Integrative modeling of the genome structure and dynamics in fission yeast
- Soya Shinkai
- Toshinori Namba
- Takeshi Sugawara
- Soya Hagiwara
- Shuichi Onami
- Tokuko Haraguchi
- Yasushi Hiraoka
- Akinori Awazu
- Masaru Ueno
- Shin-ichi Tate
2026-09-08
Genome organization in the nucleus is highly structured and dynamic. Recent advances in genomic technology have enabled the measurement of genome-wide architecture and locus-specific motion, yielding contact maps and live-cell trajectories. However, these outcomes are derived from different modalities and are not directly comparable, with their quantitative integration being a key challenge. Here we establish a genome-wide live-cell imaging platform in fission yeast Schizosaccharomyces pombe , tracking 131 chromosomal loci, along with the spindle pole body (SPB) and nucleolus, to construct a quantitative map of locus dynamics. By integrating these dynamics with contact data through polymer modeling of Hi-C data, we build a physics-based “digital twin” of the S. pombe genome consistent with the spatiotemporal dynamics of interphase chromatin. We validate it against genome-wide mobility patterns and known architectural features, including centromere and telomere clustering. The model also identifies distinct dynamical regimes: centromere- and telomere-proximal loci relax within ∼ 150 s, whereas the remaining loci relax within ∼ 70 s. We measure semiperiodic dynamics of SPB motion, including a characteristic peak near 225 s and 1 / f fluctuations. We use the model with SPB-directed forcing to show how these low-frequency components propagate through the genome to drive genome-wide chromatin displacements. Together, this predictive physics-based modeling framework integrates genome structure and dynamics to reveal how nuclear mechanical driving forces shape chromosome motion, linking mechanically driven chromatin responses to genome maintenance and regulation.