Loop extrusion: theory meets single-molecule experiments.
Sign Up to like & getrecommendations! Published in 2020 at "Current opinion in cell biology"
DOI: 10.1016/j.ceb.2020.04.011
Abstract: Chromosomes are organized as chromatin loops that promote segregation, enhancer-promoter interactions, and other genomic functions. Loops were hypothesized to form by 'loop extrusion,' by which structural maintenance of chromosomes (SMC) complexes, such as condensin and… read more here.
Keywords: single molecule; loop extrusion; extrusion theory; extrusion ... See more keywords
How DNA loop extrusion mediated by cohesin enables V(D)J recombination.
Sign Up to like & getrecommendations! Published in 2021 at "Current opinion in cell biology"
DOI: 10.1016/j.ceb.2020.11.007
Abstract: 'Structural maintenance of chromosomes' (SMC) complexes are required for the folding of genomic DNA into loops. Theoretical considerations and single-molecule experiments performed with the SMC complexes cohesin and condensin indicate that DNA folding occurs via… read more here.
Keywords: dna loop; extrusion mediated; loop extrusion; dna ... See more keywords
SMC complexes: Lifting the lid on loop extrusion.
Sign Up to like & getrecommendations! Published in 2022 at "Current opinion in cell biology"
DOI: 10.1016/j.ceb.2021.12.003
Abstract: Loop extrusion has emerged as a prominent hypothesis for how SMC complexes shape chromosomes - single molecule in vitro observations have yielded fascinating images of this process. When not extruding loops, SMC complexes are known to… read more here.
Keywords: loop extrusion; smc complexes; extrusion; biology ... See more keywords
Dilution of contact frequency between superenhancers by loop extrusion at interfaces.
Sign Up to like & getrecommendations! Published in 2019 at "Soft matter"
DOI: 10.1039/c9sm01454c
Abstract: The loop extrusion theory predicts that cohesin acts as a molecular motor that extrudes chromatin fibers to produce loops. Hi-C experiments have detected relatively high contact frequencies between superenhancers. These probably result from the fact… read more here.
Keywords: extrusion; frequency superenhancers; contact frequency; loop extrusion ... See more keywords
Chromosome compaction and chromatin stiffness enhance diffusive loop extrusion by slip-link proteins.
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DOI: 10.1039/c9sm01875a
Abstract: We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to explain the… read more here.
Keywords: diffusive loop; chromatin; loop extrusion; slip link ... See more keywords
Cornelia de Lange syndrome mutations in NIPBL can impair cohesin-mediated DNA loop extrusion
Sign Up to like & getrecommendations! Published in 2022 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2201029119
Abstract: Cornelia de Lange syndrome (CdLS) is a developmental multisystem disorder frequently associated with mutations in NIPBL. CdLS is thought to arise from developmental gene regulation defects, but how NIPBL mutations cause these is unknown. Here… read more here.
Keywords: mutations nipbl; lange syndrome; dna loop; extrusion ... See more keywords
Theory of chromatin organization maintained by active loop extrusion.
Sign Up to like & getrecommendations! Published in 2023 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2222078120
Abstract: The active loop extrusion hypothesis proposes that chromatin threads through the cohesin protein complex into progressively larger loops until reaching specific boundary elements. We build upon this hypothesis and develop an analytical theory for active… read more here.
Keywords: loop extrusion; chromatin organization; active loop;
Regulation of loop extrusion on the interphase genome
Sign Up to like & getrecommendations! Published in 2023 at "Critical Reviews in Biochemistry and Molecular Biology"
DOI: 10.1080/10409238.2023.2182273
Abstract: Abstract In the human cell nucleus, dynamically organized chromatin is the substrate for gene regulation, DNA replication, and repair. A central mechanism of DNA loop formation is an ATPase motor cohesin-mediated loop extrusion. The cohesin… read more here.
Keywords: extrusion interphase; regulation loop; regulation; loop extrusion ... See more keywords
Preprint Highlight: Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms
Sign Up to like & getrecommendations! Published in 2023 at "Molecular Biology of the Cell"
DOI: 10.1091/mbc.p23-03-0010
Abstract: Cohesins organize chromatin within the nucleus by promoting loop extrusion via cis contacts on chromatin and sister chromatid cohesion via trans contacts between chromatids. Whether cohesins employ a distinct mechanism for these two functions is… read more here.
Keywords: extrusion; sister chromatid; chromatid cohesion; loop extrusion ... See more keywords
3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1101/2022.04.15.488456
Abstract: Motivation Recent studies suggest that the loop extrusion activity of Structural Maintenance of Chromosomes complexes is central to proper organization of genomes in vivo. Polymer physics-based modeling of chromosome structure has been instrumental to assess… read more here.
Keywords: simulation framework; chromatin loop; loop extrusion;
Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks
Sign Up to like & getrecommendations! Published in 2022 at "Science Advances"
DOI: 10.1126/sciadv.abn7063
Abstract: Genome function depends on regulated chromosome folding, and loop extrusion by the protein complex cohesin is essential for this multilayered organization. The chromosomal positioning of cohesin is controlled by transcription, and the complex also localizes… read more here.
Keywords: transcription; chromosome; replication; loop extrusion ... See more keywords