Cited by 866Genomics and Chromatin DynamicsDNA Repair MechanismsNuclear Structure and Function

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DNA loop extrusion by human cohesin

Davidson, Iain F., Bauer, Benedikt, Goetz, Daniela, Tang, Wen, Wutz, Gordana, Peters, Jan-Michael·2019·Science

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Abstract

Eukaryotic genomes are folded into loops and topologically associating domains, which contribute to chromatin structure, gene regulation, and gene recombination. These structures depend on cohesin, a ring-shaped DNA-entrapping adenosine triphosphatase (ATPase) complex that has been proposed to form loops by extrusion. Such an activity has been observed for condensin, which forms loops in mitosis, but not for cohesin. Using biochemical reconstitution, we found that single human cohesin complexes form DNA loops symmetrically at rates up to 2.1 kilo-base pairs per second. Loop formation and maintenance depend on cohesin's ATPase activity and on NIPBL-MAU2, but not on topological entrapment of DNA by cohesin. During loop formation, cohesin and NIPBL-MAU2 reside at the base of loops, which indicates that they generate loops by extrusion. Our results show that cohesin and NIPBL-MAU2 form an active holoenzyme that interacts with DNA either pseudo-topologically or non-topologically to extrude genomic interphase DNA into loops.

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Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity
Ran, F. A., Hsu, P. D., Lin, C.-Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., Scott, D. A., Inoue, A., Matoba, S., Zhang, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.08.021 · Cited by 3,299
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895
Formation of chromosomal domains by loop extrusion
Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003
Cohesin Loss Eliminates All Loop Domains
Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730
Two independent modes of chromatin organization revealed by cohesin removal
Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., et al. (2017) · Nature · doi:10.1038/nature24281 · Cited by 1,196
Cohesin mediates transcriptional insulation by CCCTC-binding factor
Wendt, K. S., Yoshida, K., Itoh, T., Bando, M., Koch, B., Schirghuber, E., Tsutsumi, S., Nagae, G., Ishihara, K., Mishiro, T., et al. (2008) · Nature · doi:10.1038/nature06634 · Cited by 1,193
Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms
Parelho, V., Hadjur, S., Spivakov, M., Leleu, M., Sauer, S., Gregson, H. C., Jarmuz, A., Canzonetta, C., Webster, Z., Nesterova, T., et al. (2008) · Cell · doi:10.1016/j.cell.2008.01.011 · Cited by 900

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Han, R., Huang, Y., Robers, M., Magnitov, M. D., Vaandrager, I., Allahyar, A., Verstegen, M. J. A. M., Zhang, K., de Wit, E., de Laat, W. L., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.04.522689 · Cited by 6
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Lee, U., Laguillo-Diego, A., Magliulo, D., Wong, W., Kasliwal, K., Ni, Z., Cheng, L., Li, J., Pelham‐Webb, B., Pertsinidis, A., et al. (2026) · Nature Genetics · doi:10.1038/s41588-026-02556-4 · Cited by 10
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Holub, M., Birnie, A., Japaridze, A., van der Torre, J., den Ridder, M., de Ram, C., Pabst, M., & Dekker, C. (2022) · Cell Reports Methods · doi:10.1016/j.crmeth.2022.100366 · Cited by 5
Corticosteroid‐induced chromatin loop dynamics at the FKBP5 gene
Wang, C., Manders, F., Groh, L., Oldenkamp, R., & Logie, C. (2023) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.15064 · Cited by 3
“Remarkably, the interactomes of viewpoints 9–12, which encompass the FKBP5 promoter and its two GR-bound enhancers, are not detectably affected by glucocorticoid stimulation.”
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Structural Maintenance of Chromosomes Complexes
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“How can a continuous stretch of DNA be subdivided into separated interaction spaces? The power lies in the ring – DNA can be extruded through circular cohesin molecules, which leads to formation of DNA loops that can have sizes up to several megabases [12].”
