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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]
Citations
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Chan, B., & Rubinstein, M. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2401494121 · Cited by 34
3D genome folding in epigenetic regulation and cellular memory
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“Recent work provides experimental support for the loop extrusion model: condensin [160] and later cohesin [161,162] complexes were observed to extrude naked DNA loops in vitro.”
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“We evaluated cohesin contribution to enhancer/promoter contacts by varying cohesin density, residency time (dwell-time), and velocity on the basis of published in vitro and cellular assessments of these biophysical properties ( 34 , 35 ).”
BackgroundInfluentialCohesin organizes 3D DNA contacts surrounding active enhancers in C. elegansPreprint
Kim, J., Wang, H., & Ercan, S. (2025) · Genome Research · doi:10.1101/gr.279365.124 · Cited by 31
“In vitro, cohesin performs two-sided loop extrusion (Davidson et al. 2019; Kim et al. 2019).”
InfluentialKant, A., Guo, Z., Vinayak, V., Neguembor, M. V., Li, W. S., Agrawal, V., Pujadas-Liwag, E. M., Almassalha, L. M., Backman, V., Lakadamyali, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48698-z · Cited by 31
“…decomposed as, In addition to the extrusion of loops via RNAPII mediated DNA supercoiling activity 12,13,19,28 – 30 , in vitro experiments proposed that cohesin once transiently loaded onto DNA, could independently drive the formation of loops via its ATPase machinery 9,11,31 – 33 .”
BackgroundInfluentialSMC-based immunity against extrachromosomal DNA elements
Liu, H. W., Roisné-Hamelin, F., & Gruber, S. (2023) · Biochemical Society Transactions · doi:10.1042/bst20221395 · Cited by 31
Barton, R. E., Massari, L. F., Robertson, D., & Marston, A. L. (2022) · eLife · doi:10.7554/elife.74447 · Cited by 33
Predicting genome organisation and function with mechanistic modelling
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Rec8 Cohesin-mediated Axis-loop chromatin architecture is required for meiotic recombination
Sakuno, T., Tashiro, S., Tanizawa, H., Iwasaki, O., Ding, D., Haraguchi, T., Noma, K.-I., & Hiraoka, Y. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac183 · Cited by 29
“pombe, respectively); human Scc2 and Scc4 are required for the DNA extruding activity of human Rad21 cohesin complex at least in vitro (98).”
BackgroundDynamics of microcompartment formation at the mitosis-to-G1 transition
Goel, V. Y., Aboreden, N. G., Jusuf, J. M., Zhang, H., Mori, L., Mirny, L. A., Blobel, G. A., Banigan, E. J., & Hansen, A. S. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01687-2 · Cited by 35
“Following in vitro observations 8,112–115 , v = 1 kb s −1 unless noted.”
A low Smc flux avoids collisions and facilitates chromosome organization in Bacillus subtilis
Anchimiuk, A., Lioy, V., Bock, F., Minnen, A., Boccard, F., & Gruber, S. (2021) · eLife · doi:10.7554/elife.65467 · Cited by 19
“Purified yeast condensin and vertebrate cohesin extrude DNA loops at rates of ~1 kb/s in an asymmetric (one-sided) or symmetric (two-sided) manner, respectively (Davidson et al., 2019; Ganji et al., 2018; Kim et al., 2019).”
BackgroundESA1 regulates meiotic chromosome axis and crossover frequency via acetylating histone H4
Wang, Y., Zhai, B., Tan, T., Xiao, Y., Zhang, J., Song, M., Tan, Y., Yang, X., Chu, T., Zhang, S., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab722 · Cited by 30
A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH
Jia, B. B., Jussila, A., Kern, C., Zhu, Q., & Ren, B. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01568-9 · Cited by 30
A joint-ParB interface promotes Smc DNA recruitment
Bock, F. P., Liu, H. W., Anchimiuk, A., Diebold-Durand, M.-L., & Gruber, S. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111273 · Cited by 28
“The hawk subunit Scc2 is a loading and processivity factor for DNA loop extrusion by cohesin (Davidson et al., 2019).”
