Results 1 to 10 of about 2,219,993 (156)

A Brownian ratchet model for DNA loop extrusion by the cohesin complex [PDF]

eLife, 2021
The cohesin complex topologically encircles DNA to promote sister chromatid cohesion. Alternatively, cohesin extrudes DNA loops, thought to reflect chromatin domain formation. Here, we propose a structure-based model explaining both activities.
Torahiko L Higashi, Georgii Pobegalov, Minzhe Tang, Maxim I Molodtsov, Frank Uhlmann   +4 more
doaj   +10 more sources

DNA double-strand break end synapsis by DNA loop extrusion [PDF]

Nature Communications, 2023
DNA double-strand breaks (DSBs) occur every cell cycle and must be repaired. Here the authors combine theory and simulations to establish a likely role for loop extrusion in bringing the DSB ends back into proximity for repair.
Jin H. Yang, Hugo B. Brandão, Anders S. Hansen   +2 more
doaj   +6 more sources

Telomeres stall DNA loop extrusion by condensin

Cell Reports
Summary: DNA loop extrusion by SMC proteins is a key process underlying chromosomal organization. It is unknown how loop extruders interact with telomeres where DNA is densely covered with proteins.
Brian T. Analikwu, Alice Deshayes, Jaco van der Torre, Thomas M. Guérin, Allard J. Katan, Claire Béneut, Roman Barth, Jamie Phipps, Vittore Scolari, Xavier Veaute, Didier Busso, Karine Dubrana, Stefano Mattarocci, Cees Dekker, Stéphane Marcand   +14 more
doaj   +7 more sources

Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments [PDF]

Scientific Reports, 2023
DNA loop extrusion by structural-maintenance-of-chromosome (SMC) complexes has emerged as a primary organizing principle for chromosomes. The mechanism by which SMC motor proteins extrude DNA loops is still unresolved and much debated.
Roman Barth, Biswajit Pradhan, Eugene Kim, Iain F. Davidson, Jaco van der Torre, Jan-Michael Peters, Cees Dekker   +6 more
doaj   +4 more sources

MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions [PDF]

Genome Biology, 2022
DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns ...
Roberto Rossini, Vipin Kumar, Anthony Mathelier, Torbjørn Rognes, Jonas Paulsen   +4 more
doaj   +6 more sources

The interplay between asymmetric and symmetric DNA loop extrusion [PDF]

eLife, 2020
Chromosome compaction is essential for reliable transmission of genetic information. Experiments suggest that ∼1000-fold compaction is driven by condensin complexes that extrude chromatin loops, by progressively collecting chromatin fiber from one or ...
Edward J Banigan, Leonid A Mirny
doaj   +6 more sources

Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion. [PDF]

PLoS Computational Biology
The SMC complex cohesin mediates interphase chromatin structural formation in eukaryotic cells through DNA loop extrusion. Here, we sought to investigate its mechanism using molecular dynamics simulations.
Chenyang Gu, Shoji Takada, Giovanni B Brandani, Tsuyoshi Terakawa   +3 more
doaj   +3 more sources

Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae [PDF]

The EMBO Journal
The in vivo mechanism, cis-acting roadblocks, and biological functions of DNA loop extrusion by eukaryotic SMC complexes remain incompletely defined. Here, we identify condensin-dependent Hi-C contact stripes at the recombination enhancer (RE) and at ...
Vinciane Piveteau, Chloé Dupont, Hossein Salari, Agnès Dumont, Jérôme Savocco, Daniel Jost, Aurèle Piazza   +6 more
doaj   +3 more sources

Nested TAD hierarchy defines cohesion zones on replicated chromosomes [PDF]

The EMBO Journal
During each cell cycle, cells must not only duplicate the DNA sequence but also preserve the three-dimensional genome architecture required for gene regulation and DNA repair.
Zsuzsanna Takacs, Dmitry Mylarshchikov, Sofia Kolesnikova, Christoph C H Langer, Anton Goloborodko, Daniel W Gerlich   +5 more
doaj   +3 more sources

Author Correction: Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments [PDF]

Scientific Reports, 2023
Roman Barth, Biswajit Pradhan, Eugene Kim, Iain F. Davidson, Jaco van der Torre, Jan‑Michael Peters, Cees Dekker   +6 more
doaj   +2 more sources