Crumpled Globule Model of the Three-Dimensional Structure of DNA

Grosberg, Alexander Y.; Rabin, Yitzhak; Havlin, Shlomo; Neer, Ada

doi:10.1209/0295-5075/23/5/012

Cited by 313 publications

(314 citation statements)

References 17 publications

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“…We have shown that loop structures lead to a strong effective repulsion and for a first time quantitatively analyzed the strength of the resulting interactions. Surely, the formation of multiple loops in the system of chromatin which has been proposed in several models 6,20,45,46 induces even stronger effects and therefore might be responsible for maintaining the segregated state of chromosomes found in several experiments 9 . Indeed, studies of looping polymers have revealed an effect on the abundance of inter-chromosomal contacts 12,13 .…”

Section: Discussionmentioning

confidence: 94%

Topological interactions between ring polymers: Implications for chromatin loops

Bohn

Heermann²

2010

The Journal of Chemical Physics

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Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The detailed topological and entropic forces between loops still remain elusive. Here, we quantitatively determine the potential of mean force between the centers of mass of two ring polymers, i.e. loops. We find that the transition from a linear to a ring polymer induces a strong increase in the entropic repulsion between these two polymers. On top, topological interactions such as the non-catenation constraint further reduce the number of accessible conformations of close-by ring polymers by about 50%, resulting in an additional effective repulsion. Furthermore, the transition from linear to ring polymers displays changes in the conformational and structural properties of the system. In fact, ring polymers adopt a markedly more ordered and aligned state than linear ones. The forces and accompanying changes in shape and alignment between ring polymers suggest an important regulatory function of such a topology in biopolymers. We conjecture that dynamic loop formation in chromatin might act as a versatile control mechanism regulating and maintaining different local states of compaction and order.

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Section: Discussionmentioning

confidence: 94%

Topological interactions between ring polymers: Implications for chromatin loops

Bohn

Heermann²

2010

The Journal of Chemical Physics

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“…The static properties of rings in solution have been studied for some decades, and it is nowadays thought that rings assume crumpled conformations characterized by a scaling law for their gyration radius R g ≈ M ν with ν ' 1=3 in the limit of rings with large polymerization M (11,(28)(29)(30)(31). On the other hand, they also have been found to maintain numerous contacts with their neighbors.…”

Section: Rings In Solution Assume Crumpled But Largely Overlapping Comentioning

confidence: 99%

A topologically driven glass in ring polymers

Michieletto

Turner

2016

Proc. Natl. Acad. Sci. U.S.A.

104

184

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The static and dynamic properties of ring polymers in concentrated solutions remains one of the last deep unsolved questions in polymer physics. At the same time, the nature of the glass transition in polymeric systems is also not well understood. In this work, we study a novel glass transition in systems made of circular polymers by exploiting the topological constraints that are conjectured to populate concentrated solutions of rings. We show that such rings strongly interpenetrate through one another, generating an extensive network of topological interactions that dramatically affects their dynamics. We show that a kinetically arrested state can be induced by randomly pinning a small fraction of the rings. This occurs well above the classical glass transition temperature at which microscopic mobility is lost. Our work both demonstrates the existence of long-lived inter-ring penetrations and realizes a novel, topologically induced, glass transition.glass transition | ring polymers | topology | topological glass | molecular dynamics T he physics of ring polymers remains one of the last big mysteries in polymer physics (1). Concentrated systems of ring polymers have been observed, in both simulations and experiments, to display unique features that are not easily reconciled with the standard reptation theory of linear polymers (2-6). The main reason for this is that ring polymers do not possess free terminal segments, or ends, essential for end-directed curvilinear diffusion. In contrast, ring polymers possess a closed contour, which leads to markedly different relaxation and diffusion mechanisms. Recently, there has been much improvement in the production of purified systems of rings (6-8), with the consequent result that more and more experimental puzzling evidence requires a deeper understanding of their motion in concentrated solutions and melts from a theoretical point of view.Recently, it has been conjectured that ring polymers assume crumpled, segregated conformations in concentrated solution or the melt (5). On the other hand, numerical and experimental findings (5, 6) suggest that rings exhibit strong intercoil correlations, which have proved difficult to address in simplified theoretical models (9-12). Because of this, there have been many recent attempts to rigorously characterize these interchains' interactions (13-16), although a precise definition and unambiguous identification of these "threadings" in concentrated solutions of rings remains elusive. The primary reason for this is that the rings are assumed to remain strictly topologically unlinked from one another throughout if synthesized in this state.In the case of concentrated solutions of rings embedded in a gel, a method to identify these interpenetrating threadings has recently been proposed (13). Here it was shown that the number of threadings scales extensively in the polymer length (or mass) and can therefore be numerous for long rings, creating a hierarchical sequence of constraints that can span the entire system. It has also been con...

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“…First, we have performed systematic genome-wide studies of LRC in complete genomes over scale ranges which were as largely extended as possible (up to thousands of base-pairs) and this in an overview of organisms belonging to the three kingdoms, eukaryotes, eubacteria, archaebacteria, as well as in DNA and RNA viral genomes. Second, we have analyzed these genomes in a new perspective: our aim was to evidence LRC related to structural properties of the DNA molecule [139] involved in the processes of chromatin packaging associated to the various mechanisms of gene expression, and during the successive stages of the cell cycle. This implied not to search genome sequences only for correlations between 'one-character' motifs (DNA text), but rather between DNA segments or 'words' known to be associated to the structural properties of the DNA double helix.…”

Section: A Small-scale Lrc Regime Is Observed In Eukaryotic Sequencesmentioning

confidence: 99%

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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Abstract. Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called 'wavelet transform microscope' reveals a characteristic scale of 100 − 200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime ( 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called waveletbased multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1,2].

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Crumpled Globule Model of the Three-Dimensional Structure of DNA

Cited by 313 publications

References 17 publications

Topological interactions between ring polymers: Implications for chromatin loops

Topological interactions between ring polymers: Implications for chromatin loops

A topologically driven glass in ring polymers

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

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