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Biophys J. 2020 Mar 3. pii: S0006-3495(20)30185-5. doi: 10.1016/j.bpj.2020.02.020. [Epub ahead of print]

Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization.

Author information

1
Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan. Electronic address: soya.shinkai@riken.jp.
2
Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
3
Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
4
Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan. Electronic address: sonami@riken.jp.

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 fluctuations. However, the mechanism underlying the dynamic regulation of such hierarchical and structural chromatin units within the microscale thermal medium remains unclear. Microrheology is a way to measure dynamic viscoelastic properties coupling between thermal microenvironment and mechanical response. Here, we propose a new, to our knowledge, microrheology for Hi-C data to analyze the dynamic compliance property as a measure of rigidness and flexibility of genomic regions along with the time evolution. Our method allows the conversion of an Hi-C matrix into the spectrum of the dynamic rheological property along the genomic coordinate of a single chromosome. To demonstrate the power of the technique, we analyzed Hi-C data during the neural differentiation of mouse embryonic stem cells. We found that TAD boundaries behave as more rigid nodes than the intra-TAD regions. The spectrum clearly shows the dynamic viscoelasticity of chromatin domain formation at different timescales. Furthermore, we characterized the appearance of synchronous and liquid-like intercompartment interactions in differentiated cells. Together, our microrheology data derived from Hi-C data provide physical insights into the dynamics of the 3D genome organization.

PMID:
32191860
DOI:
10.1016/j.bpj.2020.02.020
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