BackgroundCoordination of cohesin and DNA replication observed with purified proteins
Murayama, Y., Endo, S., Kurokawa, Y., Kurita, A., Iwasaki, S., & Araki, H. (2024) · Nature · doi:10.1038/s41586-023-07003-6 · Cited by 28
“After an extensive high-salt wash (750 mM NaCl) to remove non-topological associations including DNA loops 33,34 , bound DNA was recovered and analysed by agarose gel electrophoresis.”
Sister chromatid cohesion halts DNA loop expansion
Bastié, N., Chapard, C., Cournac, A., Nejmi, S., Mboumba, H., Gadal, O., Thierry, A., Beckouët, F., & Koszul, R. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.02.004 · Cited by 27
All eukaryotic SMC proteins induce a twist of −0.6 at each DNA loop extrusion step
Janissen, R., Barth, R., Davidson, I., Taschner, M., Gruber, S., Peters, J.-M., & Dekker, C. (2024) · bioRxiv · doi:10.1126/sciadv.adt1832 · Cited by 26
Nucleosome fibre topology guides transcription factor binding to enhancers
O’Dwyer, M. R., Azagury, M., Furlong, K., Alsheikh, A., Hall-Ponselé, E., Pinto, H. B., Fyodorov, D. V., Jaber, M., Papachristoforou, E., Benchetrit, H., et al. (2024) · Nature · doi:10.1038/s41586-024-08333-9 · Cited by 32
Single cell analysis pushes the boundaries of TAD formation and function
Luppino, J. M., & Joyce, E. F. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.03.005 · Cited by 29
“Indeed, cohesin has been shown to have extrusion capabilities in vitro (Davidson et al., 2019; Kim et al., 2019).”
BackgroundMany facades of CTCF unified by its coding for three-dimensional genome architecture
Wu, Q., Liu, P., & Wang, L. (2020) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2020.06.008 · Cited by 26
Genome-in-a-Box: Building a Chromosome from the Bottom Up
Birnie, A., & Dekker, C. (2020) · ACS Nano · doi:10.1021/acsnano.0c07397 · Cited by 30
Hill, L., Wutz, G., Jaritz, M., Tagoh, H., Calderón, L., Peters, J., Goloborodko, A. A., & Busslinger, M. (2023) · Nature Communications · doi:10.1038/s41467-023-37994-9 · Cited by 30
“Cohesin, in associationwithNipbl, functionsastheloopextrusionfactor 15,16 ,which continuously extrudes a chromatin loop until the process is halted by CTCF at the base of a loop 2 .”
Cohesin‐mediated DNA loop extrusion resolves sister chromatids in G2 phase
Batty, P., Langer, C. C. H., Takács, Z., Tang, W., Blaukopf, C., Peters, J., & Gerlich, D. W. (2023) · The EMBO Journal · doi:10.15252/embj.2023113475 · Cited by 28
“Indeed, NIPBL, which is an essential factor for cohesin-mediated loop extrusion (Schwarzer et al , 2017; Davidson et al , 2019; Kim et al , 2019; Mitter et al , 2020), dissociates from chromosomes during mitotic prophase, in wild-type and WAPL-depleted cells (Rhodes et al , 2017), raising the…”
InfluentialMembers of an array of zinc-finger proteins specify distinct Hox chromatin boundaries
Ortabozkoyun, H., Huang, P., González-Buendía, E., Cho, H., Kim, S. Y., Tsirigos, A., Mazzoni, E. O., & Reinberg, D. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.08.007 · Cited by 28
Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers
Liu, N. Q., Magnitov, M. D., Schijns, M. M. G. A., van Schaik, T., Teunissen, H., van Steensel, B., & de Wit, E. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf549 · Cited by 30
Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription
Shaban, H. A., Barth, R., & Bystricky, K. (2020) · Genome biology · doi:10.1186/s13059-020-02185-y · Cited by 28
“The loop extruding activity of cohesin was recently illustrated by in vitro experiments [157, 166, 167].”
