Comparison of loop extrusion and diffusion capture as mitotic chromosome formation pathways in fission yeast

• Published in: Nucleic acids research Vol. 49; no. 3; pp. 1294 - 1312
• Main Authors: Gerguri, Tereza, Fu, Xiao, Kakui, Yasutaka, Khatri, Bhavin S, Barrington, Christopher, Bates, Paul A, Uhlmann, Frank
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 22-02-2021
• Subjects: Adenosine Triphosphatases - analysis; Chromatin - chemistry; Chromosomes, Fungal; Computational Biology; Computer Simulation; Diffusion; DNA-Binding Proteins - analysis; Mitosis - genetics; Models, Genetic; Models, Molecular; Multiprotein Complexes - analysis; Schizosaccharomyces - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkaa1270

Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (loop extrusion), or that they sequentially entrap two DNAs that come into proximity by Brownian motion (diffusion capture). To explore the implications of these two mechanisms, we perform biophysical simulations of a 3.76 Mb-long chromatin chain, the size of the long Schizosaccharomyces pombe chromosome I left arm. On it, the SMC complex condensin is modeled to perform loop extrusion or diffusion capture. We then compare computational to experimental observations of mitotic chromosome formation. Both loop extrusion and diffusion capture can result in native-like contact probability distributions. In addition, the diffusion capture model more readily recapitulates mitotic chromosome axis shortening and chromatin compaction. Diffusion capture can also explain why mitotic chromatin shows reduced, as well as more anisotropic, movements, features that lack support from loop extrusion. The condensin distribution within mitotic chromosomes, visualized by stochastic optical reconstruction microscopy (STORM), shows clustering predicted from diffusion capture. Our results inform the evaluation of current models of mitotic chromosome formation.