Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells

The mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using chromosome conformation capture-based methods. Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleo...

Full description

Saved in:
Bibliographic Details
Published in:PLoS computational biology 2016-10, Vol.12 (10), p.e1005136-e1005136
Main Authors: Shinkai, Soya, Nozaki, Tadasu, Maeshima, Kazuhiro, Togashi, Yuichi
Format: Article
Language:English
Subjects:
Binding Sites
Biology and Life Sciences
Chromatin
Chromatin - chemistry
Chromatin - genetics
Chromatin - ultrastructure
Chromatin Assembly and Disassembly - genetics
Chromosomes
Computer Simulation
Gene expression
Genomes
HeLa Cells
Humans
Laboratories
Life sciences
Models, Chemical
Models, Genetic
Models, Molecular
Molecular Conformation
Molecular Imaging - methods
Motion
Nucleosomes - chemistry
Nucleosomes - genetics
Nucleosomes - ultrastructure
Observations
Physical Sciences
Physiological aspects
R&D
Research & development
Research and analysis methods
Scholarships & fellowships
Software
Viscoelasticity
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:The mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using chromosome conformation capture-based methods. Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleosome movement. It is unclear how single nucleosomes within CDs fluctuate and how the CD structure reflects the nucleosome movement. Here, we present a polymer model wherein CDs are characterized by fractal dimensions and the nucleosome fibers fluctuate in a viscoelastic medium with memory. We analytically show that the mean-squared displacement (MSD) of nucleosome fluctuations within CDs is subdiffusive. The diffusion coefficient and the subdiffusive exponent depend on the structural information of CDs. This analytical result enabled us to extract information from the single-nucleosome imaging data for HeLa cells. Our observation that the MSD is lower at the nuclear periphery region than the interior region indicates that CDs in the heterochromatin-rich nuclear periphery region are more compact than those in the euchromatin-rich interior region with respect to the fractal dimensions as well as the size. Finally, we evaluated that the average size of CDs is in the range of 100-500 nm and that the relaxation time of nucleosome movement within CDs is a few seconds. Our results provide physical and dynamic insights into the genome architecture in living cells.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1005136