BackgroundCarico, Z. M., Stefan, H. C., Justice, M., Yimit, A., & Dowen, J. M. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009435 · Cited by 28
“For proliferation assays, cells transfected with the Nipbl- and Wapl-targeting siRNA pools were seeded into 6-well plates 24 hours post-transfection, and cells transfected with the Pds5a- and Pds5b-targeting siRNA pools were seeded 48 hours post-transfection.”
BackgroundInfluentialSpatial Organization of Chromatin: Transcriptional Control of Adaptive Immune Cell Development
Pongubala, J. M. R., & Murre, C. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.633825 · Cited by 29
“Once sequestered at chromatin, cohesin actively extrudes the chromatin fiber until it encounters two convergently bound CTCF sites (Figure 3) (87, 98, 101, 105, 106).”
BackgroundBansal, K., Michelson, D. A., Ramírez, R. N., Viny, A. D., Levine, R. L., Benoist, C. O., & Mathis, D. J. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2110991118 · Cited by 26
“Most recently, it was reported that NIPBL translocates along the DNA and is actually required for ongoing loop extrusion by cohesin (26).”
BackgroundCTCF 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) · Genome biology · doi:10.1186/s13059-022-02754-3 · Cited by 29
“Once loaded on DNA, cohesin is thought to establish long-range DNA contacts through a processive increase in chromatin loop size, a process known as extrusion ( [19, 20], reviewed in [21]).”
BackgroundFunction and Evolution of the Loop Extrusion Machinery in Animals
Kabirova, E., Nurislamov, A. R., Shadskiy, A., Smirnov, A. V., Popov, A., Salnikov, P., Баттулин, Н. Р., & Fishman, V. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24055017 · Cited by 25
“calculated in different systems [28,56,146,153], which hinted that cohesin might facilitate the process.”
BackgroundConnecting the dots: key insights on ParB for chromosome segregation from single-molecule studies
Tišma, M., Kaljević, J., Gruber, S., Le, T. B. K., & Dekker, C. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad067 · Cited by 27
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break
Roy, S., Adhikary, H., & D’Amours, D. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae103 · Cited by 24
“Importantly, the arm regions of cohesin and condensin are longer than those of the SMC5 / 6 complex ( 53 ,66 ) and bend sharply at so-called pseudo-elbow sites causing the hinge to contact the head-proximal coiled-coil or head-bound non-SMC proteins ( 26 ,66–70 ).”
BackgroundQuantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis
Brunner, A., Morero, N. R., Zhang, W., Hossain, M. J., Lampe, M., Pflaumer, H., Halavatyi, A. A., Peters, J., Beckwith, K. S., & Ellenberg, J. (2024) · The Journal of Cell Biology · doi:10.1083/jcb.202405169 · Cited by 23
“I am not suggesting a very extensive analysis, but the polymer simulations studies have typically processivity/separation ratios that produce interphase and mitotic chromosomes.”
Cohesin drives chromatin scanning during the RAD51-mediated homology search
Marín-González, A., Rybczynski, A. T., Nilavar, N. M., Nguyen, D., Karwacki-Neisius, V., Li, A. G., Zou, R. S., Avilés-Vázquez, F. J., Kanemaki, M. T., Scully, R., et al. (2025) · Science · doi:10.1126/science.adw1928 · Cited by 34
Cornelia de Lange syndrome mutations in NIPBL can impair cohesin-mediated DNA loop extrusion
Panarotto, M., Davidson, I. F., Litos, G., Schleiffer, A., & Peters, J. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2201029119 · Cited by 27
“All NIPBL mutants that are impaired in stimulating cohesin’s ATPase activity are therefore also impaired in supporting loop extrusion, as expected given that cohesin’s ATPase activity is required for this process (5, 6).”
