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pro vyhledávání: '"Bonato, Andrea"'
Autor:
Bonato, Andrea, Corbett, Dom, Kitaev, Sergey, Marenduzzo, Davide, Morozov, Alexander, Orlandini, Enzo
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors and RNA po
Externí odkaz:
http://arxiv.org/abs/2312.12159
Autor:
Bonato, Andrea, Corbett, Dom, Kitaev, Sergey, Marenduzzo, Davide, Morozov, Alexander, Orlandini, Enzo
Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop networks, bo
Externí odkaz:
http://arxiv.org/abs/2312.12154
DNA loop extrusion is arguably one of the most important players in genome organization. The precise mechanism by which loop extruding factors (LEFs) work is still unresolved and much debated. One of the major open questions in this field is how do L
Externí odkaz:
http://arxiv.org/abs/2309.08371
Autor:
Bonato, Andrea <1980>
Citokines are proteins produced by several cell types and secreted in response to various stimuli. These molecules are able to modify the behaviour of other cells inducing activities like growth, differentiation and apoptosis. In the last years, vete
Externí odkaz:
http://amsdottorato.unibo.it/738/
Autor:
Bonato, Andrea, Michieletto, Davide
Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations showing that
Externí odkaz:
http://arxiv.org/abs/2111.00332
Topological entanglements are abundant, and often detrimental, in polymeric systems in biology and materials science. Here we theoretically investigate the topological simplification of knots by diffusing slip-links (SLs), which may represent biologi
Externí odkaz:
http://arxiv.org/abs/2010.16205
Chromosome Compaction and Chromatin Stiffness Enhance Diffusive Loop Extrusion by Slip-Link Proteins
Publikováno v:
Soft Matter, 2020,16, 2406-2414
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 th
Externí odkaz:
http://arxiv.org/abs/1909.07108
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