Crowding-Activity Coupling Effect on Conformational Change of a Semi-Flexible Polymer

Cao, Xiuli; Zhang, Bingjie; Zhao, Nanrong

doi:10.3390/polym11061021

Cited by 14 publications

(6 citation statements)

References 52 publications

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“…Activity was independently shown to enhance the looping probability of chromatin segments [ 52 ]. Of note, there are hints that crowding may further promote blob formation in a crowder size- and concentration-dependent manner [ 53 ], and taking into account hydrodynamic interactions may result in even further shrinkage of polymers [ 54 ]. Interestingly, a simulation involving ensembles of active semiflexible polymers showed that the different polymers also get closer with increasing activity [ 38 ], suggesting that activity can enhance chromatin fiber density which may, in turn, promote blob formation.…”

Section: Discussionmentioning

confidence: 99%

Dynamics as a cause for the nanoscale organization of the genome

Barth

Fourel

Shaban

2020

Nucleus

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Chromatin 'blobs' were recently identified by live super-resolution imaging of labeled nucleosomes as pervasive but fleeting structural entities. However, the mechanisms leading to the formation of these blobs and their functional implications are unknown. We explore here whether causal relationships exist between parameters that characterize the chromatin blob dynamics and structure, by adapting a framework for spatio-temporal Granger-causality inference. Our analysis reveals that chromatin dynamics is a key determinant for both blob area and local density. Such causality, however, could be demonstrated only in 10-20% of the nucleus, suggesting that chromatin dynamics and structure at the nanometer scale are dominated by stochasticity. We show that the theory of active semiflexible polymers can be invoked to provide potential mechanisms leading to the organization of chromatin into blobs. Our results represent a first step toward elucidating the mechanisms that govern the dynamic and stochastic organization of chromatin in the cell nucleus.

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Section: Discussionmentioning

confidence: 99%

Dynamics as a cause for the nanoscale organization of the genome

Barth

Fourel

Shaban

2020

Nucleus

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“…Looping may be further stabilized by DNA bridging factors and/or SMC proteins at the loop bases 48 as well as a host of transcription factors operating as dimers. Of note, there are hints that crowding may further promote blob formation in a crowder size and concentration-dependent manner 49 , and taking into account hydrodynamic interactions can lead to even further shrinkage of polymers 50 .…”

Section: Discussionmentioning

confidence: 99%

Dynamics as a cause for the nanoscale organization of the genome

Barth

Fourel

Shaban

2020

Preprint

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13Chromatin 'blobs' were recently identified by live super-resolution imaging as pervasive, but transient and 14 dynamic structural entities consisting of a few associating nucleosomes. The origin and functional 15 implications of these blobs are, however, unknown. Following these findings, we explore whether causal 16 relationships exist between parameters characterizing the chromatin blob dynamics and structure, by 17 adapting a framework for spatio-temporal Granger-causality inference. Our analysis reveals that chromatin 18 dynamics is a key determinant of both blob area and local density. However, such causality can only be 19 demonstrated in small areas (10 -20%) of the nucleus, highlighting that chromatin dynamics and structure 20 at the nanoscale is dominated by stochasticity. Pixels for which the inter-blob distance can be effectively 21 demonstrated to depend on chromatin dynamics appears as clump in the nucleus, and display both a higher 22 blob density and higher local dynamics as compared with the rest of the nucleus. Furthermore, we show 23 that the theory of active semiflexible polymers can be invoked to provide potential mechanisms leading to 24 the organization of chromatin into blobs. Based on active motion-inducing effectors, this framework 25 qualitatively recapitulates experimental observations and predicts that chromatin blobs might be formed 26 stochastically by a collapse of local polymer segments consisting of a few nucleosomes. Our results 27 represent a first step towards elucidating the mechanisms that govern the dynamic and stochastic 28 organization of chromatin in a cell nucleus. 29 30 Keywords 31 Genome organization, chromatin dynamics, 4D genome, Deep-PALM, Granger-causality, active polymers 32 14,15 , thereby quantifying simultaneously the dynamics, size and distance between chromatin blobs in space 55 and time. These results indicated a strong relationship between the flow magnitude of blobs (i.e. their 56 dynamics) and their local density. Notably, the blob dynamics appear enhanced in regions of high blob 57 density and conversely isolated blobs in chromatin-void regions appear less mobile. 58This and other studies resulted in complex high-dimensional datasets, which reflect stochastic and 59 heterogeneous quantities characterizing chromatin in space and time. In order to allow inferences of 60Note that the second sum runs from 2 to in the base and the full model and the contribution of the cause-131 variable # is written explicitly in the latter. Granger-causality from # to is present if the predictions U of 132 the full model (including the past value of # ) are significantly better than those of the base model. 133 411 de Lyon for providing computational resources and further thank the Institut Rhônalpin des Systèmes 412 Complexe IXXI for supporting us. 413 414 Declaration of interests: The authors declare no competing financial interest. 415 416

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“…The phenomenology exhibited by active polymers is heterogeneous, ranging from translational [94,95] to reptation motion [88,89], swelling [52,53,96], looping [55], swirling [97], or shrinkage [98,99], according to the different parameters characterizing the active polymer model scrutinized.…”

Section: Introductionmentioning

confidence: 99%

Diffusion of an Active Particle Bound to a Generalized Elastic Model: Fractional Langevin Equation

Taloni

2024

Fractal Fract

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We investigate the influence of a self-propelling, out-of-equilibrium active particle on generalized elastic systems, including flexible and semi-flexible polymers, fluid membranes, and fluctuating interfaces, while accounting for long-ranged hydrodynamic effects. We derive the fractional Langevin equation governing the dynamics of the active particle, as well as that of any other passive particle (or probe) bound to the elastic system. This equation analytically demonstrates how the active particle dynamics is influenced by the interplay of both the non-equilibrium force and of the viscoelastic environment. Our study explores the diffusional behavior emerging for both the active particle and a distant probe. The active particle undergoes three different surprising and counter-intuitive regimes identified by the distinct dynamical time-scales: a pseudo-ballistic initial phase, a drastic decrease in the mobility, and an asymptotic subdiffusive regime.

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Crowding-Activity Coupling Effect on Conformational Change of a Semi-Flexible Polymer

Cited by 14 publications

References 52 publications

Dynamics as a cause for the nanoscale organization of the genome

Dynamics as a cause for the nanoscale organization of the genome

Dynamics as a cause for the nanoscale organization of the genome

Diffusion of an Active Particle Bound to a Generalized Elastic Model: Fractional Langevin Equation

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