BackgroundMethodCo-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression
Luppino, J. M., Field, A. R., Nguyen, S. C., Park, D. S., Shah, P. P., Abdill, R. J., Lan, Y., Yunker, R., Jain, R., Adelman, K., et al. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010528 · Cited by 34
“NIPBL, together with MAU2, have been proposed to both load cohesin and activate its ATPase domain to initiate loop extrusion [4,5,3,6,7].”
BackgroundRETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
Lee, J., Chen, L., Gaudin, S., Gupta, K., Novačić, A., Spakowitz, A. J., & Boettiger, A. N. (2025) · Science · doi:10.1126/science.adx2202 · Cited by 34
RetractedCommon Features of the Pericentromere and Nucleolus
Lawrimore, C. J., & Bloom, K. (2019) · Genes · doi:10.3390/genes10121029 · Cited by 25
“However, other studies suggest a cohesin-mediated loop extrusion model, particularly during interphase [62,68].”
BackgroundCharacterizing chromatin folding coordinate and landscape with deep learning
Xie, W. J., Qi, Y., & Zhang, B. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008262 · Cited by 23
“Several predictions of the extrusion model have been validated with perturbative Hi-C [21–25] and in vitro experiments [26, 27].”
MethodThe RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination
Beilinson, H. A., Glynn, R. A., Yadavalli, A. D., Xiao, J., Corbett, E., Saribasak, H., Arya, R., Miot, C., Bhattacharyya, A., Jones, J. M., et al. (2021) · The Journal of Experimental Medicine · doi:10.1084/jem.20210250 · Cited by 25
“For RSSs separated by a short distance from one another in the RC (2–3 kb for the Igh and Tcrb RCs), loop extrusion (measured to occur at 0.5–2 kb/s; Davidson et al., 2019; Kim et al., 2019) would be predicted to move a potential partner RSS to the opposite side of the cohesin ring from the RAG-bound RSS very rapidly,…”
BackgroundInfluentialBuilding the genome architecture during the maternal to zygotic transition
Zhang, Y., & Xie, W. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2021.11.002 · Cited by 25
Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage
Martínez‐García, B., Dyson, S., Segura, J., Ayats-Fraile, A., Cutts, E., Gutiérrez-Escribano, P., Aragón, L., & Roca, J. (2022) · The EMBO Journal · doi:10.15252/embj.2022111913 · Cited by 23
Cohesin forms fountains at active enhancers in C. elegans
Lüthi, B. N., Semple, J. I., Haemmerli, A., Thapliyal, S., Ghadage, K., Stojanovski, K., D'Asaro, D., Das, M., Gilbert, N., Glauser, D. A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-67302-6 · Cited by 29
“Fountains may also act to locally restrict the dissipation of torsional stress generated by enhancer transcription or by the loop extrusion activity of cohesin loaded onto enhancers 22 .”
Relating SMCHD1 structure to its function in epigenetic silencing
Gurzau, A. D., Blewitt, M. E., Czabotar, P. E., Murphy, J. M., & Birkinshaw, R. W. (2020) · Biochemical Society Transactions · doi:10.1042/bst20200242 · Cited by 24
Awakening of the zygotic genome by pioneer transcription factors
Kobayashi, W., & Tachibana, K.-E. K. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.05.013 · Cited by 26
Galupa, R., Picard, C., Servant, N., Nora, E. P., Zhan, Y., van Bemmel, J. G., Marjou, F. E., Johanneau, C., Borensztein, M., Ancelin, K., et al. (2022) · Development · doi:10.1242/dev.200568 · Cited by 23
Nanoscale 3D DNA tracing in single human cells visualizes loop extrusion directly in situPreprint
Beckwith, K. S., Ødegård-Fougner, Ø., Morero, N. R., Barton, C., Schueder, F., Tang, W., Alexander, S., Peters, J., Jungmann, R., Birney, E., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.12.439407 · Cited by 24
Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations
Tjalsma, S. J. D., Rinzema, N. J., Verstegen, M. J. A. M., Robers, M. J., Nieto-Aliseda, A., Gremmen, R., Allahyar, A., Muraro, M. J., Krijger, P. H. L., & de Laat, W. L. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100778 · Cited by 23
“Cohe-sinformsandextrudesloopswhenloadedontoDNA, 13 aprocess that is constrained by CCCTC-binding factor (CTCF) binding at convergently oriented sites.”
