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DNA loop extrusion by human cohesin
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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“Loop extrusion was initially proposed theoretically based on molecular dynamics simulations [342, 435] and then validated in single-molecule assays [436, 437].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [436]
In the citing paper
“loop extrusion mediated by cohesin and CTCF mediates the formation of chromatin loops and self-interacting Topologically Associating Domains (TADs)”
From Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration (2023) · cites this paper as [82]
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“Formation of such chromatin loops by loop extrusion relies on an active holoenzyme consisting of cohesin and NIPBL-MAU2 (Davidson et al., 2019; Kim et al., 2019).”
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InfluentialFactors that determine cell type–specific CTCF binding in health and disease
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“This finding, together with the sister chromatid cohesion assays presented herein, suggests that USP13-mediated ubiquitination of cohesin subunits is not required for their canonical activity in controlling cell cycle progression (or in their more recently defined essential function as engines for chromatin loop extru…”
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Cohesin ATPase activities regulate DNA binding and coiled-coil configuration
Xu, X., Kanai, R., Wang, L., & Yanagida, M. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2208004119 · Cited by 10
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Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions
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Molecular mechanisms insulating proliferation from genotoxic stress in B lymphocytes
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“Together with Ame1 and Okp1, the Ctf19-Mcm21 dimer forms the COMA Ctf19csubcomplex (De Wulf et al. 2003) (Figure 3A).”
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Aboreden, N. G., Zhao, H., Shan, F., Liu, F., Zhang, H., & Blobel, G. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.12.632634 · Cited by 10
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Chang, L., & Noordermeer, D. (2024) · BioEssays · doi:10.1002/bies.202400137 · Cited by 9
“27–30] When Cohesin is blocked on both sides, the CTCF-bound anchors will be in spatial proximity, which creates a noticeable “corner dot” at the summit of the TAD in the Hi-C map (Figure 1A–”
Cohesin positions the epigenetic reader Phf2 within the genome
Tang, W., Costantino, L., Stocsits, R. R., Wutz, G., Ladurner, R., Hudecz, O., Mechtler, K., & Peters, J. (2025) · The EMBO Journal · doi:10.1038/s44318-024-00348-2 · Cited by 9
“…of cohesin (~5 min; (Gerlich et al, 2006)) does not contradict this hypothesis, as NIPBL also has a short chromatin residence time (~50 s; (Rhodes et al, 2017)) but translocates with cohesin during loop extrusion and is in fact essential for this process (Barth et al, 2023; Davidson et al, 2019).”
Active Loop Extrusion Guides DNA-Protein Condensation
Takaki, R., Savich, Y., Jan Brugués, A., & Jülicher, F. (2025) · Physical Review Letters · doi:10.1103/physrevlett.134.128401 · Cited by 9
The SMC Hinge is a Selective Gate for Obstacle Bypass
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“Interestingly, the apparently ef fi - cient incorporation of large obstacles into DNA loops formed by permanently circularized SMC rings 11,27 led to the proposal that DNA loops might be held outside the SMC ring during LE 19 .”
Núñez-Olvera, S. I., Puente-Rivera, J., Ramos‐Payán, R., Pérez‐Plasencia, C., Salinas-Vera, Y. M., Aguilar‐Arnal, L., & López‐Camarillo, C. (2021) · Cells · doi:10.3390/cells11010075 · Cited by 8
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Pallotta, M. M., Nardo, M. D., Hennekam, R. C. M., Kaiser, F. J., Parenti, I., Pié, J., Ramos, F. J., Kline, A. D., & Musio, A. (2022) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.62992 · Cited by 9
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Mahrik, L., Štefanovie, B., Marešová, A., Princová, J., Kolesár, P., Lelkes, E., Faux, C., Helmlinger, D., Převorovský, M., & Palecek, J. J. (2023) · Epigenetics & Chromatin · doi:10.1186/s13072-023-00480-z · Cited by 12
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“Two years later the biochemical basis of this was reported – remarkably, that cohesin is actually the biochemical engine responsible for the generation (often referred to as “ extrusion ” ) of those chromatin loops (13, 14).”
BackgroundPolymer perspective of genome mobilization
Lawrimore, C. J., Lawrimore, J., He, Y., Chavez, S., & Bloom, K. (2020) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2020.111706 · Cited by 9
Keeping intracellular DNA untangled: A new role for condensin?
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Super-Enhancers Dysregulations in Hematological Malignancies
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“We know that SE regulate their target genes via the formation of chromatin loops, mediated by cohesin complexes and NIPBL [44].”
