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

Abstract

The 1-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in 3-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 micro-scale thermal medium remains unclear. Microrheology is a way to measure dynamic viscoelastic properties coupling between thermal microenvironment and mechanical response. Here, we propose, to our knowledge, a new microrheology for Hi-C data to analyze the compliance property as a barometer of rigidness and flexibility of genomic regions along with the time evolution. Our method allows conversion of a Hi-C matrix into the spectrum of the rheological property along the genomic coordinate of a single chromosome. To demonstrate 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 region. The spectrum clearly shows the rheological property of the dynamic chromatin domain formations at an individual time scale. Furthermore, we characterized the appearance of synchronous and liquid-like inter-compartment interactions in differentiated cells. Together, our microrheology provides physical insights revealing the dynamic 3D genome organization from Hi-C data.\n\nSIGNIFICANCEGenomic DNA is hierarchically packed inside the eukaryotic cell nucleus, and the genome organization in 3D contributes to proper genome functions at the multiscale chromatin domains. Although thermal fluctuations inevitably drive movements of the genome molecules in the micro-scale cell environment, there is no method, as yet, to quantify such dynamic 3D genome organization of hierarchical and structural chromatin units. Here, we describe a method to calculate rheological properties as barometers of flexibility and liquid-like behavior of genomic regions. We show that biologically relevant boundaries between chromatin domains are more rigid than the inside at a particular time scale. Our method allows interpretation of static and population-averaged genome conformation data as dynamic and hierarchical 3D genome picture.