DNA loop extrusion by human cohesin

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

DOI 10.1126/science.aaz3418

Cited by (866)

Items 101–200 of 866

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Jinshou Yang, Feihan Zhou, Xiyuan Luo, Yuan Fang, Xing Wang, Xiaohong Liu, Ruiling Xiao, Decheng Jiang, Yuemeng Tang, Gang Yang et al. · 2025 · Cell Death Discovery
The macro and micro of chromosome conformation capture
Viraat Y. Goel, Anders S. Hansen · 2020 · Wiley Interdisciplinary Reviews Developmental Biology
4D nucleome modeling
Marco Di Stefano, Jonas Paulsen, Daniel Jost, Marc A. Martı́-Renom · 2020 · Current Opinion in Genetics & Development
Disruption of NIPBL/Scc2 in Cornelia de Lange Syndrome provokes cohesin genome-wide redistribution with an impact in the transcriptome
Patricia Garcia, R. Fernández‐Hernández, Ana Cuadrado, Ignacio Coca, Antonio Gómez, María Maqueda, Ana Latorre, Beatriz Puisac, Feliciano J. Ramos, Juan Sandoval et al. · 2021 · Nature Communications
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A unified model for cohesin function in sister chromatid cohesion and chromatin loop formation
Frank Uhlmann · 2025 · Molecular Cell
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Naomichi Takemata, Stephen D. Bell · 2020 · Molecular Cell
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Ekaterini Platanitis, Stephan Gruener, Aarathy Ravi Sundar Jose Geetha, Laura Boccuni, Alexander Vogt, Maria Novatchkova, Andreas Sommer, Iros Barozzi, Mathias M. Müller, Thomas Decker · 2022 · iScience
XerD unloads bacterial SMC complexes at the replication terminus
Xheni Karaboja, Zhongqing Ren, Hugo B. Brandão, Payel Paul, David Z. Rudner, Xindan Wang · 2021 · Molecular Cell
Theory of chromatin organization maintained by active loop extrusion
Brian Chan, Michael Rubinstein · 2023 · Proceedings of the National Academy of Sciences
A Condensed View of the Chromosome Passenger Complex
Prasad Trivedi, P. Todd Stukenberg · 2020 · Trends in Cell Biology
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Kevin Li, Gabriel Bronk, Jané Kondev, James E. Haber · 2020 · Proceedings of the National Academy of Sciences
Cohesin Mutations in Cancer: Emerging Therapeutic Targets
Jisha Antony, Chue Vin Chin, Julia A. Horsfield · 2021 · International Journal of Molecular Sciences
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Martín A. Rivas, Cem Meydan, Christopher R. Chin, Matt F. Challman, Daleum Kim, Bhavneet Bhinder, Andreas Kloetgen, Aaron D. Viny, Matt R. Teater, Dylan R. McNally et al. · 2021 · Nature Immunology
The Stochastic Genome and Its Role in Gene Expression
Christopher H. Bohrer, Daniel R. Larson · 2021 · Cold Spring Harbor Perspectives in Biology
Nucleosome positioning and chromatin organization
Jyotsana J. Parmar, Ranjith Padinhateeri · 2020 · Current Opinion in Structural Biology
cLoops2: a full-stack comprehensive analytical tool for chromatin interactions
Yaqiang Cao, Shuai Liu, Gang Ren, Qingsong Tang, Keji Zhao · 2021 · Nucleic Acids Research
Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops
Shuai Liu, Yaqiang Cao, Kairong Cui, Qingsong Tang, Keji Zhao · 2022 · Nature Communications
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Dácil Alonso Gil, Ana Cuadrado, Daniel Giménez-Llorente, Miriam Rodríguez-Corsino, Ana Losada · 2023 · Nature Communications
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George Cameron, Dominika T. Gruszka, Rhian Gruar, Sherry Xie, Çağla Kaya, Kim Nasmyth, Jonathan Baxter, Madhusudhan Srinivasan, Hasan Yardimci · 2024 · Science