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Soft-matter properties of multilayer chromosomes
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“It will be of interest to explore whether such a motor mechanism also applies to other SMC complexes such as cohesin (Davidson et al., 2019; Kim et al., 2019).”
BackgroundCohesin chromatin loop formation by an extrinsic motorPreprint
Guérin, T. M., Barrington, C., Pobegalov, G. E., Molodtsov, M. I., & Uhlmann, F. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.30.569410 · Cited by 9
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RNAP II antagonizes mitotic chromatin folding and chromosome segregation by condensin
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STAG2 loss in Ewing sarcoma alters enhancer-promoter contacts dependent and independent of EWS::FLI1
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Bonato, A., Jang, J., Kim, D., Moon, K.-W., Michieletto, D., & Ryu, J. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf725 · Cited by 7
“Despite extensive structural and mechanistic studies, conflicting evidence persists regarding the exact topology and mechanics necessary for achieving systematic DNA loop growth, as observed in tethered DNA experiments [ 7 , 8 , 10 ].”
NIPBL and STAG1 enable loop extrusion by providing differential DNA–cohesin affinity
van Wee, R., Asor, R., Li, Y., Drechsel, D. N., Popova, M., Litos, G., Davidson, I. F., Peters, J., & Kukura, P. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2514190122 · Cited by 8
Right on target: Chromatin jets arise from targeted cohesin loading in wild-type cells
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García-Luis, J., Bordelet, H., Thierry, A., Koszul, R., & Aragón, L. (2022) · eLife · doi:10.7554/elife.80147 · Cited by 8
“While cohesive 409 cohesin topologically embraces DNA (Srinivasan et al., 2018), loop extruding 410 complexes rely on non-topological interactions (Davidson et al., 2019a).”
BackgroundBirot, A., Tormos-Pérez, M., Vaur, S., Feytout, A., Jaegy, J., Gil, D. A., Vazquez, S., Ekwall, K., & Javerzat, J. (2020) · eLife · doi:10.7554/elife.50556 · Cited by 8
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BackgroundEncounters in Three Dimensions: How Nuclear Topology Shapes Genome Integrity
Sebastian, R., Aladjem, M. I., & Oberdoerffer, P. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.746380 · Cited by 8
“The organization of the genome into TADs involves ATPdependent, active extrusion of DNA loops through a cohesin ring (Rao et al., 2017; Ganji et al., 2018; Davidson et al., 2019; Davidson and Peters, 2021).”
BackgroundKinetic organization of the genome revealed by ultra-resolution, multiscale live imagingPreprint
Lee, J., Chen, L., Gaudin, S., Gupta, K., Spakowitz, A. J., & Boettiger, A. N. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.27.645817 · Cited by 8
“4L ), modestly faster than average ~1 kb/s observed in vitro under opposing flow ( 25 , 26 ).”
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“TADs form via ‘ loop-extrusion ’ , with cohesin rings extruding DNA until they encounter two convergently oriented CTCF binding sites, which form the base of a loop 30 .”
Cohesin-mediated stabilization of the CCAN complex at kinetochores in mitosis
Haase, J., Aktar, K., Bonner, M. K., Colin, L., Gupta, H., Marinoni, B. E., Morgan, D. O., & Kelly, A. E. (2025) · Current Biology · doi:10.1016/j.cub.2025.07.011 · Cited by 7
Replisomes restrict SMC translocation in vivo
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“4, 5 and Supplementary Movies 2, 3), and DNA zipping beyond the moving replisome in head-on collisions (Figs.”
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Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology
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“Another extrusion model based on ‘elbow’ bending proposed by the Peters group [123] suggests that binding of DNA by the hinge domains and bending of ‘elbows’ (‘swing’) precedes formation of gripping configuration, hence, this model was named ‘swing-and-clamp’ [124].”
InfluentialPushing 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
“[51,52] Interestingly, the size of extruded DNA loops appears to be larger for SA1 than for SA2, consistent with enriched SA1 at TAD boundaries.”
Eykelenboom, J. K., Gierliński, M., Yue, Z., & Tanaka, T. U. (2025) · Current Biology · doi:10.1016/j.cub.2025.02.047 · Cited by 6
Observing Protein One-Dimensional Sliding: Methodology and Biological Significance
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The Cohesin Complex and Its Interplay with Non-Coding RNAs
Kuru-Schors, M., Hämmerle, M., & Gutschner, T. (2021) · Non-Coding RNA · doi:10.3390/ncrna7040067 · Cited by 7
Genetically induced redox stress occurs in a yeast model for Roberts syndrome
Mfarej, M. G., & Skibbens, R. V. (2021) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkab426 · Cited by 7
Mao, A. H., Chen, C., Portillo‐Ledesma, S., & Tamar Schlick, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24076395 · Cited by 7
“Thus, changes in TAD size resulting from altered CTCF function can affect normal gene expression [7].”
