Motorized chain models of the ideal chromosome

• 成果类型: Article
• 署名作者: Cao, Zhiyu; Wolynes, Peter G.
• 署名单位: Rice University; Chinese Academy of Sciences; University of Science & Technology of China, CAS; Rice University; Rice University
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-9529
• DOI: 10.1073/pnas.2407077121
• 发表日期: 2024-07-09
• 关键词: dna loop extrusion; chromatin-structure; polymer molecule; in-vivo; cohesin; ORGANIZATION; principles; DYNAMICS; genome; architecture

摘要

An array of motor proteins consumes chemical energy in setting up the architectures of chromosomes. Here, we explore how the structure of ideal polymer chains is influenced by two classes of motors. The first class which we call swimming motors acts to propel the chromatin fiber through three-dimensional space. They represent a caricature of motors such as RNA polymerases. Previously, they have often been described by adding a persistent flow onto Brownian diffusion of the chain. The second class of motors, which we call grappling motors caricatures the loop extrusion processes in which segments of chromatin fibers some distance apart are brought together. We analyze these models using a self-consistent variational phonon approximation to a many-body Master equation incorporating motor activities. We show that whether the swimming motors lead to contraction or expansion depends on the susceptibility of the motors, that is, how their activity depends on the forces they must exert. Grappling motors in contrast to swimming motors lead to long-ranged correlations that resemble those first suggested for fractal globules and that are consistent with the effective interactions inferred by energy landscape analyses of Hi-C data on the interphase chromosome.