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
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Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries [PDF]
Nature Communications, 2023 Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered ...
Li-Hsin Chang +14 more
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CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igκ repertoire [PDF]
Nature CommunicationsDynamic genome folding is important for V(D)J recombination at the immunoglobulin kappa (Igκ) locus, which recombines Jκ and Vκ gene segments across a 3.2 Mb region in both deletional and inversional orientations.
Emma L. Bush +10 more
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Biology, 2021 We propose a model for cohesin-mediated loop extrusion, where the loop extrusion is driven entropically by the energy difference between supercoiled and torsionally relaxed chromatin fibers.
Renáta Rusková, Dušan Račko
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Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion [PDF]
Genome BiologyBackground Inhomogeneous patterns of chromatin-chromatin contacts within 10–100-kb-sized regions of the genome are a generic feature of chromatin spatial organization.
Tianyu Yuan +5 more
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Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion [PDF]
eLifeTwo different models have been proposed to explain how the endpoints of chromatin looped domains (‘TADs’) in eukaryotic chromosomes are determined.
Xinyang Bing +7 more
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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
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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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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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Loop Extrusion Machinery Impairments in Models and Disease [PDF]
CellsStructural maintenance of chromosomes (SMC) complexes play a crucial role in organizing the three-dimensional structure of chromatin, facilitating key processes such as gene regulation, DNA repair, and chromosome segregation.
Anastasiya Ryzhkova +3 more
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