National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)
R01HL115153
米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01GM104427
米国
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)
R01MH077303
米国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)
R01DK042667
米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R35GM127018
米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01GM032543
米国
引用
ジャーナル: Mol Cell / 年: 2022 タイトル: Molecular organization of the early stages of nucleosome phase separation visualized by cryo-electron tomography. 著者: Meng Zhang / César Díaz-Celis / Bibiana Onoa / Cristhian Cañari-Chumpitaz / Katherinne I Requejo / Jianfang Liu / Michael Vien / Eva Nogales / Gang Ren / Carlos Bustamante / 要旨: It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, ...It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of the resulting heterogeneous condensates. We used cryo-electron tomography and deep-learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.
ダウンロード / ファイル: emd_24916.map.gz / 形式: CCP4 / 大きさ: 200 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Intermediate stage of irregular tetranucleosome condensate (3)
ボクセルのサイズ
X=Y=Z: 11.68 Å
密度
最小 - 最大
-1.8701404 - 3.9895062
平均 (標準偏差)
0.008321038 (±0.08850213)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
0
サイズ
512
512
200
Spacing
512
512
200
セル
A: 5980.16 Å / B: 5980.16 Å / C: 2336.0 Å α=β=γ: 90.0 °
-
添付データ
-
試料の構成要素
-
全体 : Intermediate stage of irregular tetranucleosome condensates
全体
名称: Intermediate stage of irregular tetranucleosome condensates
要素
複合体: Intermediate stage of irregular tetranucleosome condensates
-
超分子 #1: Intermediate stage of irregular tetranucleosome condensates
超分子
名称: Intermediate stage of irregular tetranucleosome condensates タイプ: complex / ID: 1 / 親要素: 0 詳細: Irregular condensates formed at physiological salt condition (20 mM HEPES-KOH pH 7.5; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT) after 2 min incubation.
由来(天然)
生物種: Xenopus laevis (アフリカツメガエル)
組換発現
生物種: Escherichia coli (大腸菌)
-
実験情報
-
構造解析
手法
クライオ電子顕微鏡法
解析
電子線トモグラフィー法
試料の集合状態
particle
-
試料調製
緩衝液
pH: 7.5
凍結
凍結剤: ETHANE / チャンバー内湿度: 95 %
切片作成
その他: NO SECTIONING
-
電子顕微鏡法
顕微鏡
FEI TITAN KRIOS
撮影
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 実像数: 40 / 平均露光時間: 2.5 sec. / 平均電子線量: 7.0 e/Å2