Cohesin supercoils DNA during loop extrusion
Davidson, I. F., Barth, R., Nagasaka, K., Tang, W., Wutz, G., Horn, S., Janissen, R., Stocsits, R. R., Chlosta, E., Bauer, B. W., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115856 · Cited by 24
A role of the Nse4 kleisin and Nse1/Nse3 KITE subunits in the ATPase cycle of SMC5/6
Vondrová, L., Kolesár, P., Adamus, M., Nociar, M., Oliver, A. W., & Palecek, J. J. (2020) · Scientific Reports · doi:10.1038/s41598-020-66647-w · Cited by 23
Feng, Y., Huang, W. C., Paul, C., Liu, X., Sadayappan, S., Wang, Y., & Pauklin, S. (2021) · Basic Research in Cardiology · doi:10.1007/s00395-021-00889-1 · Cited by 22
Three-dimensional loop extrusion
Bonato, A., & Michieletto, D. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.11.015 · Cited by 23
The 3D genome and its impacts on human health and disease
Wang, S., Luo, Z., Liu, W., Hu, T., Zhao, Z., Rosenfeld, M. G., & Song, X. (2023) · Life Medicine · doi:10.1093/lifemedi/lnad012 · Cited by 22
“One is the loop extrusion model [22, 23], where cohesin loads on chromatin and forms a small loop that then extrudes on the chromatin and stops when it encounters two convergently oriented CTCF.”
The interplay between asymmetric and symmetric DNA loop extrusion
Banigan, E., & Mirny, L. (2020) · bioRxiv · doi:10.7554/elife.63528 · Cited by 19
“DNA loop extrusion by condensins (Ganji et al., 2018; Golfier et al., 2020; Kong et al., 2020; Kim et al., 2020) and other SMC complexes (Kim et al., 2019; Davidson et al., 2019; Golfier et al., 2020) has recently been observed in single-molecule experiments in vitro .”
BackgroundMethodInfluentialUniform dynamics of cohesin-mediated loop extrusion in living human cells
Sabaté, T., Lelandais, B., Robert, M.-C., Szalay, M., Tinevez, J.-Y., Bertrand, E., & Zimmer, C. (2025) · Nature Genetics · doi:10.1038/s41588-025-02406-9 · Cited by 32
“…quantities, both expressed in bp s −1 : (1) the motor speed, that is, the molecular speed at which cohesin pulls out DNA strands to form a loop (estimated at 0.5–1 kb s −1 in vitro 10,11 ) and (2) the closing rate (CR), that is, the rate at which the unextruded DNA between anchors is reduced (Fig.”
InfluentialActive regulatory elements recruit cohesin to establish cell specific chromatin domains
Georgiades, E., Harrold, C., Roberts, N., Kassouf, M. T., Riva, S. G., Sanders, E., Downes, D., Francis, H. S., Blayney, J., Oudelaar, A. M., et al. (2023) · bioRxiv · doi:10.1038/s41598-025-96248-4 · Cited by 18
“Cohesin is known to play an important role in the establishment of 3D genome structure through its role in loop extrusion 39–42 .”