Background
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Lebdy, R., Patouillard, J., Larroque, M., Urbach, S., Merhi, R. A., Larroque, C., & Ribeyre, C. (2023) · Life Science Alliance · doi:10.26508/lsa.202101186 · Cited by 6
“Cohesins generate loops by extrusion (Davidson et al., 2019; Kim et al., 2019).”
HiCognition: a visual exploration and hypothesis testing tool for 3D genomics
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Method
The Mechanism, Regulation and Evolution of V(D)J Recombination
Schatz, D. G., Zhang, Y., Xiao, J., Zha, S., Zhang, Y., & Alt, F. W. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95895-0.00004-0 · Cited by 5
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Moon, K.-W., Kim, D.-G., & Ryu, J. (2024) · Communications Biology · doi:10.1038/s42003-024-06557-z · Cited by 5
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Lovejoy, C. A., Wessel, S. R., Bhowmick, R., Hatoyama, Y., Kanemaki, M. T., Zhao, R., & Cortez, D. (2025) · Nature Communications · doi:10.1038/s41467-025-56911-w · Cited by 5
“Importantly, loop extrusion is a common mechanism regulating genome architecture in interphase as well as mitosis, again involving topoisomerases, condensin II, and other closely related proteins 11,63,64 .”
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Selivanovskiy, A. V., Molodova, M. N., Khrameeva, E. E., Ulianov, S. V., & Razin, S. V. (2025) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05559-8 · Cited by 6
“These complexes have been identified at loop anchors genome-wide by ChIP-seq [3] and their loop-extruding activity has been demonstrated in vitro [4–6].”
Conformational statistics of non-equilibrium polymer loops in Rouse model with active loop extrusion.
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“Besides, DNA loop extrusion by another SMC complex – cohesin – is found to be largely symmetric [8, 41, 42].”
Background
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Gupta, K., Wang, G., Zhang, S., Gao, X.-L., Zheng, R., Zhang, Y., Meng, Q., Zhang, L.-L., Cao, Q., & Chen, K.-F. (2022) · Science Advances · doi:10.1126/sciadv.abk2246 · Cited by 4
A Tremendous Reorganization Journey for the 3D Chromatin Structure from Gametes to Embryos
Chen, Z., & Chen, X. (2022) · Genes · doi:10.3390/genes13101864 · Cited by 6
“CTCF sites to form TAD boundaries [67,78,79].”
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“Examples include DNA tethers extruded by ATP-driven cohesin [68], cross-linked biopoly-mer networks (active gels [1]), and membrane-embedded enzymes [50,69–71], or active mechanosensitive channels [72].”
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“…1 and Table 1; Rudra and Skibbens, 2013b; Jeppsson et al., 2014; Marston, 2014; Nichols and Corces, 2018; Skibbens, 2019; Marko et al., 2019; Davidson et al., 2019; Kim et al., 2019; Banigan and Mirny, 2020; Golfier et al., 2020; Mayerova et al., 2020; Higashi et al., 2021; Matityahu and…”
Influential
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Yuan, T., Yan, H., Li, K., Surovtsev, I. V., King, M. C., & Mochrie, S. G. J. (2024) · Genome biology · doi:10.1186/s13059-024-03432-2 · Cited by 7
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Barrier effects on the kinetics of cohesin-mediated loop extrusion
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(2025) · doi:10.1016/j.str.2025.06.004 · Cited by 4
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Seba, M., Boccard, F., & Duigou, S. (2024) · eLife · doi:10.7554/elife.91185.3 · Cited by 4
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Yamauchi, M., Brandani, G. B., Terakawa, T., & Takada, S. (2026) · eLife · doi:10.7554/elife.106752.3 · Cited by 4
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“Upon SMC complex loading, the ATP binding and hydrolysis drive complex translocation along DNA or loop extrusion (Davidson et al., 2019; Ganji et al., 2018; Pradhan et al., 2023).”
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Gomes, M. V., Landwerlin, P., Diebold, M.-L., Shaik, T. B., Durand, A., Troesch, E., Weber, C., Brillet, K., Lemée, M. V., Decroos, C., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114656 · Cited by 4
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Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions
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“The complex is essential in the proper functioning of the cell nucleus—as is fundamental for the loop extrusion 15 , it stabilises the topologically associating domains (cohesin-SA1) 16 , allows interactions between enhancers and promoters (cohesin-SA2) 16 .”
