title: Crowding-induced formation and structural alteration of nuclear compartments: insights from computer simulations.
abstract: Our understanding of the structural and dynamical characteristics of nuclear structures such as chromosomes and nuclear bodies (NBs) has increased significantly in recent days owing to advances in biophysical and biochemical techniques. These techniques include the use of computer simulations, which have provided further physical insights complementary to findings from experiments. In this chapter, we review recent computer simulation studies on the structural alteration of chromosome subcompartments and the formation and maintenance of NBs in the highly crowded cell nucleus. It is found that because of macromolecular crowding, the degree of chromosome compaction changes significantly and the formation of NBs is facilitated. We further discuss the physical consequences of these phenomena, which may be of critical importance in understanding genome processes.
authors.affiliation: Department of Chemistry and Nano Science, Global Top5 Research Program, Ewha Womans University, Seoul, Republic of Korea. Electronic address: jkim@ewha.ac.kr.
authors.forename: Jun Soo
authors.initials: JS
authors.lastname: Kim
authors.affiliation: Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, USA; Department of Chemistry, Northwestern University, Evanston, Illinois, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA.
authors.forename: Igal
authors.initials: I
authors.lastname: Szleifer
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000502:physiology*; D002877:Chromosomes, Human / Q000502:physiology*; D015894:Genome, Human / Q000502:physiology*; D006801:Humans; D045586:Intranuclear Inclusion Bodies / Q000502:physiology*
keywords: Chromosome subcompartments; Computer simulation; Crowding; Nuclear bodies; Nuclear structures