Principles of chromosome folding. I. Schemating cartoon of the 10nm-fiber structure resulting from DNA wrapping around the histone complex. Chromatin folding beyond the 10nm-fiber up to the scale of the whole chromosome remains controversial. Reproduced with permission from Ref. [13].

Contexts in source publication

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... eukaryotes, every ≈ 200 basepairs of the long DNA filament of each chromosome wrap around the histone complex [14], by creating a necklace-like linear sequence of nucleosomes, commonly known as the 10nm chromatin fiber, see Fig. 1. The present understanding of chromosome organization on spatial scales beyond the 10nm-fiber (in particular with respect to the existence of the * Electronic address: alessandra.merlotti2@unibo.it † Electronic address: anrosa@sissa.it ‡ Electronic address: daniel.remondini@unibo.it "elusive" 30nm-fiber [13,[15][16][17][18][19]) ...

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... its level of activity (proportional to gene density) and coupled to a specific, effective temperature. Thus, a higher effective temperature means a larger activity. With the addition of a given amount of permanent loops between chromatin fibers, this models shows that chromosomes tend to be partitioned into clusters of different temperatures, see Fig. 10(A). A rigorous physical explanation of this phenomenon was provided in Ref. [67] and later confirmed in Ref. [68] by means of systematic computer simulations: even small temperature gaps induce phase separation in systems of colloids or polymer chains. In spite of the intrinsic out-of-equilibrium nature of the system, it can nonetheless ...

Context 3

... it has been pointed out that active loop extrusion may be universally responsible for chromosome A B segregation during mitosis [65,69] and for chromosome compartmentalization into TADs [70]. Specific proteins called "condensins" assemble into complexes and bond together spatially close loci on the chromatin fiber, see Fig. 10(B). Then, the chromatin filament fixed by the condensins starts to be effectively extruded when the complex moves into opposite directions along the fiber. When two condensins collide into each other the translocation process stops. Moreover, with the addition of topoisomerase-II the loop extrusion mechanism is able to simplify chromosome ...

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... two related studies, Di Stefano and coworkers showed that by just enforcing colocalization of coexpressed genes in a polymer model for human chromosome 19 first [73] and then for the entire human genome [77] without major additional constraints, the resulting conformations (see the example shown in Fig. 11(A)) appear compatible with chromatin classification in A/B sub-domains and with the non-random locations of chromosome territories correlated to gene content (see Sec. ...

Context 5

... order to exploit the nature of TADs and of chromatin-chromatin interactions measured within a single TAD, Giorgetti et al. [74] introduced a computational polymer model (see. Fig. 11(B)) where sequencedependent monomer-monomer interactions were obtained upon maximizing the agreement between contact frequencies predicted by the model and the ones measured by ordinary conformation capture techniques. The model, targeted onto a specific region of mouse chromosome X, reveals that the structure of a single TAD measured by ...

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... to export the derived forcefield to describe the whole diploid nucleus. Specifically, polymer loci were classified into chromatin types (as in some of the models considered in Sec. III A 2) and the energy parameters describing the interactions between them were trained by using HiC data for human chromosome 10 from a specific cell line, see Fig. 11(C). The model was then used to predict an ensemble of possible structures for the other chromosomes not used for the training of the energy function: interestingly, the ob-tained maps match well the ones obtained by HiC and the simulated chromosome structures recapitulate other notable features of interphase chromatin, like microphase ...

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... chromatin to remain at the periphery of its territory. Finally, Bianco et al. refined the SBS model discussed in Sec. III A 2, by introducing the Polymer-based Recursive Statistical Inference Method (PRISMR) [76]: PRISMR works by minimizing a cost function whichagain -takes into account the predicted vs. the measured HiC contact frequencies, see Fig. 11(D). The "optimal" polymer model is then exported to construct chromosome conformations for a number of so-called structural variants of chromosomes which are known to produce anomalous chromatin folding and diseases. The protocol is then shown to be very efficient in detecting mutated chromatin-chromatin interactions which are involved in ...

