Flexible and dynamic nucleosome fiber in living mammalian cells.
Genomic DNA is organized three dimensionally within cells as chromatin and is searched and read by various proteins by an unknown mechanism; this mediates diverse cell functions. Recently, several pieces of evidence, including our cryomicroscopy and synchrotron X-ray scattering analyses, have demonstrated that chromatin consists of irregularly folded nucleosome fibers without a 30-nm chromatin fiber (i.e., a polymer melt-like structure). This melt-like structure implies a less physically constrained and locally more dynamic state, which may be crucial for protein factors to scan genomic DNA. Using a combined approach of fluorescence correlation spectroscopy, Monte Carlo computer simulations, and single nucleosome imaging, we demonstrated the flexible and dynamic nature of the nucleosome fiber in living mammalian cells. We observed local nucleosome fluctuation (~50 nm movement/30 ms) caused by Brownian motion. Our in vivo/in silico results suggest that local nucleosome dynamics facilitate chromatin accessibility and play a critical role in the scanning of genome information.
Biological Macromolecules Laboratory; Structural Biology Center; National Institute of Genetics; Mishima, Japan; Institute for Advanced Biosciences; Keio University; Fujisawa, Japan; Laboratory for Biochemical Simulation; RIKEN Quantitative Biology Center; Suita, Japan; Cellular Informatics Laboratory; RIKEN; Wako, Japan; Cellular Dynamics Program; Marine Biological Laboratory; Woods Hole, MA USA; Department of Genetics; School of Life Science; Graduate University for Advanced Studies (Sokendai); Mishima, Japan; The Institute of Scientific and Industrial Research; Osaka University; Ibaraki, Japan.
Tadasu
T
Nozaki
Kazunari
K
Kaizu
Chan-Gi
CG
Pack
Sachiko
S
Tamura
Tomomi
T
Tani
Saera
S
Hihara
Takeharu
T
Nagai
Koichi
K
Takahashi
Kazuhiro
K
Maeshima
D000818:Animals; D002470:Cell Survival; D002875:Chromosomes / Q000235:genetics / Q000378:metabolism; D003198:Computer Simulation; D023281:Genomics; D006801:Humans; D007399:Interphase / Q000235:genetics; D008938:Mitosis / Q000235:genetics; D057054:Molecular Imaging; D009010:Monte Carlo Method; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism*
D009707:Nucleosomes
30-nm chromatin fiber; Monte Carlo computer simulations; fluorescence correlation spectroscopy (FCS); interphase chromatin; irregular folding; mitotic chromosomes; nucleosome fiber (10-nm fiber); nucleosome fluctuation; polymer-melt; single nucleosome imaging; transcriptional regulation