BackgroundGenome Topology Control of Antigen Receptor Gene Assembly
Allyn, B. M., Lee, K. D., & Bassing, C. H. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.1901356 · Cited by 6
“Consistent with this model, cohesin protein complexes can compact naked and nucleosome-bound DNA in vitro by extending DNA loops symmetrically in both directions (74, 75).”
MethodCohesin depleted cells pass through mitosis and reconstitute a functional nuclear architecturePreprint
Cremer, M., Brandstetter, K., Maiser, A., Rao, S. S. P., Schmid, V. J., Mitra, N., Mamberti, S., Klein, K. N., Gilbert, D. M., Leonhardt, H., et al. (2019) · Open access LMU (Ludwid Maxmilian's Universitat Munchen) · doi:10.1101/816611 · Cited by 5
Transcription-Driven Translocation of Cohesive and Non-Cohesive Cohesin In Vivo
Borrie, M. S., Kraycer, P. M., & Gartenberg, M. R. (2023) · Molecular and Cellular Biology · doi:10.1080/10985549.2023.2199660 · Cited by 6
“More recent biochemical work showed that cohesin, in combination with NIPBL/Scc2, possesses an intrinsic motor activity that enables processive translocation.(23,24) Importantly, these complexes extruded DNA loops, a process that is thought to form the large chromosomal loops that typify genomes.”
BackgroundXiang, J.-W., Lai, Y., & He, Z. (2025) · Research · doi:10.34133/research.0757 · Cited by 6
“The binding of the cohesin complex to chromatin is dependent on the ATP hydrolysis process, which is facilitated by the NIPBL–MAU2 heterodimer (Scc2–Scc4 in yeast) [ 28 – 30 ].”
A 3D genome compendium of breast cancer progression
van den Brand, T., Collier, M. D., Flach, K. D., Gregoricchio, S., Mayayo‐Peralta, I., Dauyey, Z., Schuurman, K. G., Teunissen, H., Zwart, W. T., & de Wit, E. (2025) · iScience · doi:10.1016/j.isci.2025.113268 · Cited by 7
Dynamical properties of chromatin provide insights into key folding principles
Kadam, S., Sahoo, S., Kumar, P., & Padinhateeri, R. (2025) · Biophysical Journal · doi:10.1016/j.bpj.2025.08.018 · Cited by 5
The mitotic STAG3–cohesin complex shapes male germline nucleome
Nagano, M., Hu, B., Ogata, K., Umemura, F., Ishikura, Y., Suzuki, S., Katsifis, C. C., Yoshinaga, M., Litos, G., Nagasaka, K., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01647-w · Cited by 6
Many faces of mammalian NSD methyltransferases
Tiukacheva, E. A., Vassetzky, Y. S., Razin, S. V., Fang, D., & Ulianov, S. V. (2026) · Cellular & Molecular Biology Letters · doi:10.1186/s11658-025-00848-x · Cited by 7
“A critical feature of TAD and loop organization is the enrichment of CTCF and cohe-sin proteins at their boundaries [110, 112].”
Condensin accelerates long-range intra-chromosomal interactions
Zou, F., Li, Y., Földes, T., Pinholt, H. D., Smith, C. B., Mirny, L. A., & Bai, L. (2026) · Nature Communications · doi:10.1038/s41467-026-70538-5 · Cited by 7
Shah, R., Tortora, M. M. C., Louafi, N., Rahmaninejad, H., Hansen, K. L., Anderson, E. C., Bonitto, K., Wen, D., Giorgetti, L., Fudenberg, G., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.03.037 · Cited by 21
A dual‐function SNF2 protein drives chromatid resolution and nascent transcript removal in mitosis
Carmo, C., Coelho, J., Silva, R. D., Tavares, A., Boavida, A., Gaetani, P., Guilgur, L. G., Martinho, R. G., & Oliveira, R. A. (2023) · EMBO Reports · doi:10.15252/embr.202256463 · Cited by 6
“Condensins are ring-like protein complexes known to extrude DNA molecules in an ATP-dependent manner (Ganji et al , 2018; Davidson et al , 2019; Kim et al , 2019), thereby leading to chromosome compaction.”
