Integrative modeling of the genome structure and dynamics in fission yeast.

Authors

Soya Shinkai, Toshinori Namba, Takeshi Sugawara, Soya Hagiwara, Shuichi Onami, Tokuko Haraguchi, Yasushi Hiraoka, Akinori Awazu, Masaru Ueno, Shin-Ichi Tate

Published in

Proceedings of the National Academy of Sciences of the United States of America. Volume 123. Issue 37. Pages e2612002123. Sep 15, 2026. Epub Sep 08, 2026.

Abstract

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 [Formula: see text]150 s, whereas the remaining loci relax within [Formula: see text]70 s. We measure semiperiodic dynamics of SPB motion, including a characteristic peak near 225 s and [Formula: see text] 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.

PMID:
42709822
Bibliographic data and abstract were imported from PubMed on 09 Sep 2026.

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