Description
Chromatin, in which genetic information in a eukaryotic cell is stored, is a long polymer-like composite of DNA and proteins densely packed in the nucleus. It is now recognized that physical spacing of chromatin is critical in regulating bio-chemical and transcriptional abilities of genes, and proper functionality depends on the nonrandom organization of chromatin. Meanwhile, in a living cell, other subnuclear molecules, like polymerases and topoisomerases, act to facilitate cellular functions; such actions of subnuclear molecules may bring mechanical perturbations on chromatin, which can affect its organization and dynamics. In addition, reflecting the fact that chromatin is packed in the nucleus, the existence and features of the nucleus envelop may also affect chromatin organization and dynamics. In this presentation, we will introduce our computational studies about such possible effects, based on polymer-physics concepts. We will share the results of our computer simulations on (i) how chromatin organization and dynamics are affected by the mechanical perturbations caused by actions of subnuclear molecules affects, focusing on a type of actions of molecules described as a catch-and-release [1,2], and (ii) how its organization is affected by the envelop features, such as the shape of the envelop and the interaction between chromatin and the envelop.
References: [1] Das, Sakaue, Shivashankar, Prost, Hiraiwa “Chromatin Remodeling Due to Transient-Link-and-Pass Activity Enhances Subnuclear Dynamics" PRL 132, 058401 (2024). [2] Das, Sakaue, Shivashankar, Prost, Hiraiwa "How enzymatic activity is involved in chromatin organization" eLife 11, e79901 (2022).