Background
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Tavares-Cadete, F., Norouzi, D., Dekker, B., Liu, Y., & Dekker, J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.03.975425 · Cited by 4
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Rico, D., Kent, D., Karataraki, N., Mikulášová, A., Palmini, R. B., Walker, B. A., Javierre, B. M., Russell, L. J., & Brackley, C. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.12.434963 · Cited by 4
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Chahar, S., Zouari, Y. B., Salari, H., Molitor, A., Kobi, D., Maroquenne, M., Erb, C., Mossler, A., Karasu, N., Jost, D., et al. (2022) · bioRxiv · doi:10.1101/2022.07.01.498405 · Cited by 4
“In combination with more sophisticated single-molecule (Davidson et al., 2019) and live-imaging (Gabriele et al., 2022), going beyond basic principles to understanding the context-specific nature of chromatin architecture at specific loci is becoming a more achievable goal.”
Background
High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamicsPreprint
Sept, C. E., Tak, Y. E., Cerda-Smith, C. G., Hutchinson, H. M., Goel, V. Y., Blanchette, M., Bhakta, M. S., Hansen, A. S., Joung, J. K., Johnstone, S. E., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.20.563340 · Cited by 4
“Although conventional 3C techniques give an impression of static loops, cohesin-mediated chromatin loops are actually dynamic with an extrusion rate of ~1kb/s 12 .”
Background
The NHEJ machinery is translocated off DNA ends to enable resectionPreprint
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“Since Rad50 belongs to the SMC family of proteins, which includes known loop extruders such as cohesin, Smc5/6 and condensin [46, 47, 48], we postulated that the NHEJ machinery is mechanochemically removed from DNA ends.”
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“We therefore employed polymer simulations to determine whether cohesin might function as a DNA loop extruding motor, as suggested by studies in vertebrate systems 23,26,31 .”
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Do, C., Jiang, G., Zappile, P., Heguy, A., & Skok, J. A. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117316 · Cited by 3
“1,2 The two factors are enriched at TAD boundaries, where they function as insulators promoting interactions between enhancers and promoters within a domain and restricting the action of regulatory elements to target genes outside a domain.”
Active loop extrusion modulates the mechanical response of chromatin under tension
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A universal polymer signature in Hi-C resolves cohesin loop density and supports monomeric extrusion
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“The genome is folded by molecular motors, yet how many motors are required to generate a single chromatin loop has remained unknown.”
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Chromatin organization in myelodysplastic syndrome
Xu, J. J., & Viny, A. D. (2024) · Experimental Hematology · doi:10.1016/j.exphem.2024.104216 · Cited by 4
Nature of barriers determines first passage times in heterogeneous media.
Dasgupta, M., Guha, S., Armbruster, L., Das, D., & Mitra, M. K. (2022) · Soft Matter · doi:10.1039/d4sm00908h · Cited by 2
Adding a twist to the loops: the role of DNA superhelicity in the organization of chromosomes by SMC protein complexes
Valdés, A., & Haering, C. H. (2024) · Biochemical Society Transactions · doi:10.1042/bst20240650 · Cited by 3
Gene Doping Detection From the Perspective of 3D Genome
Ren, X., Shi, Y., Xiao, B., Su, X., Shi, H., He, G., Chen, P., Wu, D., & Shi, Y. Y. (2025) · Drug Testing and Analysis · doi:10.1002/dta.3850 · Cited by 3
Conformational asymmetry of replicated human chromosomes
Corsi, F., Kolesnikova, S., Steinacker, T. L., Takács, Z., Batty, P., Mitter, M., Gerlich, D. W., & Goloborodko, A. A. (2026) · Science · doi:10.1126/science.aea4611 · Cited by 3
DNA actively regulates the “safety-belt” dynamics of condensin during loop extrusion
Chen, J., Feng, C., Wang, Y., & Chu, X. (2026) · Nature Communications · doi:10.1038/s41467-025-68239-6 · Cited by 3
“However, simultaneous closure of all three SMC–kleisin ring interfaces does not inhibit DNA loop extrusion by cohesin and condensin, thereby challenging the hypothesis that DNA passes through the SMC–kleisin ring in a strictly topological manner [11, 15].”
