Detail of nuc_0.5_20



Project
Title
BDML file for the result of the Monte Carlo computer simulation of nucleosome dynamics in EGFP-pentamers resembling "a dog on a leash" situation (parameters: 13 nm spheres representing EGFP-pentamers in 0.5 mM 10 nm spheres representing a nucleosome with 20 nm as maximum displacement from the initial position)
Description
NA
Release, Updated
2017-10-03,
2018-11-15
License
CC BY
Kind
Quantitative data based on Simulation
File Formats
Data size
58.4 MB

Organism
-
Strain(s)
-
Cell Line
-

Datatype
single molecule dynamics
Molecular Function (MF)
Biological Process (BP)
-
Cellular Component (CC)
nucleuosome ( GO:0000786 )
Biological Imaging Method
XYZ Scale
XY: 1 micrometer, Z: 1 micrometer
T scale
1 microsecond for each time interval

Image Acquisition
Experiment type
-
Microscope type
-
Acquisition mode
-
Contrast method
-
Microscope model
-
Detector model
-
Objective model
-
Filter set
-

Summary of Methods
See details in Hihara et al. (2012) Cell Reports, 2(6): 1645-1656.
Related paper(s)

Saera Hihara, Chan-Gi Pack, Kazunari Kaizu, Tomomi Tani, Tomo Hanafusa, Tadasu Nozaki, Satoko Takemoto, Tomohiko Yoshimi, Hideo Yokota, Naoko Imamoto, Yasushi Sako, Masataka Kinjo, Koichi Takahashi, Takeharu Nagai, Kazuhiro Maeshima (2012) Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells., Cell reports, Volume 2, Number 6, pp. 1645-56

Published in 2012 Dec 27 (Electronic publication in Dec. 13, 2012, midnight )

(Abstract) Genome information, which is three-dimensionally organized within cells as chromatin, is searched and read by various proteins for diverse cell functions. Although how the protein factors find their targets remains unclear, the dynamic and flexible nature of chromatin is likely crucial. Using a combined approach of fluorescence correlation spectroscopy, single-nucleosome imaging, and Monte Carlo computer simulations, we demonstrate local chromatin dynamics in living mammalian cells. We show that similar to interphase chromatin, dense mitotic chromosomes also have considerable chromatin accessibility. For both interphase and mitotic chromatin, we observed local fluctuation of individual nucleosomes (~50 nm movement/30 ms), which is caused by confined Brownian motion. Inhibition of these local dynamics by crosslinking impaired accessibility in the dense chromatin regions. Our findings show that local nucleosome dynamics drive chromatin accessibility. We propose that this local nucleosome fluctuation is the basis for scanning genome information.
(MeSH Terms)

Contact
Kazunari Kaizu , RIKEN , Quantitative Biology Center , Laboratory for Biochemical Simulation
Contributors
Saera Hihara, Chan-Gi Pack, Kazunari Kaizu, Tomomi Tani, Tomo Hanafusa, Tadasu Nozaki, Satoko Takemoto, Tomohiko Yoshimi, Hideo Yokota, Naoko Imamoto, Yasushi Sako, Masataka Kinjo, Koichi Takahashi, Takeharu Nagai, Kazuhiro Maeshima

Local ID
nuc_0.5_20
BDML ID
936a7bff-164c-4506-9fa9-253727f7cd78
BDML/BD5
External Link