Summary of 44-Hihara-NucleosomeDyn

SSBD:database
SSBD:database URL
Title
-
Description
-
Relase date
2017-10-03
Updated date
2018-11-15
License
CC BY
Kind
Quantitative data based on Simulation
Number of Datasets
3 ( Image datasets: 0, Quantitative data datasets: 3 )
Size of Datasets
132.9 MB ( Image datasets: 0 bytes, Quantitative data datasets: 132.9 MB )

Organism(s)

Datatype
single molecule dynamics
Molecular Function (MF)
Biological Process (BP)
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Cellular Component (CC)
nucleuosome
Biological Imaging Method
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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
-

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


Dataset List of 44-Hihara-NucleosomeDyn

#
Dataset ID
Kind
Size
4D View
SSBD:OMERO
Download BDML
Download Images
# 1238
Datast ID nuc_0.1_0/
Dataset Kind Quantitative data
Dataset Size 16.2 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 1239
Datast ID nuc_0.5_0
Dataset Kind Quantitative data
Dataset Size 58.4 MB
4D view
SSBD:OMERO
Download BDML
Download Image data

# 1240
Datast ID nuc_0.5_20
Dataset Kind Quantitative data
Dataset Size 58.4 MB
4D view
SSBD:OMERO
Download BDML
Download Image data