Foundation model reveals the shared organization of transcription and topologically associating domains
Liang, H., Berger, B., & Singh, R. (2026) · Cell Systems · doi:10.1016/j.cels.2026.101675 · Cited by 3
Dysregulation of chromatin organization in pediatric and adult brain tumors: oncoepigenomic contributions to tumorigenesis and cancer stem cell properties
Paik, S., Maule, F., & Gallo, M. (2020) · Genome · doi:10.1139/gen-2020-0097 · Cited by 5
“…convergent 74 orientations and emerge through loop extrusion (Fudenberg et al., 2016; Haarhuis et al., 2017; Sanborn 75 et al., 2015) mediated by cohesins (Davidson et al., 2019) and condensins (Ganji et al., 2018) (Figure Page 3 of 39 © The Author(s) or their Institution(s) Genome Draft 4 76 1A).”
Background
Disorder of three‐dimensional chromosome structure plays a role in carcinogenesis
Zhang, L., Liu, F., Wu, L., Fu, S., Xing, L., Zhang, L., Wang, X., & Wang, Y.-X. (2021) · Clinical and Translational Discovery · doi:10.1002/ctd2.17 · Cited by 3
The Interplay of Cohesin and RNA Processing Factors: The Impact of Their Alterations on Genome Stability
Osadská, M., Selicky, T., Kretová, M., Jurcik, J., Sivakova, B., Cipakova, I., & Cipak, L. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23073939 · Cited by 2
G1-Cyclin2 (Cln2) promotes chromosome hypercondensation in eco1/ctf7 rad61 null cells during hyperthermic stress in Saccharomyces cerevisiae
Buskirk, S. W., & Skibbens, R. V. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac157 · Cited by 3
Locality of contacts determines the subdiffusion exponents in polymeric models of chromatin
Marchi, E., Zhan, Y., & Tiana, G. (2023) · Physical review. E · doi:10.1103/physreve.107.064406 · Cited by 3
Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease
Pandupuspitasari, N. S., Khan, F. A., Huang, C., Ali, A., Yousaf, M. R., Shakeel, F., Putri, E. M., Negara, W., Muktiani, A., Prasetiyono, B. W. H. E., et al. (2023) · Functional & Integrative Genomics · doi:10.1007/s10142-023-01146-5 · Cited by 3
“2019) until it is stopped by a barrier (Davidson et al. 2019).”
Background
Loops are geometric catalysts for DNA integration
Battaglia, C., & Michieletto, D. (2023) · bioRxiv · doi:10.1093/nar/gkae484 · Cited by 3
“Beyond classic enhancer-promoter interactions ( 45 ), several new mechanisms of loop formation have been identified recently, for instance those mediated by CTCF ( 43 ) ( ∼ 0.1–1 Mb), cohesin ( 46 ,47 ) and condensin ( 48–50 ) ( ∼ 1–10 kb).”
BackgroundInfluential
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
“However, being an active ATPase, Nipbl-cohesin can extrude DNA loops in cis, thereby structuring chromatids into topologically associated domains (TADs) and in ﬂ uencing transcription (Davidson et al, 2019, Kim et al, 2019, Petela et al, 2018).”
Loop Extrusion Machinery Impairments in Models and Disease
Ryzhkova, A. S., Maltseva, E., Баттулин, Н. Р., & Kabirova, E. (2024) · Cells · doi:10.3390/cells13221896 · Cited by 2
SMC translocation is unaffected by an excess of nucleoid associated proteins in vivo
Ren, Z., Way, L. E., & Wang, X. (2025) · Scientific Reports · doi:10.1038/s41598-025-86946-4 · Cited by 3
Sister chromatid cohesion through the lens of biochemical experiments
Murayama, Y. (2025) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2025.102464 · Cited by 3
Multilayered Mechanisms for Long-range Regulatory Interactions in Eukaryotic Transcription
Fukaya, T. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169311 · Cited by 3
Transcription factors organize into functional groups on the linear genome and in 3D chromatin
Vadnala, R. N., Hannenhalli, S. S., Narlikar, L., & Siddharthan, R. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e18211 · Cited by 4
“This has been recently observed in vitro [28].”
