Results 1 to 10 of about 10,514 (131)
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
doaj +6 more sources
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
doaj +6 more sources
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
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
Two CTCF motifs impede cohesin-mediated DNA loop extrusion
Molecular CellCohesin extrudes DNA into loops and is positioned along the genome by stalling at CTCF upon encountering its N-terminal region (NTR). The mechanism underlying this stalling, however, is unresolved. Using single-molecule assays that monitor DNA loop extrusion (LE) in the presence of NTR fragments, we identify two amino acid motifs, YDF and KTYQR, that ...
Cees Dekker +2 more
exaly +5 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
Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase. [PDF]
EMBO J, 2023 Abstract Genetic information is stored in linear DNA molecules, which are highly folded inside cells. DNA replication along the folded template path yields two sister chromatids that initially occupy the same nuclear region in an intertwined arrangement.
Batty P +6 more
europepmc +4 more sources
Theory and simulations of condensin mediated loop extrusion in DNA [PDF]
Nature Communications, 2021 How chromosomes, which are polymers with nearly billion base pairs, are packaged in the restricted nuclear volume is not well understood. Here, the authors combine polymer physics, nonequilibrium fluctuation theorem, and simulations to quantitatively ...
Ryota Takaki +3 more
doaj +5 more sources