BRWD1 orchestrates small pre-B cell chromatin topology by converting static to dynamic cohesin
Mandal, M., Maienschein‐Cline, M., Hu, Y., Mohsin, A., Veselits, M., Wright, N., Okoreeh, M. K., Yoon, Y. M., Veselits, J., Georgopoulos, K., et al. (2023) · Nature Immunology · doi:10.1038/s41590-023-01666-z · Cited by 6
“5a), the protein product of which both loads the cohesin complex and enhances loop extrusion processivity 26,28,29 .”
Coßmann, J., Kos, P. I., Varamogianni‐Mamatsi, V., Assenheimer, D. S., Bischof, T. A., Kuhn, T., Vomhof, T., Papantonis, A., Giorgetti, L., & Gebhardt, J. C. M. (2025) · Nature Communications · doi:10.1038/s41467-025-56889-5 · Cited by 6
“Its ATPase activity and, thereby, the loop extrusion function of the core complex depend on Mau2-Nibpl 17 – 20 , while Wapl determines the release of cohesin from DNA 21,22 .”
InfluentialStrasser, A. S., Gonzalez-Reiche, A. S., Zhou, X., Valdebenito‐Maturana, B., Ye, X., Zhang, B., Wu, M., van Bakel, H., & Jabs, E. W. (2024) · Nature Communications · doi:10.1038/s41467-024-51328-3 · Cited by 6
Phase Separation Mediated Sub-Nuclear Compartmentalization of Androgen Receptors
Yavuz, S., Abraham, T. E., Houtsmuller, A. B., & van Royen, M. E. (2024) · Cells · doi:10.3390/cells13201693 · Cited by 6
“Within TADs, various epigenetic marks promote or suppress gene transcription [78] by facilitating or blocking spatial interactions between CREs and promoters, aided by cohesin complexes during loop extrusion processes (Figure 3) [79].”
BackgroundFontana, A., Bianco, S., Tafuri, F., Esposito, A., Abraham, A., Conte, M., Vercellone, F., Pierno, F. D., Kundu, S., Guha, S., et al. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0243454 · Cited by 6
Pioneer factors outline chromatin architecture
Gómora‐García, J. C., & Furlan-Magaril, M. (2025) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2025.102480 · Cited by 7
Linking DNA-packing density distribution and TAD boundary locations
Meng, L., Sheong, F. K., & Luo, Q. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2418456122 · Cited by 6
Genome folding and refolding in differentiation and cellular senescence
Mizi, A., Zhang, S., & Papantonis, A. (2020) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.08.002 · Cited by 6
Intersubunit and intrasubunit interactions driving the MukBEF ATPase
Bahng, S., Kumar, R., & Marians, K. J. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101964 · Cited by 6
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) · BMC Genomics · doi:10.1186/s12864-022-08574-w · Cited by 6
“The ring-shaped cohesin complex is thought to be loaded onto DNA at active enhancers and promoters, translocate along or extrude DNA, and then unload at sites distal to the loading sites [3].”
BackgroundGitchev, T., Zala, G., Meister, P., & Jost, D. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac705 · Cited by 6
It’s all in the numbers: Cohesin stoichiometry
Matityahu, A., & Onn, I. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.1010894 · Cited by 7
“These discrepancies can be explained if extrusion is mediated by a cohesin dimer (Davidson et al., 2019; Golfier et al., 2020).”
BackgroundRosa, C., Singh, P., Chen, P. B., Sinha, A., Claës, A., Preiser, P. R., Dedon, P. C., Baumgarten, S., Scherf, A., & Bryant, J. M. (2023) · EMBO Reports · doi:10.15252/embr.202357090 · Cited by 5
Belan, S., & Parfenyev, V. (2024) · The Journal of Chemical Physics · doi:10.1063/5.0199573 · Cited by 8
Biology on track: single-molecule visualisation of protein dynamics on linear DNA substrates
Kaur, G., & Spenkelink, L. M. (2020) · Essays in Biochemistry · doi:10.1042/ebc20200019 · Cited by 6
Studying chromosome biology with single-molecule resolution in Xenopus laevis egg extracts
Cameron, G., & Yardimci, H. (2021) · Essays in Biochemistry · doi:10.1042/ebc20200026 · Cited by 6
Lombardi, E. P., & Tarsounas, M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.21.348946 · Cited by 6
“Loop extrusion is completed when both sides of the loop encountered convergent CTCF binding sites (Fudenberg et al. 2016; Davidson et al. 2019; Kim et al. 2019).”
Background
Metadata
- 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
- Venue
- Science
- Published
- 2019-12-13
- Volume
- 366
- Issue
- 6471
- Pages
- 1338-1345
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- 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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