Shinkai, S.*, Nakagawa, M., Sugawara, T., Togashi, Y., Ochiai, H., Nakato, R., Onami, S.* (2020) PHi-C: deciphering Hi-C data into polymer dynamics. NAR Genomics and Bioinformatics 2(2), lqaa020. Full Text
(Left) A 4D simulation with intra- and interdomain interactions. (Right) The corresponding 3D distance map.
(Left) A 4D simulation during mitotic chromosome formation of chromosome 7 in chicken DT-40 cells. (Right) The optimized contact matrix.
Spinning 3D structures at G2 (0 min), 5, 15, 30 and 60 min in the 4D simulation (Supplementary Video S4).
Shinkai, S.*, Sugawara, T., Miura, H., Hiratani, I., Onami, S.* (2020) Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization. Biophysical Journal 118, 2220–2228. Full Text
A PHi-C simulation for chromosome 6 in mouse embryonic stem cells. Pink and blue dots represent the genomic positions at the TAD insides and boundaries.
Spinning 3D structure of cumulative dots of the peaks and troughs in the simulation (Supplementary Video S1).
Time evolution of the Cole-Cole plots between the normalized storage and loss compliances within chromosome 6 in mouse embryonic stem (Left; blue), neural progenitor (Middle; green), and cortical neuron (Right; red) cells.
A PHi-C simulation for chromosome 6 in mouse embryonic stem cells within time, which is identical to the dynamics in Supplementary Video S1. According to an eigenvector profile of a Hi-C matrix, compartment regions with positive and negative eigenvectors are labeled by green and red colors, respectively.
Spinning green- and red-labeled 3D compartments (Upper) with positive and negative eigenvectors, respectively, for chromosome 6 in mouse embryonic stem cells and the labeled cumulative dots (Lower) in the PHi-C simulation for time intervals 10 (Left), 100 (Middle), and 1000 (Right).
A PHi-C simulation for chromosome 6 in mouse neural progenitor cells. According to an eigenvector profile of a Hi-C matrix, compartment regions with positive and negative eigenvectors are labeled by green and red colors, respectively.
Spinning green- and red-labeled 3D compartments (Upper) with positive and negative eigenvectors, respectively, for chromosome 6 in mouse neural progenitor cells and the labeled cumulative dots (Lower) in the PHi-C simulation for time intervals 10 (Left), 100 (Middle), and 1000 (Right).
A PHi-C simulation for chromosome 6 in mouse cortical neuron cells.
Spinning green- and red-labeled 3D compartments (Upper) with positive and negative eigenvectors, respectively, for chromosome 6 in mouse cortical neuron cells and the labeled cumulative dots (Lower) in the PHi-C simulation for time intervals 10 (Left), 100 (Middle), and 1000 (Right).