Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs.

Autor:	Ohno M; Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan., Ando T; Laboratory for Biomolecular Function Simulation, Quantitative Biology Center, RIKEN, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan., Priest DG; Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan., Kumar V; Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan., Yoshida Y; Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan., Taniguchi Y; Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan. Electronic address: taniguchi@riken.jp.
Jazyk:	angličtina
Zdroj:	Cell [Cell] 2019 Jan 24; Vol. 176 (3), pp. 520-534.e25. Date of Electronic Publication: 2019 Jan 17.
DOI:	10.1016/j.cell.2018.12.014
Abstrakt:	Elucidating the global and local rules that govern genome-wide, hierarchical chromatin architecture remains a critical challenge. Current high-throughput chromosome conformation capture (Hi-C) technologies have identified large-scale chromatin structural motifs, such as topologically associating domains and looping. However, structural rules at the smallest or nucleosome scale remain poorly understood. Here, we coupled nucleosome-resolved Hi-C technology with simulated annealing-molecular dynamics (SA-MD) simulation to reveal 3D spatial distributions of nucleosomes and their genome-wide orientation in chromatin. Our method, called Hi-CO, revealed distinct nucleosome folding motifs across the yeast genome. Our results uncovered two types of basic secondary structural motifs in nucleosome folding: α-tetrahedron and β-rhombus analogous to α helix and β sheet motifs in protein folding. Using mutants and cell-cycle-synchronized cells, we further uncovered motifs with specific nucleosome positioning and orientation coupled to epigenetic features at individual loci. By illuminating molecular-level structure-function relationships in eukaryotic chromatin, our findings establish organizational principles of nucleosome folding. (Copyright © 2018 Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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