Context 8

... eukaryotes, every ≈ 200 basepairs of the long DNA filament of each chromosome wrap around the histone complex [14], by creating a necklace-like linear sequence of nucleosomes, commonly known as the 10nm chromatin fiber, see Fig. 1. The present understanding of chromosome organization on spatial scales beyond the 10nm-fiber (in particular with respect to the existence of the * Electronic address: alessandra.merlotti2@unibo.it † Electronic address: anrosa@sissa.it ‡ Electronic address: daniel.remondini@unibo.it "elusive" 30nm-fiber [13,[15][16][17][18][19]) ...

Context 9

... its level of activity (proportional to gene density) and coupled to a specific, effective temperature. Thus, a higher effective temperature means a larger activity. With the addition of a given amount of permanent loops between chromatin fibers, this models shows that chromosomes tend to be partitioned into clusters of different temperatures, see Fig. 10(A). A rigorous physical explanation of this phenomenon was provided in Ref. [67] and later confirmed in Ref. [68] by means of systematic computer simulations: even small temperature gaps induce phase separation in systems of colloids or polymer chains. In spite of the intrinsic out-of-equilibrium nature of the system, it can nonetheless ...

Context 10

... it has been pointed out that active loop extrusion may be universally responsible for chromosome A B segregation during mitosis [65,69] and for chromosome compartmentalization into TADs [70]. Specific proteins called "condensins" assemble into complexes and bond together spatially close loci on the chromatin fiber, see Fig. 10(B). Then, the chromatin filament fixed by the condensins starts to be effectively extruded when the complex moves into opposite directions along the fiber. When two condensins collide into each other the translocation process stops. Moreover, with the addition of topoisomerase-II the loop extrusion mechanism is able to simplify chromosome ...

Context 11

... two related studies, Di Stefano and coworkers showed that by just enforcing colocalization of coexpressed genes in a polymer model for human chromosome 19 first [73] and then for the entire human genome [77] without major additional constraints, the resulting conformations (see the example shown in Fig. 11(A)) appear compatible with chromatin classification in A/B sub-domains and with the non-random locations of chromosome territories correlated to gene content (see Sec. ...

Context 12

... order to exploit the nature of TADs and of chromatin-chromatin interactions measured within a single TAD, Giorgetti et al. [74] introduced a computational polymer model (see. Fig. 11(B)) where sequencedependent monomer-monomer interactions were obtained upon maximizing the agreement between contact frequencies predicted by the model and the ones measured by ordinary conformation capture techniques. The model, targeted onto a specific region of mouse chromosome X, reveals that the structure of a single TAD measured by ...

Context 13

... to export the derived forcefield to describe the whole diploid nucleus. Specifically, polymer loci were classified into chromatin types (as in some of the models considered in Sec. III A 2) and the energy parameters describing the interactions between them were trained by using HiC data for human chromosome 10 from a specific cell line, see Fig. 11(C). The model was then used to predict an ensemble of possible structures for the other chromosomes not used for the training of the energy function: interestingly, the ob-tained maps match well the ones obtained by HiC and the simulated chromosome structures recapitulate other notable features of interphase chromatin, like microphase ...

Context 14

... chromatin to remain at the periphery of its territory. Finally, Bianco et al. refined the SBS model discussed in Sec. III A 2, by introducing the Polymer-based Recursive Statistical Inference Method (PRISMR) [76]: PRISMR works by minimizing a cost function whichagain -takes into account the predicted vs. the measured HiC contact frequencies, see Fig. 11(D). The "optimal" polymer model is then exported to construct chromosome conformations for a number of so-called structural variants of chromosomes which are known to produce anomalous chromatin folding and diseases. The protocol is then shown to be very efficient in detecting mutated chromatin-chromatin interactions which are involved in ...