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 +2 more
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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 +4 more
doaj +6 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 +4 more
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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
Telomeres stall DNA loop extrusion by condensin
Cell ReportsSummary: 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 +14 more
doaj +6 more sources
DNA actively regulates the “safety-belt” dynamics of condensin during loop extrusion [PDF]
Nature CommunicationsCondensin plays an essential role in genome folding through its active DNA loop extrusion activity. Condensin contains a binding interface between its Ycg1 HEAT-repeat subunit and the Brn1 kleisin, together forming a “safety-belt” DNA-binding groove ...
Jinyu Chen +3 more
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Cohesin mediates DNA loop extrusion by a “swing and clamp” mechanism [PDF]
Cell, 2021 Structural maintenance of chromosomes (SMC) complexes organize genome topology in all kingdoms of life and have been proposed to perform this function by DNA loop extrusion. How this process works is unknown. Here, we have analyzed how loop extrusion is mediated by human cohesin-NIPBL complexes, which enable chromatin folding in interphase cells.
Daniel Canena +2 more
exaly +4 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 +6 more
doaj +2 more sources
Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae [PDF]
The EMBO JournalThe 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 +6 more
doaj +2 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 +6 more
doaj +2 more sources