“Looping In” Mechanics: Mechanobiologic Regulation of the Nucleus and the Epigenome
Dai, E. N., Heo, S., & Mauck, R. L. (2020) · Advanced Healthcare Materials · doi:10.1002/adhm.202000030 · Cited by 22
Uncovering the Principles of Genome Folding by 3D Chromatin ModelingPreprint
Yıldırım, A., Boninsegna, L., Zhan, Y., & Alber, F. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a039693 · Cited by 25
Mach, P., Kos, P., Zhan, Y., Cramard, J., Gaudin, S., Tünnermann, J., Marchi, E., Eglinger, J., Zuin, J., Kryzhanovska, M., et al. (2022) · bioRxiv · doi:10.1101/2022.03.03.482826 · Cited by 18
Cohesin guides homology search during DNA repair using loops and sister chromatid linkages
Teloni, F., Takács, Z., Mitter, M., Langer, C. C. H., Prlesi, I., Steinacker, T. L., Reuter, V. P., Mylarshchikov, D. E., & Gerlich, D. W. (2025) · Science · doi:10.1126/science.adw0566 · Cited by 28
Liu, L., Zhang, L., Dao, F., Yang, Y., & Lin, H. (2020) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2020.11.011 · Cited by 21
“Based on the loop extrusion model, 25,48 these skip genes are good background for our study.”
BackgroundOpening of cohesin’s SMC ring is essential for timely DNA replication and DNA loop formation
Sakata, R., Niwa, K., Torre, D. U. L., Gu, C., Tahara, E., Takada, S., & Nishiyama, T. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108999 · Cited by 21
Vicioso‐Mantis, M., Fueyo, R., Navarro, C., Cruz-Molina, S., van IJcken, W. F. J., Rebollo, E., Rada-Iglesias, Á., & Martínez‐Balbás, M. A. (2022) · Nature Communications · doi:10.1038/s41467-022-30614-y · Cited by 22
Cuadrado, A., Giménez-Llorente, D., Koninck, M. D., Ruiz‐Torres, M., Kojic, A., Rodríguez-Corsino, M., & Losada, A. (2022) · Epigenetics & Chromatin · doi:10.1186/s13072-022-00469-0 · Cited by 21
“Recent in vitro reconstitution of loop extrusion by cohesin has demonstrated the requirement for NIPBL to activate the SMC1/3 ATPase [28, 29].”
BackgroundWhat AlphaFold tells us about cohesin’s retention on and release from chromosomes
Nasmyth, K. A., Lee, B.-G., Roig, M. B., & Löwe, J. (2023) · eLife · doi:10.7554/elife.88656.4 · Cited by 21
Recombination-mediated genome rearrangements
Savocco, J., & Piazza, A. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2021.06.008 · Cited by 21
Epigenetic regulation by ASXL1 in myeloid malignancies
Yang, F., & Agosto-Peña, J. (2023) · International Journal of Hematology · doi:10.1007/s12185-023-03586-y · Cited by 22
“It has also been reported 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 [96].”
BackgroundStructure and Function of the Separase-Securin Complex
Luo, S., & Tong, L. (2020) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-030-58971-4_4 · Cited by 20
Matityahu, A., & Onn, I. (2021) · Journal of Cell Science · doi:10.1242/jcs.247577 · Cited by 22
“To this end, the effect of alternative cohesin subunits on cohesin processivity has not been addressed in detail; it stands as a future challenge to provide biochemical systems that can be used to test loop extrusion activity for complexes with alternative subunit composition to either confirm or reject this idea (Dav…”
BackgroundChromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue
Janowski, M., Milewska, M., Zare, P., & Pękowska, A. (2021) · Pharmaceuticals · doi:10.3390/ph14080765 · Cited by 21
Kimura, S., Park, C. S., Montefiori, L. E., Iacobucci, I., Pölönen, P., Gao, Q., Arnold, E. D., Attarbaschi, A., Brown, A. R., Buldini, B., et al. (2024) · Cancer Discovery · doi:10.1158/2159-8290.cd-23-1452 · Cited by 24
The Impact of Space and Time on the Functional Output of the GenomePreprint
Nollmann, M., Bennabi, I., Götz, M., & Gregor, T. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040378 · Cited by 23
“In addition, loop extrusion by the cohesin complex occurs at a maximum rate of ∼2 kb/sec in vitro (Davidson et al. 2019; Kim et al. 2019); thus, loops could likely play a role in the dynamics of enhancer–promoter interactions.”
