by the same author The Physics of Liquid Crystals Superconductivity of Metals and Alloys Scaling Concepts in Polymer. Scaling Concepts in Polymer Physics. P. G. de Gennes · Thomas A. Physics Today 33, 6, 51 (); cucurboldnegel.cf Free first page. false. The first stage of the physics of long, flexible chains was pioneered by eminent scientists such as Debye, Kuhn, Kramers, and Flory, who formulated the basic.
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Nov 30, Scaling Concepts in Polymer Physics. The first stage of the physics of long, flexible chains was pioneered by eminent scientists such as Debye. Scaling Concepts in Polymer Physics - De Gennes - Ebook download as PDF File .pdf) or read book online. cucurboldnegel.cf - Ebook download as PDF File .pdf) or read book online.
Taken together our results support a view whereby basic mechanism of polymer folding could play key functional roles in the regulation of the genome by controlling the spatial organisation of chromatin. Figure 4: Polymer physics captures the folding of the Sox9 locus.
Bottom: the SBS polymer model that best explain the Hi-C contact map of the Sox9 region has the shown different types of binding sites, as seen in the zoom different colors ; their abundance is represented as an histogram over the genomic sequence. The bar at the bottom highlights three main regional areas to help 3D visualization. Chromatin domains self-assemble hierarchically in higher-order structures, in approx. First, we considered a 6 Mbs sequence around the Sox9 gene chr, mm9 , an important genomic locus linked to severe congenital diseases 11 , including gene rich areas as well as gene deserts Fig.
To capture the details of Sox9, we generalized our polymer model to accommodate different types of binding sites colors and molecular binders Fig. With a Monte Carlo recursive optimization method Supplementary Materials , we estimated the minimal arrangement and different types of binding sites that best reproduces the 40 kb Hi-C map available in mESC-J1 cells 6.
Scaling concepts in polymer physics
We informed our polymer model with the obtained arrangement of binding sites and run full-scale Molecular Dynamics simulations to derive the ensemble of 3D conformations of the locus see Supplementary Materials and Methods. Figure 4a represents the histograms of the abundance of our inferred binding sites along the locus different types in different colors , ordered left-to-right according to the location of the domain center of mass.
Binding domains tend to overlap with the different TADs in the locus, but importantly they also overlap with each other producing higher-order interactions across TADs, i. A snapshot of a single typical configuration, in the closed state, is shown in Fig. The Sox9 locus is marked by many-body contacts that are exponentially more abundant than expected in a randomly folded conformation Fig.
Scaling Concepts in Polymer Physics 1979 - De Gennes
The self-assembly of the locus architecture from initial open states proceeds hierarchically, with early formed local domains folding into larger and larger 3D structures encompassing the entire locus Fig. The variety of information on Sox9 and its folding mechanisms that can be inferred from polymer physics extends well beyond the Hi-C pair-wise contact data used to infer the model.
To check the general validity of our approach, we applied our polymer models to a different locus, a 2 Mb wide region around the Bmp7 gene chr important in tissue development, where Hi-C data at 30 kb resolution are available in mESCC cells Starting from a 20 kb resolution 5C map in mESC-E14 cells 7 , we derived our polymer model describing the wild-type locus and after MD simulations we found a good agreement with 5C data Fig.
In the above calculation there are no adjustable parameters.
Such findings are in agreement with those of a similar interacting polymer model introduced for the Xist locus Summarizing, the binding domains identified in-silico by our model can describe the folding of Sox9 with high accuracy and predict the effects of genomic rearrangements based only on polymer physics.
Full size image Discussion We have discussed a polymer model of chromatin where 3D conformations are shaped by the interactions of binding domains with their cognate binding molecular factors, such as DNA-binding molecules.
Genome-wide, and loci specific chromatin contact data can be explained by classical scaling concepts of polymer physics over orders of magnitude in genomic separation, up to chromosomal scales, across mammalian cell types. Consistent with our SBS picture, a model has been recently proposed focused, in particular, on the role of CTFC binding sites and cohesin mediated interactions to explain folding of loci at short scales, in the 10— kb range 23 , Contrary to previous approaches, our model does not require a previous knowledge of the molecular factors responsible for folding e.
That supports the view that our model captures some of the key folding mechanisms of chromatin. By combining polymer models and Hi-C data, a quantitative scenario emerges of the large-scale features of chromatin architecture where chromatin folding is determined by a complex system of binding domains and molecular factors, regulated by general mechanisms of polymer physics.
How does the scaling for the polymer chain in the dissipative particle dynamics hold
As our polymer physics approach identifies the molecular determinants of folding and their mechanisms of action, it can help understanding the link between architecture and function, and the design of novel approaches to personalized diagnosis and treatment of human diseases. Materials and Methods A detailed description of the materials and methods is provided in the Supplementary Materials. All the details about the model and computational parameters, as well as on the analyses performed are reported in the Supplementary Materials and Methods.
Additional Information How to cite this article: Chiariello, A. Polymer physics of chromosome large-scale 3D organisation. Acta Polymerica Volume 32, Issue 5. Straube Search for more papers by this author. First published: May Tools Request permission Export citation Add to favorites Track citation.
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Share Give access Share full text access. Share full text access. Please review our Terms and Conditions of Use and check box below to share full-text version of article. No abstract is available for this article. Excluded volume interaction[ edit ] The ideal chain model assumes that polymer segments can overlap with each other as if the chain were a phantom chain.
In reality, two segments cannot occupy the same space at the same time. This interaction between segments is called the excluded volume interaction. The simplest formulation of excluded volume is the self-avoiding random walk, a random walk that cannot repeat its previous path.
A path of this walk of N steps in three dimensions represents a conformation of a polymer with excluded volume interaction. Because of the self-avoiding nature of this model, the number of possible conformations is significantly reduced. The radius of gyration is generally larger than that of the ideal chain.
Flexibility and reptation[ edit ] Whether a polymer is flexible or not depends on the scale of interest.The sections of this book summarize the properties of polymers and the models that were devised to explain those. Hoy and to ring polymers of tangent hard spheres for which the G. Chromatin structure: a repeating unit of histones and DNA.
Contrary to previous approaches, our model does not require a previous knowledge of the molecular factors responsible for folding e. Truskett, and P.
Grest, Macromolecules 40,  J. Maeshima, R. English ISBN Pc s only depends on the thermodynamics state of the system Figure S2.