Background
Human cohesin extrudes interphase DNA to make loops
Baumann, K. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0198-z · Cited by 3
Chromosome Territories in Hematological Malignancies
de Lima, M. F., Lisboa, M. D. O., Terceiro, L. E. L., Pozzo, A. R., & Mai, S. (2022) · Cells · doi:10.3390/cells11081368 · Cited by 3
Drosophila SUMM4 complex couples insulator function and DNA replication control
Andreyeva, E. N., Emelyanov, A. V., Nevil, M., Sun, L., Vershilova, E., Hill, C. A., Keogh, M., Duronio, R. J., Skoultchi, A. I., & Fyodorov, D. V. (2022) · eLife · doi:10.7554/elife.81828 · Cited by 3
“In mammals, CTCF-dependent loop formation requires ATP-driven motor activity of SMC complex cohesin ( Davidson et al., 2019 ).”
Regulation of loop extrusion on the interphase genome
Shin, H., & Kim, Y. (2023) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2023.2182273 · Cited by 4
“reported that cohesin plays as a monomer or dimer during loop extrusion (Davidson et al. 2019; Kim et al. 2019).”
BackgroundInfluential
A CRISPR Screen Identifies Myc-associated Zinc Finger Protein (MAZ) as an Insulator Functioning at CTCF boundaries in Hox ClustersPreprint
Ortabozkoyun, H., Huang, P., Cho, H., Narendra, V. K., LeRoy, G., Skok, J. A., Tsirigos, A., Mazzoni, E. O., & Reinberg, D. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.25.267237 · Cited by 3
“(E) Proposed model for the effect of MAZ on loops via its interaction with cohesin (middle) or binding adjacent to CTCF and interaction with cohesin (right), in addition to existing loop-extrusion model of CTCF and cohesin (left, (44, 45)).”
Method
Can pseudotopological models for SMC-driven DNA loop extrusion explain the traversal of physical roadblocks bigger than the SMC ring size?Preprint
Pradhan, B., Barth, R., Kim, E., Davidson, I. F., van der Torre, J., Peters, J., & Dekker, C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.02.502451 · Cited by 3
Observation of Higher-Order Assemblies Controlled by Protein One-dimensional MovementPreprint
Han, X., Rao, M., Wu, S.-R., Zhang, Q., Hou, F., Zhang, S., Chen, L., & Liu, J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.06.597732 · Cited by 3
Post-mitotic transcriptional activation and 3D regulatory interactions show locus- and differentiation-specific sensitivity to cohesin depletion
Lee, U., Laguillo-Diego, A., Wong, W., Ni, Z., Cheng, L., Li, J., Pelham-Webb, B., Pertsinidis, A., Leslie, C., & Apostolou, E. (2025) · doi:10.1101/2025.02.13.638153 · Cited by 3
Loop extrusion provides mechanical robustness to chromatinPreprint
Salari, H., & Jost, D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.16.676638 · Cited by 3
Cooperative CTCF-nucleosome oligomerization stabilizes chromatin loop anchorsPreprint
Osorio‐Valeriano, M., Stone, A. C., Nagano, M., Su, B. G., Caccianini, L., Hansen, A. S., Farnung, L., & Vos, S. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.06.704447 · Cited by 4
“Chromatin loops are thought to be formed largely through the action of cohesin, which can actively extrude DNA loops 14 .”
Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation
Yang, J. H., Pinholt, H. D., Toppen, J., Huseyin, M. K., Jusuf, J. M., Katsifis, C. C., Kæstel-Hansen, J., Mirny, L. A., Zechner, C., & Hansen, A. S. (2026) · doi:10.64898/2026.06.21.733446 · Cited by 3
“This physical alignment predicts that E-P-mediated transcription might be particularly sensitive to perturbations of cohesin-extrusion ( 65–69 ) mediated interactions.”