BackgroundKoide, H., Kodera, N., Bisht, S., Takada, S., & Terakawa, T. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009265 · Cited by 19
Mechanical disengagement of the cohesin ring
Richeldi, M., Pobegalov, G. E., Higashi, T. L., Gmurczyk, K., Uhlmann, F., & Molodtsov, M. I. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01122-4 · Cited by 19
“During interphase, cohesin is thought to translocate along DNA and extrude DNA loops 14–17 .”
BackgroundCohesin regulation and roles in chromosome structure and function
Rittenhouse, N., & Dowen, J. M. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102159 · Cited by 19
Effective model of loop extrusion predicts chromosomal domains
Crippa, M., Zhan, Y., & Tiana, G. (2020) · Physical review. E · doi:10.1103/physreve.102.032414 · Cited by 21
Structural insights into DNA loop extrusion by SMC protein complexes
Datta, S., Lecomte, L., & Haering, C. H. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.06.009 · Cited by 18
“In single-molecule imaging experiments, purified yeast condensin complexes [12] or human cohesin complexes [13,14] were indeed able to track along tens of kilobase pairs and progressively extrude DNA into loops.”
BackgroundFunctions of Polycomb Proteins on Active Targets
Giner-Laguarda, N., & Vidal, M. (2020) · Epigenomes · doi:10.3390/epigenomes4030017 · Cited by 20
“These long-range contacts withstand removal of cohesins [102], the molecules involved in chromatin organization through DNA loop extrusion [103,104] and, therefore, represent an independent element of chromatin organization.”
BackgroundDNA Binding by the Mis4Scc2 Loader Promotes Topological DNA Entrapment by the Cohesin Ring
Kurokawa, Y., & Murayama, Y. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108357 · Cited by 19
Physical mechanisms of chromatin spatial organization
Chiariello, A. M., Bianco, S., Esposito, A., Fiorillo, L., Conte, M., Irani, E., Musella, F., Abraham, A., Prisco, A., & Nicodemi, M. (2021) · FEBS Journal · doi:10.1111/febs.15762 · Cited by 20
Impacts of chromatin dynamics and compartmentalization on DNA repair
Yasuhara, T., & Zou, L. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103162 · Cited by 18
Signaling‐to‐chromatin pathways in the immune system
de Paz, A. M., & Josefowicz, S. Z. (2021) · Immunological Reviews · doi:10.1111/imr.12955 · Cited by 18
Models behind the mystery of establishing enhancer-promoter interactions
Monfils, K., & Barakat, T. S. (2021) · European Journal of Cell Biology · doi:10.1016/j.ejcb.2021.151170 · Cited by 19
“3 fiber in one or both directions (Davidson et al., 2019; Fudenberg et al., 2016; Kim et al., 2019).”
BackgroundSTAG2 Promotes the Myelination Transcriptional Program in Oligodendrocytes
Cheng, N., Li, G., Kanchwala, M., Evers, B. M., Xing, C., & Yu, H. (2021) · eLife · doi:10.7554/elife.77848 · Cited by 18
Modulation of the high-order chromatin structure by Polycomb complexes
Guo, Y., & Wang, G. G. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.1021658 · Cited by 19
“Further studies demonstrated that cohesin complex is loaded to DNA through the Nipped-B-like (NIPBL) protein and its binding partner MAU2, which are strong activators of cohesin’s ATPase activity (Davidson et al., 2019; Kim et al., 2019).”
