s retention on and release from chromosomes
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Abstract
Cohesin is a trimeric complex containing a pair of SMC proteins (Smc1 and Smc3) whose ATPase domains at the end of long coiled coils (CC) are interconnected by Scc1. During interphase, it organizes chromosomal DNA topology by extruding loops in a manner dependent on Scc1’s association with two large hook-shaped proteins called SA (yeast: Scc3) and Nipbl (Scc2). The latter’s replacement by Pds5 recruits Wapl, which induces release from chromatin via a process requiring dissociation of Scc1’s N-terminal domain (NTD) from Smc3. If blocked by Esco (Eco)-mediated Smc3 acetylation, cohesin containing Pds5 merely maintains pre-existing loops, but a third fate occurs during DNA replication, when Pds5-containing cohesin associates with Sororin and forms structures that hold sister DNAs together. How Wapl induces and Sororin blocks release has hitherto remained mysterious. In the 20 years since their discovery, not a single testable hypothesis has been proposed as to their role. Here, AlphaFold 2 (AF) three-dimensional protein structure predictions lead us to propose formation of a quarternary complex between Wapl, SA, Pds5, and Scc1’s NTD, in which the latter is juxtaposed with (and subsequently sequestered by) a highly conserved cleft within Wapl’s C-terminal domain. AF also reveals how Scc1’s dissociation from Smc3 arises from a distortion of Smc3’s CC induced by engagement of SMC ATPase domains, how Esco acetyl transferases are recruited to Smc3 by Pds5, and how Sororin prevents release by binding to the Smc3/Scc1 interface. Our hypotheses explain the phenotypes of numerous existing mutations and are highly testable.
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Mota, I. P., Gálová, M., Schleiffer, A., Nguyen, T.-T., Kováčiková, I., Saad, C. F., Litos, G., Nishiyama, T., Gregáň, J., Peters, J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49178-0 · Cited by 16 · see citing works
Flagged first, then by citations
1 of the 81 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
From interaction networks to interfaces, scanning intrinsically disordered regions using AlphaFold2
Bret, H., Gao, J., Zea, D. J., Andreani, J., & Guerois, R. (2024) · Nature Communications · doi:10.1038/s41467-023-44288-7 · Cited by 103 · see citing works
Shah, R., Tortora, M. M. C., Louafi, N., Rahmaninejad, H., Hansen, K. L., Anderson, E. C., Wen, D., Giorgetti, L., Fudenberg, G., & Nora, E. P. (2025) · doi:10.1101/2025.08.14.667581 · Cited by 15 · see citing works
Molecular mechanism and functional significance of Wapl interaction with the Cohesin complex
Yuan, X., Yan, L., Chen, Q., Zhu, S., Zhou, X., Zeng, L., Liu, M., He, X., Huang, J., Lü, W., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2405177121 · Cited by 13 · see citing works
The physical chemistry of interphase loop extrusion
Tortora, M. M. C., & Fudenberg, G. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.101098 · Cited by 2 · see citing works
Pushing the TAD boundary: Decoding insulator codes of clustered CTCF sites in 3D genomes
Huang, H., & Wu, Q. (2024) · BioEssays · doi:10.1002/bies.202400121 · Cited by 7 · see citing works
Regulation of pericentromeric DNA loop size via Scc2-cohesin interaction
Nguyen, S. A., Sakata, T., Shirahige, K., & Sutani, T. (2025) · iScience · doi:10.1016/j.isci.2025.112322 · Cited by 5 · see citing works
Requirement of Nek2a and cyclin A2 for Wapl-dependent removal of cohesin from prophase chromatin
Hellmuth, S., & Stemmann, O. (2024) · The EMBO Journal · doi:10.1038/s44318-024-00228-9 · Cited by 3 · see citing works
Helical coiled nucleosome chromosome architectures during cell cycle progression
McDonald, A., Murre, C., & Sedat, J. W. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2410584121 · Cited by 2 · see citing works
A chromatin-remodeling-independent role for ATRX in protecting centromeric cohesion
Zhao, L., Yuan, X., Chen, Q., Yan, H., & Wang, F. (2025) · The EMBO Journal · doi:10.1038/s44318-025-00465-6 · Cited by 2 · see citing works
The intrinsically disordered tail of ESCO1 binds DNA in a charge-dependent mannerPreprint
Schoen, J. R., Chen, J., & Rankin, S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.05.570177
Collier, J., & Srinivasan, M. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-5005-9_8
- Authors
- Nasmyth, K. A., Lee, B.-G., Roig, M. B., & Löwe, J.
- Affiliations
- Gachon University (KR)
- Corresponding author
- Nasmyth, Kim A
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2023-11-17
- Volume
- 12
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC10656103
- OpenAlex
- W4380787280
- Cited by
- 12
- References
- 81
- Citations by year
- 2025: 5 · 2024: 5 · 2023: 2
- FWCI
- 1.07
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Medical Research Council (U105184326)
- Cancer Research UK (26747)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
- Keywords
- cohesin, WAPL, Pds5, SMC3, Sororin, sister chromatid cohesion, chromatin loop extrusion
- MeSH terms
- Cohesins, Adenosine Triphosphatases, Chromatids, Chromosomes, DNA, Saccharomyces cerevisiae, Cell Cycle Proteins, Saccharomyces cerevisiae Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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