Solution AFM Imaging and Coarse-grained Molecular Modeling of Yeast Condensin Structural Variation Coupled to the ATP Hydrolysis Cycle
Koide, H., Kodera, N., Takada, S., & Terakawa, T. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169185 · Cited by 3
Deciphering the 3D structures of plant genomes: building blocks of hierarchically organized chromatin domains
Lee, H., & Seo, P. J. (2025) · Journal of Experimental Botany · doi:10.1093/jxb/eraf218 · Cited by 3
The Biological Function of Genome Organization
Yang, X., Zhu, H., Liu, Y., Wang, J., Song, Y., Liao, S., & Dong, P. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26189058 · Cited by 3
“Ring-shaped cohesin complexes are loaded onto chromatin by loader proteins and act as molecular motors to extrude DNA loops through their ring structure by utilizing energy from ATP hydrolysis [30].”
Chromatin looping-based CRISPR screen identifies TLK2 as chromatin loop formation regulator in cancer stemness plasticity
Wang, Z., Liu, F., Chen, N., Wu, J., Li, X., Fang, M., Yan, M., Zhang, J., Deng, B., Wang, L., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-64066-x · Cited by 3
“Cohesin, loaded at NIPBL binding sites, extrudes chromatin ﬁ bers and halts extrusion until engaging CTCF anchors to shape chromatin into loops 11,12 .”
STAG2-truncating variants reveal a mosaic STAG2 inactivation pattern and compensatory mechanisms involving cohesin complex remodeling
Gines, M. M., Wessels, M. W., Casà, V., van Staveren, T., Hof, A., Chung, W. K., Willems, M., Sandestig, A., Hüning, I., Turnpenny, P. D., et al. (2025) · iScience · doi:10.1016/j.isci.2025.114195 · Cited by 2
Crosstalk between cohesins and axis proteins determines meiotic chromosome architecture in Sordaria macrospora
Yefsah, K., Habbi, M., Budin, K., Bourbon, H.-M. G., Zickler, D., Espagne, E., & Boisnard, S. (2025) · PLoS Genetics · doi:10.1371/journal.pgen.1012001 · Cited by 2
“Their ring-like structure allows them to entrap DNA molecules, which, in turn, generates a higher-order chromatin organization whose regulation and dynamics ensure a wide range of essential cellular functions [5–7].”

Authors: Davidson, I. F., Bauer, B., Goetz, D., Tang, W., Wutz, G., & Peters, J.-M.
Affiliations: Research Institute of Molecular Pathology (AT)
Corresponding author: Peters, Jan-Michael
ORCID: Davidson, Iain F.
Bauer, Benedikt
Wutz, Gordana
Peters, Jan-Michael
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2019-12-13
Volume: 366
Issue: 6471
Pages: 1338-1345
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.aaz3418
OpenAlex: W2991248607
Cited by: 863
References: 46
Citations by year: 2026: 117 · 2025: 126 · 2024: 109 · 2023: 121 · 2022: 123 · 2021: 148 · 2020: 113 · 2019: 5
FWCI: 32.36
Type: journal article
Language: en
Open access: closed
Locations: Science (publishedVersion)
PubMed (publishedVersion)
Funders: Boehringer Ingelheim
European Molecular Biology Organization (Long-term Fellowship)
H2020 European Research Council (693949)
Human Frontier Science Program (Long-term Fellowship)
Austrian Research Promotion Agency (FFG-852936)
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 › Molecular Biology › Nuclear Structure and Function
Keywords: cohesin, DNA loop extrusion, topologically associating domains, chromatin folding, interphase chromatin, holoenzyme, condensin
MeSH terms: Cohesins, Chromosomal Proteins, Non-Histone, DNA, DNA-Binding Proteins, Proton-Translocating ATPases, HeLa Cells, Humans, Nucleic Acid Conformation, Cell Cycle Proteins, Holoenzymes

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DNA loop extrusion by human cohesin

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