Polymer physics of Hi-C data reveals linear viscoelasticity of the 3D genome
Chromatin fibers are biopolymers packed inside eukaryotic cells. Hi-C has unveiled the hierarchical division of chromosomes into 3D structural units, but its fixation limits chromatin's dynamic understanding. Meanwhile, live-cell imaging captures chromatin dynamics. To bridge the gap, we developed PHi-C, a computational tool interpreting Hi-C data as a dynamic 3D genome state. PHi-C constructs a polymer model from an input Hi-C matrix. Analyzing a segment's dynamics reveals that it follows the generalized Langevin equation. Then, the segment's linear-response function relates to mean-square displacement. Thus, we established a theoretical approach to unveil the linear viscoelasticity of the 3D genome itself from Hi-C data or stochastic motion of a labeled locus.