2020
DOI: 10.1016/j.bpj.2020.02.020
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Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization

Abstract: The one-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in a three-dimensional (3D) space. Genome-wide chromosome conformation capture (Hi-C) methods have uncovered the 3D genome organization and revealed multiscale chromatin domains of compartments and topologically associating domains (TADs). Moreover, single-nucleosome live-cell imaging experiments have revealed the dynamic organization of chromatin domains caused by stochastic thermal fluctua… Show more

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Cited by 19 publications
(22 citation statements)
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“…In our polymer modeling system, the interaction matrix also allows us to create simulations of 4D polymer dynamics featuring stochastic thermal fluctuations. With these simulations, we can conduct conformational sampling, calculate mean-squared displacement (MSD) curves of modeled monomers, and depict microrheology spectra [15] , [16] ( Fig. 2 B).…”
Section: Polymer Modeling Of Hi-c Datamentioning
confidence: 99%
See 3 more Smart Citations
“…In our polymer modeling system, the interaction matrix also allows us to create simulations of 4D polymer dynamics featuring stochastic thermal fluctuations. With these simulations, we can conduct conformational sampling, calculate mean-squared displacement (MSD) curves of modeled monomers, and depict microrheology spectra [15] , [16] ( Fig. 2 B).…”
Section: Polymer Modeling Of Hi-c Datamentioning
confidence: 99%
“…Furthermore, we can sample many polymer conformations in thermal equilibrium and quantitatively analyze the structural information such as the gyration radius. Moreover, recently, we developed a method, microrheology for Hi-C data, that can analyze the dynamic rheology property as a measure of the rigidity and flexibility of genomic regions along with the time evolution [16] . We can obtain a microrheology spectrum using the microrheology transformation formula [41] of the MSD curves derived from the matrix .…”
Section: Polymer Modeling Of Hi-c Datamentioning
confidence: 99%
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“…A perspective by Moller and de Pablo describes various approaches to multiscale chromatin modeling (12). In addition, many novel algorithms are described for modeling the biophysical properties of nucleosomes associated with cancer cells (13), tracking beads in singlemolecule biophysical experiments (14), computing interaction strengths among chromatin units compatible with measured values in chromosome conformation experiments (15), analyzing the spatial arrangement of tRNA genes in budding yeast to help interpret experimental discrepancies (16), simulating and visualizing genome elements from their constituent DNA components (17), analyzing dynamic 3D genome organization inferred from Hi-C data (18), simulating sequence-dependent DNA mechanics involved in nucleosome unspooling (19), and capturing the diffusion of DNA binding species (20).…”
Section: Multiscale Genome Organization: Dazzling Subject and Inventimentioning
confidence: 99%