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Barth, Roman, Davidson, Iain F., van der Torre, Jaco, Taschner, Michael, Gruber, Stephan, Peters, Jan-Michael, Dekker, Cees · 2025 · Cell
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Honggui Wu, Jiankun Zhang, Longzhi Tan, Xiaoliang Sunney Xie · 2025 · Nature Genetics
Wapl releases Scc1-cohesin and regulates chromosome structure and segregation in mouse oocytes
Mariana C.C. Silva, Sean T. Powell, Sabrina Ladstätter, Johanna Gassler, Roman R. Stocsits, Antonio Tedeschi, Jan‐Michael Peters, Kiku-e K. Tachibana · 2020 · The Journal of Cell Biology
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Sílvia Dyson, Joana Segura, Belén Martínez‐García, Antonio Valdés, Joaquím Roca · 2020 · The EMBO Journal
Loop competition and extrusion model predicts CTCF interaction specificity
Xi Wang, M Beer · 2021 · Nature Communications
DNA segment capture by Smc5/6 holocomplexes
Taschner, Michael, Gruber, Stephan · 2023 · Nature Structural & Molecular Biology
SMC complexes organize the bacterial chromosome by lengthwise compaction
Jarno Mäkelä, David J. Sherratt · 2020 · Current Genetics
Cohesin architecture and clustering in vivo
Siheng Xiang, Douglas E. Koshland · 2021 · eLife
Epigenetic regulatory layers in the 3D nucleus
Andréa Willemin, Dominik Szabó, Ana Pombo · 2024 · Molecular Cell
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Polina S. Belokopytova, Veniamin Fishman · 2021 · Frontiers in Genetics
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Sugako Ogushi, Ahmed Rattani, Jonathan Godwin, Jean Metson, Lothar Schermelleh, Kim Nasmyth · 2021 · Developmental Cell
DNA double-strand break end synapsis by DNA loop extrusion
Yang, Jin H., Brandão, Hugo B., Hansen, Anders S. · 2023 · Nature Communications
Establishment of dsDNA-dsDNA interactions by the condensin complex
Minzhe Tang, Georgii E. Pobegalov, Hideki Tanizawa, Zhuo Angel Chen, Juri Rappsilber, Maxim I. Molodtsov, Ken-ichi Noma, Frank Uhlmann · 2023 · Molecular Cell
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Claudia Rabuffo, Markus R. Schmidt, Prateek Yadav, Pin Tong, Roberta Carloni, Anna Barcons-Simon, Raúl O. Cosentino, Stefan Krebs, Keith R. Matthews, Robin C. Allshire et al. · 2024 · Nature Communications
Shaping of the 3D genome by the ATPase machine cohesin
Yoori Kim, Hongtao Yu · 2020 · Experimental & Molecular Medicine
Single‐cell imaging of genome organization and dynamics
Liangqi Xie, Zhe J. Liu · 2021 · Molecular Systems Biology
Loop-extrusion-mediated plasmid DNA cleavage by the bacterial SMC Wadjet complex
Biswajit Pradhan, Amar Deep, Jessica König, Martin Dieter Baaske, Kevin D. Corbett, Eugene Kim · 2024 · Molecular Cell
Rec8 Cohesin: A Structural Platform for Shaping the Meiotic Chromosomes
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Jan‐Michael Peters · 2021 · Current Opinion in Cell Biology
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Ning-Qing Liu, Mikhail D. Magnitov, Marijne M G A Schijns, T. van Schaik, Robin H. van der Weide, Hans Teunissen, B. van Steensel, Elzo de Wit · 2021 · bioRxiv
Structural biology of SMC complexes across the tree of life
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Structural basis for plasmid restriction by SMC JET nuclease
Roisné-Hamelin, Florian, Liu, Hon Wing, Taschner, Michael, Li, Yan, Gruber, Stephan · 2024 · Molecular Cell
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