BackgroundLoops and the activity of loop extrusion factors constrain chromatin dynamics
Bailey, M. L. P., Surovtsev, I. V., Williams, J. F., Yan, H., Yuan, T., Li, K., Duseau, K., Mochrie, S. G. J., & King, M. C. (2023) · Molecular Biology of the Cell · doi:10.1091/mbc.e23-04-0119 · Cited by 22
“, 2017), it has been widely suggested that SMC complexes are loop extrusion factors (LEFs) that drive the formation of chromatin loops, an activity that can be observed in vitro or in extracts (Ganji et al., 2018; Davidson et al., 2019; Kim et al., 2019; Golfier et al., 2020).”
InfluentialPolovnikov, K., & Slavov, B. (2023) · Physical Review E · doi:10.1103/physreve.107.054135 · Cited by 16
Do, C., Jiang, G., Cova, G., Katsifis, C. C., Narducci, D. N., Sakellaropoulos, T., Vidal, R. S., Lhoumaud, P., Tsirigos, A., Regis, F. F., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100813 · Cited by 20
Polymer models for the mechanisms of chromatin 3D folding: review and perspective
Zhou, R., & Gao, Y. Q. (2020) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp01877e · Cited by 18
Myosin VI moves on nuclear actin filaments and supports long-range chromatin rearrangementsPreprint
Große-Berkenbusch, A., Hettich, J., Kuhn, T., Fili, N., Cook, A. W., Hari‐Gupta, Y., Palmer, A., Streit, L. M., Ellis, P. J. I., Toseland, C. P., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.03.023614 · Cited by 19
“…Cremer et al., 2003; T. Cremer & Cremer, 2010; Fraser & Bickmore, 2007), are compartmentalized (Lieberman-Aiden et al., 2009) and exhibit topologically associating domains (Dixon et al., 2012) extruded by a motor function of cohesin (Davidson et al., 2019; Kim, Shi, Zhang, Finkelstein, & Yu, 2019).”
BackgroundChromatin domains in the cell: Phase separation and condensation
Fujishiro, S., Sasai, M., & Maeshima, K. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103006 · Cited by 21
Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome
Papantonis, A., & Oudelaar, A. M. (2025) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120423-012301 · Cited by 19
preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution
Stilianoudakis, S. C., Marshall, M. A., & Dozmorov, M. G. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab743 · Cited by 19
Regulation of cohesin‐mediated chromosome folding by PDS5 in mammals
Yu, D., Chen, G., Wang, Y., Wang, Y., Lin, R., Liu, N., Zhu, P., Liu, H., Hu, T., Feng, R., et al. (2022) · EMBO Reports · doi:10.15252/embr.202254853 · Cited by 15
“Single-molecular imaging studies indicate recombinant human cohesin-NIPLB-MAU2 complex can extrude DNA and form loops in a manner dependent on cohesin’s ATPase activity (Davidson et al , 2019; Kim et al , 2019).”
Kean, C. M., Tracy, C. J., Mitra, A., Rahat, B., Winkle, M. T. V., Gebert, C. M., Noeker, J. A., Calof, A. L., Lander, A. D., Kassis, J. A., et al. (2022) · Science Advances · doi:10.1126/sciadv.add4136 · Cited by 16
“Cohesin, stimulated by NIPBL, acts as an adenosine triphosphate (ATP)– dependent molecular motor extruding DNA and folding the genome into topologically associated domains (TADs) ( 10 – 13 ).”
Transcription induces context-dependent remodeling of chromatin architecture during differentiation
Chahar, S., Zouari, Y. B., Salari, H., Molitor, A. M., Kobi, D., Maroquenne, M., Erb, C., Mossler, A., Karasu, N., Jost, D., et al. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002424 · Cited by 21
Liu, C., Nagashima, H., Fernando, N., Bass, V., Gopalakrishnan, J., Signorella, S., Montgomery, W., Lim, A. I., Harrison, O. J., Reich, L. N., et al. (2024) · Immunity · doi:10.1016/j.immuni.2024.04.007 · Cited by 18
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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